Browsing by Author "Ternus, Krista"

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    SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission
    (Cold Spring Harbor Laboratory Press, 2021) Sapoval, Nicolae; Mahmoud, Medhat; Jochum, Michael D.; Liu, Yunxi; Elworth, R. A. Leo; Wang, Qi; Albin, Dreycey; Ogilvie, Huw A.; Lee, Michael D.; Villapol, Sonia; Hernandez, Kyle M.; Berry, Irina Maljkovic; Foox, Jonathan; Beheshti, Afshin; Ternus, Krista; Aagaard, Kjersti M.; Posada, David; Mason, Christopher E.; Sedlazeck, Fritz J.; Treangen, Todd J.
    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.
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    Synthetic DNA and biosecurity: Nuances of predicting pathogenicity and the impetus for novel computational approaches for screening oligonucleotides
    (Public Library of Science, 2020) Elworth, R.A. Leo; Diaz, Christian; Yang, Jing; de Figueiredo, Paul; Ternus, Krista; Treangen, Todd