RacCS203

RacCS203
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:
RacCS203

RacCS203 is a bat-derived strain of severe acute respiratory syndrome–related coronavirus collected in acuminate horseshoe bats from sites in Thailand and sequenced by Lin-Fa Wang. It has 91.5% sequence similarity to SARS-CoV-2 and is most related to the RmYN02 strain. Its spike protein is closely related to RmYN02's spike, both highly divergent from SARS-CoV-2's spike.[1][2]

Phylogenetics

Phylogenetic tree

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, 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]

 
 
 
 

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

 
 

SARS-CoV-2

 
 
 
 
 
 
 
 

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

 

Genome comparison

SARS-CoV-2 compared to other SARSr-CoV (by nucleotide %)[11]
Strain Full-length genome ORF1ab S RBM ORF3a E M ORF6 ORF7a ORF7b ORF8 N ORF10
RaTG13 96.10% 96.50% 92.30% 86.30% 96.30% 99.60% 95.50% 98.40% 95.60% 99.20% 97.00% 96.90% 99.20%
RmYN02 93.60% 97.10% 72.50% 61.90% 96.40% 98.70% 94.80% 96.80% 96.20% 91.00% 48.70% 97.30% 99.20%
RacCS203 91.50% 94.30% 71.30% 61.60% 91.90% 99.10% 94.60% 96.20% 92.40% 93.90% 91.60% 93.20% 99.20%
GD/1/2019 90.20% 90.20% 83.70% 86.90% 93.20% 99.10% 93.30% 95.70% 93.40% 91.70% 92.10% 96.20% 99.20%
SL-ZC45 87.70% 89.00% 75.50% 62.50% 87.80% 98.70% 93.40% 94.60% 88.80% 94.70% 88.50% 91.10% 99.20%
SL-ZXC21 87.50% 88.70% 74.90% 61.60% 88.90% 98.70% 93.40% 94.60% 89.10% 95.50% 88.50% 91.20% 99.20%
GX-P4L 85.40% 84.80% 83.60% 80.00% 86.80% 97.40% 91.30% 90.90% 86.60% 83.50% 81.30% 91.00% 88.90%
GX-P5L 85.20% 84.60% 83.30% 79.90% 87.00% 97.40% 91.30% 90.90% 86.40% 83.50% 80.70% 91.00% 94.00%
SARS-CoV 79.30% 79.70% 72.30% 71.90% 75.30% 93.50% 85.50% 75.50% 82.10% 83.80% 45.80% 88.20% 93.20%
Rc-o319 79.20% 79.80% 72.20% 70.10% 83.30% 97.40% 86.60% 86.60% 78.40% 77.30% 52.30% 88.30% 94.90%
SARS-CoV-2 compared to other SARSr-CoV (by amino acid %)[11]
Strain Full-length genome ORF1ab S RBM ORF3a E M ORF6 ORF7a ORF7b ORF8 N ORF10
RaTG13 98.50% 97.30% 90.10% 97.80% 100.00% 99.60% 100.00% 97.50% 97.70% 95.00% 99.10% 97.40%
RmYN02 98.80% 72.40% 63.20% 96.70% 100.00% 98.70% 96.70% 95.90% 83.70% 28.20% 98.60% 97.40%
RacCS203 97.30% 72.30% 63.70% 97.50% 100.00% 99.10% 98.40% 95.90% 93.00% 94.20% 95.70% -
GD/1/2019 96.70% 90.00% 96.90% 97.10% 100.00% 98.70% 96.70% 97.50% 95.40% 95.00% 97.90% 97.40%
SL-ZC45 95.60% 80.20% 65.90% 90.90% 100.00% 98.70% 93.40% 87.60% 93.00% 94.20% 94.30% 97.40%
SL-ZXC21 95.20% 79.70% 65.90% 92.00% 100.00% 98.70% 93.40% 88.40% 93.00% 94.20% 94.30% -
GX-P4L 92.50% 92.30% 86.60% 89.50% 100.00% 98.20% 95.10% 88.40% - 87.60% 93.60% 73.70%
GX-P5L 92.50% 92.40% 86.60% 89.80% 100.00% 98.20% 95.10% 88.40% 72.10% 87.60% 93.80% 84.20%
SARS-CoV 86.10% 75.80% 73.10% 72.40% 94.70% 90.50% 67.20% 85.30% 81.40% - 90.50% 81.60%
Rc-o319 87.60% 76.20% 73.50% 87.00% 98.70% 91.00% 83.60% 73.80% 69.80% 26.80% 89.50% 86.80%

See also

  • RaTG13, 96.2% similarity to SARS-COV-2
  • RmYN02, 93.3% similarity to SARS-COV-2

References

  1. ↑ Wacharapluesadee, S; Tan, CW; Maneeorn, P; Duengkae, P; Zhu, F; Joyjinda, Y; Kaewpom, T; Chia, WN; Ampoot, W; Lim, BL; Worachotsueptrakun, K; Chen, VC; Sirichan, N; Ruchisrisarod, C; Rodpan, A; Noradechanon, K; Phaichana, T; Jantarat, N; Thongnumchaima, B; Tu, C; Crameri, G; Stokes, MM; Hemachudha, T; Wang, LF (9 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.
  2. ↑ "Coronavirus: Bat scientists find new evidence". BBC News. 10 February 2021.
  3. 1 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.
  4. 1 2 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. 1 2 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. ↑ 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. PMC 7224457. PMID 32407364.
  9. 1 2 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.
  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. 1 2 Wacharapluesadee, Supaporn; Tan, Chee Wah; Maneeorn, Patarapol; Duengkae, Prateep; Zhu, Feng; Joyjinda, Yutthana; Kaewpom, Thongchai; Chia, Wan Ni; Ampoot, Weenassarin; Lim, Beng Lee; Worachotsueptrakun, Kanthita (2021-02-09). "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. ISSN 2041-1723. PMC 7873279. PMID 33563978.
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