SARS-CoV-2 population dynamics in immunocompetent individuals in a closed transmission chain shows genomic diversity over the course of infection

• DOI: 10.1186/s13073-024-01360-1
• Publication Date: 2024-07-16T11:02:23Z
• Authors: Hannah Goldswain; Rebekah Penrice-R...; I’ah Donovan-Banf...; Craig W. Duffy; Xiaofeng Dong; Nadine Randle; Yan Ryan; Aleksandra M. Rze...; Jack Pilgrim; Emma Keyser; Simon A. Weller; Emma J. Hutley; Catherine Hartley; Tessa Prince; Alistair C. Darby; Niall Aye Maung; Henry Nwume; Julian A. Hiscox; Stevan R. Emmett
• Keywords: Indel; Viral evolution; Pandemic

Abstract Background SARS-CoV-2 remains rapidly evolving, and many biologically important genomic substitutions/indels have characterised novel lineages, which emerged during successive global waves of the pandemic. Worldwide sequencing has been able to monitor these waves, track transmission clusters, examine viral evolution in real time help inform healthcare policy. One school thought is that an apparent greater than average divergence emerging lineage from contemporary variants may require persistent infection, for example immunocompromised host. Due nature COVID-19 pandemic sampling, there were few studies examined evolutionary trajectory healthy individuals. Methods We investigated trends participant symptomatology within a cluster 16 infected, immunocompetent individuals with no co-morbidities closed chain. Longitudinal nasopharyngeal swab sampling allowed characterisation intra-host variation over at both dominant minor variant levels through Nimagen-Illumina sequencing. Results A change assignment was observed individual infections; however, only one indel evidence recombination period acute infection. Minor modifications varied between participants, some increasing abundance become sequence Conclusions Data this cohort SARS-CoV-2-infected participants demonstrated long-term infection host not necessarily prerequisite generating frequency amino acid substitutions. Amino substitutions level showing changes can occur diversity.