ArticleClinical infectious diseases : an official publication of the Infectious Diseases Society of America2025
Utilizing Whole Genome Sequencing to Investigate a COVID-19 Cluster Among Healthcare Workers in a Tertiary Care Facility in the Philippines: Insights and Implications for Infection Prevention and Control.
Article in Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
backgroundThe coronavirus disease 2019 (COVID-19) pandemic has highlighted the importance of genomic surveillance and whole genome sequencing (WGS) for identifying mutations and supporting epidemiologic investigations. Healthcare workers (HCWs) face unique risks for COVID-19, potentially amplifying outbreaks within healthcare facilities (HCFs). This report details the use of WGS to retrospectively investigate a COVID-19 cluster among HCWs in a tertiary care HCF in the Philippines.
methodsEpidemiologic investigation was conducted by the HCF infection prevention and control (IPC) staff. The Global Action in Healthcare Network (GAIHN) COVID-19 variant characterization project retrospectively conducted WGS on selected HCW and inpatient respiratory specimens associated with the cluster with reverse-transcription polymerase chain reaction cycle threshold ≤32. Phylogenetic analyses were conducted using Nextstrain. Subclusters were defined by shared severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage and epidemiologic data.
resultsInvestigation by IPC staff identified 19 HCWs with COVID-19 diagnosed during 2-9 September 2022 from a single nursing unit. Specimens for WGS were collected from 8 of these HCWs and from 43 additional HCF staff and inpatients with COVID-19 diagnosed from 1 August through 30 September 2022. Phylogenetic analyses identified 12 unique SARS-CoV-2 lineages and 2 subclusters: subcluster A (BA.5.2 lineage, n = 6) and subcluster B (BA.5.10.1 lineage, n = 7). Pairwise substitution-by-site analyses, combined with epidemiological data, provided support for multiple potential transmission events.
conclusionsWGS identified SARS-CoV-2 subclusters associated with high-risk exposure settings among HCWs in a tertiary care facility, providing essential insights into transmission pathways and demonstrating its potential to guide targeted IPC interventions and improve outbreak response strategies.
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