Analysis of genomic distributions of SARS-CoV-2 reveals a dominant strain type with strong allelic associations
學年 109
學期 1
出版（發表）日期 2020-12-01
作品名稱 Analysis of genomic distributions of SARS-CoV-2 reveals a dominant strain type with strong allelic associations
作品名稱（其他語言）
著者 Hsin-Chou Yang; Chun-houh Chen; Jen-Hung Wang; Hsiao-Chi Liao; Chih-Ting Yang; Chia-Wei Chen; Yin-Chun Lin; Chiun-How Kao; Mei-Yeh Jade Lu; James C. Liao
單位
出版者
著錄名稱、卷期、頁數 Proceedings of the National Academy of Sciences 117(48), p.30679-30686
摘要 Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causal agent of COVID 19, continues to evolve since its first emergence in December 2019. Using the complete sequences of 1,932 SARS-CoV-2 genomes, various clustering analyses consistently identified six types of the strains. Independent of the dendrogram construction, 13 signature variations in the form of single nucleotide variations (SNVs) in protein coding regions and one SNV in the 5′ untranslated region (UTR) were identified and provided a direct interpretation for the six types (types I to VI). The six types of the strains and their underlying signature SNVs were validated in two subsequent analyses of 6,228 and 38,248 SARS-CoV-2 genomes which became available later. To date, type VI, characterized by the four signature SNVs C241T (5′UTR), C3037T (nsp3 F924F), C14408T (nsp12 P4715L), and A23403G (Spike D614G), with strong allelic associations, has become the dominant type. Since C241T is in the 5′ UTR with uncertain significance and the characteristics can be captured by the other three strongly associated SNVs, we focus on the other three. The increasing frequency of the type VI haplotype 3037T-14408T-23403G in the majority of the submitted samples in various countries suggests a possible fitness gain conferred by the type VI signature SNVs. The fact that strains missing one or two of these signature SNVs fail to persist implies possible interactions among these SNVs. Later SNVs such as G28881A, G28882A, and G28883C have emerged with strong allelic associations, forming new subtypes. This study suggests that SNVs may become an important consideration in SARS-CoV-2 classification and surveillance.
關鍵字 COVID-19;mutation;single nucleotide variation;allelic association;sequencing
語言 en_US
ISSN
期刊性質 國外
收錄於 SCI
產學合作
通訊作者
審稿制度 否
國別 USA
公開徵稿
出版型式 ,電子版,紙本
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