Molecular Epidemiology of SARS-CoV-2 by Sequencing

Yan Yan; Qinxue Hu

doi:10.1007/978-1-0716-2111-0_2

Molecular Epidemiology of SARS-CoV-2 by Sequencing

Methods Mol Biol. 2022:2452:19-32. doi: 10.1007/978-1-0716-2111-0_2.

Authors

Yan Yan¹, Qinxue Hu^{2

3}

Affiliations

¹ Infection and Immunity Laboratory, The Fifth People's Hospital of Wuxi, Affiliated Hospital of Jiangnan University, Wuxi, China.
² State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China. [email protected].
³ Institute for Infection and Immunity, St. George's, University of London, London, UK. [email protected].

PMID: 35554898
DOI: 10.1007/978-1-0716-2111-0_2

Abstract

Sequences of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) contains preliminary information on the phylodynamics and phylogeography of this new virus. A maximum clade credibility tree (MCCT) was constructed using available whole genome sequences of SARS-CoV-2 and highly similar whole genome sequences from bat SARS-like coronavirus, which are available in GenBank. In this chapter, we describe the molecular epidemiology of SARS-CoV-2 by sequencing the viral genomes from confirmed COVID-19 patients, utilizing methods such as target fragment amplification, sequencing, alignment, and maximum similarity mapping.

Keywords: COVID-19; Genotype; Molecular epidemiology; SARS-CoV-2; Sequencing.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

COVID-19* / epidemiology
Genome, Viral
Humans
Molecular Epidemiology
Phylogeny
SARS-CoV-2* / genetics