THE EVOLUTION SUBTYPES OF THE SARS-CoV-2 LINEAGES

Abstract

Thirty two spike protein (S) sequences of SARS-CoV-2 variants were collected from USA GenBank database. The results of multiple S sequence alignment of SARS-CoV-2 variants identified nine SARS-CoV-2 lineages with WHO codes: Origin, Alpha, Beta, Gamma, Delta, Delta Plus, Iota, Kappa and Omicron. The lineages closely related to the Origin lineage are Iota (distance 0.00468), Delta (0.00545), Kappa (0.00546), Alpha (0.00548) and Beta (0.00665). The lineages with average evolutionary relationship with the Origin lineage are Delta Plus (0.00782) and Gamma (0.00938). All other SARS-CoV-2 lineages are distantly related to the Omicron lineage with a distance of 0.02473 to 0.02837. Based on the mutations on the S sequence and the genetic distance, two evolutionary subtypes from the Origin lineage to the SARS-CoV-2 lineages were predicted