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

Significance In this study, we discovered that the genome of SARS-CoV-2 to date 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. 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.