Classification of a Massive Number of Viral Genomes and Estimation of Time of Most Recent Common Ancestor (tMRCA) of SARS-CoV-2 Using Phylodynamic Analysis.

Xiaowen Hu, Siqin Guan, Yiliang He, Guohui Yi, Lei Yao, Jiaming Zhang

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Article in Bio-protocol, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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6 authors.

Xiaowen HuKey Laboratory of Microbiology of Hainan, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.

Siqin GuanKey Laboratory of Microbiology of Hainan, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.

Yiliang HeKey Laboratory of Microbiology of Hainan, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.

Guohui YiPublic Research Laboratory, Hainan Medical University, Haikou, China.

Lei YaoSichuan Provincial Key Laboratory for Human Disease Gene Study and the Center for Medical Genetics, Department of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology, Chengdu, China.

Jiaming ZhangKey Laboratory of Microbiology of Hainan, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Estimating the time of most recent common ancestor (tMRCA) is important to trace the origin of pathogenic viruses. This analysis is based on the genetic diversity accumulated in a certain time period. There have been thousands of mutant sites occurring in the genomes of SARS-CoV-2 since the COVID-19 pandemic started; six highly linked mutation sites occurred early before the start of the pandemic and can be used to classify the genomes into three main haplotypes. Tracing the origin of those three haplotypes may help to understand the origin of SARS-CoV-2. In this article, we present a complete protocol for the classification of SARS-CoV-2 genomes and calculating tMRCA using Bayesian phylodynamic method. This protocol may also be used in the analysis of other viral genomes. Key features • Filtering and alignment of a massive number of viral genomes using custom scripts and ViralMSA. • Classification of genomes based on highly linked sites using custom scripts. • Phylodynamic analysis of viral genomes using Bayesian evolutionary analysis sampling trees (BEAST). • Visualization of posterior distribution of tMRCA using Tracer.v1.7.2. • Optimized for the SARS-CoV-2.

Indexed as

Bayesian phylodynamic analysisDiversityGenetic linkageGenome classificationRedundant genomeSARS-CoV-2Viral origin

Identifiers

PMID38835995

DOI10.21769/BioProtoc.4955

PMCPMC10958167

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