TY - JOUR
T1 - Systematic Exploration of SARS-CoV-2 Adaptation to Vero E6, Vero E6/TMPRSS2, and Calu-3 Cells
AU - Aiewsakun, Pakorn
AU - Phumiphanjarphak, Worakorn
AU - Ludowyke, Natali
AU - Purwono, Priyo Budi
AU - Manopwisedjaroen, Suwimon
AU - Srisaowakarn, Chanya
AU - Ekronarongchai, Supanuch
AU - Suksatu, Ampa
AU - Yuvaniyama, Jirundon
AU - Thitithanyanont, Arunee
N1 - Publisher Copyright:
© The Author(s) 2023. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.
PY - 2023/4/1
Y1 - 2023/4/1
N2 - Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to spread globally, and scientists around the world are currently studying the virus intensively in order to fight against the on-going pandemic of the virus. To do so, SARS-CoV-2 is typically grown in the lab to generate viral stocks for various kinds of experimental investigations. However, accumulating evidence suggests that such viruses often undergo cell culture adaptation. Here, we systematically explored cell culture adaptation of two SARS-CoV-2 variants, namely the B.1.36.16 variant and the AY.30 variant, a sub lineage of the B.1.617.2 (Delta) variant, propagated in three different cell lines, including Vero E6, Vero E6/TMPRSS2, and Calu-3 cells. Our analyses detected numerous potential cell culture adaptation changes scattering across the entire virus genome, many of which could be found in naturally circulating isolates. Notable ones included mutations around the spike glycoprotein’s multibasic cleavage site, and the Omicron-defining H655Y mutation on the spike glycoprotein, as well as mutations in the nucleocapsid protein’s linker region, all of which were found to be Vero E6-specific. Our analyses also identified deletion mutations on the nonstructural protein 1 and membrane glycoprotein as potential Calu-3-specific adaptation changes. S848C mutation on the non-structural protein 3, located to the protein’s papain-like protease domain, was also identified as a potential adaptation change, found in viruses propagated in all three cell lines. Our results highlight SARS-CoV-2 high adaptability, emphasize the need to deep-sequence cultured viral samples when used in intricate and sensitive biological experiments, and illustrate the power of experimental evolutionary study in shedding lights on the virus evolutionary landscape.
AB - Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to spread globally, and scientists around the world are currently studying the virus intensively in order to fight against the on-going pandemic of the virus. To do so, SARS-CoV-2 is typically grown in the lab to generate viral stocks for various kinds of experimental investigations. However, accumulating evidence suggests that such viruses often undergo cell culture adaptation. Here, we systematically explored cell culture adaptation of two SARS-CoV-2 variants, namely the B.1.36.16 variant and the AY.30 variant, a sub lineage of the B.1.617.2 (Delta) variant, propagated in three different cell lines, including Vero E6, Vero E6/TMPRSS2, and Calu-3 cells. Our analyses detected numerous potential cell culture adaptation changes scattering across the entire virus genome, many of which could be found in naturally circulating isolates. Notable ones included mutations around the spike glycoprotein’s multibasic cleavage site, and the Omicron-defining H655Y mutation on the spike glycoprotein, as well as mutations in the nucleocapsid protein’s linker region, all of which were found to be Vero E6-specific. Our analyses also identified deletion mutations on the nonstructural protein 1 and membrane glycoprotein as potential Calu-3-specific adaptation changes. S848C mutation on the non-structural protein 3, located to the protein’s papain-like protease domain, was also identified as a potential adaptation change, found in viruses propagated in all three cell lines. Our results highlight SARS-CoV-2 high adaptability, emphasize the need to deep-sequence cultured viral samples when used in intricate and sensitive biological experiments, and illustrate the power of experimental evolutionary study in shedding lights on the virus evolutionary landscape.
KW - COVID-19
KW - Calu-3
KW - SARS-CoV-2
KW - Vero E6
KW - Vero E6/TMPRSS2
KW - experimental evolutionary study
UR - http://www.scopus.com/inward/record.url?scp=85152167810&partnerID=8YFLogxK
U2 - 10.1093/gbe/evad035
DO - 10.1093/gbe/evad035
M3 - Article
C2 - 36852863
AN - SCOPUS:85152167810
SN - 1759-6653
VL - 15
JO - Genome Biology and Evolution
JF - Genome Biology and Evolution
IS - 4
M1 - evad035
ER -