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Developing an appropriate evolutionary baseline model for the study of SARS-CoV-2 patient samples

Authors :
John W. Terbot
Parul Johri
Schuyler W. Liphardt
Vivak Soni
Susanne P. Pfeifer
Brandon S. Cooper
Jeffrey M. Good
Jeffrey D. Jensen
Source :
PLOS Pathogens. 19:e1011265
Publication Year :
2023
Publisher :
Public Library of Science (PLoS), 2023.

Abstract

Over the past 3 years, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has spread through human populations in several waves, resulting in a global health crisis. In response, genomic surveillance efforts have proliferated in the hopes of tracking and anticipating the evolution of this virus, resulting in millions of patient isolates now being available in public databases. Yet, while there is a tremendous focus on identifying newly emerging adaptive viral variants, this quantification is far from trivial. Specifically, multiple co-occurring and interacting evolutionary processes are constantly in operation and must be jointly considered and modeled in order to perform accurate inference. We here outline critical individual components of such an evolutionary baseline model—mutation rates, recombination rates, the distribution of fitness effects, infection dynamics, and compartmentalization—and describe the current state of knowledge pertaining to the related parameters of each in SARS-CoV-2. We close with a series of recommendations for future clinical sampling, model construction, and statistical analysis.

Details

ISSN :
15537374
Volume :
19
Database :
OpenAIRE
Journal :
PLOS Pathogens
Accession number :
edsair.doi...........d7fe4c39aa83a4e518eed1bf9ab8461a
Full Text :
https://doi.org/10.1371/journal.ppat.1011265