SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission.

TitleSARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission.
Publication TypeJournal Article
Year of Publication2021
AuthorsSapoval, N, Mahmoud, M, Jochum, MD, Liu, Y, Elworth, RALeo, Wang, Q, Albin, D, Ogilvie, HA, Lee, MD, Villapol, S, Hernandez, KM, Berry, IMaljkovic, Foox, J, Beheshti, A, Ternus, K, Aagaard, KM, Posada, D, Mason, CE, Sedlazeck, FJ, Treangen, TJ
JournalGenome Res
Date Published2021 04
KeywordsCOVID-19, Genetic Variation, Genome, Viral, Host-Pathogen Interactions, Humans, Polymorphism, Single Nucleotide, Real-Time Polymerase Chain Reaction, SARS-CoV-2

The COVID-19 pandemic has sparked an urgent need to uncover the underlying biology of this devastating disease. Though RNA viruses mutate more rapidly than DNA viruses, there are a relatively small number of single nucleotide polymorphisms (SNPs) that differentiate the main SARS-CoV-2 lineages that have spread throughout the world. In this study, we investigated 129 RNA-seq data sets and 6928 consensus genomes to contrast the intra-host and inter-host diversity of SARS-CoV-2. Our analyses yielded three major observations. First, the mutational profile of SARS-CoV-2 highlights intra-host single nucleotide variant (iSNV) and SNP similarity, albeit with differences in C > U changes. Second, iSNV and SNP patterns in SARS-CoV-2 are more similar to MERS-CoV than SARS-CoV-1. Third, a significant fraction of insertions and deletions contribute to the genetic diversity of SARS-CoV-2. Altogether, our findings provide insight into SARS-CoV-2 genomic diversity, inform the design of detection tests, and highlight the potential of iSNVs for tracking the transmission of SARS-CoV-2.

Alternate JournalGenome Res
PubMed ID33602693
PubMed Central IDPMC8015855
Grant ListR01 HD091731 / HD / NICHD NIH HHS / United States
U19 AI144297 / AI / NIAID NIH HHS / United States