Within-host genetic diversity of SARS-CoV-2 in the context of large-scale hospital-associated genomic surveillance.
Alexandra MushegianScott Wesley LongRandall James OlsenPaul James ChristensenSishir SubediMatthew ChungJames DavisJames MusserElodie GhedinPublished in: medRxiv : the preprint server for health sciences (2022)
The COVID-19 pandemic has resulted in extensive surveillance of the genomic diversity of SARS-CoV-2. Sequencing data generated as part of these efforts can also capture the diversity of the SARS-CoV-2 virus populations replicating within infected individuals. To assess this within-host diversity of SARS-CoV-2 we quantified low frequency (minor) variants from deep sequence data of thousands of clinical samples collected by a large urban hospital system over the course of a year. Using a robust analytical pipeline to control for technical artefacts, we observe that at comparable viral loads, specimens from patients hospitalized due to COVID-19 had a greater number of minor variants than samples from outpatients. Since individuals with highly diverse viral populations could be disproportionate drivers of new viral lineages in the patient population, these results suggest that transmission control should pay special attention to patients with severe or protracted disease to prevent the spread of novel variants.
Keyphrases
- sars cov
- genetic diversity
- copy number
- respiratory syndrome coronavirus
- end stage renal disease
- public health
- healthcare
- electronic health record
- ejection fraction
- chronic kidney disease
- newly diagnosed
- big data
- prognostic factors
- genome wide
- acute care
- dna methylation
- early onset
- health insurance
- emergency department
- gene expression
- coronavirus disease
- machine learning
- patient reported outcomes
- drug induced