Rapid SARS-CoV-2 surveillance using clinical, pooled, or wastewater sequence as a sensor for population change.

ABSTRACT: The COVID-19 pandemic has highlighted the critical role of genomic surveillance for guiding policy and control. Timeliness is key, but sequence alignment and phylogeny slow most surveillance techniques. Millions of SARS-CoV-2 genomes have been assembled. Phylogenetic methods are ill equipped to handle this sheer scale. We introduce a pangenomic measure that examines the information diversity of a k-mer library drawn from a country's complete set of clinical, pooled, or wastewater sequence. Quantifying diversity is central to ecology. Hill numbers, or the effective number of species in a sample, provide a simple metric for comparing species diversity across environments. The more diverse the sample, the higher the Hill number. We adopt this ecological approach and consider each k<

SUBMITTER: Narechania A 

PROVIDER: S-EPMC11529847 | biostudies-literature | 2024 Oct

REPOSITORIES: biostudies-literature