RmYN02

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. ^[1] Other researchers have questioned the validity of this as an authentic furin cleavage site insertion, noting that it appears more likely to be a deletion of two amino acids at that locus. ^[2]

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. ^[1]

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. ^[1] 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: ^{[3] [4]}

SARS‑CoV‑2 related coronavirus	(Bat) Rc-o319, 81% to SARS-CoV-2, Rhinolophus cornutus , Iwate, Japan [5] Bat SL-ZXC21, 88% to SARS-CoV-2, Rhinolophus pusillus , Zhoushan, Zhejiang [6] Bat SL-ZC45, 88% to SARS-CoV-2, Rhinolophus pusillus, Zhoushan, Zhejiang [6] Pangolin SARSr-CoV-GX, 85.3% to SARS-CoV-2, Manis javanica , smuggled from Southeast Asia [7] Pangolin SARSr-CoV-GD, 90.1% to SARS-CoV-2, Manis javanica, smuggled from Southeast Asia [8] Bat RshSTT182, 92.6% to SARS-CoV-2, Rhinolophus shameli , Steung Treng, Cambodia [9] Bat RshSTT200, 92.6% to SARS-CoV-2, Rhinolophus shameli, Steung Treng, Cambodia [9] (Bat) RacCS203, 91.5% to SARS-CoV-2, Rhinolophus acuminatus , Chachoengsao, Thailand [4] (Bat) RmYN02, 93.3% to SARS-CoV-2, Rhinolophus malayanus , Mengla, Yunnan [10] (Bat) RpYN06, 94.4% to SARS-CoV-2, Rhinolophus pusillus, Xishuangbanna, Yunnan [3] (Bat) RaTG13, 96.1% to SARS-CoV-2, Rhinolophus affinis , Mojiang, Yunnan [11] (Bat) BANAL-52, 96.8% to SARS-CoV-2, Rhinolophus malayanus , Vientiane, Laos [12] SARS-CoV-2
	SARS-CoV-1, 79% to SARS-CoV-2

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. Segreto, Rossana. "Should we discount the laboratory origin of COVID-19?". Environmental Chemistry Letters. 19: 2743–2757. The reliability of the conclusions of Zhou et al. (2020a) has been questioned by Deigin and Segreto (2020), who particularly challenge the claim that RmYN02 has an insertion around the site of the FCS insertion in SARS-CoV-2 and instead point to a two amino acid deletion in RmYN02 at that locus. Therefore, RmYN02 should not be used as evidence of the natural origin of SARS-CoV-2′s FCS until its claimed insertion is properly validated.
3. 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.
4. 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.
5. 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.
6. 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.
7. 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.
8. 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.
9. 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.
10. 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.
11. 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.
12. 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.