SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission

Nicolae Sapoval, Medhat Mahmoud, Michael D. Jochum, Yunxi Liu, R. A.Leo Elworth, Qi Wang, Dreycey Albin, Huw A. Ogilvie, Michael D. Lee, Sonia Villapol, Kyle M. Hernandez, Irina Maljkovic Berry, Jonathan Foox, Afshin Beheshti, Krista Ternus, Kjersti M. Aagaard, David Posada, Christopher E. Mason, Fritz J. Sedlazeck, Todd J. Treangen

Research output: Contribution to journalArticlepeer-review

25 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)635-644
Number of pages10
JournalGenome Research
Issue number4
StatePublished - Apr 1 2021


  • COVID-19/diagnosis
  • Genetic Variation
  • Genome, Viral
  • Host-Pathogen Interactions
  • Humans
  • Polymorphism, Single Nucleotide
  • Real-Time Polymerase Chain Reaction/methods
  • SARS-CoV-2/genetics

ASJC Scopus subject areas

  • Genetics(clinical)
  • Genetics


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