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.

本研究对2020年1月至12月期间印度收集的516个独立且完整的SARS-CoV-2分离株基因组进行了突变和选择景观分析，历时12个月，旨在探究该病毒在该地理区域内的进化趋势。我们识别出953个全基因组位点的单核苷酸多态性（SNP），通过主成分分析和突变图谱分析该数据集，发现遗传变异随时间推移而增加。其中42%的多态性位点表现出密码子第三位核苷酸上的替换，表明非同义替换更为普遍。这些分离株在ORF1ab、刺突、核衣壳和膜糖蛋白等基因中显示出强烈的净化选择证据。