Division of Life Science, Institute of Advanced Study in Science and Technology, Paschim Boragaon, Guwahati, Assam, 781035, India.
Department of Microbiology, Gauhati Medical College and Hospital, Guwahati, Assam, 781032, India.
Virol J. 2023 Sep 1;20(1):201. doi: 10.1186/s12985-023-02139-3.
To understand the mechanism underlying the evolution of SARS-CoV-2 in a population, we sequenced 92 viral genomes from Assam, India. Analysis of these and database sequences revealed a complete selective sweep of a haplotype in Assam carrying 13 pre-existing variants, including a high leap in frequency of a variant on ORF8, which is involved in immune evasion. A comparative study between sequences of same lineage and similar time frames in and outside Assam showed that 10 of the 13 pre-existing variants had a frequency ranging from 96 to 99%, and the remaining 3 had a low frequency outside Assam. Using a phylogenetic approach to infer sequential occurrences of variants we found that the variant Phe120del on ORF8, which had a low frequency (1.75%) outside Assam, is at the base of the phylogenetic tree of variants and became totally fixed (100%) in Assam population. Based on this observation, we inferred that the variant on ORF8 had a selective advantage, so it carried the haplotype to reach the100% frequency. The haplotype also carried 32 pre-existing variants at a frequency from 1.00 to 80.00% outside Assam. Those of these variants that are more closely linked to the S-protein locus, which often carries advantageous mutations and is tightly linked to the ORF8 locus, retained higher frequencies, while the less tightly linked variants showed lower frequencies, likely due to recombination among co- circulating variants in Assam. The ratios of non-synonymous substitutions to synonymous substitutions suggested that some genes such as those coding for the S-protein and non-structural proteins underwent positive selection while others were subject to purifying selection during their evolution in Assam. Furthermore, we observed negative correlation of the Ct value of qRT-PCR of the patients with abundant ORF6 transcripts, suggesting that ORF6 can be used as a marker for estimating viral titer. In conclusion, our in-depth analysis of SARS-CoV-2 genomes in a regional population reveals the mechanism and dynamics of viral evolution.
为了了解 SARS-CoV-2 在人群中进化的机制，我们对来自印度阿萨姆邦的 92 个病毒基因组进行了测序。对这些基因组和数据库序列的分析揭示了一个携带 13 种先前存在变异的单倍型在阿萨姆邦的完全选择清除，包括 ORF8 上一个变异的频率的大幅跃升，该变异参与免疫逃避。在阿萨姆邦内外具有相同谱系和相似时间框架的序列之间的比较研究表明，13 种先前存在的变异中有 10 种的频率在 96%至 99%之间，其余 3 种在阿萨姆邦以外的频率较低。使用系统发育方法推断变异的连续发生，我们发现 ORF8 上的变异 Phe120del 的频率（阿萨姆邦以外的频率为 1.75%）很低，它位于变异的系统发育树的底部，在阿萨姆邦人群中完全固定（100%）。根据这一观察结果，我们推断该 ORF8 上的变异具有选择优势，因此它携带单倍型达到 100%的频率。该单倍型在阿萨姆邦以外的频率也携带 32 种先前存在的变异，频率为 1.00%至 80.00%。这些变异中与 S 蛋白基因座更紧密相关的变异，该基因座经常携带有利突变且与 ORF8 基因座紧密相关，保留了更高的频率，而与 S 蛋白基因座联系不那么紧密的变异则显示出较低的频率，这可能是由于阿萨姆邦内循环变异之间的重组所致。非同义替换与同义替换的比例表明，某些基因（如编码 S 蛋白和非结构蛋白的基因）在阿萨姆邦的进化过程中经历了正选择，而其他基因则受到了纯化选择。此外，我们观察到 qRT-PCR 的 Ct 值与大量 ORF6 转录物的患者呈负相关，这表明 ORF6 可以用作估计病毒滴度的标志物。总之，我们对区域性人群中 SARS-CoV-2 基因组的深入分析揭示了病毒进化的机制和动态。
