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Wikipedia

SARS-CoV-2 Omicron variant

January 09, 2023

Omicron (B.1.1.529) is a variant of SARS-CoV-2 first reported to the World Health Organization (WHO) by the Network for Genomics Surveillance in South Africa on 24 November 2021.[12][13] It was first detected in Botswana and has spread to become the predominant variant in circulation around the world.[14] Following the original B.1.1.529 variant, several subvariants of Omicron have emerged including: BA.1, BA.2, BA.3, BA.4, and BA.5.[15] Since October 2022, two subvariants of BA.5 called BQ.1 and BQ.1.1 have emerged.

SARS-CoV-2 Variant
Omicron
General details
WHO DesignationOmicron
LineageB.1.1.529
First detectedSouth Africa
Date reported24 November 2021; 13 months ago (2021-11-24)
StatusVariant of concern
Symptoms
Cases map
Cumulative confirmed Omicron variant cases by country and territory
  •   100,000–999,999
  •   10,000–99,999
  •   1,000–9,999
  •   100–999
  •   10–99
  •   1–9
  •   0
Major variants

Three doses of a COVID-19 vaccine provide protection against severe disease and hospitalisation caused by Omicron and its subvariants.[16][17][18][19] For three-dose vaccinated individuals, the BA.4 and BA.5 variants are more infectious than previous subvariants but there is no evidence of greater sickness or severity.[15][20][21]

Classification

 
Omicron variant and other major or previous variants of concern of SARS-CoV-2 depicted in a tree scaled radially by genetic distance, derived from Nextstrain on 1 December 2021

On 26 November, the WHO's Technical Advisory Group on SARS-CoV-2 Virus Evolution declared PANGO lineage B.1.1.529 a variant of concern and designated it with the Greek letter omicron.[12] The WHO skipped the preceding letters nu and xi in the Greek alphabet to avoid confusion with the similarities of the English word "new" and the Chinese surname Xi.[22]

The name of the variant has occasionally been mistaken as "Omnicron" among some English speakers, due to a lack of familiarity with the Greek alphabet, and the relative frequency of the Latin prefix "omni" in other common speech.[23][24]

The GISAID project has assigned it the clade identifier GR/484A,[25] and the Nextstrain project has assigned it the clade identifiers 21K and 21L, both belonging to a larger Omicron group 21M.[26]

History

Omicron was first detected on 22 November 2021 in laboratories in Botswana and South Africa based on samples collected on 11–16 November,[27] with the first known samples collected in Johannesburg, South Africa on 8 November 2021.[28] The first known cases outside of South Africa were two people who travelled on 11 November: one who flew from South Africa to Hong Kong via Qatar, and another who travelled from Egypt to Belgium via Turkey.[29][30] On 26 November 2021, WHO designated B.1.1.529 as a variant of concern and named it "Omicron", after the fifteenth letter in the Greek alphabet.[12] As of 6 January 2022, the variant had been confirmed in 149 countries.[31]

Origin hypotheses

Omicron did not evolve from any other variant, but instead diverged on a distinct track, perhaps in mid-2020.[31][32] Competing hypotheses are being examined.

One origin hypothesis is that various mutations in the Omicron variant, comprising a 9-nucleotide sequence, may have been acquired from another coronavirus (known as HCoV-229E), responsible for the common cold.[33] This is not entirely unexpected — at times, viruses within the body acquire and swap segments of genetic material from each other, and this is one common means of mutation.[33]

A link with HIV infection may explain a large number of mutations in the sequence of the Omicron variant.[34] Indeed, in order to be affected by such a high number of mutations, the virus must have been able to evolve a long time without killing its host, which can occur in people with a weakened immune system who receive enough medical care to survive.[34][35] This is the case in HIV patients in South Africa, who represent about 14% of the population (as of 2017).[36] HIV prevention could be key to reducing the risk of uncontrolled HIV driving the emergence of SARS-CoV-2 variants.[34]

One hypothesis to explain the novel mutations is that SARS-CoV-2 was transmitted from humans to mice and mutated in a population of mice sometime between mid-2020 and late 2021 before reinfecting humans.[32]

On 1 December 2022, a team of researchers from the Charité (Berlin) published a study in Science (journal) that claimed that "data revealed genetically diverse Omicron ancestors already existed across Africa by August 2021".[37] After a re-analysis because of doubts,[38] the team has retracted the article on 20 December 2022 due to contamination of the samples.[39][40]

Spread

On 24 November 2021, the variant was first reported to the WHO from South Africa based on samples that had been collected from 14 to 16 November.[27] South African scientists were first alerted by samples from the very beginning of November where the PCR tests had S gene target failure (occurs in a few variants, but not in Delta which dominated in the country in October) and by a sudden increase of COVID-19 cases in Gauteng; sequencing revealed that more than 70 percent of samples collected in the province between 14 and 23 November were a new variant.[41]

The first confirmed specimens of Omicron were collected on 8 November 2021 in South Africa and on 9 November in Botswana.[42] Likely Omicron (SGTF) samples had occurred on 4 November 2021 in Pretoria, South Africa.

When WHO was alerted on 24 November, Hong Kong was the only place outside Africa that had confirmed a case of Omicron; one person who traveled from South Africa on 11 November, and another traveler who was cross-infected by this case while staying in the same quarantine hotel.[29]

On 25 November, one confirmed case was identified in Israel from a traveler returning from Malawi,[43] along with two who returned from South Africa and one from Madagascar.[44] All four initial cases reported from Botswana occurred among fully vaccinated individuals.[45]

On 26 November, Belgium confirmed its first case; an unvaccinated person who had travelled from Egypt via Turkey on 11 November.[30] All three initial confirmed and suspected cases reported from Israel occurred among fully vaccinated individuals,[43] as did a single suspected case in Germany.[46]

On 27 November, two cases were detected in the United Kingdom, another two in Munich, Germany and one in Milan, Italy.[47]

On 28 November, 13 cases were confirmed in the Netherlands among the 624 airline passengers who arrived from South Africa on 26 November.[48] Confirmation of a further 5 cases among these passengers followed later.[49] Entry into the Netherlands generally required having been vaccinated or PCR-tested, or having recovered. The passengers of these two flights had been tested upon arrival because of the newly imposed restrictions (which were set in place during their flight), after which 61 tested positive for SARS-CoV-2.[50] A further two cases were detected in Australia. Both people landed in Sydney the previous day, and travelled from southern Africa to Sydney Airport via Doha Airport. The two people, who were fully vaccinated, entered isolation; 12 other travellers from southern Africa also entered quarantine for fourteen days, while about 260 other passengers and crew on the flight were directed to isolate.[51] Two travellers from South Africa who landed in Denmark tested positive for COVID-19; it was confirmed on 28 November that both carried the Omicron variant.[52][53] On the same day, Austria also confirmed its first Omicron case.[54] A detected Omicron case was reported in the Czech Republic, from a traveler who spent time in Namibia.[55] Canada also reported its first Omicron cases, with two from travelers from Nigeria, therefore becoming the first North American country to report an Omicron case.[56]

On 29 November, a positive case was recorded in Darwin, Australia. The person arrived in Darwin on a repatriation flight from Johannesburg, South Africa on 25 November, and was taken to a quarantine facility, where the positive test was recorded.[57] Two more people who travelled to Sydney from southern Africa via Singapore tested positive.[58] Portugal reported 13 Omicron cases, all of them members of a soccer club.[59] Sweden also confirmed their first case on 29 November,[60] as did Spain, when a traveler came from South Africa.[61]

On 30 November, the Netherlands reported that Omicron cases had been detected in two samples dating back as early as 19 November.[62] A positive case was recorded in Sydney from a traveller who had visited southern Africa before travel restrictions were imposed, and was subsequently active in the community.[63] Japan also confirmed its first case.[64] Two Israeli doctors tested positive and entered isolation. Both of them had received three shots of the Pfizer vaccine prior to testing positive.[65] In Brazil, three cases of the Omicron variant were confirmed in São Paulo.[66] Another five are under suspicion.[67][68] A person in Leipzig, Germany with no travel history nor contact with travellers tested positive for Omicron.[69]

On 1 December, the Omicron variant was detected in three samples in Nigeria that had been collected from travelers from South Africa within the last week.[70][71] On the same day, public health authorities in the United States announced the country's first confirmed Omicron case. A resident of San Francisco who had been vaccinated returned from South Africa on 22 November, began showing mild symptoms on 25 November[72] and was confirmed to have a mild case of COVID-19 on 29 November.[73] Ireland and South Korea also reported their first cases.[74] South Korea reported its cases from five travelers arriving in South Korea from Nigeria.[75]

On 2 December, Dutch health authorities confirmed that all 14 passengers with confirmed Omicron infection on 26 November had been previously vaccinated.[76] The same day, the Norwegian Institute of Public Health confirmed that 50 attendees of a company Christmas party held at a restaurant in Norway's capital, Oslo, were infected with the Omicron variant.[77] France has confirmed only 25 cases of the new Omicron variant but officials say the number could jump significantly in the coming weeks.[78]

By 6 December, Malaysia confirmed its first case of the variant. The case was a South African student entering to study at a private university.[79] In Namibia, 18 cases out of 19 positive COVID-19 samples that had been collected between 11 and 26 November were found to be Omicron, indicating a high level of prevalence in the country.[80] Fiji also confirmed two positive cases of the variant. They travelled from Nigeria arriving in Fiji on November 25.[81]

On 9 December, Richard Mihigo, coordinator of the World Health Organisation's Immunisation and Vaccine Development Programme for Africa, announced that Africa accounted for 46% of reported cases of the Omicron variant globally.[82]

On 13 December, the first death of a person with Omicron was reported in the UK.[83]

On 16 December, New Zealand confirmed its first case of the Omicron variant, an individual who had traveled from Germany via Dubai.[84]

The first death of a person with Omicron was reported in Germany on 23 December[85] and in Australia on 27 December.[86]

By Christmas 2021, the Omicron Strain became dominant in the US.[87]

On 3 January 2022, South Korea reported the first two deaths of people who tested positive post mortem for Omicron.[88]

On 29 March 2022, Omicron subvariant BA.2 overtook BA.1 and became the dominant strain in the U.S.[89][90][91]

As of May 2022, BA.2.12.1 was spreading in the US and two new subvariants of Omicron named BA.4 and BA.5, first detected in January 2022, spread in South Africa. All 3 subvariants have spike protein mutations of L452 and elude immunity from prior BA1 infection.[92]

Reactions

Vaccine producers

On 26 November 2021, BioNTech said it would know in two weeks whether the current vaccine is effective against the variant and that an updated vaccine could be shipped in 100 days if necessary. AstraZeneca, Moderna and Johnson & Johnson were also studying the variant's impact on the effectiveness of their vaccines.[93] On the same day, Novavax stated that it was developing an updated vaccine requiring two doses for the Omicron variant, which the company expected to be ready for testing and manufacturing within a few weeks.[94][95] On 29 November 2021, The Gamaleya Institute said that Sputnik Light should be effective against the variant, that it would begin adapting Sputnik V, and that a modified version could be ready for mass production in 45 days.[96] Sinovac said it could quickly mass-produce an inactivated vaccine against the variant and that it was monitoring studies and collecting samples of the variant to determine if a new vaccine is needed.[97]

On 7 December 2021, at a symposium in Brazil with its partner Instituto Butantan, Sinovac said it would update its vaccine to the new variant and make it available in three months.[98] On 2 December, the Finlay Institute was already developing a version of Soberana Plus against the variant.[99] Pfizer hoped to have a vaccine targeted to immunize against Omicron ready by March 2022.[100]

World Health Organization

On 26 November 2021, the WHO asked nations to enhance surveillance and sequencing efforts, submit complete genome sequences and associated metadata to a publicly available database, such as GISAID, report initial cases/clusters associated with virus-of-concern infection to WHO through the IHR mechanism, where capacity exists and in coordination with the international community, perform field investigations and laboratory assessments to improve understanding of the potential impacts of the virus of concern on COVID-19 epidemiology, severity, and the effectiveness of public health and social measures, diagnostic methods, immune responses, antibody neutralization, or other relevant characteristics.[101] On 26 November 2021, WHO advised countries not to impose new restrictions on travel, instead recommending a "risk-based and scientific" approach to travel measures.[102] On the same day, the European Centre for Disease Prevention and Control (ECDC) reported modeling indicating that strict travel restrictions would delay the variant's impact on European countries by two weeks, possibly allowing countries to prepare for it.[103] As with other variants, the WHO recommended that people continue to keep enclosed spaces well ventilated, avoid crowding and close contact, wear well-fitting masks, clean hands frequently, and get vaccinated.[104][105] On 29 November 2021, the WHO said cases and infections were expected among those vaccinated, albeit in a small and predictable proportion.[106]

International response

After the WHO announcement, on the same day, several countries announced travel bans from southern Africa in response to the identification of the variant, including the United States, which banned travel from eight African countries,[107] although as of 30 November 2021 it notably did not ban travel from any European countries, Israel, Canada, or Australia where cases were also detected at the time the bans were announced. Other countries that also implemented travel bans include Japan, Canada, the European Union, Israel, Australia, the United Kingdom, Singapore, Malaysia, Indonesia, Morocco, and New Zealand.[108][109]

On 26 November 2021 the Brazilian Health Regulatory Agency recommended flight restrictions regarding the new variant.[110] The state of New York declared a state of emergency ahead of a potential Omicron spike, although no cases had yet been detected in the state or the rest of the United States.[111] On 27 November 2021, Switzerland introduced obligatory tests and quarantine for all visitors arriving from countries where the variant was detected, which originally included Belgium and Israel.[112]

On 26 November 2021 South African Minister of Health Joe Phaahla defended his country's handling of the pandemic and said that travel bans went against the "norms and standards" of the World Health Organization.[113]

Some speculated that travel bans could have a significant impact on South Africa's economy by limiting tourism and could lead to other countries with economies that are reliant on tourism to hide the discovery of new variants of concern. Low vaccine coverage in less-developed nations could create opportunities for the emergence of new variants, and these nations also were struggling to gain intellectual property to develop and produce vaccines locally.[114] At the same time, inoculation had slowed in South Africa due to vaccine hesitancy and apathy, with a nationwide vaccination rate of only 35% as of November 24, 2021.[115]

On 29 November 2021, the WHO warned countries that the variant poses a very high global risk with severe consequences and that they should prepare by accelerating vaccination of high-priority groups and strengthening health systems. WHO director-general Tedros Adhanom described the global situation as dangerous and precarious and called for a new agreement on the handling of pandemics, as the current system disincentivizes countries from alerting others to threats that will inevitably land on their shores. CEPI CEO Richard Hatchett said that the variant fulfilled predictions that transmission of the virus in low-vaccination areas would accelerate its evolution.[106]

In preparation for the Omicron variant arriving in the United States, President Joe Biden stated that the variant is "cause for concern, not panic", reiterated that the government was prepared for the variant and would have it under control and that large-scale lockdowns, similar to the ones in 2020 near the beginning of the pandemic, were "off the table for now."[116]

In mid-December 2021, multiple Canadian provinces reinstated restrictions on gatherings and events such as sports tournaments, and tightened enforcement of proof of vaccination orders. British Columbia expressly prohibited any non-seated "organized New Year's Eve event",[117][118][119] while Quebec announced a partial lockdown on 20 December 2021, ordering the closure of all bars, casinos, gyms, schools, and theatres, as well as imposing restrictions on the capacity and operating hours of restaurants, and the prohibition of spectators at professional sporting events.[120]

On 18 December 2021, the Netherlands government announced a lockdown intended to prevent spread of the variant during the holiday period.[121]

In late December 2021, some countries shortened the typical six-month interval for a booster dose of the vaccine to prepare for a wave of Omicron, as two doses are not enough to stop the infection. UK, South Korea and Thailand reduced to three months; Belgium, four months; France, Singapore, Taiwan, Italy and Australia, five months. Finland reduced it to three months for risk groups. Other countries continued with a six-month booster schedule. While antibody levels begin to drop at four months, a longer interval usually allows time for the immune system's response to mature.[122]

Market reactions

Main article: Financial market impact of the COVID-19 pandemic

On 26 November 2021, worry about the potential economic impact of the Omicron variant led to a drop in global markets, including the worst drop of the Dow Jones Industrial Average in 2021, led by travel-related stocks. The price of Brent Crude and West Texas Intermediate oil fell 10% and 11.7%, respectively[123] Cryptocurrency markets were also routed.[124][125] and the South African rand also hit an all-time low for 2021, trading at over 16 rand to the dollar, losing 6% of its value in November.[126][127][128]

In early December 2021, Jerome Powell, the chairman of the Federal Reserve, testified before the U.S. Senate Committee on Banking that "The recent rise in COVID-19 cases and the emergence of the Omicron variant pose downside risks to employment and economic activity and increased uncertainty for inflation."[129]

Biology

 
The genomic sequence of the Omicron variant is pictured above

Mutations

As of June 2022, Omicron had about 50 mutations, which is more than any previous SARS-CoV-2 variant, 32 of which pertained to the spike protein, which most vaccines target to neutralise the virus.[130] As of December 2021, many mutations were novel and not found in previous variants.[42] As of April 2022 the variant was characterised by 30 amino acid changes, three small deletions, and one small insertion in the spike protein compared with the original virus, of which 15 are located in the receptor-binding domain (residues 319–541).[131] As of December 2022 the virus carried a number of changes and deletions in other genomic regions. For example three mutations at the furin cleavage site, which facilitates its transmission.[132][133]

 
 
Illustration of the locations of the Omicron mutations in the spike protein, top view (left) and side view (right), showing amino acid substitutions (yellow), deletions (red), and insertions (green). In this trimeric structure, two monomers (gray and light blue) have their receptor-binding domains in the "down" conformation while one (dark blue) is in the "up" or "open" conformation. Mutation data from WHO,[104] structure from PDB: 6VYB​.[134]




 
Comparison of mutation prevalence for ORF1a, ORF1b, and S genes of Omicron lineages that are designated Variants of Concern. Characteristic mutations for a lineage are defined as nonsynonymous substitutions or deletions that occur in > 75% of sequences within that lineage.[135]







Subvariants

Several subvariants of Omicron have been discovered and new ones continue to emerge.[14] There are 310 Pango lineages currently associated with the Omicron variant.[136] The 'standard' sublineage is now referred to as BA.1 (or B.1.1.529.1), and the two other sublineages are known as BA.2 (or B.1.1.529.2) and BA.3 (or B.1.1.529.3).[137] In mid-2022, BA.4 (or B.1.1.529.4) and BA.5 (or B.1.1.529.5) were detected in several countries.[138] They share many mutations, but also significantly differ. In general, BA.1 and BA.2 share 32 mutations, but differ by 28.[139] BA.1 has itself been divided in two, the original BA.1 and BA.1.1 (or B.1.1.529.1.1) where the main difference is that the latter has a R346K mutation.[140]

Standard PCR and rapid tests continue to detect all Omicron subvariants as COVID-19, but further tests are necessary to distinguish the subvariants from each other and from other COVID-19 variants.[141]

Defining mutations in the
SARS-CoV-2 Omicron variant
Gene Amino acid
ORF1ab nsp3: K38R
nsp3: V1069I
nsp3: Δ1265
nsp3: L1266I
nsp3: A1892T
nsp4: T492I
nsp5: P132H
nsp6: Δ105-107
nsp6: A189V
nsp12: P323L
nsp14: I42V
Spike A67V
Δ69-70
T95I
G142D,
Δ143-145
Δ211
L212I
ins214EPE
G339D
S371L
S373P
S375F
K417N
N440K
G446S
S477N
T478K
E484A
Q493R
G496S
Q498R
N501Y
Y505H
T547K
D614G
H655Y
N679K
P681H
N764K
D796Y
N856K
Q954H
N969K
L981F
E T9I
M D3G
Q19E
A63T
N P13L
Δ31-33
R203K
G204R
Sources: UK Health Security Agency[142] CoVariants[26]

BA.2

A laboratory study on hamsters and mice in Japan published as a non-peer-reviewed preprint in mid-February 2022 suggested that BA.2, is not only more transmissible than BA.1, but may cause more severe disease.[143] This was later disproven by a study in late-October 2022, that found BA.2 actually caused less severe disease relative to BA.1 (which in turn, caused less severe disease compared to the delta variant).[144] Therapeutic monoclonal antibodies used to treat people infected with COVID-19 did not have much effect on BA.2, which was "almost completely resistant" to casirivimab and imdevimab, and 35 times more resistant to sotrovimab than the BA.1 subvariant.

Affected countries and transmissibility

According to early research, BA.2 is roughly 30% to 60% more transmissible than BA.1.[145][146]

The first known sequence of BA.2 was in a sample from 15 November 2021.[147] As of 17 January 2022, BA.2 had been detected in at least 40 countries and in all continents except Antarctica.[148] By 31 January, it had been detected in at least 57 countries.[149] In global samples collected from 4 February to 5 March and uploaded to GISAID, BA.2 accounted for c. 34%, compared to 41% for BA.1.1, 25% for BA.1 and less than 1% for BA.3.[150] In a review two weeks later, covering 16 February to 17 March, BA.2 had become the most frequent.[151] However, the data is geographically skewed due to sequencing rate and speed; for example, among the c. 205,000 COVID-19 sequences from March that had been uploaded to GISAID as of 22 March, United Kingdom and Denmark accounted for more than 3⁄4, and most of the remaining were from other European countries, Australia, Canada and the United States (altogether, c. 6,000 were from Africa, Asia and Latin America).[152] Based on GISAID uploads, BA.1 peaked in early January 2022, after which it was overtaken by both BA.1.1 and BA.2.[153] In North America, parts of Europe and parts of Asia, BA.1 was first outcompeted by BA.1.1. For example, in the United States, France and Japan, BA.1.1 became the dominant subvariant in January 2022.[154][155][156]

By late December 2021/early January 2022, BA.2 appeared to have become dominant in at least parts of India (already making up almost 80 percent in Kolkata in late December 2021[157]) and the Philippines, had become frequent in Scandinavia, South Africa and Singapore, and was showing signs of growth in Germany and the United Kingdom.[158][159][160][161] In Japan, which has quarantine and detailed screening of all international travellers, as of 24 January, the vast majority of BA.2 had been detected in people that had arrived from India or the Philippines with cases going back at least to 1 December 2021 (far fewer BA.1 or other variants were detected among arrivals from the two countries in that period), but small numbers had also been detected in people arriving from other countries.[162][163][164]

In Denmark, the first BA.2 was in a sample collected on 5 December 2021 and extremely few were found in the directly following period.[165] By week fifty (13–19 December) it had started to increase, with BA.2 being at around 2 percent of sequenced cases compared to 46 percent BA.1 (remaining Delta). The frequency of both Omicron subvariants continued to increase throughout the last half of December; in week fifty-two (27 December–2 January), BA.2 had reached 20 percent and BA.1 peaked at 72 percent. In January 2022, BA.1 began decreasing, whereas BA.2 continued its increase. By the second week (10–16 January) of 2022, the frequency of the two was almost equal, both being near 50 percent (around one percent was the rapidly disappearing Delta).[165] In the following week, BA.2 became clearly dominant in Denmark with 65 percent of new cases being the BA.2 subvariant.[166] Trends from the other Scandinavian countries, India, South Africa and the United Kingdom also showed that BA.2 was increasing in proportion to BA.1.[167][168] In early February 2022, it had become the dominant subvariant in South Africa, in late February it had become dominant in Germany and in early March it had become dominant in the United Kingdom.[169][170][171] In early March, BA.1.1 was still heavily dominant in the United States (having overtaken BA.1 in January), but BA.2 was increasing in frequency, later becoming dominant in the US by 29 March.[154][172]

BA.2.12

There were two new BA.2 subvariants detected in the US state of New York, which are BA.2.12 (or B.1.1.529.2.12) and BA.2.12.1 (or B.1.1.529.2.12.1), both of which have a significant growth advantage of 23–27% over BA.2 and contributing to a rise in infections in central New York, centred on Syracuse and Lake Ontario, which later became dominant by May 24 in the US.[173]

BA.2.75 and BA.2.75.2

The subvariant BA.2.75 (or B.1.1.529.2.75, nicknamed Centaurus by the media[174]), first detected in India in May 2022, has been classified as variant under monitoring by the WHO.[175] Additional newer mutations in this line (like BA.2.75.2 aka B.1.1.529.2.75.2 or Chiron) may be capable of escaping neutralizing antibodies.[176]

XBB and XBB.1

XBB, a recombinant of the BA.2.10.1 and BA.2.75 sublineages,[177] is an Omicron subvariant first detected in August 2022.[178] Described as "immune-evasive", it has caused a small surge of cases in countries including Singapore and Bangladesh.[179]

On 20 October 2022, the chief scientist of the World Health Organization (WHO), Soumya Swaminathan, warned that the XBB subvariant of Omicron may cause infections in some countries while the severity of the new variants is not yet known.[180]

Early observations from Singapore indicated the possibility of XBB being less severe compared to the omicron BA.5 variant, with data from the first two weeks in October 2022 indicating that the XBB variant had a 30% lower hospitalisation risk.[181] However, this could also be due to high levels of population immunity from vaccination and previous waves.

BA.3

The third Omicron sublineage, BA.3, is very rare. It has the same S-gene target failure (SGTF) deletion (Δ69-70) as BA.1.

XE

A new BA.1–BA.2 recombinant isolated from the UK in January 2022, dubbed the "XE" recombinant, was found by the WHO to be potentially 10% more transmissible than BA.2, making it about 43% to 76% to more transmissible than BA.1, and making the XE recombinant the most contagious variant identified.[182]

BA.4 and BA.5

In April 2022, the WHO announced it was tracking the BA.4 and BA.5 subvariants with BA.4 having been detected in South Africa, Botswana, Denmark, Scotland and England.[183] Early indications from data collected in South Africa suggested BA.4 and BA.5 have a significant growth advantage over BA.2, which by 12 May earned the status Variant of Concern by the European Centre for Disease Prevention and Control, and, by 20 May, by the UK Health Security Agency.[184][185][186][187] BA.5 was dominant in Portugal by 25 May, accounting for two-thirds of all new cases there.[188] By 24 June, BA.4 and BA.5 together had become dominant variants in the UK and Germany.[189][190][191][192] These two subvariants became dominant in the United States by 28 June.[193][194] By late June, BA.5 became the dominant subvariant in France, with 59% of new cases linked to it.[195][196]

On 10 May 2022, a case of a new subvariant BA.5.2.1 was reported in California.[197] On 10 July, the city of Shanghai reported its first case of BA.5.2.1, in a man who had flown in from Uganda, sparking a new wave of testing.[198] On 22 July, the province of Ontario, Canada announced that subvariant BA.5.2.1 overtook BA.2.12.1 as the main variant in circulation in Ontario around 2 July.[199] Regeneron is reporting that BA.5.2.1 is the main variant in Australia, Belgium, Brunei, Greece and Iceland.[200] The government of Canada is also reporting that in late June and July, of the travelers arriving by air who test positive for COVID-19, a substantial proportion are BA.5.2.1.[201] BF.7 is a shortened version of the sub-variants full name, which is BA.5.2.1.7. This sub-variant is part of Omicron's BA.5 variant, which has the highest number of reported cases globally, accounting for 76.2% of all cases.[202]

BQ.1 and BQ.1.1

Since October 2022, two BA.5 subvariants were found: BQ.1 (or B.1.1.529.5.3.1.1.1.1.1, nicknamed Typhon by the media) and BQ.1.1 (or B.1.1.529.5.3.1.1.1.1.1.1, nicknamed Cerberus).[203][204][205] They have been more prevalent in France than any other European country.[206] As of 17 November, 93% of sequences in France were Omicron sub-lineage BA.5 and among the BA.5 sub-lineages, BQ.1.1 continued to rise (32% vs 25% in the prior week).[207] according to Nextclade even 55%.[208] they were reported in the US to have become dominant, accounting for 44% of new infections, up from 33% the previous week. Early laboratory tests found that these subvariants were better at escaping first and booster vaccines than previous variants; however, no new treatments appeared to be in development. Virologist Andy Pekosz said that "the mutations have pretty much eliminated every single monoclonal antibody on the market right now in terms of their efficacy".[209]

Transmission

 
False-color transmission electron micrograph of an Omicron variant coronavirus, shown in pink, replicating within the cytoplasm of an infected Vero cell

In humans

In January 2022, William Schaffner, professor of infectious diseases at Vanderbilt University Medical Center, compared the contagiousness of the Omicron variant to that of the measles.[210]

Vaccinated

It was not known in November 2021 how Omicron would spread in populations with high levels of immunity or if it causes a milder or more severe disease. On 15 December 2021, Jenny Harries, head of the UK Health Security Agency, told a parliamentary committee that the doubling time of COVID-19 in most regions of the UK was now less than two days despite the country's high vaccination rate. She said that the Omicron variant of COVID-19 is "probably the most significant threat since the start of the pandemic", and that the number of cases in the next few days would be "quite staggering compared to the rate of growth that we've seen in cases for previous variants".[211]

Natural immunity

Relating to naturally acquired immunity, Anne von Gottberg, an expert at the South African National Institute for Communicable Diseases, believed at the beginning of December 2021 that immunity granted by previous variants would not protect against Omicron.[212]

Vaccinated or natural immunity

A study suggests that mutations that promote breakthrough infections or antibody-resistance "like those in Omicron" could be a new mechanism for viral evolution success of SARS-CoV-2 and that such may become a dominating mechanism of its evolution.[213] A preprint supports such an explanation of Omicron's spread, suggesting that it "primarily can be ascribed to the immune evasiveness rather than an inherent increase in the basic transmissibility".[214][215] Studies showed the variant to escape the majority of existing SARS-CoV-2 neutralizing antibodies, including those in sera from vaccinated and convalescent individuals.[216][217][218][219] Nevertheless, current vaccines are expected to protect against severe illness, hospitalizations, and deaths due to Omicron[220] and, on an individual level, the Omicron variant is milder than earlier variants that evolved when the antibody/vaccination share was lower than it was when Omicron emerged.[221]

In contrast to other investigated variants, Omicron showed substantial, population-level, evasion of immunity from prior infection as well as a higher ability to evade immunity induced by vaccines.[222]

In non-human animals

In February 2022, the first confirmed case infecting a wild animal was confirmed by researchers at Pennsylvania State University in white-tailed deer in Staten Island, N.Y.[223]

Surfaces

Although transmission via fomites is rare, preliminary data indicate that the variant lasts for 194 hours on plastic surfaces and 21 hours on skin, compared with just 56 and 7 hours, respectively, for the original strain.[224][225]

Vaccine effectiveness

Pfizer-BioNTech (BNT162b2) and Moderna (mRNA-1273) mRNA vaccines provide reduced protection against asymptomatic disease but do reduce the risk of serious illness.[226][227][228] On 22 December 2021, the Imperial College COVID-19 Response Team reported an about 41% (95% CI, 37–45%) lower risk of a hospitalization requiring a stay of at least 1 night compared to the Delta variant, and that the data suggested that recipients of 2 doses of the Pfizer–BioNTech, the Moderna or the Oxford–AstraZeneca vaccine were substantially protected from hospitalization.[229] In January 2022, results from Israel suggested that a fourth dose is only partially effective against Omicron. Many cases of infection broke through, albeit "a bit less than in the control group", even though trial participants had higher antibody levels after the fourth dose.[230] On 23 December 2021, Nature indicates that, though Omicron likely weakens vaccine protection, reasonable effectiveness against Omicron may be maintained with currently available vaccination and boosting approaches.[231][232]

In December, studies, some of which using large nationwide datasets from either Israel and Denmark, found that vaccine effectiveness of multiple common two-dosed COVID-19 vaccines is substantially lower against the Omicron variant than for other common variants including the Delta variant, and that a new (often a third) dose – a booster dose – is needed and effective, as it substantially reduces deaths from the disease compared to cohorts who received no booster but two doses.[233][234][235][236][237][238]

Vaccines continue to be recommended for Omicron and its subvariants. Professor Paul Morgan, immunologist at Cardiff University said, "I think a blunting rather than a complete loss [of immunity] is the most likely outcome. The virus can't possibly lose every single epitope on its surface, because if it did that spike protein couldn't work any more. So, while some of the antibodies and T cell clones made against earlier versions of the virus, or against the vaccines may not be effective, there will be others, which will remain effective. (...) If half, or two-thirds, or whatever it is, of the immune response is not going to be effective, and you're left with the residual half, then the more boosted that is the better."[239] Professor Francois Balloux of the Genetics Institute at University College London said, "From what we have learned so far, we can be fairly confident that – compared with other variants – Omicron tends to be better able to reinfect people who have been previously infected and received some protection against COVID-19. That is pretty clear and was anticipated from the mutational changes we have pinpointed in its protein structure. These make it more difficult for antibodies to neutralise the virus."[240]

BA.1 and BA.2

A January 2022 study by the UK Health Security Agency found that vaccines afforded similar levels of protection against symptomatic disease by BA.1 and BA.2, and in both it was considerably higher after two doses and a booster than two doses without booster,[241][242] though because of the gradually waning effect of vaccines, further booster vaccination may later be necessary.[171]

BA.4 and BA.5

In May 2022, a preprint indicated Omicron subvariants BA.4 and BA.5 could cause a large share of COVID-19 reinfections, beyond the increase of reinfections caused by the Omicron lineage, even for people who were infected by Omicron BA.1 due to increases in immune evasion, especially for the unvaccinated. However, the observed escape of BA.4 and BA.5 from immunity by a BA.1 infection is more moderate than of BA.1 against studied prior cases of immunity (such as immunity from specific vaccines).[243][244]

Immunity from an Omicron infection for unvaccinated and previously uninfected was found to be weak "against non-Omicron variants",[245] albeit at the time Omicron is, by a large margin, the dominant variant in sequenced human cases.[246]

BQ.1 and BQ.1.1

Subvariants BQ.1 and BQ.1.1 were found in late 2022 to be better at escaping first and booster vaccines than previous variants, and "to have pretty much eliminated every single monoclonal antibody on the market right now in terms of their efficacy".[citation needed]

Vaccine adjustments

See also: Universal coronavirus vaccine

As of June 2022, researchers, health organizations and regulators are discussing, investigating (including with preliminary laboratory studies and trials) and partly recommending COVID-19 vaccine boosters that mix the original vaccine formulation with Omicron-adjusted parts – such as spike proteins of a specific Omicron subvariant – to better prepare the immune system to recognize a wide variety of variants amid substantial and ongoing immune evasion by Omicron (and other SARS-CoV-2 variants).[247]

In June 2022 Pfizer and Moderna developed bivalent vaccines to protect against the SARS-COV-2 wild-type and the Omicron variant. The bivalent vaccines are well-tolerated and offer immunity to omicron superior to previous mRNA vaccines.[248] The United States Food and Drug Administration (FDA) has authorized the bivalent vaccines for use in the USA .[249]

Signs and symptoms

Main article: Symptoms of COVID-19

Loss of taste and smell seem to be uncommon compared to other strains.[6][7] A unique reported symptom of the Omicron variant is night sweats,[8][250] particularly with the BA.5 subvariant.[251][252] A study performed between 1 and 7 December 2021 by the Center for Disease Control found that: "The most commonly reported symptoms [were] cough, fatigue, and congestion or runny nose" making it difficult to distinguish from a less damaging variant or another virus.[253] Research published in London on 25 December 2021 suggested the most frequent symptoms stated by users of the Zoe Covid app were "a runny nose, headaches, fatigue, sneezing and sore throats."[11]

A British omicron case-control observational study until March 2022 showed a reduction in odds of long COVID with the omicron variant versus the delta variant of 0·24–0·5 depending on age and time since vaccination.[254]

Virulence

As of 6 January 2022, Omicron multiplied around 70 times faster than the Delta variant in the bronchi (lung airways) but evidence suggested it is less severe than previous variants, especially compared to Delta,[255][221] since it might be less able to penetrate deep lung tissue.[256] As of January 2022, in southern California infections were 91 percent less fatal than the delta variant, with 51 percent less risk of hospitalization.[257] However, the estimated difference in the intrinsic risk of hospitalization in England largely decreased to 0–30 percent, when reinfections were excluded.[258]

BA.1 and BA.2 differences

As of 21 January 2022 the risk of hospitalization was the same in BA.1 and BA.2 based on reviews from Denmark, India, South Africa and the United Kingdom.[259][150][166][260] Norwegian studies showed that the amount of virus in the upper airways was similar in those infected with BA.1 and BA.2.[168]

Diagnosis

See also: COVID-19 testing

As of November 2021, the chance of detecting an Omicron case particularly depended on a country's sequencing rate, with South Africa sequencing far more samples than any other country in Africa, but at a considerably lower rate than most Western nations.[261][262] Furthermore, it could take up to two weeks to return a viral sequence in places with the technical capability, hence solid statistics on confirmed cases have lagged the actual situation.[263]

PCR testing

In December 2021, the US FDA published guidelines on how PCR tests would be affected by Omicron.[264] Tests that detect multiple gene targets were to continue to identify the testee as positive for COVID-19. S-gene dropout or target failure was proposed as a shorthand way of differentiating Omicron from Delta. besides sequencing and genotyping.[265]

As of December 2021, Denmark and Norway have regarded cases found by their variant qPCR test, which is relatively fast and checks several genes,[266] as sufficient for counting it as Omicron, before full sequencing.[267][268]

BA.1 and BA.2 differences

As of 7 December 2021 it was known that BA.2 -unlike Ba1- lacks the characteristic S-gene target failure (SGTF) causing deletion (Δ69-70), by which many qPCR tests have been able to rapidly detect a case as an Omicron (or Alpha) variant, from the previously dominant Delta variant.[269][270] Thus, countries which primarily rely on SGTF for detection may overlook BA.2,[269] and British authorities consider SGTF alone as insufficient for monitoring the spread of Omicron.[259] This has resulted in it having been nicknamed 'Stealth Omicron',[259] but because BA.2 still can be separated from other variants through normal full sequencing, or checks of certain other mutations, the nickname is not quite accurate.[139][271] As of January 2022, some countries, such as Denmark and Japan, have been using a variant qPCR which tests for several mutations, including L452R.[266][162] It can also distinguish Delta, which has L452R,[272] and all Omicron subvariants, which do not have L452R.[273][148] As Omicron became dominant and the Delta variant became rare in early 2022, the SGTF mutation that had made Delta and BA.2 similar in qPCR tests was found to be useful for separating BA.1 and BA.2 from each other.[274]

Rapid antigen testing

In January 2022 the medicine and therapeutic regulatory agency Therapeutic Goods Administration (TGA) of the Australian Government found that only one of their 23 approved COVID-19 rapid antigen tests (RAT) stated that it detected Omicron.[275]In June 2022, the German federal Paul-Ehrlich-Institute published their findings, that most RATs detected the Omicron Variant.[276]

Treatment

See also: Treatment and management of COVID-19

As of 28 November 2021, Corticosteroids such as dexamethasone and IL6 receptor blockers such as tocilizumab (Actemra) were known to be effective for managing patients with the earlier strains of severe COVID-19 but the impact on the effectiveness of other treatments was being assessed.[277][278]

Relating to monoclonal antibodies (mAbs) treatments, similar testing and research is ongoing. Preclinical data on in vitro pseudotyped virus data demonstrate that some mAbs designed to use highly conserved epitopes retain neutralizing activity against key mutations of Omicron substitutions.[279] Similar results are confirmed by cryo-electron microscopy and X-ray data, also providing the structural approach and molecular basis for the evasion of humoral immunity exhibited by Omicron antigenic shift as well as the importance of targeting conserved epitopes for vaccine and therapeutics design. While 7 clinical mAbs or mAb cocktails experienced loss of neutralizing activity of 1-2 orders of magnitude or greater relative to the prototypic virus, the S309 mAb, the parent mAb of sotrovimab, neutralized Omicron with only 2-3-fold reduced potency.[280]

As of December 2021, most monoclonal antibodies had lost in vitro neutralizing activity against Omicron, with only 3 out of 29 mAbs examined in another study retaining unaltered potency. Furthermore, a fraction of broadly neutralizing sarbecovirus mAbs neutralized Omicron through recognition of antigenic sites outside the RBM, including sotrovimab (VIR-7831), S2X259 and S2H97.[281] However, sotrovimab was not fully active against the BA.2 Omicron sublineage, and in March2022 the office of the U.S. ASPR stopped distributing the antibody treatment to states where BA.2 was dominant.[282] February 2022 data suggested Omicron caused significant humoral immune evasion, while neutralizing antibodies targeting the sarbecovirus conserved region remained most effective.[283]

Epidemiology

On 26 November 2021, the South African National Institute for Communicable Diseases announced that 30,904 COVID-19-tests (in one day) detected 2,828 new COVID-19 infections (a 9.2% positivity rate).[284] One week later, on 3 December 2021, the NICD announced that 65,990 COVID-19 tests had found 16,055 new infections (5.7 times as many as seven days before; positive rate 24.3%) and that 72 percent of them were found in Gauteng.[285][286] This province of South Africa is densely populated at about 850 inhabitants per km2. Gauteng's capital Johannesburg is a megacity (about 5.5 million inhabitants in the city itself plus 9.5 million in the urban region).

In November 2021, the transmissibility of the Omicron variant, as compared to the Delta variant or other variants of the COVID-19 virus, was still uncertain.[287] Omicron is frequently able to infect previously COVID-19-positive people.[288][289]

It has been estimated the Omicron variant diverged in late September or early October 2021, based on Omicron genome comparisons.[290] Sequencing data suggests that Omicron had become the dominant variant in South Africa by November 2021, the same month where it had been first identified in the country.[291][292]

Phylogeny suggests a recent emergence. Data from South Africa suggests that Omicron has a pronounced growth advantage there. However, this may be due to transmissibility or immune escape related, or both."[293] Also the serial interval plays a role in the growth.

Detectable changes in levels of COVID-19 in wastewater samples from South Africa's Gauteng province were seen as early as 17–23 October (week 42).[294] The National Institute for Communicable Diseases reports that children under the age of 2 make up 10% of total hospital admissions in the Omicron point of discovery Tshwane in South Africa.[295] Data on the S gene target failure (SGTF) of sampled cases in South Africa indicates a growth of 21% per day relative to Delta, generating an increased reproduction number by a factor of 2.4.[a] Omicron became the majority strain in South Africa around 10 November.[296][297] Another analysis showed 32% growth per day in Gauteng, South Africa, having become dominant there around 6 November.[298]

In the UK, the logarithmic growth rate of Omicron-associated S gene target failure (SGTF) cases over S gene target positive (SGTP) cases was estimated at 0.37 per day,[b] which is exceptionally high.[299] Furthermore, by 14 December it appears to have become the most dominant strain.[c][300] Without presuming behavior change in response to the variant, a million infections per day by 24 December are projected for a 2.5 days doubling time.[d][265] In Denmark, the growth rate has been roughly similar with a doubling time of about 2–3 days, it having become the most prevalent strain on 17 December.[301][302][303] Switzerland is not far behind.[304] In Germany Omicron became the most prevalent variant on 1 January.[305] In Scotland, Omicron apparently became the most prevalent variant on 17 December.[306][307] In the Canadian province of Ontario it became the most prevalent strain on 13 December.[308] In the US, the variant appears to have become the most prevalent strain on 18 December, growing at 0.24 per day.[309] In Portugal, Omicron had reached 61.5% of cases on 22 December.[310] In Belgium, the strain has become the most prevalent on 25 December,[311] and in the Netherlands on 28 December.[312] In Italy, it had reached 28% of cases on 20 December and was doubling every two days,[313] while it became the dominant variant in Norway on 25 December.[314] In France, it made up about 15% of COVID-19 cases in mid-December, but around 27 December it had increased to more than 60%.[315][316] Researchers recommend sampling at least 5% of COVID-19 patient samples in order to detect Omicron or other emerging variants.[317]

During January 2022, in Denmark the BA.2 variant grew at ~0.10 per day (+11% per day) as a ratio to BA.1 (the legacy Omicron variant), and became the dominant strain in week 2, 2022.[165] In the United Kingdom, the BA.2 variant was growing at ~0.11 per day (+12% per day) as a ratio to BA.1.[318]

On 13 January 2022, the BBC reported that the hospitalization rate was higher in the US and Canada than in Europe and South Africa. This was attributed to a combination of a greater number of elderly people than in South Africa, greater prevalence of comorbidities such as hypertension and obesity than in Europe, higher indoor transmission due to the winter, lower vaccination rate in the US than in Europe and Canada, and a possible still high prevalence of the Delta variant, which more often leads to hospitalization.[319]

Reported cases

Confirmed and suspected cases by country and territory
Country/Territory Confirmed cases (PANGOLIN)[320]
as of 5 May, 2022 		Confirmed cases (GISAID)[321]
as of July 29, 2022 		Confirmed cases (other sources)
As of 24 June 2022		 Suspected cases
  United States 801,020 1,431,772 62,480[322]As of January 8, 2022 –
  United Kingdom 998,552 1,253,700 246,780[323] 600,041[323]
  Germany 207,407 365,837 268,661[324] –
  Austria 6,809 57,379 290,378[325][326] –
  Denmark 196,746 264,998 66,563[327] –
  France 83,564 184,880 5,591[328] –
  Canada 73,584 147,223 174,248[329] –
  Japan 67,203 153,110 12,453[330] –
  India 37,542 81 017 8,209[331][332] –
  Australia 33,905 80,013 11,071[333] –
  Norway 14,729 24,529 45,296[267] –
  Thailand 6,778 12,811 5,397[334] –
  Indonesia 9,761 12,028 3,779[335] –
  Singapore 4,543 7,300 4,322[336][337][338][339] –
  Estonia 1,982 3,778 3,857[340][341][342] –
  Israel 22,164 60,435 1,741[343][344] 861[343]
  South Africa 9,631 16,451 1,095[345] 19,070[346]
  South Korea 7,731 27,705 1,318[347] –
  Spain 24,607 31,992 51[324][348] –
  Belgium 26,448 30,865 121[325][348] –
  Sweden 38,397 42,525 53.760[349] –
  Switzerland 30,034 32,635 19,269[325][350] –
  Argentina 2,228 2,583 455[351][352] 80[353]
  Botswana 931 1,594 23[354] –
  Netherlands 24,381 26,601 123[355][348] –
  Ireland 24,654 29,518 29,576[356] –
  Gibraltar 112 122 24[357] –
  Iceland – – 84[358] –
  Italy 23,707 27,292 84[359] –
  Chile 4,097 4,572 684[360][361][362] –
  Portugal 7,683 8,870 69[363][348] 6[364][325]
  Morocco 128 138 76[365] 246[365]
  Zimbabwe 185 219 50[366] –
  Ghana 441 605 33[354] –
  Brazil 27,787 32,224 203[367] –
  Finland 4,029 5,239 523[368][369] –
  Cyprus – – 31[370][371] –
  Kenya 1,653 2,329 27[372] –
  Russia 1,273 1,738 8,239[373] –
  Cayman Islands – – 44[374] 59[374]
  Uganda 12 38 25[375][376] –
  Mexico 12,736 13,678 1[377] –
  New Zealand 3,169 3,739 116[378] –
  Namibia 125 213 18[379] –
  Hong Kong 1,432 3,526 102[380][381] –
  Senegal 14 229 3[382] –
  Mozambique 133 176 2[383] 2[322]
  Greece 3,268 3,276 17[325][384] –
  Bermuda – 24 144[385][386] –
  Latvia 407 407 644[387][348][388] –
  Romania 4,034 4,282 25[389][390][391] –
  Malaysia 5,330 7,353 245[392] –
  Zambia 141 365 11[393] –
  Nigeria 827 1,638 6[394] –
  Czech Republic 13,264 15,147 10[325][395][348] –
  Kosovo 245 262 9[396] –
  Slovenia 15,684 17,106 1,418[397][348][398][399] –
  Lebanon 85 107 433[400][401] 16[400]
  Reunion 2,014 2,402 2[402] –
  Mauritius – 763 7[322] –
  Poland 31,766 33,327 1[403] –
  Rwanda 70 178 6[403] –
  Turkey 9,135 10,239 6[404] –
  Montenegro 142 211 5[405] –
  Cambodia 950 974 31[406] –
  Peru 5,653 5,960 10,032[407] –
  Jordan 83 83 832[408] –
  China 89 96 4[409][410][411] –
  Cuba – – 92[412][413][414] –
  Croatia 10,379 11,742 3[325] –
  Egypt 15 40 3[403] –
  Malawi 133 166 3[415] –
  Palestinian Territory – 9 126[416][417] –
  Taiwan 32 34 89[418] –
  Lithuania 7,063 9,136 2[419] –
  Colombia 1,629 3,816 3[420]
  Slovakia 13,501 15,625 3[421] –
  Trinidad and Tobago 291 499 1[422] –
  Puerto Rico 3,166 3,558 1[423] –
  Fiji – – 2[424] –
    Nepal 255 349 2[425] –
  Myanmar 25 28 4[426] –
  Philippines 1,281 1,549 535[427][428][429][430][431][432] –
  Northern Cyprus – – 9[433] –
  Bangladesh 690 998 10[434] –
  Liechtenstein 246 736 1[435] 3[322]
  Hungary 28 28 61[436][348][437] –
  Oman 71 85 2[438] –
  Pakistan 359 463 75[439][440] –
  Sri Lanka 626 927 1[441] –
  Georgia 718 822 600[442] –
  Algeria 61 73 1[403] –
  Bahrain – – 1[443] –
  Ecuador 1,177 1,561 1[444] –
  Kuwait 54 72 1[445] –
  Luxembourg 4,031 11,149 1[325] –
  Maldives – 281 5[446][447] –
  Sierra Leone – 1 1[448] –
  Saudi Arabia 28 30 1[449] –
  Tunisia 51 52 1[450] –
  United Arab Emirates – 1 1[451] –
  Iran 595 682 467[452] –
  Ukraine 73 99 1[453] –
  Panama 821 822 1[454] –
  Costa Rica 1,430 1,529 1[455] –
  Aruba 61 61 1[456] –
  North Macedonia 46 47 9[457][458] –
  Vietnam 1,085 1,790 108[459] –
  Brunei 1,163 1,253 8[460] –
  Malta 138 162 2[461] –
  Venezuela 60 62 7[462] –
  French Guiana – 366 20[463] –
  Republic of the Congo 50 78 1[464] –
  Qatar 267 290 4[465] –
  Paraguay 122 139 3[466] –
  Burkina Faso – 17 2[467] –
  Curacao 482 487 1[468] –
  Saint Kitts and Nevis – 16 2[469] –
  Libya – – 2[470] –
  Albania 1 1 1[471] –
  Barbados 1 7 1[472] –
  Saint Vincent and the Grenadines – 62 1[473] –
  Dominican Republic 69 73 1[474] –
  Jamaica 443 622 1[475] –
  Serbia 81 81 1[476] –
  Tanzania 2 3 1[477] –
  Togo – – 5[478] –
  Belarus – 71 4[479] –
  Bosnia and Herzegovina 118 122 10[480] –
  Angola 25 37 16[481] –
  Democratic Republic of the Congo 34 204 1[482] –
  Bulgaria 2,516 2,520 12[483] –
  Mayotte 123 130 1[484] –
  Martinique – 593 1[485] –
  Gambia 30 155 26[486] –
  Seychelles – 235 464[487] –
  Saint Martin 224 240 2[488] –
  Laos – – 1[489] –
  Iraq 36 103 5[490] –
  Mauritania – – 14[491] –
  South Sudan 28 28 41[492] –
  Ivory Coast 41 60 78[493] –
  Cape Verde – 152 175[494] –
  Antigua and Barbuda – 36 1[495] –
  Gabon – – 1[496] –
  Bolivia 2 7 1[497] –
  Moldova 287 314 29[498] –
  Kazakhstan 8 8 8[499] –
  Guadeloupe 264 300 1[500] –
  Azerbaijan 12 12 12[501] –
  Suriname 81 96 146[487] –
  Sint Maarten – 479 753[487] –
  British Virgin Islands 20 26 39[487] –
  Mali 1 2 – –
  Anguilla – 24 30[487] –
  Bonaire – 400 692[487] –
  Bhutan – – 14[502] –
  Papua New Guinea 379 565 1[503] –
  Mongolia 133 133 12[504] –
  Antarctica – – 24[505] –
  Uzbekistan – – 1[506] –
  Saint Lucia 1 9 54[487] –
  Burundi – 1 28[487] –
  American Samoa – 35 84[487] –
  Armenia 4 16 17[487] –
  Guinea 48 167 159[487] –
  Guam 168 274 348[487] –
  Belize 223 240 441[487] –
  Eswatini 124 133 – –
  Djibouti 306 308 337[487] –
 World total (170 countries and territories) 2,986,573 3,517,102 1,168,383 620,384


See also

Notes

  1. ^ With a presumed identical person-to-person serial interval of loge(2.4)/0.21 ~ 4.2 days, or a distribution thereof to the same effect.
  2. ^ Logarithmic growth rate of 0.37/day means that the log odds loge(SGTF/SGTP) is increasing by 0.37 in a day. So SGTF/SGTP was increasing by a multiplicative factor of exp(0.37) ~ 1.45. This is substantially higher than a naive increase to 100%+37%. The difference is mathematically due to compound growth within the day, which does not imply that epidemically people are already infectious within a day. Rather, simplified (non-delay) differential equations are used for convenience for the modeling. This also indicates a doubling time of loge(2)/(0.37/day) ~ 1. days for the Omicron to Delta prevalence ratio.
  3. ^ Referring to ref 12 in the reference, where the x-axis is crossed at 14 December.
  4. ^ A doubling time of 2.5 days corresponds to an exponential growth rate of ln(2)/(2.5 days) ~ 0.28/day. Direct comparison to the logistic growth rate needs to take the growth/decline of Delta into account.

References

  1. ^ a b c Yadav PD, Gupta N, Potdar V, Mohandas S, Sahay RR, Sarkale P, et al. (January 2022). An in vitro and in vivo approach for the isolation of Omicron variant from human clinical specimens. pp. 2022–01.02.474750. doi:10.1101/2022.01.02.474750. from the original on 16 January 2022. Retrieved 16 January 2022.
  2. ^ a b Padin M (17 January 2022). "Feeling light-headed may be an early indication you have Omicron Covid variant". mirror. from the original on 28 January 2022. Retrieved 30 January 2022.
  3. ^ Poudel S, Ishak A, Perez-Fernandez J, Garcia E, León-Figueroa DA, Romaní L, et al. (December 2021). "Highly mutated SARS-CoV-2 Omicron variant sparks significant concern among global experts – What is known so far?". Travel Medicine and Infectious Disease. 45: 102234. doi:10.1016/j.tmaid.2021.102234. PMC 8666662. PMID 34896326.
  4. ^ "How Omicron Symptoms Compare with Other Variants". Healthline. 14 January 2022. from the original on 21 January 2022. Retrieved 30 January 2022.
  5. ^ a b Omicron's cold-like symptoms mean UK guidance 'needs urgent update'. 25 December 2021 at the Wayback Machine. The Guardian.
  6. ^ a b "Omicron Symptoms: Here's How They Differ From Other Variants". NBC Chicago. from the original on 24 January 2022. Retrieved 30 January 2022.
  7. ^ a b Slater, Jack (23 January 2022). "Is a change to your taste or smell a sign of Omicron?". Metro. from the original on 26 January 2022. Retrieved 30 January 2022.
  8. ^ a b Scribner H (21 December 2021). "Doctor reveals new nightly omicron variant symptom". Deseret News. from the original on 2 January 2022. Retrieved 1 January 2022.
  9. ^ "Does Omicron cause less damage to the lungs?". www.medicalnewstoday.com. 14 January 2022.
  10. ^ Murrison P (18 January 2022). "Omicron symptoms: Three distinctive rashes to watch for". Express.co.uk. from the original on 12 January 2022. Retrieved 30 January 2022.
  11. ^ a b Omicron's cold-like symptoms mean UK guidance 'needs urgent update' 25 December 2021 at the Wayback Machine The Guardian
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January 09, 2023
sars, omicron, variant, omicron, variant, sars, first, reported, world, health, organization, network, genomics, surveillance, south, africa, november, 2021, first, detected, botswana, spread, become, predominant, variant, circulation, around, world, following. Omicron B 1 1 529 is a variant of SARS CoV 2 first reported to the World Health Organization WHO by the Network for Genomics Surveillance in South Africa on 24 November 2021 12 13 It was first detected in Botswana and has spread to become the predominant variant in circulation around the world 14 Following the original B 1 1 529 variant several subvariants of Omicron have emerged including BA 1 BA 2 BA 3 BA 4 and BA 5 15 Since October 2022 two subvariants of BA 5 called BQ 1 and BQ 1 1 have emerged SARS CoV 2 VariantOmicronGeneral detailsWHO DesignationOmicronLineageB 1 1 529First detectedSouth AfricaDate reported24 November 2021 13 months ago 2021 11 24 StatusVariant of concernSymptomsAsymptomatic infection 1 Body ache 1 Cough 1 Fainting 2 Fatigue 3 Fever 4 Headache 5 Loss of smell or taste 6 7 less common Nasal congestion or running nose 5 Night sweats 8 unique Omicron symptom Upper respiratory tract infection 9 Skin rash 10 Sneezing 11 Sore throat 2 Cases mapCumulative confirmed Omicron variant cases by country and territory 100 000 999 999 10 000 99 999 1 000 9 999 100 999 10 99 1 9 0Major variantsAlpha B 1 1 7 Beta B 1 351 Gamma P 1 Delta B 1 617 2 Omicron B 1 1 529 BA 1 B 1 1 529 1 BA 2 B 1 1 529 2 BA 3 B 1 1 529 3 BA 4 B 1 1 529 4 BA 5 B 1 1 529 5 vteThree doses of a COVID 19 vaccine provide protection against severe disease and hospitalisation caused by Omicron and its subvariants 16 17 18 19 For three dose vaccinated individuals the BA 4 and BA 5 variants are more infectious than previous subvariants but there is no evidence of greater sickness or severity 15 20 21 Contents 1 Classification 2 History 2 1 Origin hypotheses 2 2 Spread 3 Reactions 3 1 Vaccine producers 3 2 World Health Organization 3 3 International response 3 4 Market reactions 4 Biology 4 1 Mutations 5 Subvariants 5 1 BA 2 5 1 1 Affected countries and transmissibility 5 1 2 BA 2 12 5 1 3 BA 2 75 and BA 2 75 2 5 1 3 1 XBB and XBB 1 5 2 BA 3 5 3 XE 5 4 BA 4 and BA 5 5 4 1 BQ 1 and BQ 1 1 6 Transmission 6 1 In humans 6 1 1 Vaccinated 6 1 2 Natural immunity 6 1 3 Vaccinated or natural immunity 6 2 In non human animals 6 3 Surfaces 7 Vaccine effectiveness 7 1 BA 1 and BA 2 7 2 BA 4 and BA 5 7 2 1 BQ 1 and BQ 1 1 8 Vaccine adjustments 9 Signs and symptoms 10 Virulence 10 1 BA 1 and BA 2 differences 11 Diagnosis 11 1 PCR testing 11 1 1 BA 1 and BA 2 differences 11 2 Rapid antigen testing 12 Treatment 13 Epidemiology 13 1 Reported cases 14 See also 15 Notes 16 References 17 Further reading 18 External linksClassification Edit Omicron variant and other major or previous variants of concern of SARS CoV 2 depicted in a tree scaled radially by genetic distance derived from Nextstrain on 1 December 2021 On 26 November the WHO s Technical Advisory Group on SARS CoV 2 Virus Evolution declared PANGO lineage B 1 1 529 a variant of concern and designated it with the Greek letter omicron 12 The WHO skipped the preceding letters nu and xi in the Greek alphabet to avoid confusion with the similarities of the English word new and the Chinese surname Xi 22 The name of the variant has occasionally been mistaken as Omnicron among some English speakers due to a lack of familiarity with the Greek alphabet and the relative frequency of the Latin prefix omni in other common speech 23 24 The GISAID project has assigned it the clade identifier GR 484A 25 and the Nextstrain project has assigned it the clade identifiers 21K and 21L both belonging to a larger Omicron group 21M 26 History EditOmicron was first detected on 22 November 2021 in laboratories in Botswana and South Africa based on samples collected on 11 16 November 27 with the first known samples collected in Johannesburg South Africa on 8 November 2021 28 The first known cases outside of South Africa were two people who travelled on 11 November one who flew from South Africa to Hong Kong via Qatar and another who travelled from Egypt to Belgium via Turkey 29 30 On 26 November 2021 WHO designated B 1 1 529 as a variant of concern and named it Omicron after the fifteenth letter in the Greek alphabet 12 As of 6 January 2022 the variant had been confirmed in 149 countries 31 Origin hypotheses Edit Omicron did not evolve from any other variant but instead diverged on a distinct track perhaps in mid 2020 31 32 Competing hypotheses are being examined One origin hypothesis is that various mutations in the Omicron variant comprising a 9 nucleotide sequence may have been acquired from another coronavirus known as HCoV 229E responsible for the common cold 33 This is not entirely unexpected at times viruses within the body acquire and swap segments of genetic material from each other and this is one common means of mutation 33 A link with HIV infection may explain a large number of mutations in the sequence of the Omicron variant 34 Indeed in order to be affected by such a high number of mutations the virus must have been able to evolve a long time without killing its host which can occur in people with a weakened immune system who receive enough medical care to survive 34 35 This is the case in HIV patients in South Africa who represent about 14 of the population as of 2017 36 HIV prevention could be key to reducing the risk of uncontrolled HIV driving the emergence of SARS CoV 2 variants 34 One hypothesis to explain the novel mutations is that SARS CoV 2 was transmitted from humans to mice and mutated in a population of mice sometime between mid 2020 and late 2021 before reinfecting humans 32 On 1 December 2022 a team of researchers from the Charite Berlin published a study in Science journal that claimed that data revealed genetically diverse Omicron ancestors already existed across Africa by August 2021 37 After a re analysis because of doubts 38 the team has retracted the article on 20 December 2022 due to contamination of the samples 39 40 Spread Edit On 24 November 2021 the variant was first reported to the WHO from South Africa based on samples that had been collected from 14 to 16 November 27 South African scientists were first alerted by samples from the very beginning of November where the PCR tests had S gene target failure occurs in a few variants but not in Delta which dominated in the country in October and by a sudden increase of COVID 19 cases in Gauteng sequencing revealed that more than 70 percent of samples collected in the province between 14 and 23 November were a new variant 41 The first confirmed specimens of Omicron were collected on 8 November 2021 in South Africa and on 9 November in Botswana 42 Likely Omicron SGTF samples had occurred on 4 November 2021 in Pretoria South Africa When WHO was alerted on 24 November Hong Kong was the only place outside Africa that had confirmed a case of Omicron one person who traveled from South Africa on 11 November and another traveler who was cross infected by this case while staying in the same quarantine hotel 29 On 25 November one confirmed case was identified in Israel from a traveler returning from Malawi 43 along with two who returned from South Africa and one from Madagascar 44 All four initial cases reported from Botswana occurred among fully vaccinated individuals 45 On 26 November Belgium confirmed its first case an unvaccinated person who had travelled from Egypt via Turkey on 11 November 30 All three initial confirmed and suspected cases reported from Israel occurred among fully vaccinated individuals 43 as did a single suspected case in Germany 46 On 27 November two cases were detected in the United Kingdom another two in Munich Germany and one in Milan Italy 47 On 28 November 13 cases were confirmed in the Netherlands among the 624 airline passengers who arrived from South Africa on 26 November 48 Confirmation of a further 5 cases among these passengers followed later 49 Entry into the Netherlands generally required having been vaccinated or PCR tested or having recovered The passengers of these two flights had been tested upon arrival because of the newly imposed restrictions which were set in place during their flight after which 61 tested positive for SARS CoV 2 50 A further two cases were detected in Australia Both people landed in Sydney the previous day and travelled from southern Africa to Sydney Airport via Doha Airport The two people who were fully vaccinated entered isolation 12 other travellers from southern Africa also entered quarantine for fourteen days while about 260 other passengers and crew on the flight were directed to isolate 51 Two travellers from South Africa who landed in Denmark tested positive for COVID 19 it was confirmed on 28 November that both carried the Omicron variant 52 53 On the same day Austria also confirmed its first Omicron case 54 A detected Omicron case was reported in the Czech Republic from a traveler who spent time in Namibia 55 Canada also reported its first Omicron cases with two from travelers from Nigeria therefore becoming the first North American country to report an Omicron case 56 On 29 November a positive case was recorded in Darwin Australia The person arrived in Darwin on a repatriation flight from Johannesburg South Africa on 25 November and was taken to a quarantine facility where the positive test was recorded 57 Two more people who travelled to Sydney from southern Africa via Singapore tested positive 58 Portugal reported 13 Omicron cases all of them members of a soccer club 59 Sweden also confirmed their first case on 29 November 60 as did Spain when a traveler came from South Africa 61 On 30 November the Netherlands reported that Omicron cases had been detected in two samples dating back as early as 19 November 62 A positive case was recorded in Sydney from a traveller who had visited southern Africa before travel restrictions were imposed and was subsequently active in the community 63 Japan also confirmed its first case 64 Two Israeli doctors tested positive and entered isolation Both of them had received three shots of the Pfizer vaccine prior to testing positive 65 In Brazil three cases of the Omicron variant were confirmed in Sao Paulo 66 Another five are under suspicion 67 68 A person in Leipzig Germany with no travel history nor contact with travellers tested positive for Omicron 69 On 1 December the Omicron variant was detected in three samples in Nigeria that had been collected from travelers from South Africa within the last week 70 71 On the same day public health authorities in the United States announced the country s first confirmed Omicron case A resident of San Francisco who had been vaccinated returned from South Africa on 22 November began showing mild symptoms on 25 November 72 and was confirmed to have a mild case of COVID 19 on 29 November 73 Ireland and South Korea also reported their first cases 74 South Korea reported its cases from five travelers arriving in South Korea from Nigeria 75 On 2 December Dutch health authorities confirmed that all 14 passengers with confirmed Omicron infection on 26 November had been previously vaccinated 76 The same day the Norwegian Institute of Public Health confirmed that 50 attendees of a company Christmas party held at a restaurant in Norway s capital Oslo were infected with the Omicron variant 77 France has confirmed only 25 cases of the new Omicron variant but officials say the number could jump significantly in the coming weeks 78 By 6 December Malaysia confirmed its first case of the variant The case was a South African student entering to study at a private university 79 In Namibia 18 cases out of 19 positive COVID 19 samples that had been collected between 11 and 26 November were found to be Omicron indicating a high level of prevalence in the country 80 Fiji also confirmed two positive cases of the variant They travelled from Nigeria arriving in Fiji on November 25 81 On 9 December Richard Mihigo coordinator of the World Health Organisation s Immunisation and Vaccine Development Programme for Africa announced that Africa accounted for 46 of reported cases of the Omicron variant globally 82 On 13 December the first death of a person with Omicron was reported in the UK 83 On 16 December New Zealand confirmed its first case of the Omicron variant an individual who had traveled from Germany via Dubai 84 The first death of a person with Omicron was reported in Germany on 23 December 85 and in Australia on 27 December 86 By Christmas 2021 the Omicron Strain became dominant in the US 87 On 3 January 2022 South Korea reported the first two deaths of people who tested positive post mortem for Omicron 88 On 29 March 2022 Omicron subvariant BA 2 overtook BA 1 and became the dominant strain in the U S 89 90 91 As of May 2022 BA 2 12 1 was spreading in the US and two new subvariants of Omicron named BA 4 and BA 5 first detected in January 2022 spread in South Africa All 3 subvariants have spike protein mutations of L452 and elude immunity from prior BA1 infection 92 Reactions EditVaccine producers Edit On 26 November 2021 BioNTech said it would know in two weeks whether the current vaccine is effective against the variant and that an updated vaccine could be shipped in 100 days if necessary AstraZeneca Moderna and Johnson amp Johnson were also studying the variant s impact on the effectiveness of their vaccines 93 On the same day Novavax stated that it was developing an updated vaccine requiring two doses for the Omicron variant which the company expected to be ready for testing and manufacturing within a few weeks 94 95 On 29 November 2021 The Gamaleya Institute said that Sputnik Light should be effective against the variant that it would begin adapting Sputnik V and that a modified version could be ready for mass production in 45 days 96 Sinovac said it could quickly mass produce an inactivated vaccine against the variant and that it was monitoring studies and collecting samples of the variant to determine if a new vaccine is needed 97 On 7 December 2021 at a symposium in Brazil with its partner Instituto Butantan Sinovac said it would update its vaccine to the new variant and make it available in three months 98 On 2 December the Finlay Institute was already developing a version of Soberana Plus against the variant 99 Pfizer hoped to have a vaccine targeted to immunize against Omicron ready by March 2022 100 World Health Organization Edit On 26 November 2021 the WHO asked nations to enhance surveillance and sequencing efforts submit complete genome sequences and associated metadata to a publicly available database such as GISAID report initial cases clusters associated with virus of concern infection to WHO through the IHR mechanism where capacity exists and in coordination with the international community perform field investigations and laboratory assessments to improve understanding of the potential impacts of the virus of concern on COVID 19 epidemiology severity and the effectiveness of public health and social measures diagnostic methods immune responses antibody neutralization or other relevant characteristics 101 On 26 November 2021 WHO advised countries not to impose new restrictions on travel instead recommending a risk based and scientific approach to travel measures 102 On the same day the European Centre for Disease Prevention and Control ECDC reported modeling indicating that strict travel restrictions would delay the variant s impact on European countries by two weeks possibly allowing countries to prepare for it 103 As with other variants the WHO recommended that people continue to keep enclosed spaces well ventilated avoid crowding and close contact wear well fitting masks clean hands frequently and get vaccinated 104 105 On 29 November 2021 the WHO said cases and infections were expected among those vaccinated albeit in a small and predictable proportion 106 International response Edit After the WHO announcement on the same day several countries announced travel bans from southern Africa in response to the identification of the variant including the United States which banned travel from eight African countries 107 although as of 30 November 2021 it notably did not ban travel from any European countries Israel Canada or Australia where cases were also detected at the time the bans were announced Other countries that also implemented travel bans include Japan Canada the European Union Israel Australia the United Kingdom Singapore Malaysia Indonesia Morocco and New Zealand 108 109 On 26 November 2021 the Brazilian Health Regulatory Agency recommended flight restrictions regarding the new variant 110 The state of New York declared a state of emergency ahead of a potential Omicron spike although no cases had yet been detected in the state or the rest of the United States 111 On 27 November 2021 Switzerland introduced obligatory tests and quarantine for all visitors arriving from countries where the variant was detected which originally included Belgium and Israel 112 On 26 November 2021 South African Minister of Health Joe Phaahla defended his country s handling of the pandemic and said that travel bans went against the norms and standards of the World Health Organization 113 Some speculated that travel bans could have a significant impact on South Africa s economy by limiting tourism and could lead to other countries with economies that are reliant on tourism to hide the discovery of new variants of concern Low vaccine coverage in less developed nations could create opportunities for the emergence of new variants and these nations also were struggling to gain intellectual property to develop and produce vaccines locally 114 At the same time inoculation had slowed in South Africa due to vaccine hesitancy and apathy with a nationwide vaccination rate of only 35 as of November 24 2021 115 On 29 November 2021 the WHO warned countries that the variant poses a very high global risk with severe consequences and that they should prepare by accelerating vaccination of high priority groups and strengthening health systems WHO director general Tedros Adhanom described the global situation as dangerous and precarious and called for a new agreement on the handling of pandemics as the current system disincentivizes countries from alerting others to threats that will inevitably land on their shores CEPI CEO Richard Hatchett said that the variant fulfilled predictions that transmission of the virus in low vaccination areas would accelerate its evolution 106 In preparation for the Omicron variant arriving in the United States President Joe Biden stated that the variant is cause for concern not panic reiterated that the government was prepared for the variant and would have it under control and that large scale lockdowns similar to the ones in 2020 near the beginning of the pandemic were off the table for now 116 In mid December 2021 multiple Canadian provinces reinstated restrictions on gatherings and events such as sports tournaments and tightened enforcement of proof of vaccination orders British Columbia expressly prohibited any non seated organized New Year s Eve event 117 118 119 while Quebec announced a partial lockdown on 20 December 2021 ordering the closure of all bars casinos gyms schools and theatres as well as imposing restrictions on the capacity and operating hours of restaurants and the prohibition of spectators at professional sporting events 120 On 18 December 2021 the Netherlands government announced a lockdown intended to prevent spread of the variant during the holiday period 121 In late December 2021 some countries shortened the typical six month interval for a booster dose of the vaccine to prepare for a wave of Omicron as two doses are not enough to stop the infection UK South Korea and Thailand reduced to three months Belgium four months France Singapore Taiwan Italy and Australia five months Finland reduced it to three months for risk groups Other countries continued with a six month booster schedule While antibody levels begin to drop at four months a longer interval usually allows time for the immune system s response to mature 122 Market reactions Edit Main article Financial market impact of the COVID 19 pandemic On 26 November 2021 worry about the potential economic impact of the Omicron variant led to a drop in global markets including the worst drop of the Dow Jones Industrial Average in 2021 led by travel related stocks The price of Brent Crude and West Texas Intermediate oil fell 10 and 11 7 respectively 123 Cryptocurrency markets were also routed 124 125 and the South African rand also hit an all time low for 2021 trading at over 16 rand to the dollar losing 6 of its value in November 126 127 128 In early December 2021 Jerome Powell the chairman of the Federal Reserve testified before the U S Senate Committee on Banking that The recent rise in COVID 19 cases and the emergence of the Omicron variant pose downside risks to employment and economic activity and increased uncertainty for inflation 129 Biology Edit The genomic sequence of the Omicron variant is pictured above Mutations Edit As of June 2022 Omicron had about 50 mutations which is more than any previous SARS CoV 2 variant 32 of which pertained to the spike protein which most vaccines target to neutralise the virus 130 As of December 2021 many mutations were novel and not found in previous variants 42 As of April 2022 the variant was characterised by 30 amino acid changes three small deletions and one small insertion in the spike protein compared with the original virus of which 15 are located in the receptor binding domain residues 319 541 131 As of December 2022 the virus carried a number of changes and deletions in other genomic regions For example three mutations at the furin cleavage site which facilitates its transmission 132 133 Illustration of the locations of the Omicron mutations in the spike protein top view left and side view right showing amino acid substitutions yellow deletions red and insertions green In this trimeric structure two monomers gray and light blue have their receptor binding domains in the down conformation while one dark blue is in the up or open conformation Mutation data from WHO 104 structure from PDB 6VYB 134 Comparison of mutation prevalence for ORF1a ORF1b and S genes of Omicron lineages that are designated Variants of Concern Characteristic mutations for a lineage are defined as nonsynonymous substitutions or deletions that occur in gt 75 of sequences within that lineage 135 Subvariants EditSeveral subvariants of Omicron have been discovered and new ones continue to emerge 14 There are 310 Pango lineages currently associated with the Omicron variant 136 The standard sublineage is now referred to as BA 1 or B 1 1 529 1 and the two other sublineages are known as BA 2 or B 1 1 529 2 and BA 3 or B 1 1 529 3 137 In mid 2022 BA 4 or B 1 1 529 4 and BA 5 or B 1 1 529 5 were detected in several countries 138 They share many mutations but also significantly differ In general BA 1 and BA 2 share 32 mutations but differ by 28 139 BA 1 has itself been divided in two the original BA 1 and BA 1 1 or B 1 1 529 1 1 where the main difference is that the latter has a R346K mutation 140 Standard PCR and rapid tests continue to detect all Omicron subvariants as COVID 19 but further tests are necessary to distinguish the subvariants from each other and from other COVID 19 variants 141 Defining mutations in theSARS CoV 2 Omicron variant Gene Amino acidORF1ab nsp3 K38Rnsp3 V1069Insp3 D1265nsp3 L1266Insp3 A1892Tnsp4 T492Insp5 P132Hnsp6 D105 107nsp6 A189Vnsp12 P323Lnsp14 I42VSpike A67VD69 70T95IG142D D143 145D211L212Iins214EPEG339DS371LS373PS375FK417NN440KG446SS477NT478KE484AQ493RG496SQ498RN501YY505HT547KD614GH655YN679KP681HN764KD796YN856KQ954HN969KL981FE T9IM D3GQ19EA63TN P13LD31 33R203KG204RSources UK Health Security Agency 142 CoVariants 26 BA 2 Edit A laboratory study on hamsters and mice in Japan published as a non peer reviewed preprint in mid February 2022 suggested that BA 2 is not only more transmissible than BA 1 but may cause more severe disease 143 This was later disproven by a study in late October 2022 that found BA 2 actually caused less severe disease relative to BA 1 which in turn caused less severe disease compared to the delta variant 144 Therapeutic monoclonal antibodies used to treat people infected with COVID 19 did not have much effect on BA 2 which was almost completely resistant to casirivimab and imdevimab and 35 times more resistant to sotrovimab than the BA 1 subvariant Affected countries and transmissibility Edit According to early research BA 2 is roughly 30 to 60 more transmissible than BA 1 145 146 The first known sequence of BA 2 was in a sample from 15 November 2021 147 As of 17 January 2022 BA 2 had been detected in at least 40 countries and in all continents except Antarctica 148 By 31 January it had been detected in at least 57 countries 149 In global samples collected from 4 February to 5 March and uploaded to GISAID BA 2 accounted for c 34 compared to 41 for BA 1 1 25 for BA 1 and less than 1 for BA 3 150 In a review two weeks later covering 16 February to 17 March BA 2 had become the most frequent 151 However the data is geographically skewed due to sequencing rate and speed for example among the c 205 000 COVID 19 sequences from March that had been uploaded to GISAID as of 22 March United Kingdom and Denmark accounted for more than 3 4 and most of the remaining were from other European countries Australia Canada and the United States altogether c 6 000 were from Africa Asia and Latin America 152 Based on GISAID uploads BA 1 peaked in early January 2022 after which it was overtaken by both BA 1 1 and BA 2 153 In North America parts of Europe and parts of Asia BA 1 was first outcompeted by BA 1 1 For example in the United States France and Japan BA 1 1 became the dominant subvariant in January 2022 154 155 156 By late December 2021 early January 2022 BA 2 appeared to have become dominant in at least parts of India already making up almost 80 percent in Kolkata in late December 2021 157 and the Philippines had become frequent in Scandinavia South Africa and Singapore and was showing signs of growth in Germany and the United Kingdom 158 159 160 161 In Japan which has quarantine and detailed screening of all international travellers as of 24 January the vast majority of BA 2 had been detected in people that had arrived from India or the Philippines with cases going back at least to 1 December 2021 far fewer BA 1 or other variants were detected among arrivals from the two countries in that period but small numbers had also been detected in people arriving from other countries 162 163 164 In Denmark the first BA 2 was in a sample collected on 5 December 2021 and extremely few were found in the directly following period 165 By week fifty 13 19 December it had started to increase with BA 2 being at around 2 percent of sequenced cases compared to 46 percent BA 1 remaining Delta The frequency of both Omicron subvariants continued to increase throughout the last half of December in week fifty two 27 December 2 January BA 2 had reached 20 percent and BA 1 peaked at 72 percent In January 2022 BA 1 began decreasing whereas BA 2 continued its increase By the second week 10 16 January of 2022 the frequency of the two was almost equal both being near 50 percent around one percent was the rapidly disappearing Delta 165 In the following week BA 2 became clearly dominant in Denmark with 65 percent of new cases being the BA 2 subvariant 166 Trends from the other Scandinavian countries India South Africa and the United Kingdom also showed that BA 2 was increasing in proportion to BA 1 167 168 In early February 2022 it had become the dominant subvariant in South Africa in late February it had become dominant in Germany and in early March it had become dominant in the United Kingdom 169 170 171 In early March BA 1 1 was still heavily dominant in the United States having overtaken BA 1 in January but BA 2 was increasing in frequency later becoming dominant in the US by 29 March 154 172 BA 2 12 Edit There were two new BA 2 subvariants detected in the US state of New York which are BA 2 12 or B 1 1 529 2 12 and BA 2 12 1 or B 1 1 529 2 12 1 both of which have a significant growth advantage of 23 27 over BA 2 and contributing to a rise in infections in central New York centred on Syracuse and Lake Ontario which later became dominant by May 24 in the US 173 BA 2 75 and BA 2 75 2 Edit The subvariant BA 2 75 or B 1 1 529 2 75 nicknamed Centaurus by the media 174 first detected in India in May 2022 has been classified as variant under monitoring by the WHO 175 Additional newer mutations in this line like BA 2 75 2 aka B 1 1 529 2 75 2 or Chiron may be capable of escaping neutralizing antibodies 176 XBB and XBB 1 Edit XBB a recombinant of the BA 2 10 1 and BA 2 75 sublineages 177 is an Omicron subvariant first detected in August 2022 178 Described as immune evasive it has caused a small surge of cases in countries including Singapore and Bangladesh 179 On 20 October 2022 the chief scientist of the World Health Organization WHO Soumya Swaminathan warned that the XBB subvariant of Omicron may cause infections in some countries while the severity of the new variants is not yet known 180 Early observations from Singapore indicated the possibility of XBB being less severe compared to the omicron BA 5 variant with data from the first two weeks in October 2022 indicating that the XBB variant had a 30 lower hospitalisation risk 181 However this could also be due to high levels of population immunity from vaccination and previous waves BA 3 Edit The third Omicron sublineage BA 3 is very rare It has the same S gene target failure SGTF deletion D69 70 as BA 1 XE Edit A new BA 1 BA 2 recombinant isolated from the UK in January 2022 dubbed the XE recombinant was found by the WHO to be potentially 10 more transmissible than BA 2 making it about 43 to 76 to more transmissible than BA 1 and making the XE recombinant the most contagious variant identified 182 BA 4 and BA 5 Edit In April 2022 the WHO announced it was tracking the BA 4 and BA 5 subvariants with BA 4 having been detected in South Africa Botswana Denmark Scotland and England 183 Early indications from data collected in South Africa suggested BA 4 and BA 5 have a significant growth advantage over BA 2 which by 12 May earned the status Variant of Concern by the European Centre for Disease Prevention and Control and by 20 May by the UK Health Security Agency 184 185 186 187 BA 5 was dominant in Portugal by 25 May accounting for two thirds of all new cases there 188 By 24 June BA 4 and BA 5 together had become dominant variants in the UK and Germany 189 190 191 192 These two subvariants became dominant in the United States by 28 June 193 194 By late June BA 5 became the dominant subvariant in France with 59 of new cases linked to it 195 196 On 10 May 2022 a case of a new subvariant BA 5 2 1 was reported in California 197 On 10 July the city of Shanghai reported its first case of BA 5 2 1 in a man who had flown in from Uganda sparking a new wave of testing 198 On 22 July the province of Ontario Canada announced that subvariant BA 5 2 1 overtook BA 2 12 1 as the main variant in circulation in Ontario around 2 July 199 Regeneron is reporting that BA 5 2 1 is the main variant in Australia Belgium Brunei Greece and Iceland 200 The government of Canada is also reporting that in late June and July of the travelers arriving by air who test positive for COVID 19 a substantial proportion are BA 5 2 1 201 BF 7 is a shortened version of the sub variants full name which is BA 5 2 1 7 This sub variant is part of Omicron s BA 5 variant which has the highest number of reported cases globally accounting for 76 2 of all cases 202 BQ 1 and BQ 1 1 Edit Since October 2022 two BA 5 subvariants were found BQ 1 or B 1 1 529 5 3 1 1 1 1 1 nicknamed Typhon by the media and BQ 1 1 or B 1 1 529 5 3 1 1 1 1 1 1 nicknamed Cerberus 203 204 205 They have been more prevalent in France than any other European country 206 As of 17 November 93 of sequences in France were Omicron sub lineage BA 5 and among the BA 5 sub lineages BQ 1 1 continued to rise 32 vs 25 in the prior week 207 according to Nextclade even 55 208 they were reported in the US to have become dominant accounting for 44 of new infections up from 33 the previous week Early laboratory tests found that these subvariants were better at escaping first and booster vaccines than previous variants however no new treatments appeared to be in development Virologist Andy Pekosz said that the mutations have pretty much eliminated every single monoclonal antibody on the market right now in terms of their efficacy 209 Transmission Edit False color transmission electron micrograph of an Omicron variant coronavirus shown in pink replicating within the cytoplasm of an infected Vero cell In humans Edit In January 2022 William Schaffner professor of infectious diseases at Vanderbilt University Medical Center compared the contagiousness of the Omicron variant to that of the measles 210 Vaccinated Edit It was not known in November 2021 how Omicron would spread in populations with high levels of immunity or if it causes a milder or more severe disease On 15 December 2021 Jenny Harries head of the UK Health Security Agency told a parliamentary committee that the doubling time of COVID 19 in most regions of the UK was now less than two days despite the country s high vaccination rate She said that the Omicron variant of COVID 19 is probably the most significant threat since the start of the pandemic and that the number of cases in the next few days would be quite staggering compared to the rate of growth that we ve seen in cases for previous variants 211 Natural immunity Edit Relating to naturally acquired immunity Anne von Gottberg an expert at the South African National Institute for Communicable Diseases believed at the beginning of December 2021 that immunity granted by previous variants would not protect against Omicron 212 Vaccinated or natural immunity Edit A study suggests that mutations that promote breakthrough infections or antibody resistance like those in Omicron could be a new mechanism for viral evolution success of SARS CoV 2 and that such may become a dominating mechanism of its evolution 213 A preprint supports such an explanation of Omicron s spread suggesting that it primarily can be ascribed to the immune evasiveness rather than an inherent increase in the basic transmissibility 214 215 Studies showed the variant to escape the majority of existing SARS CoV 2 neutralizing antibodies including those in sera from vaccinated and convalescent individuals 216 217 218 219 Nevertheless current vaccines are expected to protect against severe illness hospitalizations and deaths due to Omicron 220 and on an individual level the Omicron variant is milder than earlier variants that evolved when the antibody vaccination share was lower than it was when Omicron emerged 221 In contrast to other investigated variants Omicron showed substantial population level evasion of immunity from prior infection as well as a higher ability to evade immunity induced by vaccines 222 In non human animals Edit In February 2022 the first confirmed case infecting a wild animal was confirmed by researchers at Pennsylvania State University in white tailed deer in Staten Island N Y 223 Surfaces Edit Although transmission via fomites is rare preliminary data indicate that the variant lasts for 194 hours on plastic surfaces and 21 hours on skin compared with just 56 and 7 hours respectively for the original strain 224 225 Vaccine effectiveness EditPfizer BioNTech BNT162b2 and Moderna mRNA 1273 mRNA vaccines provide reduced protection against asymptomatic disease but do reduce the risk of serious illness 226 227 228 On 22 December 2021 the Imperial College COVID 19 Response Team reported an about 41 95 CI 37 45 lower risk of a hospitalization requiring a stay of at least 1 night compared to the Delta variant and that the data suggested that recipients of 2 doses of the Pfizer BioNTech the Moderna or the Oxford AstraZeneca vaccine were substantially protected from hospitalization 229 In January 2022 results from Israel suggested that a fourth dose is only partially effective against Omicron Many cases of infection broke through albeit a bit less than in the control group even though trial participants had higher antibody levels after the fourth dose 230 On 23 December 2021 Nature indicates that though Omicron likely weakens vaccine protection reasonable effectiveness against Omicron may be maintained with currently available vaccination and boosting approaches 231 232 In December studies some of which using large nationwide datasets from either Israel and Denmark found that vaccine effectiveness of multiple common two dosed COVID 19 vaccines is substantially lower against the Omicron variant than for other common variants including the Delta variant and that a new often a third dose a booster dose is needed and effective as it substantially reduces deaths from the disease compared to cohorts who received no booster but two doses 233 234 235 236 237 238 Vaccines continue to be recommended for Omicron and its subvariants Professor Paul Morgan immunologist at Cardiff University said I think a blunting rather than a complete loss of immunity is the most likely outcome The virus can t possibly lose every single epitope on its surface because if it did that spike protein couldn t work any more So while some of the antibodies and T cell clones made against earlier versions of the virus or against the vaccines may not be effective there will be others which will remain effective If half or two thirds or whatever it is of the immune response is not going to be effective and you re left with the residual half then the more boosted that is the better 239 Professor Francois Balloux of the Genetics Institute at University College London said From what we have learned so far we can be fairly confident that compared with other variants Omicron tends to be better able to reinfect people who have been previously infected and received some protection against COVID 19 That is pretty clear and was anticipated from the mutational changes we have pinpointed in its protein structure These make it more difficult for antibodies to neutralise the virus 240 BA 1 and BA 2 Edit A January 2022 study by the UK Health Security Agency found that vaccines afforded similar levels of protection against symptomatic disease by BA 1 and BA 2 and in both it was considerably higher after two doses and a booster than two doses without booster 241 242 though because of the gradually waning effect of vaccines further booster vaccination may later be necessary 171 BA 4 and BA 5 Edit In May 2022 a preprint indicated Omicron subvariants BA 4 and BA 5 could cause a large share of COVID 19 reinfections beyond the increase of reinfections caused by the Omicron lineage even for people who were infected by Omicron BA 1 due to increases in immune evasion especially for the unvaccinated However the observed escape of BA 4 and BA 5 from immunity by a BA 1 infection is more moderate than of BA 1 against studied prior cases of immunity such as immunity from specific vaccines 243 244 Immunity from an Omicron infection for unvaccinated and previously uninfected was found to be weak against non Omicron variants 245 albeit at the time Omicron is by a large margin the dominant variant in sequenced human cases 246 BQ 1 and BQ 1 1 Edit Subvariants BQ 1 and BQ 1 1 were found in late 2022 to be better at escaping first and booster vaccines than previous variants and to have pretty much eliminated every single monoclonal antibody on the market right now in terms of their efficacy citation needed Vaccine adjustments EditSee also Universal coronavirus vaccineAs of June 2022 researchers health organizations and regulators are discussing investigating including with preliminary laboratory studies and trials and partly recommending COVID 19 vaccine boosters that mix the original vaccine formulation with Omicron adjusted parts such as spike proteins of a specific Omicron subvariant to better prepare the immune system to recognize a wide variety of variants amid substantial and ongoing immune evasion by Omicron and other SARS CoV 2 variants 247 In June 2022 Pfizer and Moderna developed bivalent vaccines to protect against the SARS COV 2 wild type and the Omicron variant The bivalent vaccines are well tolerated and offer immunity to omicron superior to previous mRNA vaccines 248 The United States Food and Drug Administration FDA has authorized the bivalent vaccines for use in the USA 249 Signs and symptoms EditMain article Symptoms of COVID 19 Loss of taste and smell seem to be uncommon compared to other strains 6 7 A unique reported symptom of the Omicron variant is night sweats 8 250 particularly with the BA 5 subvariant 251 252 A study performed between 1 and 7 December 2021 by the Center for Disease Control found that The most commonly reported symptoms were cough fatigue and congestion or runny nose making it difficult to distinguish from a less damaging variant or another virus 253 Research published in London on 25 December 2021 suggested the most frequent symptoms stated by users of the Zoe Covid app were a runny nose headaches fatigue sneezing and sore throats 11 A British omicron case control observational study until March 2022 showed a reduction in odds of long COVID with the omicron variant versus the delta variant of 0 24 0 5 depending on age and time since vaccination 254 Virulence EditAs of 6 January 2022 Omicron multiplied around 70 times faster than the Delta variant in the bronchi lung airways but evidence suggested it is less severe than previous variants especially compared to Delta 255 221 since it might be less able to penetrate deep lung tissue 256 As of January 2022 in southern California infections were 91 percent less fatal than the delta variant with 51 percent less risk of hospitalization 257 However the estimated difference in the intrinsic risk of hospitalization in England largely decreased to 0 30 percent when reinfections were excluded 258 BA 1 and BA 2 differences Edit As of 21 January 2022 the risk of hospitalization was the same in BA 1 and BA 2 based on reviews from Denmark India South Africa and the United Kingdom 259 150 166 260 Norwegian studies showed that the amount of virus in the upper airways was similar in those infected with BA 1 and BA 2 168 Diagnosis EditSee also COVID 19 testingAs of November 2021 the chance of detecting an Omicron case particularly depended on a country s sequencing rate with South Africa sequencing far more samples than any other country in Africa but at a considerably lower rate than most Western nations 261 262 Furthermore it could take up to two weeks to return a viral sequence in places with the technical capability hence solid statistics on confirmed cases have lagged the actual situation 263 PCR testing Edit In December 2021 the US FDA published guidelines on how PCR tests would be affected by Omicron 264 Tests that detect multiple gene targets were to continue to identify the testee as positive for COVID 19 S gene dropout or target failure was proposed as a shorthand way of differentiating Omicron from Delta besides sequencing and genotyping 265 As of December 2021 Denmark and Norway have regarded cases found by their variant qPCR test which is relatively fast and checks several genes 266 as sufficient for counting it as Omicron before full sequencing 267 268 BA 1 and BA 2 differences Edit As of 7 December 2021 it was known that BA 2 unlike Ba1 lacks the characteristic S gene target failure SGTF causing deletion D69 70 by which many qPCR tests have been able to rapidly detect a case as an Omicron or Alpha variant from the previously dominant Delta variant 269 270 Thus countries which primarily rely on SGTF for detection may overlook BA 2 269 and British authorities consider SGTF alone as insufficient for monitoring the spread of Omicron 259 This has resulted in it having been nicknamed Stealth Omicron 259 but because BA 2 still can be separated from other variants through normal full sequencing or checks of certain other mutations the nickname is not quite accurate 139 271 As of January 2022 some countries such as Denmark and Japan have been using a variant qPCR which tests for several mutations including L452R 266 162 It can also distinguish Delta which has L452R 272 and all Omicron subvariants which do not have L452R 273 148 As Omicron became dominant and the Delta variant became rare in early 2022 the SGTF mutation that had made Delta and BA 2 similar in qPCR tests was found to be useful for separating BA 1 and BA 2 from each other 274 Rapid antigen testing Edit In January 2022 the medicine and therapeutic regulatory agency Therapeutic Goods Administration TGA of the Australian Government found that only one of their 23 approved COVID 19 rapid antigen tests RAT stated that it detected Omicron 275 In June 2022 the German federal Paul Ehrlich Institute published their findings that most RATs detected the Omicron Variant 276 Treatment EditSee also Treatment and management of COVID 19 As of 28 November 2021 Corticosteroids such as dexamethasone and IL6 receptor blockers such as tocilizumab Actemra were known to be effective for managing patients with the earlier strains of severe COVID 19 but the impact on the effectiveness of other treatments was being assessed 277 278 Relating to monoclonal antibodies mAbs treatments similar testing and research is ongoing Preclinical data on in vitro pseudotyped virus data demonstrate that some mAbs designed to use highly conserved epitopes retain neutralizing activity against key mutations of Omicron substitutions 279 Similar results are confirmed by cryo electron microscopy and X ray data also providing the structural approach and molecular basis for the evasion of humoral immunity exhibited by Omicron antigenic shift as well as the importance of targeting conserved epitopes for vaccine and therapeutics design While 7 clinical mAbs or mAb cocktails experienced loss of neutralizing activity of 1 2 orders of magnitude or greater relative to the prototypic virus the S309 mAb the parent mAb of sotrovimab neutralized Omicron with only 2 3 fold reduced potency 280 As of December 2021 most monoclonal antibodies had lost in vitro neutralizing activity against Omicron with only 3 out of 29 mAbs examined in another study retaining unaltered potency Furthermore a fraction of broadly neutralizing sarbecovirus mAbs neutralized Omicron through recognition of antigenic sites outside the RBM including sotrovimab VIR 7831 S2X259 and S2H97 281 However sotrovimab was not fully active against the BA 2 Omicron sublineage and in March2022 the office of the U S ASPR stopped distributing the antibody treatment to states where BA 2 was dominant 282 February 2022 data suggested Omicron caused significant humoral immune evasion while neutralizing antibodies targeting the sarbecovirus conserved region remained most effective 283 Epidemiology EditOn 26 November 2021 the South African National Institute for Communicable Diseases announced that 30 904 COVID 19 tests in one day detected 2 828 new COVID 19 infections a 9 2 positivity rate 284 One week later on 3 December 2021 the NICD announced that 65 990 COVID 19 tests had found 16 055 new infections 5 7 times as many as seven days before positive rate 24 3 and that 72 percent of them were found in Gauteng 285 286 This province of South Africa is densely populated at about 850 inhabitants per km2 Gauteng s capital Johannesburg is a megacity about 5 5 million inhabitants in the city itself plus 9 5 million in the urban region In November 2021 the transmissibility of the Omicron variant as compared to the Delta variant or other variants of the COVID 19 virus was still uncertain 287 Omicron is frequently able to infect previously COVID 19 positive people 288 289 It has been estimated the Omicron variant diverged in late September or early October 2021 based on Omicron genome comparisons 290 Sequencing data suggests that Omicron had become the dominant variant in South Africa by November 2021 the same month where it had been first identified in the country 291 292 Phylogeny suggests a recent emergence Data from South Africa suggests that Omicron has a pronounced growth advantage there However this may be due to transmissibility or immune escape related or both 293 Also the serial interval plays a role in the growth Detectable changes in levels of COVID 19 in wastewater samples from South Africa s Gauteng province were seen as early as 17 23 October week 42 294 The National Institute for Communicable Diseases reports that children under the age of 2 make up 10 of total hospital admissions in the Omicron point of discovery Tshwane in South Africa 295 Data on the S gene target failure SGTF of sampled cases in South Africa indicates a growth of 21 per day relative to Delta generating an increased reproduction number by a factor of 2 4 a Omicron became the majority strain in South Africa around 10 November 296 297 Another analysis showed 32 growth per day in Gauteng South Africa having become dominant there around 6 November 298 In the UK the logarithmic growth rate of Omicron associated S gene target failure SGTF cases over S gene target positive SGTP cases was estimated at 0 37 per day b which is exceptionally high 299 Furthermore by 14 December it appears to have become the most dominant strain c 300 Without presuming behavior change in response to the variant a million infections per day by 24 December are projected for a 2 5 days doubling time d 265 In Denmark the growth rate has been roughly similar with a doubling time of about 2 3 days it having become the most prevalent strain on 17 December 301 302 303 Switzerland is not far behind 304 In Germany Omicron became the most prevalent variant on 1 January 305 In Scotland Omicron apparently became the most prevalent variant on 17 December 306 307 In the Canadian province of Ontario it became the most prevalent strain on 13 December 308 In the US the variant appears to have become the most prevalent strain on 18 December growing at 0 24 per day 309 In Portugal Omicron had reached 61 5 of cases on 22 December 310 In Belgium the strain has become the most prevalent on 25 December 311 and in the Netherlands on 28 December 312 In Italy it had reached 28 of cases on 20 December and was doubling every two days 313 while it became the dominant variant in Norway on 25 December 314 In France it made up about 15 of COVID 19 cases in mid December but around 27 December it had increased to more than 60 315 316 Researchers recommend sampling at least 5 of COVID 19 patient samples in order to detect Omicron or other emerging variants 317 During January 2022 in Denmark the BA 2 variant grew at 0 10 per day 11 per day as a ratio to BA 1 the legacy Omicron variant and became the dominant strain in week 2 2022 165 In the United Kingdom the BA 2 variant was growing at 0 11 per day 12 per day as a ratio to BA 1 318 On 13 January 2022 the BBC reported that the hospitalization rate was higher in the US and Canada than in Europe and South Africa This was attributed to a combination of a greater number of elderly people than in South Africa greater prevalence of comorbidities such as hypertension and obesity than in Europe higher indoor transmission due to the winter lower vaccination rate in the US than in Europe and Canada and a possible still high prevalence of the Delta variant which more often leads to hospitalization 319 Reported cases Edit Confirmed and suspected cases by country and territory viewtalkedit Country Territory Confirmed cases PANGOLIN 320 as of 5 May 2022 Confirmed cases GISAID 321 as of July 29 2022 Confirmed cases other sources As of 24 June 2022 update Suspected cases United States 801 020 1 431 772 62 480 322 As of January 8 2022 update United Kingdom 998 552 1 253 700 246 780 323 600 041 323 Germany 207 407 365 837 268 661 324 Austria 6 809 57 379 290 378 325 326 Denmark 196 746 264 998 66 563 327 France 83 564 184 880 5 591 328 Canada 73 584 147 223 174 248 329 Japan 67 203 153 110 12 453 330 India 37 542 81 017 8 209 331 332 Australia 33 905 80 013 11 071 333 Norway 14 729 24 529 45 296 267 Thailand 6 778 12 811 5 397 334 Indonesia 9 761 12 028 3 779 335 Singapore 4 543 7 300 4 322 336 337 338 339 Estonia 1 982 3 778 3 857 340 341 342 Israel 22 164 60 435 1 741 343 344 861 343 South Africa 9 631 16 451 1 095 345 19 070 346 South Korea 7 731 27 705 1 318 347 Spain 24 607 31 992 51 324 348 Belgium 26 448 30 865 121 325 348 Sweden 38 397 42 525 53 760 349 Switzerland 30 034 32 635 19 269 325 350 Argentina 2 228 2 583 455 351 352 80 353 Botswana 931 1 594 23 354 Netherlands 24 381 26 601 123 355 348 Ireland 24 654 29 518 29 576 356 Gibraltar 112 122 24 357 Iceland 84 358 Italy 23 707 27 292 84 359 Chile 4 097 4 572 684 360 361 362 Portugal 7 683 8 870 69 363 348 6 364 325 Morocco 128 138 76 365 246 365 Zimbabwe 185 219 50 366 Ghana 441 605 33 354 Brazil 27 787 32 224 203 367 Finland 4 029 5 239 523 368 369 Cyprus 31 370 371 Kenya 1 653 2 329 27 372 Russia 1 273 1 738 8 239 373 Cayman Islands 44 374 59 374 Uganda 12 38 25 375 376 Mexico 12 736 13 678 1 377 New Zealand 3 169 3 739 116 378 Namibia 125 213 18 379 Hong Kong 1 432 3 526 102 380 381 Senegal 14 229 3 382 Mozambique 133 176 2 383 2 322 Greece 3 268 3 276 17 325 384 Bermuda 24 144 385 386 Latvia 407 407 644 387 348 388 Romania 4 034 4 282 25 389 390 391 Malaysia 5 330 7 353 245 392 Zambia 141 365 11 393 Nigeria 827 1 638 6 394 Czech Republic 13 264 15 147 10 325 395 348 Kosovo 245 262 9 396 Slovenia 15 684 17 106 1 418 397 348 398 399 Lebanon 85 107 433 400 401 16 400 Reunion 2 014 2 402 2 402 Mauritius 763 7 322 Poland 31 766 33 327 1 403 Rwanda 70 178 6 403 Turkey 9 135 10 239 6 404 Montenegro 142 211 5 405 Cambodia 950 974 31 406 Peru 5 653 5 960 10 032 407 Jordan 83 83 832 408 China 89 96 4 409 410 411 Cuba 92 412 413 414 Croatia 10 379 11 742 3 325 Egypt 15 40 3 403 Malawi 133 166 3 415 Palestinian Territory 9 126 416 417 Taiwan 32 34 89 418 Lithuania 7 063 9 136 2 419 Colombia 1 629 3 816 3 420 Slovakia 13 501 15 625 3 421 Trinidad and Tobago 291 499 1 422 Puerto Rico 3 166 3 558 1 423 Fiji 2 424 Nepal 255 349 2 425 Myanmar 25 28 4 426 Philippines 1 281 1 549 535 427 428 429 430 431 432 Northern Cyprus 9 433 Bangladesh 690 998 10 434 Liechtenstein 246 736 1 435 3 322 Hungary 28 28 61 436 348 437 Oman 71 85 2 438 Pakistan 359 463 75 439 440 Sri Lanka 626 927 1 441 Georgia 718 822 600 442 Algeria 61 73 1 403 Bahrain 1 443 Ecuador 1 177 1 561 1 444 Kuwait 54 72 1 445 Luxembourg 4 031 11 149 1 325 Maldives 281 5 446 447 Sierra Leone 1 1 448 Saudi Arabia 28 30 1 449 Tunisia 51 52 1 450 United Arab Emirates 1 1 451 Iran 595 682 467 452 Ukraine 73 99 1 453 Panama 821 822 1 454 Costa Rica 1 430 1 529 1 455 Aruba 61 61 1 456 North Macedonia 46 47 9 457 458 Vietnam 1 085 1 790 108 459 Brunei 1 163 1 253 8 460 Malta 138 162 2 461 Venezuela 60 62 7 462 French Guiana 366 20 463 Republic of the Congo 50 78 1 464 Qatar 267 290 4 465 Paraguay 122 139 3 466 Burkina Faso 17 2 467 Curacao 482 487 1 468 Saint Kitts and Nevis 16 2 469 Libya 2 470 Albania 1 1 1 471 Barbados 1 7 1 472 Saint Vincent and the Grenadines 62 1 473 Dominican Republic 69 73 1 474 Jamaica 443 622 1 475 Serbia 81 81 1 476 Tanzania 2 3 1 477 Togo 5 478 Belarus 71 4 479 Bosnia and Herzegovina 118 122 10 480 Angola 25 37 16 481 Democratic Republic of the Congo 34 204 1 482 Bulgaria 2 516 2 520 12 483 Mayotte 123 130 1 484 Martinique 593 1 485 Gambia 30 155 26 486 Seychelles 235 464 487 Saint Martin 224 240 2 488 Laos 1 489 Iraq 36 103 5 490 Mauritania 14 491 South Sudan 28 28 41 492 Ivory Coast 41 60 78 493 Cape Verde 152 175 494 Antigua and Barbuda 36 1 495 Gabon 1 496 Bolivia 2 7 1 497 Moldova 287 314 29 498 Kazakhstan 8 8 8 499 Guadeloupe 264 300 1 500 Azerbaijan 12 12 12 501 Suriname 81 96 146 487 Sint Maarten 479 753 487 British Virgin Islands 20 26 39 487 Mali 1 2 Anguilla 24 30 487 Bonaire 400 692 487 Bhutan 14 502 Papua New Guinea 379 565 1 503 Mongolia 133 133 12 504 Antarctica 24 505 Uzbekistan 1 506 Saint Lucia 1 9 54 487 Burundi 1 28 487 American Samoa 35 84 487 Armenia 4 16 17 487 Guinea 48 167 159 487 Guam 168 274 348 487 Belize 223 240 441 487 Eswatini 124 133 Djibouti 306 308 337 487 World total 170 countries and territories 2 986 573 3 517 102 1 168 383 620 384See also Edit COVID 19 portal Medicine portal Viruses portal Africa portalCOVID 19 pandemic in Africa COVID 19 vaccination in Africa COVID 19 vaccination in Botswana COVID 19 vaccination in South Africa Timeline of the SARS CoV 2 Omicron variant November 2021 February 2022 Variants of SARS CoV 2 Other variants of either interest or concern Alpha Beta Gamma Delta Epsilon Zeta Eta Theta Iota Kappa Lambda Mu Sikhulile Moyo scientist who discovered SARS CoV 2 OmicronNotes Edit With a presumed identical person to person serial interval of loge 2 4 0 21 4 2 days or a distribution thereof to the same effect Logarithmic growth rate of 0 37 day means that the log odds loge SGTF SGTP is increasing by 0 37 in a day So SGTF SGTP was increasing by a multiplicative factor of exp 0 37 1 45 This is substantially higher than a naive increase to 100 37 The difference is mathematically due to compound growth within the day which does not imply that epidemically people are already infectious within a day Rather simplified non delay differential equations are used for convenience for the modeling This also indicates a doubling time of loge 2 0 37 day 1 days for the Omicron to Delta prevalence ratio Referring to ref 12 in the reference where the x axis is crossed at 14 December A doubling time of 2 5 days corresponds to an exponential growth rate of ln 2 2 5 days 0 28 day Direct comparison to the logistic growth rate needs to take the growth decline of Delta into account References Edit a b c Yadav PD Gupta N Potdar V Mohandas S Sahay RR Sarkale P et al January 2022 An in vitro and in vivo approach for the isolation of Omicron variant from human clinical specimens pp 2022 01 02 474750 doi 10 1101 2022 01 02 474750 Archived from the original on 16 January 2022 Retrieved 16 January 2022 a b Padin M 17 January 2022 Feeling light headed may be an early indication you have Omicron Covid variant mirror Archived from the original on 28 January 2022 Retrieved 30 January 2022 Poudel S Ishak A Perez Fernandez J Garcia E Leon Figueroa DA Romani L et al December 2021 Highly mutated SARS CoV 2 Omicron variant sparks significant concern among global experts What is known so far Travel Medicine and Infectious Disease 45 102234 doi 10 1016 j tmaid 2021 102234 PMC 8666662 PMID 34896326 How Omicron Symptoms Compare with Other Variants Healthline 14 January 2022 Archived from the original on 21 January 2022 Retrieved 30 January 2022 a b Omicron s cold like symptoms mean UK guidance needs urgent update Archived 25 December 2021 at the Wayback Machine The Guardian a b Omicron Symptoms Here s How They Differ From Other Variants NBC Chicago Archived from the original on 24 January 2022 Retrieved 30 January 2022 a b Slater Jack 23 January 2022 Is a change to your taste or smell a sign of Omicron Metro Archived from the original on 26 January 2022 Retrieved 30 January 2022 a b Scribner H 21 December 2021 Doctor reveals new nightly omicron variant symptom Deseret News Archived from the original on 2 January 2022 Retrieved 1 January 2022 Does Omicron cause less damage to the lungs www medicalnewstoday com 14 January 2022 Murrison P 18 January 2022 Omicron symptoms Three distinctive rashes to watch for Express co uk Archived from the original on 12 January 2022 Retrieved 30 January 2022 a b Omicron s cold like symptoms mean UK guidance needs urgent update Archived 25 December 2021 at the Wayback Machine The Guardian a b c Quarleri J Galvan V Delpino MV February 2022 Omicron variant of the SARS CoV 2 a quest to define the consequences of its high mutational load GeroScience 44 1 53 56 doi 10 1007 s11357 021 00500 4 PMC 8683309 PMID 34921354 Gowrisankar A Priyanka TM Banerjee S 10 January 2022 Omicron a mysterious variant of concern European Physical Journal Plus 137 1 100 Bibcode 2022EPJP 137 100G doi 10 1140 epjp s13360 021 02321 y PMC 8743750 PMID 35036269 a b Vitiello A Ferrara F Auti AM Di Domenico M Boccellino M July 2022 Advances in the Omicron variant development Journal of Internal Medicine 292 1 81 90 doi 10 1111 joim 13478 PMC 9115048 PMID 35289434 a b Yao L Zhu KL Jiang XL Wang XJ Zhan BD Gao HX et al June 2022 Omicron subvariants escape antibodies elicited by vaccination and BA 2 2 infection The Lancet Infectious Diseases 22 8 1116 1117 doi 10 1016 s1473 3099 22 00410 8 PMC 9212811 PMID 35738299 Ahmed SF Quadeer AA McKay MR January 2022 SARS CoV 2 T Cell Responses Elicited by COVID 19 Vaccines or Infection Are Expected to Remain Robust against Omicron Viruses 14 1 79 doi 10 3390 v14010079 PMC 8781795 PMID 35062283 Al Jurdi A Gassen RB Borges TJ Lape IT Morena L Efe O et al June 2022 Suboptimal antibody response against SARS CoV 2 Omicron variant after third dose of mRNA vaccine in kidney transplant recipients Kidney International 101 6 1282 1286 doi 10 1101 2022 01 03 22268649 PMC 9006415 PMID 35429496 S2CID 245739956 Archived from the original on 11 January 2022 Retrieved 16 January 2022 Altarawneh HN Chemaitelly H Ayoub HH Tang P Hasan MR Yassine HM et al July 2022 Effects of Previous Infection and Vaccination on Symptomatic Omicron Infections The New England Journal of Medicine 387 1 21 34 doi 10 1056 NEJMoa2203965 PMC 9258753 PMID 35704396 S2CID 249677809 Nemet I Kliker L Lustig Y Zuckerman N Erster O Cohen C et al February 2022 Third BNT162b2 Vaccination Neutralization of SARS CoV 2 Omicron Infection The New England Journal of Medicine 386 5 492 494 doi 10 1056 NEJMc2119358 PMC 8823651 PMID 34965337 Cao Y Yisimayi A Jian F Song W Xiao T Wang L et al June 2022 BA 2 12 1 BA 4 and BA 5 escape antibodies elicited by Omicron infection Nature 608 7923 593 602 Bibcode 2022Natur 608 593C doi 10 1038 s41586 022 04980 y PMC 9385493 PMID 35714668 Hachmann NP Miller J Collier AY Ventura JD Yu J Rowe M et al July 2022 Neutralization Escape by SARS CoV 2 Omicron Subvariants BA 2 12 1 BA 4 and BA 5 The New England Journal of Medicine 387 1 86 88 doi 10 1056 NEJMc2206576 PMC 9258748 PMID 35731894 S2CID 249956777 Patel V 27 November 2021 How Omicron the New Covid 19 Variant Got Its Name The New York Times ISSN 0362 4331 Archived from the original on 28 November 2021 Retrieved 28 November 2021 Tcholakian D 15 December 2021 Omni is everywhere why do so many people struggle to say Omicron The Guardian Archived from the original on 23 December 2021 Retrieved 23 December 2021 Zimmer B 2 December 2021 Omicron Greek s Little O Will Loom Larger Now Wall Street Journal ISSN 0099 9660 Archived from the original on 3 December 2021 Retrieved 23 December 2021 President Joe Biden stumbled over the pronunciation in a press conference on Monday calling the variant omnicron with an extra n sound It has also been frequently misspelled that way online The confusion is understandable since we re more familiar with words that have the Latin prefix omni meaning all as in omnipresent or omnivore In focus gisaid org GISAID 28 November 2021 Archived from the original on 21 January 2021 Retrieved 28 November 2021 The unique mix of spike amino acid changes in Omicron GR 484A B 1 1 529 is of interest as it comprises several that were previously known to affect receptor binding and antibody escape a b Variant 21K Omicron covariants org CoVariants 28 November 2021 Archived from the original on 28 November 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