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Volume 26, Number 7—July 2020
Dispatch

Possible Bat Origin of Severe Acute Respiratory Syndrome Coronavirus 2

Susanna K.P. Lau1Comments to Author , 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. WooComments to Author 
Author affiliations: The University of Hong Kong, Hong Kong, China (S.K.P. Lau, H.K.H. Luk, A.C.P. Wong, K.S.M. Li, L. Zhu, Z. He, J. Fung, T.T.Y. Chan, P.C.Y. Woo); United Christian Hospital, Hong Kong (K.S.C. Fung)

Main Article

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..

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1These authors contributed equally to this article.

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