评估SARS-CoV-2谱系的进化和核苷酸变异之间的动态关联

Asmita Gupta, Reelina Basu, M. Bashyam
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引用次数: 1

摘要

尽管在了解SARS-CoV-2(严重急性呼吸综合征冠状病毒2)的感染机制方面取得了重大进展,但它仍在全球范围内造成严重的发病率和死亡率。虽然在一些国家实施了大规模免疫规划,但病毒传播周期以多波的形式显示出持续的进展。通过有利的选择,核苷酸变异(NVs)的积累导致了优势病毒谱系频率的不断变化,这可以理解为疾病严重程度和可能的疫苗逃逸的主要决定因素。事实上,世界范围内已经开始努力确定可能导致严重临床表现或促进疫苗接种突破的特定病毒谱系和/或NVs。由于宿主遗传学预计在塑造病毒进化中发挥重要作用,因此有必要研究全基因组SARS-CoV-2 nv在不同人群中的作用。在本研究中,我们分析了从印度特伦甘纳邦获得的3543份sars - cov -2感染样本的全基因组序列(包括我们之前研究中的210份),这些样本是在2020年4月至2021年10月的较长时间内收集的。在此期间,我们提出了流行病毒谱系和NVs进化的独特视角。我们还强调,特定NVs的存在可能与归类为疫苗接种突破的样本有利相关。最后,我们报告了新的基因组位置的全基因组内宿主变异。本文提出的结果为病毒在较长时期内的进化提供了重要见解,并为严格研究特定nv在疫苗接种突破中的作用铺平了道路。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Assessing the evolution of SARS-CoV-2 lineages and the dynamic associations between nucleotide variations
Despite seminal advances towards understanding the infection mechanism of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), it continues to cause significant morbidity and mortality worldwide. Though mass immunization programmes have been implemented in several countries, the viral transmission cycle has shown a continuous progression in the form of multiple waves. A constant change in the frequencies of dominant viral lineages, arising from the accumulation of nucleotide variations (NVs) through favourable selection, is understandably expected to be a major determinant of disease severity and possible vaccine escape. Indeed, worldwide efforts have been initiated to identify specific virus lineage(s) and/or NVs that may cause a severe clinical presentation or facilitate vaccination breakthrough. Since host genetics is expected to play a major role in shaping virus evolution, it is imperative to study the role of genome-wide SARS-CoV-2 NVs across various populations. In the current study, we analysed the whole genome sequence of 3543 SARS-CoV-2-infected samples obtained from the state of Telangana, India (including 210 from our previous study), collected over an extended period from April 2020 to October 2021. We present a unique perspective on the evolution of prevalent virus lineages and NVs during this period. We also highlight the presence of specific NVs likely to be associated favourably with samples classified as vaccination breakthroughs. Finally, we report genome-wide intra-host variations at novel genomic positions. The results presented here provide critical insights into virus evolution over an extended period and pave the way to rigorously investigate the role of specific NVs in vaccination breakthroughs.
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