Sapoval, NicolaeMahmoud, MedhatJochum, Michael D.Liu, YunxiElworth, R. A. LeoWang, QiAlbin, DreyceyOgilvie, Huw A.Lee, Michael D.Villapol, SoniaHernandez, Kyle M.Berry, Irina MaljkovicFoox, JonathanBeheshti, AfshinTernus, KristaAagaard, Kjersti M.Posada, DavidMason, Christopher E.Sedlazeck, Fritz J.Treangen, Todd J.2021-05-072021-05-072021Sapoval, Nicolae, Mahmoud, Medhat, Jochum, Michael D., et al.. "SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission." <i>Genome Research,</i> 31, no. 4 (2021) Cold Spring Harbor Laboratory Press: 635-644. https://doi.org/10.1101/gr.268961.120.https://hdl.handle.net/1911/110490The 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.engThis article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.Journal articleGenomeRes-2021-Sapoval-635-44https://doi.org/10.1101/gr.268961.120