@article{Sapoval18022021,
author = {Sapoval, Nicolae and Mahmoud, Medhat and Jochum, Michael and Liu, Yunxi and Elworth, R.A. Leo and Wang, Qi and Albin, Dreycey and Ogilvie, Huw and Lee, Michael D. and Villapol, Sonia and Hernandez, Kyle and Maljkovic Berry, Irina and Foox, Jonathan and Beheshti, Afshin and Ternus, Krista and Aagaard, Kjersti and Posada, David and Mason, Christopher and Sedlazeck, Fritz J and Treangen, Todd J}, 
title = {Hidden genomic diversity of SARS-CoV-2: implications for qRT-PCR diagnostics and transmission},
year = {2021}, 
doi = {10.1101/gr.268961.120}, 
elocation-id = {gr.268961.120}, 
abstract ={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.}, 
URL = {http://genome.cshlp.org/content/early/2021/02/18/gr.268961.120.abstract}, 
eprint = {http://genome.cshlp.org/content/early/2021/02/18/gr.268961.120.full.pdf+html}, 
journal = {Genome Research} 
}