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RacCS203

RacCS203
Virus classification
(unranked):	Virus
Realm:	Riboviria
Kingdom:	Orthornavirae
Phylum:	Pisuviricota
Class:	Pisoniviricetes
Order:	Nidovirales
Family:	Coronaviridae
Genus:	Betacoronavirus
Subgenus:	Sarbecovirus
Species:	Betacoronavirus pandemicum
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's team. 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, 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

Genome comparison

SARS-CoV-2 compared to other SARSr-CoV (by nucleotide %)^[13]
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 %)^[13]
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%

References

↑ 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.
↑ "Coronavirus: Bat scientists find new evidence". BBC News. 10 February 2021.
1 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.
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.
↑ 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.
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.
↑ 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.
↑ 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.
1 2 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.
↑ 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.
↑ 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.
↑ 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.
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.

Taxonomy of the Coronaviridae

Higher taxonomy: Riboviria > Orthornavirae > Pisuviricota > Pisoniviricetes > Nidovirales > Cornidovirineae > Coronaviridae

Coronavirus

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

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

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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Phylogenetics

Phylogenetic tree

Genome comparison

See also

References