Analysis of SARS-CoV-2 genomic surveillance data during the Delta and Omicron waves at a Saudi tertiary referral hospital.

ABSTRACT:

Background

Studying the genomic evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) may help determine outbreak clusters and virus transmission advantages to aid public health efforts during the pandemic. Thus, we tracked the evolution of SARS-CoV-2 by variant epidemiology, breakthrough infection, and patient characteristics as the virus spread during the Delta and Omicron waves. We also conducted phylogenetic analyses to assess modes of transmission.

Methods

Nasopharyngeal samples were collected from a cohort of 900 patients with positive polymerase chain reaction (PCR) test results confirming COVID-19 disease. Samples underwent real-time PCR detection using TaqPath assays. Sequencing was performed with Ion GeneStudio using the Ion AmpliSeq™ SARS-CoV-2

SUBMITTER: Obeid D 

PROVIDER: S-EPMC9747229 | biostudies-literature | 2023 Feb

REPOSITORIES: biostudies-literature