Intrahost genetic diversity and evolution of the SARS-CoV-2 B.1.517 lineage during chronic infection of an immunocompromised individual medrxivpreprint YaleSPH Sydney_Uni UNC infection genetics evolution COVID19 coronavirus covid
By Pooja Toshniwal PahariaJul 6 2022Reviewed by Danielle Ellis, B.Sc. In a recent study posted to the medRxiv* preprint server, researchers investigated the intrahost evolution and genetic diversity of the severe acute respiratory syndrome coronavirus 2 B.1.517 variant in an immunosuppressed person with chronic coronavirus disease 2019 .
The team detected the B.1.517 variant in Connecticut till March 2022 via a dataset of SARS-CoV-2 genomic surveillance. B.1.517 genetic sequences were traced to an immunosuppressed person with chronic COVID-19 for >1 year, from whom 30 nasopharyngeal swabs were obtained to sequence the SARS-CoV-2 genome. Whole-genome sequencing was used for sequencing between day 79 and day 471 to assess SARS-CoV-2 infectivity, and 12 swabs were also subjected to in vitro testing for viable SARS-CoV-2.
Results Related StoriesIn the RT-PCR analysis, swab samples obtained between day 79 and day 471 post-COVID-19 diagnosis had an average cycle threshold value of 25.5 reflective of ~ 3.1 × 108 SARS-CoV-2 copies in every mL; however, SARS-CoV-2 copies reduced with time.
Despite fluctuations, the iSNV frequencies obtained on WGS analysis largely correlated with those of the UMI-sequenced S gene. The iSNVs increased with time among the genotypes identified with average iSNVs numbers of 32.1. The second genotype had more iSNVs than the first one, and the number of iSNVs positively correlated with the sampling periods.
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