Volume 26, Number 7—July 2020
Dispatch
Possible Bat Origin of Severe Acute Respiratory Syndrome Coronavirus 2
Susanna K.P. Lau1
, Hayes K.H. Luk1, Antonio C.P. Wong1, Kenneth S.M. Li, Longchao Zhu, Zirong He, Joshua Fung, Tony T.Y. Chan, Kitty S.C. Fung, and Patrick C.Y. Woo
, Hayes K.H. Luk1, Antonio C.P. Wong1, Kenneth S.M. Li, Longchao Zhu, Zirong He, Joshua Fung, Tony T.Y. Chan, Kitty S.C. Fung, and Patrick C.Y. Woo
Table 1
Comparison of pairwise percentage amino acid identities between SARS-CoV-2 HK20, 4 other strains of SARS-CoV-2, and other SARSr-CoVs with complete genomes available*
| Virus | nsp1 | nsp2 | nsp3 | nsp4 | nsp5 | nsp6 | nsp7 | nsp8 | nsp9 | nsp10 | nsp12 | nsp13 | nsp14 | nsp15 | nsp16 | Spike | NTD | CTD | S2 | ORF3 | ORF8 | E | M | N | Genome |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SARS-CoV-2 HKU-SZ-005b_2020/Guangdong/2020 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 99.3 | 100 | 100 | 100 | 100 | 99.2 | 100 | 100 | 100 | 100 |
| SARS-CoV-2 Wuhan-Hu-1/Hubei/2019 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 99.9 |
| SARS-CoV-2 WIV02/Hubei/2019 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 99.7 | 99.3 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 99.8 |
| SARS-CoV-2 HKU-SZ-002a_2020/Guangdong/2020 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 99.3 | 100 | 100 | 100 | 100 | 99.2 | 100 | 100 | 100 | 99.8 |
| SARSr-Ra-BatCoV RaTG13/R.affinis/Yunnan/2013 | 96.7 | 98.3 | 96.7 | 99.6 | 99.3 | 99.7 | 100 | 100 | 100 | 100 | 99.6 | 99.7 | 99.2 | 97.7 | 100 | 96.7 | 98.6 | 89.3 | 99.1 | 97.8 | 95.0 | 100 | 99.5 | 99.0 | 96.1 |
| SARSr-Rp-BatCoV bat-SL-CoVZC45/R.pusillus/Zhejiang/2015 | 95.6 | 95.3 | 93.9 | 96.8 | 99.0 | 97.9 | 100 | 97.5 | 97.3 | 97.1 | 95.9 | 99.2 | 94.5 | 89.0 | 98.0 | 80.2 | 66.3 | 65.5 | 90.8 | 90.9 | 94.2 | 100 | 98.6 | 94.3 | 87.8 |
| SARSr-Rp-BatCoV bat-SL-CoVZXC21/R.pusillus/Zhejiang/2015 | 95.6 | 96.4 | 93.0 | 96.2 | 99.0 | 97.6 | 98.8 | 96.0 | 96.5 | 97.8 | 95.6 | 98.7 | 94.7 | 88.2 | 98.0 | 79.6 | 65.2 | 64.5 | 90.5 | 92.0 | 94.2 | 100 | 98.6 | 94.3 | 87.6 |
| Pangolin-SARSr-CoV Guangxi/P4L/2017 | 90.6 | 88.4 | 85.5 | 90.2 | 97.1 | 96.2 | 100 | 97.5 | 97.3 | 97.1 | 97.9 | 98.2 | 97.0 | 94.5 | 97.7 | 91.7 | 88.0 | 86.8 | 95.6 | 89.5 | 87.6 | 100 | 98.2 | 93.8 | 85.3 |
| SARSr-Rm-BatCoV Longquan-140/R.monoceros/Zhejiang/2012 | 83.9 | 82.8 | 75.9 | 81.2 | 95.8 | 86.6 | 100 | 97.5 | 97.3 | 94.3 | 95.7 | 99.0 | 94.9 | 89.0 | 94.3 | 75.8 | 49.3 | 66.0 | 90.5 | 61.5 | – | 93.4 | 90.5 | 89.5 | 80.1 |
| SARSr-Rs-BatCoV Rs4231/R.sinicus/Yunnan/2013 | 85.0 | 67.9 | 76.3 | 81.2 | 96.1 | 87.2 | 100 | 97.0 | 97.3 | 97.8 | 96.4 | 99.3 | 95.6 | 89.0 | 93.3 | 76.3 | 52.2 | 77.2 | 87.5 | 73.8 | 57.9 | 93.4 | 90.1 | 90.8 | 79.5 |
| SARSr-Rs-BatCoV Rs3367/R.sinicus/Yunnan/2012 | 85.0 | 67.4 | 76.1 | 80.4 | 96.1 | 86.9 | 100 | 97.5 | 97.3 | 97.8 | 96.4 | 99.3 | 95.4 | 88.7 | 93.0 | 76.8 | 53.7 | 76.6 | 87.8 | 74.2 | 57.9 | 94.7 | 90.1 | 90.5 | 79.5 |
| SARSr-Rs-BatCoV Rs9401/R.sinicus/Yunnan/2015 | 84.4 | 68.3 | 76.3 | 80.8 | 96.1 | 87.2 | 100 | 97.5 | 97.3 | 97.8 | 96.1 | 99.3 | 95.6 | 89.0 | 93.0 | 76.6 | 53.7 | 76.1 | 87.7 | 74.2 | 57.9 | 93.4 | 89.6 | 90.5 | 79.5 |
| SARSr-Rs-BatCoV RsSHC014/R.sinicus/Yunnan/2011 | 85.0 | 67.9 | 75.9 | 81.0 | 95.8 | 87.2 | 100 | 97.5 | 97.3 | 97.8 | 96.4 | 99.3 | 95.1 | 89.0 | 92.6 | 77.0 | 53.7 | 77.7 | 87.9 | 74.2 | 58.7 | 94.7 | 90.1 | 90.3 | 79.4 |
| SARSr-Ra-BatCoV LYRa11/R.affinis/Yunnan/2011 | 82.2 | 68.0 | 76.1 | 80.8 | 95.8 | 86.6 | 100 | 97.5 | 96.5 | 96.4 | 96.1 | 98.8 | 95.1 | 89.0 | 93.0 | 76.0 | 49.3 | 75.1 | 88.3 | 76.0 | 57.9 | 93.4 | 89.6 | 91.0 | 79.4 |
| SARSr-Rs-BatCoV Rs4237/R.sinicus/Yunnan/2013 | 83.9 | 67.7 | 76.1 | 81.0 | 96.1 | 87.6 | 98.8 | 97.5 | 97.3 | 97.8 | 96.7 | 99.5 | 95.4 | 89.0 | 94.6 | 75.0 | 50.0 | 65.0 | 89.1 | 72.0 | 57.9 | 94.7 | 90.5 | 90.8 | 79.4 |
| SARSr-Rs-BatCoV Rs4247/R.sinicus/Yunnan/2013 | 83.9 | 67.7 | 76.3 | 81.0 | 96.1 | 87.6 | 98.8 | 97.5 | 97.3 | 97.8 | 96.6 | 99.3 | 95.6 | 89.0 | 94.6 | 75.2 | 49.7 | 65.5 | 89.3 | 72.4 | 57.0 | 93.4 | 90.1 | 90.5 | 79.4 |
| Human SARS-CoV TOR2/Toronto/Mar2003 | 84.4 | 68.3 | 76.0 | 80.0 | 96.1 | 87.2 | 98.8 | 97.5 | 97.3 | 97.1 | 96.4 | 99.7 | 95.1 | 88.7 | 93.3 | 75.4 | 51.9 | 74.1 | 87.1 | 72.4 | – | 94.7 | 90.5 | 90.5 | 79.4 |
| Human SARS-CoV GZ02/Guangdong/Feb2003 | 83.9 | 68.3 | 76.1 | 79.8 | 96.1 | 87.2 | 98.8 | 97.5 | 97.3 | 97.1 | 96.4 | 99.3 | 95.1 | 88.7 | 93.6 | 75.7 | 52.6 | 74.6 | 87.3 | 73.1 | 29.7 | 94.7 | 90.5 | 90.5 | 79.4 |
| SARSr-Rs-BatCoV Rs4081/R.sinicus/Yunnan/2012 | 85.0 | 67.9 | 76.3 | 81.0 | 96.1 | 87.6 | 100 | 97.5 | 97.3 | 97.8 | 96.4 | 99.2 | 95.8 | 89.0 | 94.3 | 74.4 | 48.1 | 64.0 | 89.0 | 72.0 | 58.7 | 94.7 | 90.1 | 90.3 | 79.3 |
| SARS-As-BatCoV As6526/Aselliscus stoliczkanus/Yunnan/2014 | 84.4 | 67.9 | 76.3 | 81.0 | 95.8 | 87.2 | 100 | 97.5 | 97.3 | 97.8 | 96.1 | 99.3 | 95.6 | 89.0 | 94.6 | 75.1 | 49.7 | 66.0 | 88.9 | 71.6 | 58.7 | 94.7 | 91.0 | 90.0 | 79.3 |
| Human SARS-CoV BJ01/Beijing | 84.4 | 68.3 | 76.0 | 80.4 | 96.1 | 87.2 | 98.8 | 97.5 | 97.3 | 97.1 | 96.4 | 99.5 | 95.1 | 88.7 | 93.3 | 75.6 | 52.2 | 74.1 | 87.3 | 72.4 | – | 94.7 | 90.5 | 90.5 | 79.3 |
| Civet SARS-CoV SZ3/Shenzhen/2013 | 84.4 | 68.5 | 76.1 | 80.6 | 96.1 | 87.2 | 98.8 | 97.5 | 97.3 | 97.1 | 96.4 | 99.5 | 95.1 | 88.7 | 93.6 | 75.7 | 51.9 | 75.1 | 87.3 | 72.4 | 29.7 | 94.7 | 90.1 | 90.5 | 79.3 |
| Civet SARS-CoV SZ16/Shenzhen/2013 | 84.4 | 68.5 | 76.0 | 80.6 | 96.1 | 87.2 | 98.8 | 97.5 | 97.3 | 97.1 | 96.4 | 99.5 | 95.1 | 88.7 | 93.6 | 75.7 | 51.9 | 75.1 | 87.3 | 72.4 | 29.7 | 94.7 | 90.1 | 90.5 | 79.3 |
| SARSr-Ra-BatCoV YN2018A/R.affinis/Yunnan?/2016 | 84.4 | 67.9 | 76.3 | 80.8 | 96.1 | 86.9 | 100 | 97.5 | 97.3 | 97.8 | 96.5 | 99.5 | 95.4 | 89.0 | 64.1 | 75.2 | 49.7 | 65.5 | 89.1 | 71.3 | 57.9 | 94.7 | 89.6 | 90.3 | 79.2 |
| SARSr-Rs-BatCoV Rs4255/R.sinicus/Yunnan/2013 | 85.0 | 67.9 | 76.1 | 80.8 | 96.1 | 87.2 | 100 | 97.5 | 97.3 | 97.8 | 96.1 | 99.3 | 95.6 | 88.7 | 94.3 | 74.5 | 48.1 | 65.0 | 89.0 | 72.0 | 58.7 | 94.7 | 89.2 | 90.3 | 79.2 |
| SARSr-Rs-BatCoV Rp3/R.sinicus/Guangxi/2004 | 82.8 | 67.7 | 75.4 | 80.6 | 95.8 | 87.2 | 100 | 96.0 | 96.5 | 97.8 | 96.2 | 99.2 | 95.4 | 88.4 | 93.3 | 75.0 | 49.3 | 65.5 | 89.3 | 74.5 | 56.2 | 94.7 | 90.1 | 90.3 | 79.2 |
| SARSr-Rs-BatCoV Rs4084/R.sinicus/Yunnan/2012 | 84.4 | 68.3 | 76.3 | 80.4 | 95.8 | 87.2 | 100 | 97.5 | 97.3 | 97.8 | 96.2 | 98.5 | 95.1 | 88.7 | 92.6 | 76.9 | 53.7 | 77.2 | 87.9 | 74.2 | – | 94.7 | 90.1 | 90.0 | 79.2 |
| Civet SARS-CoV PC4–227/Guangdong/2004 | 84.4 | 68.2 | 76.0 | 80.6 | 96.1 | 86.9 | 98.8 | 97.0 | 96.5 | 97.1 | 96.2 | 99.3 | 94.9 | 88.7 | 93.0 | 75.4 | 52.2 | 75.1 | 86.7 | 72.4 | – | 94.7 | 90.1 | 90.0 | 79.2 |
| SARSr-Rs-BatCoV HuB2013/R.sinicus/Hubei/2013 | 83.9 | 69.3 | 76.0 | 81.0 | 96.1 | 86.6 | 100 | 97.5 | 97.3 | 97.8 | 96.1 | 99.0 | 95.6 | 88.2 | 94.0 | 74.9 | 47.8 | 66.0 | 89.4 | 75.3 | 49.6 | 93.4 | 91.0 | 91.0 | 79.1 |
| SARSr-Rm-BatCoV Rm1/R.macrotis/Hubei/2004 | 80.0 | 69.1 | 74.8 | 80.6 | 95.8 | 86.6 | 100 | 97.0 | 96.5 | 97.1 | 95.9 | 98.8 | 94.9 | 87.0 | 93.0 | 74.4 | 47.6 | 65.0 | 89.0 | 74.5 | 57.0 | 93.4 | 91.0 | 90.0 | 79.1 |
| SARSr-Rs-BatCoV Anlong-103/Guizhou/R.sinicus/2013 | 84.4 | 68.2 | 75.8 | 80.8 | 96.1 | 86.9 | 98.8 | 97.5 | 97.3 | 97.1 | 96.5 | 99.3 | 95.6 | 89.0 | 93.6 | 75.1 | 50.2 | 64.5 | 89.1 | 72.0 | 29.7 | 94.7 | 89.6 | 89.6 | 79.1 |
| Civet SARS-CoV civet020/Guangdong/2004 | 84.4 | 68.0 | 75.9 | 80.6 | 96.1 | 87.2 | 97.6 | 97.0 | 97.3 | 97.1 | 96.4 | 99.3 | 94.7 | 88.7 | 93.3 | 75.4 | 52.2 | 75.1 | 86.7 | 72.4 | 29.7 | 94.7 | 90.1 | 90.0 | 79.1 |
| SARSr-Rs-BatCoV HKU3-12/R.sinicus/Hong Kong/2007 | 83.9 | 68.8 | 75.3 | 81.8 | 95.8 | 86.6 | 100 | 97.5 | 96.5 | 97.8 | 95.9 | 98.7 | 94.7 | 88.2 | 93.3 | 75.8 | 49.0 | 66.5 | 90.5 | 73.5 | 57.0 | 94.7 | 91.0 | 89.1 | 79.0 |
| SARSr-Rs-BatCoV HKU3-7/R.sinicus/Guangdong/2006 | 83.9 | 68.5 | 75.5 | 81.4 | 95.8 | 87.2 | 100 | 96.5 | 97.3 | 97.8 | 95.8 | 99.2 | 94.5 | 87.9 | 94.0 | 75.7 | 49.0 | 66.5 | 90.3 | 73.5 | 57.0 | 93.4 | 90.1 | 90.3 | 79.0 |
| SARSr-Rs-BatCoV HKU3–8/R.sinicus/Guangdong/2006 | 83.9 | 68.5 | 75.6 | 81.4 | 95.4 | 87.2 | 100 | 96.5 | 97.3 | 97.8 | 95.8 | 99.2 | 94.5 | 87.9 | 94.0 | 75.9 | 49.3 | 66.5 | 90.5 | 73.5 | – | 92.1 | 89.6 | 90.3 | 79.0 |
| SARSr-Rs-BatCoV HKU3–1/R.sinicus/Hong Kong/2005 | 83.9 | 69.0 | 75.2 | 81.4 | 95.4 | 87.2 | 100 | 96.5 | 97.3 | 97.8 | 95.6 | 98.7 | 94.7 | 88.2 | 93.3 | 75.7 | 49.0 | 66.5 | 90.3 | 73.1 | 57.0 | 94.7 | 91.0 | 89.5 | 79.0 |
| SARSr-Rs-BatCoV HKU3–3/R.sinicus/Hong Kong/2005 | 83.9 | 69.0 | 75.2 | 81.4 | 95.4 | 87.2 | 100 | 96.5 | 97.3 | 97.8 | 95.6 | 98.7 | 94.7 | 88.2 | 93.3 | 75.7 | 49.0 | 66.5 | 90.3 | 73.1 | 57.0 | 94.7 | 91.0 | 89.5 | 79.0 |
| SARSr-Rs-BatCoV HKU3–9/R.sinicus/Hong Kong/2006 | 83.9 | 69.0 | 75.2 | 81.4 | 95.1 | 87.2 | 100 | 96.5 | 97.3 | 97.8 | 95.6 | 98.8 | 94.7 | 87.6 | 93.3 | 75.7 | 49.0 | 66.5 | 90.2 | 72.7 | 57.0 | 94.7 | 91.0 | 89.3 | 79.0 |
| SARSr-Rf-BatCoV Rf4092/R.ferrumequinum/Yunnan/2012 | 84.4 | 67.7 | 76.1 | 81.0 | 96.1 | 87.2 | 98.8 | 96.5 | 97.3 | 97.8 | 96.5 | 99.5 | 95.1 | 89.0 | 93.0 | 72.6 | 39.9 | 66.0 | 88.6 | 71.3 | 28.9 | 94.7 | 89.6 | 90.5 | 79.0 |
| SARSr-Rs-BatCoV Anlong-112/Guizhou/R.sinicus/2013 | 83.9 | 68.2 | 76.0 | 80.8 | 96.1 | 87.2 | 98.8 | 97.5 | 97.3 | 97.8 | 96.5 | 99.3 | 95.6 | 89.0 | 93.6 | 75.1 | 50.2 | 64.5 | 89.1 | 72.0 | 29.7 | 94.7 | 89.6 | 89.6 | 79.0 |
| SARSr-Rs-BatCoV HKU3–2/R.sinicus/Hong Kong/2005 | 83.9 | 69.0 | 75.3 | 81.4 | 95.4 | 87.2 | 100 | 96.5 | 97.3 | 97.8 | 95.6 | 98.8 | 94.7 | 87.6 | 93.3 | 75.7 | 49.0 | 66.5 | 90.3 | 73.1 | 57.0 | 94.7 | 91.0 | 89.8 | 78.9 |
| SARSr-Rs-BatCoV HKU3–13/R.sinicus/Hong Kong/2007 | 83.9 | 69.0 | 75.1 | 81.4 | 95.4 | 87.2 | 100 | 96.5 | 97.3 | 97.8 | 95.6 | 98.8 | 94.5 | 87.6 | 93.3 | 75.7 | 49.0 | 66.5 | 90.2 | 72.7 | 57.0 | 94.7 | 91.0 | 89.3 | 78.9 |
| UNVERIFIED: SARSr-Rp-BatCoV F46/R.pusillus/Yunnan/2012 | 81.7 | 68.3 | 75.8 | 80.8 | 96.1 | 86.2 | 98.8 | 97.5 | 96.5 | 97.1 | 96.4 | 99.3 | 95.6 | 89.6 | 93.6 | 72.6 | 39.9 | 66.0 | 88.9 | 70.9 | 26.6 | 94.7 | 89.6 | 90.5 | 78.9 |
| Human SARS-CoV GZ0401/Guangdong/Dec2003 | 84.4 | 68.2 | 45.9 | 80.6 | 96.1 | 87.2 | 97.6 | 97.0 | 97.3 | 97.1 | 96.2 | 99.3 | 94.9 | 88.7 | 93.3 | 75.3 | 51.9 | 75.1 | 86.7 | 64.4 | 29.7 | 94.7 | 84.7 | 90.0 | 78.9 |
| SARSr-Rl-BatCoV SC2018/Rhinolophus sp./2016 | 83.3 | 69.3 | 74.9 | 81.2 | 95.8 | 86.9 | 100 | 97.5 | 97.3 | 97.8 | 96.1 | 98.8 | 95.4 | 86.7 | 92.3 | 74.4 | 47.4 | 66.0 | 88.9 | 70.9 | 55.4 | 94.7 | 90.1 | 90.7 | 78.8 |
| SARSr-Rf-BatCoV YNLF_31C/R.ferrumequinum/Yunnan/2013 | 78.9 | 69.0 | 75.8 | 80.8 | 95.8 | 86.6 | 97.6 | 97.0 | 97.3 | 97.1 | 96.2 | 99.2 | 95.6 | 88.7 | 93.0 | 73.4 | 49.3 | 65.5 | 86.2 | 70.9 | 29.7 | 94.7 | 89.6 | 90.0 | 78.7 |
| Civet SARS-CoV B039/Guangdong/2004 | 84.4 | 68.2 | 75.9 | 80.6 | 96.1 | 87.2 | 98.8 | 97.0 | 97.3 | 97.1 | 96.4 | 99.5 | 94.7 | 88.7 | 93.3 | 75.4 | 52.2 | 75.1 | 86.7 | 72.4 | 29.7 | 94.7 | 90.1 | 90.0 | 78.6 |
| Civet SARS-CoV civet007/Guangdong/2004 | 84.4 | 68.0 | 75.9 | 80.6 | 96.1 | 87.2 | 98.8 | 97.0 | 97.3 | 97.1 | 96.4 | 99.5 | 94.9 | 88.7 | 93.0 | 75.3 | 51.9 | 75.1 | 86.6 | 72.0 | 29.7 | 94.7 | 90.1 | 90.0 | 78.6 |
| Civet SARS-CoV A022/Guangdong/2004 | 84.4 | 68.2 | 76.0 | 80.6 | 96.1 | 87.2 | 98.8 | 97.0 | 97.3 | 97.1 | 96.4 | 99.5 | 94.9 | 88.7 | 92.6 | 75.3 | 51.9 | 75.1 | 86.6 | 72.0 | 29.7 | 94.7 | 90.1 | 89.8 | 78.5 |
| SARSr-Rf-BatCoV Rf1/R.ferrumequinum/Hubei/2004 | 78.9 | 68.8 | 75.3 | 81.6 | 96.1 | 86.6 | 100 | 97.0 | 97.3 | 97.1 | 96.2 | 99.0 | 94.9 | 88.2 | 91.9 | 73.6 | 50.0 | 66.0 | 86.2 | 68.7 | 31.3 | 93.4 | 89.6 | 89.1 | 78.4 |
| SARSr-Rp-BatCoV Rp/Shaanxi2011/R.pusillus/Shaanxi/2011 | 84.4 | 69.3 | 75.8 | 81.2 | 96.1 | 86.6 | 100 | 97.5 | 97.3 | 97.8 | 96.1 | 99.2 | 96.0 | 88.4 | 93.6 | 74.7 | 48.0 | 66.0 | 89.1 | 72.4 | 58.7 | 93.4 | 90.5 | 91.0 | 78.4 |
| SARSr-Rf-BatCoV Jiyuan-84/R.ferrumequinum/ Henan/2012 | 77.8 | 68.8 | 75.3 | 81.4 | 95.4 | 86.9 | 100 | 97.0 | 97.3 | 97.1 | 96.2 | 99.0 | 95.8 | 89.0 | 91.9 | 73.3 | 49.7 | 66.0 | 85.8 | 70.2 | 28.9 | 93.4 | 89.6 | 89.8 | 78.3 |
| SARSr-Cp-BatCoV Cp/Yunnan2011/C. plicata/Yunnan/2011 | 81.7 | 68.0 | 76.5 | 81.0 | 96.1 | 86.6 | 100 | 97.0 | 96.5 | 97.8 | 96.0 | 98.0 | 94.7 | 89.3 | 93.0 | 74.5 | 49.0 | 65.5 | 88.7 | 72.0 | 57.9 | 94.7 | 91.4 | 90.3 | 78.2 |
| SARSr-Ra-BatCoV YN2018B/R.affinis/Yunnan?/2016 | 85.0 | 68.2 | 76.3 | 80.6 | 96.1 | 87.2 | 100 | 97.5 | 97.3 | 97.8 | 96.4 | 99.3 | 95.6 | 89.0 | 93.0 | 76.6 | 53.4 | 76.1 | 87.8 | 73.8 | 57.9 | 94.7 | 90.1 | 90.8 | 78.1 |
| SARSr-Rs-BatCoV Rs7327/R.sinicus/Yunnan/2014 | 84.4 | 67.9 | 76.2 | 80.8 | 96.1 | 87.2 | 100 | 97.5 | 97.3 | 97.8 | 96.2 | 99.2 | 95.6 | 89.0 | 93.0 | 76.7 | 53.7 | 76.1 | 87.8 | 73.8 | 57.0 | 94.7 | 90.1 | 90.5 | 78.1 |
| SARSr-Rs-BatCoV Rs4874/R.sinicus/Yunnan/2013 | 85.0 | 67.9 | 76.3 | 81.0 | 96.1 | 87.6 | 100 | 97.5 | 97.3 | 97.8 | 96.2 | 98.7 | 95.3 | 88.7 | 93.3 | 76.5 | 52.2 | 76.6 | 87.9 | 74.2 | 57.9 | 94.7 | 89.6 | 90.3 | 78.1 |
| SARSr-Rs-BatCoV WIV16/R.sinicus/Yunnan/2013 | 85.0 | 67.9 | 76.2 | 81.0 | 96.1 | 87.6 | 100 | 97.5 | 97.3 | 97.8 | 96.1 | 99.3 | 94.7 | 88.7 | 93.3 | 76.5 | 52.2 | 76.6 | 87.9 | 74.2 | 57.9 | 94.7 | 90.1 | 90.3 | 78.1 |
| SARSr-Ra-BatCoV YN2018D/R.affinis/Yunnan?/2016 | 85.0 | 68.2 | 76.3 | 81.0 | 96.1 | 87.2 | 100 | 97.5 | 97.3 | 97.8 | 96.5 | 99.3 | 95.4 | 89.0 | 94.0 | 74.4 | 48.1 | 64.0 | 89.1 | 72.7 | 57.9 | 94.7 | 76.1 | 90.5 | 77.9 |
| SARSr-Rf-BatCoV SX2013/R.ferrumequinum/Shanxi/2013 | 78.3 | 69.1 | 75.3 | 81.2 | 95.8 | 86.6 | 100 | 96.5 | 97.3 | 97.1 | 95.9 | 99.0 | 95.8 | 89.0 | 91.9 | 73.3 | 49.7 | 66.0 | 85.8 | 70.9 | 30.5 | 92.1 | 89.6 | 89.8 | 77.9 |
| SARSr-Rf-BatCoV HeB2013/R.ferrumequinum/Hebei/2013 | 78.9 | 69.1 | 75.1 | 81.6 | 95.8 | 86.6 | 100 | 97.0 | 97.3 | 97.1 | 96.1 | 99.0 | 95.8 | 88.7 | 91.9 | 73.4 | 49.7 | 66.0 | 85.9 | 70.5 | 30.5 | 93.4 | 89.6 | 89.8 | 77.7 |
| SARSr-Rs-BatCoV YN2013/R.sinicus/Yunnan/2013 | 83.9 | 67.9 | 76.1 | 80.6 | 96.1 | 87.2 | 100 | 97.5 | 97.3 | 97.8 | 96.4 | 99.3 | 95.8 | 88.4 | 93.3 | 75.1 | 50.9 | 64.0 | 89.0 | 71.3 | 29.7 | 94.7 | 91.0 | 90.8 | 77.5 |
| SARSr- Rs-BatCoV Rs672/2006/R.sinicus/Guizhou/2006 | 85.0 | 67.9 | 68.3 | 80.4 | 95.4 | 87.2 | 100 | 97.5 | 97.3 | 97.8 | 96.5 | 98.8 | 95.6 | 88.2 | 94.3 | 74.2 | 47.8 | 64.0 | 89.0 | 71.6 | 58.7 | 94.7 | 89.6 | 90.5 | 77.5 |
| SARSr-Rs-BatCoV GX2013/R.sinicus/Guangxi/2013 | 83.3 | 68.3 | 75.9 | 80.2 | 95.8 | 87.2 | 100 | 97.5 | 96.5 | 97.1 | 96.5 | 99.3 | 95.4 | 89.0 | 94.0 | 75.1 | 49.7 | 66.5 | 89.0 | 72.7 | 29.7 | 94.7 | 91.4 | 89.6 | 77.3 |
| SARSr-Rf-BatCoV 16BO133/R.ferrumequinum/Korea/2016 | 78.9 | 69.1 | 67.6 | 81.2 | 95.1 | 85.9 | 100 | 96.5 | 97.3 | 97.1 | 96.1 | 98.5 | 94.9 | 88.2 | 92.6 | 71.2 | 39.0 | 65.0 | 86.6 | 68.0 | – | 93.4 | 89.6 | 88.8 | 76.9 |
| SARSr-Rf-BatCoV JL2012/R.ferrumequinum/Jilin/2012 | 78.9 | 69.0 | 74.8 | 81.2 | 94.8 | 85.9 | 98.8 | 96.5 | 97.3 | 97.1 | 96.2 | 98.3 | 95.1 | 87.9 | 92.6 | 71.2 | 39.5 | 65.0 | 86.6 | 68.0 | – | 92.1 | 89.6 | 89.3 | 76.9 |
| SARSr-Rf-BatCoV JTMC15/R.ferrumequinum/Jilin/2013 | 78.9 | 69.0 | 67.2 | 81.2 | 94.8 | 85.9 | 98.8 | 96.5 | 97.3 | 97.1 | 96.2 | 98.3 | 94.9 | 88.2 | 92.6 | 71.2 | 39.3 | 65.0 | 86.6 | 68.0 | – | 90.8 | 90.1 | 89.3 | 76.4 |
| SARSr-Rs-BatCoV BtKY72/Rhinolophus sp./Kenya/2007 | 82.2 | 63.2 | 71.6 | 82.2 | 95.4 | 82.1 | 94.0 | 95.5 | 97.3 | 95.0 | 95.0 | 96.7 | 92.8 | 87.3 | 90.6 | 71.6 | 46.6 | 72.7 | 82.5 | 63.6 | 19.1 | 94.7 | 86.9 | 86.2 | 75.5 |
| SARSr-Rb-BatCoV BM48–31/BGR/2008/R.blasii/Bulgaria/2008 | 81.7 | 62.4 | 71.3 | 81.0 | 94.1 | 83.8 | 95.2 | 96.5 | 98.2 | 95.0 | 95.2 | 97.7 | 93.5 | 89.9 | 88.6 | 71.3 | 44.1 | 69.7 | 83.4 | 62.5 | – | 92.1 | 85.9 | 87.6 | 75.2 |
*SARS-CoV-2 strains are highlighted in tan, and SARSr-CoV strains that had the highest end identity for each gene with SARS-CoV-2 are highlighted in red. SARSr-CoV strains were listed in descending order according to complete genome identities to SARS-CoV-2 HK20/Hong Kong/2020.. Pairwise amino acid identities could not be calculated for some strains because of completely or partially truncated ORF8. CTD, C-terminal domain; E, envelope; M, matrix; N, nucleocapsid; nsp, nonstructural protein; NTD, N-terminal domain; ORF, open reading frame; S, spike; SARS-CoV- 2, severe acute respiratory syndrome coronavirus 2; SARSr-CoV, severe acute respiratory syndrome–related coronavirus; –, not applicable..
1These authors contributed equally to this article.
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