RT Journal Article T1 SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission A1 Sapoval, Nicolae A1 Mahmoud, Medhat A1 Jochum, Michael D. A1 Liu, Yunxi A1 Elworth, R.A. Leo A1 Wang, Qi A1 Albin, Dreycey A1 Ogilvie, Huw A. A1 Lee, Michael D. A1 Villapol, Sonia A1 Hernández, Kyle M. A1 Maljkovic Berry, Irina A1 Foox, Jonathan A1 Beheshti, Afshin A1 Ternus, Krista A1 Aagaard, Kjersti M. A1 Posada González, David A1 Mason, Christopher E. A1 Sedlazeck, Fritz J. A1 Treangen, Todd J. K1 2409 Genética K1 3202 Epidemiología AB 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. PB Genome Research SN 10889051 YR 2021 FD 2021-02-18 LK http://hdl.handle.net/11093/3015 UL http://hdl.handle.net/11093/3015 LA eng NO Genome Research, 31(4): 635-644 (2021) NO National Institutes of Health | Ref. R01HD091731 DS Investigo RD 08-feb-2025