SARS-CoV-2 variants with NSP12 P323L/G671S mutations display enhanced virus replication in ferret upper airways and higher transmissibility
Se-Mi Kim,
Eun-Ha Kim,
Mark Anthony B. Casel,
Young-Il Kim,
Rong Sun,
Mi-Jeong Kwak,
Ji-Seung Yoo,
Mina Yu,
Kwang-Min Yu,
Seung-Gyu Jang,
Rare Rollon,
Jeong Ho Choi,
Juryeon Gil,
Kiyoung Eun,
Hyunggee Kim,
Armin Ensser,
Jungwon Hwang,
Min-Suk Song,
Myung Hee Kim,
Jae U. Jung,
Young Ki Choi
Affiliations
Se-Mi Kim
Center for Study of Emerging and Re-emerging Viruses, Korea Virus Research Institute, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
Eun-Ha Kim
Center for Study of Emerging and Re-emerging Viruses, Korea Virus Research Institute, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
Mark Anthony B. Casel
College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju 28644, Republic of Korea
Young-Il Kim
Center for Study of Emerging and Re-emerging Viruses, Korea Virus Research Institute, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
Rong Sun
Department of Cancer Biology, Infection Biology Program, and Global Center for Pathogens and Human Health Research, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
Mi-Jeong Kwak
Department of Cancer Biology, Infection Biology Program, and Global Center for Pathogens and Human Health Research, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
Ji-Seung Yoo
Center for Study of Emerging and Re-emerging Viruses, Korea Virus Research Institute, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
Mina Yu
Center for Study of Emerging and Re-emerging Viruses, Korea Virus Research Institute, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
Kwang-Min Yu
College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju 28644, Republic of Korea
Seung-Gyu Jang
College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju 28644, Republic of Korea
Rare Rollon
College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju 28644, Republic of Korea
Jeong Ho Choi
College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju 28644, Republic of Korea
Juryeon Gil
College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju 28644, Republic of Korea
Kiyoung Eun
Institute of Animal Molecular Biotechnology, Korea University, Seongbuk-gu, Seoul 02841, Republic of Korea; Department of Biotechnology, School of Life Sciences and Biotechnology, Korea University, Seongbuk-gu, Seoul 02841, Republic of Korea
Hyunggee Kim
Institute of Animal Molecular Biotechnology, Korea University, Seongbuk-gu, Seoul 02841, Republic of Korea; Department of Biotechnology, School of Life Sciences and Biotechnology, Korea University, Seongbuk-gu, Seoul 02841, Republic of Korea
Armin Ensser
Institute for Clinical and Molecular Virology, University Hospital Erlangen, Friedrich Alexander University Erlangen-Nuremberg, Erlangen, Germany
Jungwon Hwang
Infection and Immunity Research Laboratory, Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
Min-Suk Song
College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju 28644, Republic of Korea
Myung Hee Kim
Infection and Immunity Research Laboratory, Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
Jae U. Jung
Department of Cancer Biology, Infection Biology Program, and Global Center for Pathogens and Human Health Research, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Corresponding author
Young Ki Choi
Center for Study of Emerging and Re-emerging Viruses, Korea Virus Research Institute, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea; College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju 28644, Republic of Korea; Corresponding author
Summary: With the emergence of multiple predominant SARS-CoV-2 variants, it becomes important to have a comprehensive assessment of their viral fitness and transmissibility. Here, we demonstrate that natural temperature differences between the upper (33°C) and lower (37°C) respiratory tract have profound effects on SARS-CoV-2 replication and transmissibility. Specifically, SARS-CoV-2 variants containing the NSP12 mutations P323L or P323L/G671S exhibit enhanced RNA-dependent RNA polymerase (RdRp) activity at 33°C compared with 37°C and high transmissibility. Molecular dynamics simulations and microscale thermophoresis demonstrate that the NSP12 P323L and P323L/G671S mutations stabilize the NSP12-NSP7-NSP8 complex through hydrophobic effects, leading to increased viral RdRp activity. Furthermore, competitive transmissibility assay reveals that reverse genetic (RG)-P323L or RG-P323L/G671S NSP12 outcompetes RG-WT (wild-type) NSP12 for replication in the upper respiratory tract, allowing markedly rapid transmissibility. This suggests that NSP12 P323L or P323L/G671S mutation of SARS-CoV-2 is associated with increased RdRp complex stability and enzymatic activity, promoting efficient transmissibility.
