RmYN02

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RmYN02
Virus classification e
(unranked): Virus
Realm: Riboviria
Kingdom: Orthornavirae
Phylum: Pisuviricota
Class: Pisoniviricetes
Order: Nidovirales
Family: Coronaviridae
Genus: Betacoronavirus
Subgenus: Sarbecovirus
Species:
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, which was the subject of a paper sent to Nature.[1]

Discovery[edit]

RmYN02 was collected between May and July, 2019, by Yunnan and Shandong researchers, based on an analysis of 302 feces samples collected from 227 bats 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:[2][3][4]

SARS‑CoV‑2 related coronavirus

Rc-o319, 81% to SARS-COV-2, Rhinolophus cornutus, Iwate, Japan[5]

SL-ZXC21, 88% to SARS-COV-2, Rhinolophus pusillus, Zhoushan, Zhejiang[6]

SL-ZC45, 88% to SARS-COV-2, Rhinolophus pusillus, Zhoushan, Zhejiang[6]

Pangolin SARSr-COV-GX, 89% to SARS-COV-2, Manis javanica, Smuggled from Southeast Asia[7]

Pangolin SARSr-COV-GD, 91% to SARS-COV-2, Manis javanica, Smuggled from Southeast Asia[8]

RshSTT182, 92.6% to SARS-COV-2, Rhinolophus shameli, Steung Treng, Cambodia[4]

RshSTT200, 92.6% to SARS-COV-2, Rhinolophus shameli, Steung Treng, Cambodia[4]

RacCS203, 91.5% to SARS-COV-2, Rhinolophus acuminatus, Chachoengsao, Thailand[3]

RmYN02, 93.3% to SARS-COV-2, Rhinolophus malayanus Mengla, Yunnan[9]

RpYN06, 94.4% to SARS-COV-2, Rhinolophus pusillus, Xishuangbanna, Yunnan[2]

RaTG13, 96.1% to SARS-COV-2, Rhinolophus affinis, Mojiang, Yunnan

SARS-CoV-2

SARS-CoV-1, 79% to SARS-COV-2

See also[edit]

References[edit]

  1. ^ a b 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. doi:10.1016/j.cub.2020.05.023. ISSN 1879-0445. PMC 7211627. PMID 32416074.
  2. ^ a b 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: S0092867421007091. doi:10.1016/j.cell.2021.06.008. PMID 34147139.
  3. ^ a b 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. doi:10.1038/s41467-021-21240-1. PMC 7873279. PMID 33563978.
  4. ^ a b c Hul V, Delaune D, Karlsson EA, Hassanin A, Tey PO, Baidaliuk A, et al. (26 January 2021). "A novel SARS-CoV-2 related coronavirus in bats from Cambodia". bioRxiv. pp. 2021.01.26.428212. doi:10.1101/2021.01.26.428212.
  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. ^ a b 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. 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. doi:10.1038/s41586-020-2169-0. PMID 32218527.
  8. ^ Liu P, Jiang JZ, Wan XF, Hua Y, Li L, Zhou J, et al. (May 2020). "Are pangolins the intermediate host of the 2019 novel coronavirus (SARS-CoV-2)?". PLoS Pathogens. 16 (5): e1008421. doi:10.1371/journal.ppat.1008421. PMID 32407364.
  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. PMID 32416074.