RpYN06

Bat coronavirus RpYN06 is a SARS-like betacoronavirus that infects the horseshoe bat Rhinolophus pusillus, it is a close relative of SARS-CoV-2 with a 94.48% sequence identity.^[1]

BatCoV RpYN06
Virus classification
(unranked):	Virus
Realm:	Riboviria
Kingdom:	Orthornavirae
Phylum:	Pisuviricota
Class:	Pisoniviricetes
Order:	Nidovirales
Family:	Coronaviridae
Genus:	Betacoronavirus
Subgenus:	Sarbecovirus
Species:	Severe acute respiratory syndrome–related coronavirus
Strain:	BatCoV RpYN06

Phylogenetics

A phylogenetic tree based on whole-genome sequences of SARS-CoV-2 and related coronaviruses is:^[2][3]

SARS‑CoV‑2 related coronavirus	(Bat) Rc-o319, 81% to SARS-CoV-2, Rhinolophus cornutus, Iwate, Japan^[4] Bat SL-ZXC21, 88% to SARS-CoV-2, Rhinolophus pusillus, Zhoushan, Zhejiang^[5] Bat SL-ZC45, 88% to SARS-CoV-2, Rhinolophus pusillus, Zhoushan, Zhejiang^[5] Pangolin SARSr-CoV-GX, 85.3% to SARS-CoV-2, Manis javanica, smuggled from Southeast Asia^[6] Pangolin SARSr-CoV-GD, 90.1% to SARS-CoV-2, Manis javanica, smuggled from Southeast Asia^[7] Bat RshSTT182, 92.6% to SARS-CoV-2, Rhinolophus shameli, Steung Treng, Cambodia^[8] Bat RshSTT200, 92.6% to SARS-CoV-2, Rhinolophus shameli, Steung Treng, Cambodia^[8] (Bat) RacCS203, 91.5% to SARS-CoV-2, Rhinolophus acuminatus, Chachoengsao, Thailand^[3] (Bat) RmYN02, 93.3% to SARS-CoV-2, Rhinolophus malayanus, Mengla, Yunnan^[9] (Bat) RpYN06, 94.4% to SARS-CoV-2, Rhinolophus pusillus, Xishuangbanna, Yunnan^[2] (Bat) RaTG13, 96.1% to SARS-CoV-2, Rhinolophus affinis, Mojiang, Yunnan^[10] (Bat) BANAL-52, 96.8% to SARS-CoV-2, Rhinolophus malayanus, Vientiane, Laos^[11] SARS-CoV-2
	SARS-CoV-1, 79% to SARS-CoV-2

References

1. Hong Zhou, Jingkai Ji, Xing Chen, Yuhai Bi, Juan Li, Tao Hu, Hao Song, Yanhua Chen, Mingxue Cui, Yanyan Zhang, Alice C. Hughes, Edward C. Holmes, Weifeng Shi (8 March 2021). "Identification of novel bat coronaviruses sheds light on the 2 evolutionary origins of SARS-CoV-2 and related viruses". Cell. 184 (17): 4380–4391.e14. doi:10.1016/j.cell.2021.06.008. PMC 8188299. PMID 34147139.{{cite journal}}: CS1 maint: uses authors parameter (link)
2. Zhou H, Ji J, Chen X, Bi Y, Li J, Wang Q, et al. (June 2021). "Identification of novel bat coronaviruses sheds light on the evolutionary origins of SARS-CoV-2 and related viruses". Cell. 184 (17): 4380–4391.e14. doi:10.1016/j.cell.2021.06.008. PMC 8188299. PMID 34147139.
3. Wacharapluesadee S, Tan CW, Maneeorn P, Duengkae P, Zhu F, Joyjinda Y, et al. (February 2021). "Evidence for SARS-CoV-2 related coronaviruses circulating in bats and pangolins in Southeast Asia". Nature Communications. 12 (1): 972. Bibcode:2021NatCo..12..972W. doi:10.1038/s41467-021-21240-1. PMC 7873279. PMID 33563978.
4. Murakami S, Kitamura T, Suzuki J, Sato R, Aoi T, Fujii M, et al. (December 2020). "Detection and Characterization of Bat Sarbecovirus Phylogenetically Related to SARS-CoV-2, Japan". Emerging Infectious Diseases. 26 (12): 3025–3029. doi:10.3201/eid2612.203386. PMC 7706965. PMID 33219796.
5. Zhou H, Chen X, Hu T, Li J, Song H, Liu Y, et al. (June 2020). "A Novel Bat Coronavirus Closely Related to SARS-CoV-2 Contains Natural Insertions at the S1/S2 Cleavage Site of the Spike Protein". Current Biology. 30 (11): 2196–2203.e3. doi:10.1016/j.cub.2020.05.023. PMC 7211627. PMID 32416074.
6. Lam TT, Jia N, Zhang YW, Shum MH, Jiang JF, Zhu HC, et al. (July 2020). "Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins". Nature. 583 (7815): 282–285. Bibcode:2020Natur.583..282L. doi:10.1038/s41586-020-2169-0. PMID 32218527. S2CID 214683303.
7. Xiao, Kangpeng; Zhai, Junqiong; Feng, Yaoyu; Zhou, Niu; Zhang, Xu; Zou, Jie-Jian; Li, Na; Guo, Yaqiong; Li, Xiaobing; Shen, Xuejuan; Zhang, Zhipeng; Shu, Fanfan; Huang, Wanyi; Li, Yu; Zhang, Ziding; Chen, Rui-Ai; Wu, Ya-Jiang; Peng, Shi-Ming; Huang, Mian; Xie, Wei-Jun; Cai, Qin-Hui; Hou, Fang-Hui; Chen, Wu; Xiao, Lihua; Shen, Yongyi (9 July 2020). "Isolation of SARS-CoV-2-related coronavirus from Malayan pangolins". Nature. 583 (7815): 286–289. doi:10.1038/s41586-020-2313-x.
8. Delaune, Deborah; Hul, Vibol; Karlsson, Erik A.; Hassanin, Alexandre; Ou, Tey Putita; Baidaliuk, Artem; Gámbaro, Fabiana; Prot, Matthieu; Tu, Vuong Tan; Chea, Sokha; Keatts, Lucy; Mazet, Jonna; Johnson, Christine K.; Buchy, Philippe; Dussart, Philippe; Goldstein, Tracey; Simon-Lorière, Etienne; Duong, Veasna (9 November 2021). "A novel SARS-CoV-2 related coronavirus in bats from Cambodia". Nature Communications. 12 (1): 6563. doi:10.1038/s41467-021-26809-4. ISSN 2041-1723.
9. Zhou H, Chen X, Hu T, Li J, Song H, Liu Y, et al. (June 2020). "A Novel Bat Coronavirus Closely Related to SARS-CoV-2 Contains Natural Insertions at the S1/S2 Cleavage Site of the Spike Protein". Current Biology. 30 (11): 2196–2203.e3. doi:10.1016/j.cub.2020.05.023. PMC 7211627. PMID 32416074.
10. Zhou, Peng; Yang, Xing-Lou; Wang, Xian-Guang; Hu, Ben; Zhang, Lei; Zhang, Wei; Si, Hao-Rui; Zhu, Yan; Li, Bei; Huang, Chao-Lin; Chen, Hui-Dong; Chen, Jing; Luo, Yun; Guo, Hua; Jiang, Ren-Di; Liu, Mei-Qin; Chen, Ying; Shen, Xu-Rui; Wang, Xi; Zheng, Xiao-Shuang; Zhao, Kai; Chen, Quan-Jiao; Deng, Fei; Liu, Lin-Lin; Yan, Bing; Zhan, Fa-Xian; Wang, Yan-Yi; Xiao, Geng-Fu; Shi, Zheng-Li (12 March 2020). "A pneumonia outbreak associated with a new coronavirus of probable bat origin". Nature. 579 (7798): 270–273. doi:10.1038/s41586-020-2012-7.
11. Temmam, Sarah; Vongphayloth, Khamsing; Baquero, Eduard; Munier, Sandie; Bonomi, Massimiliano; Regnault, Béatrice; Douangboubpha, Bounsavane; Karami, Yasaman; Chrétien, Delphine; Sanamxay, Daosavanh; Xayaphet, Vilakhan; Paphaphanh, Phetphoumin; Lacoste, Vincent; Somlor, Somphavanh; Lakeomany, Khaithong; Phommavanh, Nothasin; Pérot, Philippe; Dehan, Océane; Amara, Faustine; Donati, Flora; Bigot, Thomas; Nilges, Michael; Rey, Félix A.; van der Werf, Sylvie; Brey, Paul T.; Eloit, Marc (16 February 2022). "Bat coronaviruses related to SARS-CoV-2 and infectious for human cells". Nature. doi:10.1038/s41586-022-04532-4.