COV-IRT Collaboration (Preprint): Hidden genomic diversity of SARS-CoV-2: implications for qRT-PCR diagnostics and transmission

This research was developed by the COV-IRT Subgroup: Viral Genomics and Evolution.

Collaborators include Nicolae Sapoval, Medhat Mahmoud, Michael D. Jochum, Yunxi Liu, R. A. Leo Elworth, Dreycey Albin, Huw 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 Sedlazeck, Todd J. Treangen

This preprint was posted on July 2, 2020


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 clades that have spread throughout the world. In this study, we investigated over 7,000 SARS-CoV-2 datasets to unveil both intrahost and interhost diversity. Our intrahost and interhost diversity analyses yielded three major observations. First, the mutational profile of SARS-CoV-2 highlights iSNV and SNP similarity, albeit with high variability in C>T 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 small indels fuel 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.

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