TABLE 1.

List of analyzed strains

Strain name	GenBank ID
Wuhan-Hu-1	NC_045512.2
2019-nCoV WHU01	MN988668.1
2019-nCoV WHU02	MN988669.1
2019-nCoV_HKU-SZ-005b_2020	MN975262.1
2019-nCoV_HKU-SZ-002a_2020	MN938384.1
SARS-CoV-2/WH-09/human/2020/CHN	MT093631.1
SARS-CoV-2/IQTC01/human/2020/CHN	MT123290.1
HZ-1	MT039873.1
BetaCoV/Wuhan/IPBCAMS-WH-01/2019	MT019529.1
BetaCoV/Wuhan/IPBCAMS-WH-03/2019	MT019531.1
BetaCoV/Wuhan/IPBCAMS-WH-02/2019	MT019530.1
BetaCoV/Wuhan/IPBCAMS-WH-04/2019	MT019532.1
BetaCoV/Wuhan/IPBCAMS-WH-05/2020	MT019533.1
WIV02	MN996527.1
WIV04	MN996528.1
WIV05	MN996529.1
WIV06	MN996530.1
WIV07	MN996531.1
SARS-CoV-2/Yunnan-01/human/2020/CHN	MT049951.1
nCoV-FIN-29-Jan-2020	MT020781.1
SARS0CoV-2/61-TW/human/2020/NPL	MT072688.1
SNU01	MT039890.1
SARS-CoV-2/01/human/2020/SWE	MT093571.1
SARS-CoV-2/NTU01/2020/TWN	MT066175.1
SARS-CoV-2/NTU02/2020/TWN	MT066176.1
2019-nCoV/USA-WA1/2020	MN985325.1
2019-nCoV/USA-AZ1/2020	MN997409.1
2019-nCoV/USA-CA1/2020	MN994467.1
2019-nCoV/USA-CA2/2020	MN994468.1
2019-nCoV/USA-CA3/2020	MT027062.1
2019-nCoV/USA-CA4/2020	MT027063.1
2019-nCoV/USA-CA5/2020	MT027064.1
2019-nCoV/USA-CA6/2020	MT044258.1
2019-nCoV/USA-CA7/2020	MT106052.1
2019-nCoV/USA-CA8/2020	MT106053.1
2019-nCoV/USA-CA9/2020	MT118835.1
2019-nCoV/USA-IL2/2020	MT044257.1
2019-nCoV/USA-IL1/2020	MN988713.1
2019-nCoV/USA-MA1/2020	MT039888.1
2019-nCoV/USA-TX1/2020	MT106054.1
2019-nCoV/USA-WA1-A12/2020	MT020880.1
2019-nCoV/USA-WA1-F6/2020	MT020881.1
2019-nCoV/USA-WI1/2020	MT039887.1
Australia/VIC01/2020	MT007544.1
Bat coronavirus RaTG13	MN996532.1
Pangolin coronavirus isolate MP789	MT084071.1
Bat SARS-like coronavirus isolate bat-SL-CoVZC45	MG772933.1
Bat SARS-like coronavirus isolate bat-SL-CoVZXC21	MG772934.1
SARS-CoV tor2	NC_004718.3
SARS-CoV GZ02	AY390556.1
Bat SARS coronavirus HKU3-1	DQ022305.2
Rhinolophus affinis coronavirus isolate LYRa11	KF569996.1