From an isolated epidemic, COVID-19 has now emerged as a global pandemic. The availability of genomes in the public domain following the epidemic provides a unique opportunity to understand the evolution and spread of the SARS-CoV-2 virus across the globe. The availability of whole genomes from multiple states in India prompted us to analyse the phylogenetic clusters of genomes in India. We performed whole-genome sequencing for 64 genomes making a total of 361 genomes from India, followed by phylogenetic clustering, substitution analysis, and dating of the different phylogenetic clusters of viral genomes. We describe a distinct phylogenetic cluster (Clade I / A3i) of SARS-CoV-2 genomes from India, which encompasses 41% of all genomes sequenced and deposited in the public domain from multiple states in India. Globally 3.5% of genomes, which till date could not be mapped to any distinct known cluster fall in this newly defined clade. The cluster is characterized by a core set of shared genetic variants - C6312A (T2016K), C13730T (A88V/A97V), C23929T, and C28311T (P13L). Further, the cluster is also characterized by a nucleotide substitution rate of 1.4 x 10-3 variants per site per year, lower than the prevalent A2a cluster, and predominantly driven by variants in the E and N genes and relative sparing of the S gene. Epidemiological assessments suggest that the common ancestor emerged in the month of February 2020 and possibly resulted in an outbreak followed by countrywide spread, as evidenced by the low divergence of the genomes from across the country. To the best of our knowledge, this is the first comprehensive study characterizing the distinct and predominant cluster of SARS-CoV-2 in India.

中文翻译：

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印度SARS-CoV-2分离株的独特系统发育簇

从孤立的流行病来看，COVID-19现在已经成为一种全球流行病。流行之后，公共领域的基因组可用性为了解SARS-CoV-2病毒在全球的进化和传播提供了独特的机会。来自印度多个州的完整基因组的可用性促使我们分析了印度基因组的系统发育簇。我们对64个基因组进行了全基因组测序，总共获得了来自印度的361个基因组，然后进行了系统发育聚类，替代分析以及对病毒基因组不同系统聚类进行了日期测定。我们描述了一个来自印度的SARS-CoV-2基因组的独特的系统发育簇（I / A3i进化枝），它涵盖了来自印度多个州的41％的基因组序列，并已在公共领域存放。全球基因组的3.5％直到现在仍无法映射到任何不同的已知星团，都属于这个新定义的进化枝。该集群的特征是一组核心的共享遗传变异-C6312A（T2016K），C13730T（A88V / A97V），C23929T和C28311T（P13L）。此外，该簇的特征还在于每年每个位点1.4个10-3个变体的核苷酸取代率，低于普遍的A2a簇，并且主要由E和N基因的变体和S基因的相对稀疏驱动。流行病学评估表明，该共同祖先在2020年2月出现，并可能导致暴发，随后在全国范围内传播，这一点在全国各地的基因组差异不大的情况下得到了证明。据我们所知，