![]() Substitutions included mutations that are lineage defining for SARS-CoV-2 variants, at target sites for monoclonal antibodies and/or are commonly found in immunocompromised people 11, 12, 13, 14. In some individuals, we identified many viral amino acid substitutions, indicating periods of strong positive selection, whereas others had no consensus change in the sequences for prolonged periods, consistent with weak selection. We estimate that 0.1–0.5% of infections may become persistent with typically rebounding high viral loads and last for at least 60 days. Individuals with persistent infection had more than 50% higher odds of self-reporting long COVID than individuals with non-persistent infection. We refer to these as ‘persistent infections’ as available evidence suggests that they represent ongoing viral replication, although the persistence of non-replicating RNA cannot be ruled out in all. Here, using viral sequence data collected as part of a national infection survey, we identified 381 individuals with SARS-CoV-2 RNA at high titre persisting for at least 30 days, of which 54 had viral RNA persisting at least 60 days. However, the population prevalence of persistent infections, their viral load kinetics and evolutionary dynamics over the course of infections remain largely unknown. Persistent SARS-CoV-2 infections may act as viral reservoirs that could seed future outbreaks 1, 2, 3, 4, 5, give rise to highly divergent lineages 6, 7, 8 and contribute to cases with post-acute COVID-19 sequelae (long COVID) 9, 10. ![]() ![]() The COVID-19 Genomics UK (COG-UK) Consortium,.Wellcome Sanger Institute COVID-19 Surveillance Team,.Prevalence of persistent SARS-CoV-2 in a large community surveillance study
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