Stability of SARS-CoV-2 phylogenies.

PLoS Genetics
Yatish TurakhiaRussell Corbett-Detig

Abstract

The SARS-CoV-2 pandemic has led to unprecedented, nearly real-time genetic tracing due to the rapid community sequencing response. Researchers immediately leveraged these data to infer the evolutionary relationships among viral samples and to study key biological questions, including whether host viral genome editing and recombination are features of SARS-CoV-2 evolution. This global sequencing effort is inherently decentralized and must rely on data collected by many labs using a wide variety of molecular and bioinformatic techniques. There is thus a strong possibility that systematic errors associated with lab-or protocol-specific practices affect some sequences in the repositories. We find that some recurrent mutations in reported SARS-CoV-2 genome sequences have been observed predominantly or exclusively by single labs, co-localize with commonly used primer binding sites and are more likely to affect the protein-coding sequences than other similarly recurrent mutations. We show that their inclusion can affect phylogenetic inference on scales relevant to local lineage tracing, and make it appear as though there has been an excess of recurrent mutation or recombination among viral lineages. We suggest how samples can be scree...Continue Reading

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Citations

Feb 18, 2021·Life Science Alliance·Mengran WangSusan Dina Ghiassian
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Sep 2, 2021·Molecular Biology and Evolution·Jakob McBroomeYatish Turakhia

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Methods Mentioned

BETA
PCR
glycosylation
MDS

Software Mentioned

R
Dendroscope3
TreeCmp
cophylo
IQ
GISAID
tanglegrams
UK
MCdist
dendropy

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