Rapid feedback on hospital onset SARS-CoV-2 infections combining epidemiological and sequencing data.

ABSTRACT:

Background

Rapid identification and investigation of healthcare-associated infections (HCAIs) is important for suppression of SARS-CoV-2, but the infection source for hospital onset COVID-19 infections (HOCIs) cannot always be readily identified based only on epidemiological data. Viral sequencing data provides additional information regarding potential transmission clusters, but the low mutation rate of SARS-CoV-2 can make interpretation using standard phylogenetic methods difficult.

Methods

We developed a novel statistical method and sequence reporting tool (SRT) that combines epidemiological and sequence data in order to provide a rapid assessment of the probability of HCAI among HOCI cases (defined as first positive test >48 hr following admission) and to identify infect

SUBMITTER: Stirrup O 

PROVIDER: S-EPMC8285103 | biostudies-literature | 2021 Jun

REPOSITORIES: biostudies-literature