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RmYN02
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:	RmYN02

RmYN02 is a bat-derived strain of Severe acute respiratory syndrome–related coronavirus. It was discovered in bat droppings collected between May and October 2019 from sites in Mengla County, Yunnan Province, China. It is the second-closest known relative of SARS-CoV-2, the virus strain that causes COVID-19, sharing 93.3% nucleotide identity at the scale of the complete virus genome. RmYN02 contains an insertion at the S1/S2 cleavage site in the spike protein, similar to SARS-CoV-2, suggesting that such insertion events can occur naturally.

Genetics

It shares 93.3% genome with SARS-CoV-2. RmYN02 was 97.2% identical to SARS-CoV-2 in the 1ab. RmYN02 was 71.8% identical in nucleotide and 97.4% in amino acid to SARS-CoV-2 in the S gene, compared to 97.4% amino acid identity between RaTG13 and SARS-CoV-2. All genetic data were found by Weifeng Shi and his team.

Discovery

RmYN02 was collected between May and July, 2019, in Yunnan by Professor Alice C. Hughes from Xishuangbanna Tropical Botanical Garden, and sequenced by Weifeng Shi from Shandong Medical University, based on an analysis of 302 feces samples collected from 227 bats that were collected from Mengla County, Yunnan Province, China, within a short distance from the Xishuangbanna Tropical Botanical Garden. The genome itself was assembled from a pool of 11 samples.

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

See also

• Bat SARS-like coronavirus RsSHC014
• Bat SARS-like coronavirus WIV1

References

1. ^ Zhou, Hong; Chen, Xing; Hu, Tao; Li, Juan; Song, Hao; Liu, Yanran; Wang, Peihan; Liu, Di; Yang, Jing; Holmes, Edward C.; Hughes, Alice C. (June 8, 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. Bibcode:2020CBio...30E2196Z. doi:10.1016/j.cub.2020.05.023. ISSN 1879-0445. PMC 7211627. PMID 32416074.
2. ^ Zhou H, Ji J, Chen X, Bi Y, Li J, Wang Q, et al. (August 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 K, Zhai J, Feng Y, Zhou N, Zhang X, Zou JJ, et al. (July 2020). "Isolation of SARS-CoV-2-related coronavirus from Malayan pangolins". Nature. 583 (7815): 286–289. Bibcode:2020Natur.583..286X. doi:10.1038/s41586-020-2313-x. PMID 32380510. S2CID 256822274.
8. ^ Delaune D, Hul V, Karlsson EA, Hassanin A, Ou TP, Baidaliuk A, et al. (November 2021). "A novel SARS-CoV-2 related coronavirus in bats from Cambodia". Nature Communications. 12 (1): 6563. Bibcode:2021NatCo..12.6563D. doi:10.1038/s41467-021-26809-4. PMC 8578604. PMID 34753934.
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 P, Yang XL, Wang XG, Hu B, Zhang L, Zhang W, et al. (March 2020). "A pneumonia outbreak associated with a new coronavirus of probable bat origin". Nature. 579 (7798): 270–273. Bibcode:2020Natur.579..270Z. doi:10.1038/s41586-020-2012-7. PMC 7095418. PMID 32015507.
11. Temmam S, Vongphayloth K, Baquero E, Munier S, Bonomi M, Regnault B, et al. (April 2022). "Bat coronaviruses related to SARS-CoV-2 and infectious for human cells". Nature. 604 (7905): 330–336. Bibcode:2022Natur.604..330T. doi:10.1038/s41586-022-04532-4. PMID 35172323. S2CID 246902858.

v t e Taxonomy of the Coronaviridae
Higher taxonomy: Riboviria > Orthornavirae > Pisuviricota > Pisoniviricetes > Nidovirales > Cornidovirineae > Coronaviridae
Orthocoronavirinae Alphacoronavirus Colacovirus Bat coronavirus CDPHE15 Decacovirus Bat coronavirus HKU10 Rhinolophus ferrumequinum alphacoronavirus HuB-2013 Duvinacovirus Human coronavirus 229E Luchacovirus Lucheng Rn rat coronavirus Minacovirus Mink coronavirus 1 Minunacovirus Miniopterus bat coronavirus 1 Miniopterus bat coronavirus HKU8 Myotacovirus Myotis ricketti alphacoronavirus Sax-2011 Nyctacovirus Nyctalus velutinus alphacoronavirus SC-2013 Pipistrellus kuhlii coronavirus 3398 Pedacovirus Porcine epidemic diarrhea virus Scotophilus bat coronavirus 512 Rhinacovirus Rhinolophus bat coronavirus HKU2 Setracovirus Human coronavirus NL63 NL63-related bat coronavirus strain BtKYNL63-9b Soracovirus Sorex araneus coronavirus T14 Sunacovirus Suncus murinus coronavirus X74 Tegacovirus Alphacoronavirus 1 Feline coronavirus Canine coronavirus Canine coronavirus HuPn-2018 Transmissible gastroenteritis virus Betacoronavirus Embecovirus Betacoronavirus 1 Bovine coronavirus Human coronavirus OC43 China Rattus coronavirus HKU24 Human coronavirus HKU1 Murine coronavirus Rat coronavirus Myodes coronavirus 2JL14 Hibecovirus Bat Hp-betacoronavirus Zhejiang2013 Merbecovirus Hedgehog coronavirus 1 Middle East respiratory syndrome-related coronavirus London1_novel CoV/2012 MERS coronavirus EMC/2012 Pipistrellus bat coronavirus HKU5 Tylonycteris bat coronavirus HKU4 Nobecovirus Eidolon bat coronavirus C704 Rousettus bat coronavirus GCCDC1 Rousettus bat coronavirus HKU9 Sarbecovirus SARS-related coronavirus SARS-CoV-1 SARS-CoV-2 Variants BANAL-52 Bat SARS-like coronavirus WIV1 RacCS203 RaTG13 RmYN02 RpYN06 SHC014-CoV Gammacoronavirus Brangacovirus Goose coronavirus CB17 Cegacovirus Beluga whale coronavirus SW1 Igacovirus Avian coronavirus Avian coronavirus 9203 Duck coronavirus 2714 Deltacoronavirus Andecovirus Wigeon coronavirus HKU20 Buldecovirus Bulbul coronavirus HKU11 Common moorhen coronavirus HKU21 Coronavirus HKU15 Munia coronavirus HKU13 White-eye coronavirus HKU16 Herdecovirus Night heron coronavirus HKU19
Letovirinae Alphaletovirus Milecovirus Microhyla letovirus 1
Source: ICTV –– Wikispecies

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