Publication date: Jul 01, 2025
The 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. Epidemiologic 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. Investigation 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. WGS 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.
| Concepts | Keywords |
|---|---|
| August | cluster investigation |
| Coronavirus | COVID-19 |
| Covid | phylogenetic analysis |
| Philippines | SARS-CoV-2 |
| Staff | whole genome sequencing |
Semantics
| Type | Source | Name |
|---|---|---|
| disease | MESH | Coronavirus Disease 2019 |
| disease | IDO | facility |
| disease | MESH | Infection |
| drug | DRUGBANK | Etoperidone |
| disease | IDO | site |