Contrasting Patterns in the Early Stage of SARS-CoV-2 Evolution between Humans and Minks. (8th August 2022)

• Record Type: Journal Article
• Authors: Tai, Jui-Hung; Sun, Hsiao-Yu; Tseng, Yi-Cheng; Li, Guanghao; Chang, Sui-Yuan; Yeh, Shiou-Hwei; Chen, Pei-Jer; Chaw, Shu-Miaw; Wang, Hurng-Yi
• Editors: Yeager, Meredith
• Is Part Of: Molecular biology and evolution. Volume 39:Number 9(2022)
• Publication Date: 2022-08-08
• Subjects: positive selection -- site frequency spectrum -- genetic hitchhiking -- Ka/Ks; Molecular biology -- Periodicals; Molecular evolution -- Periodicals; Evolution, Molecular -- Periodicals; Molecular Biology -- Periodicals; 572.8
• DOI: 10.1093/molbev/msac156
• Languages: English
• ISSNs: 0737-4038

Abstract

Abstract: One of the unique features of SARS-CoV-2 is its apparent neutral evolution during the early pandemic (before February 2020). This contrasts with the preceding SARS-CoV epidemics, where viruses evolved adaptively. SARS-CoV-2 may exhibit a unique or adaptive feature which deviates from other coronaviruses. Alternatively, the virus may have been cryptically circulating in humans for a sufficient time to have acquired adaptive changes before the onset of the current pandemic. To test the scenarios above, we analyzed the SARS-CoV-2 sequences from minks ( Neovision vision ) and parental humans. In the early phase of the mink epidemic (April to May 2020), nonsynonymous to synonymous mutation ratio per site in the spike protein is 2.93, indicating a selection process favoring adaptive amino acid changes. Mutations in the spike protein were concentrated within its receptor-binding domain and receptor-binding motif. An excess of high-frequency derived variants produced by genetic hitchhiking was found during the middle (June to July 2020) and late phase I (August to September 2020) of the mink epidemic. In contrast, the site frequency spectra of early SARS-CoV-2 in humans only show an excess of low-frequency mutations, consistent with the recent outbreak of the virus. Strong positive selection in the mink SARS-CoV-2 implies that the virus may not be preadapted to a wide range of hosts and illustrates how a virus evolves to establish a continuous infection in a new host. Therefore, the lack of positive selection signal during the early pandemic in humans deserves further investigation.