Direct massively parallel sequencing of SARS-CoV-2 genome was undertaken from nasopharyngeal and oropharyngeal swab samples of infected individuals in Eastern India. Seven of the isolates belonged to the A2a clade, while one belonged to the B4 clade. Specific mutations, characteristic of the A2a clade, were also detected, which included the P323L in RNA-dependent RNA polymerase and D614G in the Spike glycoprotein. Further, our data revealed emergence of novel subclones harbouring nonsynonymous mutations, viz. G1124V in Spike (S) protein, R203K, and G204R in the nucleocapsid (N) protein. The N protein mutations reside in the SR-rich region involved in viral capsid formation and the S protein mutation is in the S 2 domain, which is involved in triggering viral fusion with the host cell membrane. Interesting correlation was observed between these mutations and travel or contact history of COVID-19 positive cases. Consequent alterations of miRNA binding and structure were also predicted for these mutations. More importantly, the possible implications of mutation D614G (in S D domain) and G1124V (in S 2 subunit) on the structural stability of S protein have also been discussed. Results report for the first time a bird’s eye view on the accumulation of mutations in SARS-CoV-2 genome in Eastern India.

中文翻译：

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在印度东部发现的 SARS-CoV-2 病毒 RNA 突变：对印度持续爆发的可能影响以及对病毒结构和宿主易感性的影响

对印度东部感染者的鼻咽和口咽拭子样本进行了 SARS-CoV-2 基因组的直接大规模平行测序。七个分离株属于 A2a 进化枝，而一个属于 B4 进化枝。还检测到 A2a 进化枝特有的特定突变，其中包括 RNA 依赖性 RNA 聚合酶中的 P323L 和 Spike 糖蛋白中的 D614G。此外，我们的数据揭示了包含非同义突变的新型亚克隆的出现，即。Spike (S) 蛋白中的 G1124V、核衣壳 (N) 蛋白中的 R203K 和 G204R。N 蛋白突变位于参与病毒衣壳形成的富含 SR 的区域，S 蛋白突变位于 S 2 结构域，其参与触发病毒与宿主细胞膜的融合。在这些突变与 COVID-19 阳性病例的旅行或接触史之间观察到了有趣的相关性。还预测了这些突变的 miRNA 结合和结构随之发生的改变。更重要的是，还讨论了突变 D614G（在 SD 域中）和 G1124V（在 S 2 亚基中）对 S 蛋白结构稳定性的可能影响。结果首次报告了印度东部 SARS-CoV-2 基因组突变积累的鸟瞰图。