Speaker
Description
Evidence suggests that persistent SARS-CoV-2 infections may contain long periods of replicating virus, creating potential viral reservoirs of high genetic diversity. An earlier analysis of SARS-CoV-2 viral sequence data from >38,000 samples collected at the Houston Methodist Medical Center identified individuals who were sampled repeatedly. This dataset was used to conduct a longitudinal clinical case series to investigate the intra-host genetic dynamics of persistent SARS-CoV-2 infections. After filtering steps, we identified 62 individuals with quality viral sequences at time points beyond 21 days after initial sampling; of these individuals, 17 had quality viral sequence data at time points beyond 50 days. These potential long-term infections were grouped as persistently infected or reinfected based on the percent change of private single nucleotide polymorphisms (SNPs), longitudinal rare synonymous mutations, and intra-host Single Nucleotide Variant (iSNV) tracking. All individuals shared 10% of their iSNVs with SNPs, and 11% percent were shared across the 62 filtered individuals, suggesting a relationship between iSNVs and emerging SNPs. Additionally, 13 persistently-infected individuals had at least one rare SNP associated with a later clade, demonstrating the importance of intra-host dynamics in understanding the rise of novel SARS-CoV-2 variants.
