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对17271个印度新冠病毒基因组进行系统发育分析，以确定时空热点突变。

Phylogenetic analysis of 17271 Indian SARS-CoV-2 genomes to identify temporal and spatial hotspot mutations.

作者信息

Ghosh Nimisha, Nandi Suman, Saha Indrajit

机构信息

Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland.

Department of Computer Science and Information Technology, Institute of Technical Education and Research, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India.

出版信息

PLoS One. 2022 Mar 28;17(3):e0265579. doi: 10.1371/journal.pone.0265579. eCollection 2022.

DOI:10.1371/journal.pone.0265579
PMID:35344550
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC8959188/
Abstract

The second wave of SARS-CoV-2 has hit India hard and though the vaccination drive has started, moderate number of COVID affected patients is still present in the country, thereby leading to the analysis of the evolving virus strains. In this regard, multiple sequence alignment of 17271 Indian SARS-CoV-2 sequences is performed using MAFFT followed by their phylogenetic analysis using Nextstrain. Subsequently, mutation points as SNPs are identified by Nextstrain. Thereafter, from the aligned sequences temporal and spatial analysis are carried out to identify top 10 hotspot mutations in the coding regions based on entropy. Finally, to judge the functional characteristics of all the non-synonymous hotspot mutations, their changes in proteins are evaluated as biological functions considering the sequences by using PolyPhen-2 while I-Mutant 2.0 evaluates their structural stability. For both temporal and spatial analysis, there are 21 non-synonymous hotspot mutations which are unstable and damaging.

摘要

新冠病毒的第二波疫情给印度带来了沉重打击，尽管疫苗接种工作已经启动，但该国仍有一定数量的新冠感染患者，因此需要对不断演变的病毒株进行分析。在这方面，使用MAFFT对17271条印度新冠病毒序列进行多序列比对，随后使用Nextstrain对其进行系统发育分析。接着，Nextstrain识别出作为单核苷酸多态性（SNP）的突变点。此后，基于比对后的序列进行时空分析，以根据熵确定编码区域中的前10个热点突变。最后，为了判断所有非同义热点突变的功能特征，使用PolyPhen-2评估它们在蛋白质中的变化作为生物学功能，而I-Mutant 2.0评估它们的结构稳定性。在时空分析中，有21个非同义热点突变不稳定且具有破坏性。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/042e/8959188/d4cc669607c9/pone.0265579.g010.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/042e/8959188/d4cc669607c9/pone.0265579.g010.jpg

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