SARS-CoV-2_Geo_India

In this study, we analyzed the mutation and selection landscape of 516 unique and complete genomes of SARS-CoV-2 isolates from India in a 12-month span (from Jan-Dec 2020) to understand how the virus is evolving in this geographical region. We identified 953 genome-wide loci displaying single nucleotide polymorphism (SNP) and the Principal Component Analysis and mutation plots of the datasets indicate an increase in genetic variance with time. The 42% of the polymorphic sites display substitutions in the third nucleotide position of codons indicating that non-synonymous substitutions are more prevalent. These isolates displayed strong evidence of purifying selection in ORF1ab, spike, nucleocapsid, and membrane glycoprotein.

本研究针对2020年1月至12月这12个月期间采集自印度的516株独立完整的严重急性呼吸综合征冠状病毒2型（SARS-CoV-2）分离株基因组，分析其突变与选择景观，以探究该病毒在这一地理区域内的演化规律。本研究共鉴定出953个全基因组范围内存在单核苷酸多态性（SNP）的位点；对数据集开展主成分分析（Principal Component Analysis, PCA）与突变位点绘图后发现，病毒的遗传方差随时间推移呈上升趋势。其中42%的多态性位点在密码子第三个核苷酸位置发生碱基替换，提示非同义替换更为普遍。上述分离株在开放阅读框1ab（ORF1ab）、刺突蛋白（spike）、核衣壳蛋白（nucleocapsid）以及膜糖蛋白（membrane glycoprotein）中均呈现出显著的纯化选择（purifying selection）信号。