Analysis of genomic distributions of SARS-CoV-2 reveals a dominant strain type with strong allelic associations

Abstract

In this study, we discovered that the genome of SARS-CoV-2 can be classified in six major types characterized by 14 signature single nucleotide variations (SNVs). In particular, Type VI that was first reported in China and spread to different countries, has become the major type (more than 95% among data collected after mid-May, 2020). The signature SNVs for this strain type C241T (5’UTR), C3037T (nsp3 F924F), C14408T (nsp12 P4715L), and A23403G (S protein D614G) exhibit high pairwise allelic associations and the haplotype 241T-3037T-14408T-23403G has the highest frequency. The fact that strains missing any of these signature SNVs fail to persist implies possible interactions among these SNVs. Understanding nucleotide variations in the SARS-CoV-2 genome will provide useful insight for the developmental history of the pandemic, and even the disease management if the biological significance is understood. We established a website for tracking SARS-CoV-2 variations https://sarscov2.sinica.edu.tw/. ? Joint work with Chun-houh Chen, Jen-Hung Wang, Hsiao-Chi Liao, Chih-Ting Yang, Chia-Wei Chen, Yin-Chun Lin, Chiun-How Kao, Mei-Yeh Lu, Ling-Jyh Chen, and James C. Liao.