TY  - JOUR
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
Y1  - 2021/02/18 
JF  - Genome Research 
JO  - Genome Research 
DO  - 10.1101/gr.268961.120 
SP  - gr.268961.120 
UR  - http://genome.cshlp.org/content/early/2021/02/18/gr.268961.120.abstract 
N2  - 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. 
ER  -