RT Journal
A1 Sapoval, Nicolae
A1 Mahmoud, Medhat
A1 Jochum, Michael
A1 Liu, Yunxi
A1 Elworth, R.A. Leo
A1 Wang, Qi
A1 Albin, Dreycey
A1 Ogilvie, Huw
A1 Lee, Michael D.
A1 Villapol, Sonia
A1 Hernandez, Kyle
A1 Maljkovic Berry, Irina
A1 Foox, Jonathan
A1 Beheshti, Afshin
A1 Ternus, Krista
A1 Aagaard, Kjersti
A1 Posada, David
A1 Mason, Christopher
A1 Sedlazeck, Fritz J
A1 Treangen, Todd J
T1 Hidden genomic diversity of SARS-CoV-2: implications for qRT-PCR diagnostics and transmission
JF Genome Research 
JO Genome Research 
YR 2021 
FD February 18 
DO 10.1101/gr.268961.120 
SP gr.268961.120 
UL http://genome.cshlp.org/content/early/2021/02/18/gr.268961.120.abstract 
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 datasets and 6,928 consensus genomes to contrast the intrahost and interhost diversity of SARS-CoV-2. Our analyses yielded three major observations. First, the mutational profile of SARS-CoV-2 highlights 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.