tetano
Editor, Senior Moderator
Clin Infect Dis
. 2025 Jul 1:ciaf057.
doi: 10.1093/cid/ciaf057. Online ahead of print. Utilizing Whole Genome Sequencing to Investigate a Coronavirus Disease 2019 Cluster Among Healthcare Workers in a Tertiary Care Facility in the Philippines: Insights and Implications for Infection Prevention and Control
Gina de Guzman Betito[SUP] 1 [/SUP], Reed Magleby[SUP] 2 [/SUP], Janice C Caoili[SUP] 1 [/SUP], Jason Caravas[SUP] 3 [/SUP], Mark Lemuel Ybañez[SUP] 1 [/SUP], Kara Moser[SUP] 2 [/SUP], Matthew Westercamp[SUP] 2 [/SUP], Maria Tarcela Gler[SUP] 1 [/SUP]; Global Action in Healthcare Network Healthcare-associated Infection Team
Collaborators, Affiliations
Background: 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.
Methods: 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.
Results: 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.
Conclusions: 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.
Keywords: COVID-19; SARS-CoV-2; cluster investigation; phylogenetic analysis; whole genome sequencing.
. 2025 Jul 1:ciaf057.
doi: 10.1093/cid/ciaf057. Online ahead of print. Utilizing Whole Genome Sequencing to Investigate a Coronavirus Disease 2019 Cluster Among Healthcare Workers in a Tertiary Care Facility in the Philippines: Insights and Implications for Infection Prevention and Control
Gina de Guzman Betito[SUP] 1 [/SUP], Reed Magleby[SUP] 2 [/SUP], Janice C Caoili[SUP] 1 [/SUP], Jason Caravas[SUP] 3 [/SUP], Mark Lemuel Ybañez[SUP] 1 [/SUP], Kara Moser[SUP] 2 [/SUP], Matthew Westercamp[SUP] 2 [/SUP], Maria Tarcela Gler[SUP] 1 [/SUP]; Global Action in Healthcare Network Healthcare-associated Infection Team
Collaborators, Affiliations
- PMID: 40590532
- DOI: 10.1093/cid/ciaf057
Background: 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.
Methods: 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.
Results: 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.
Conclusions: 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.
Keywords: COVID-19; SARS-CoV-2; cluster investigation; phylogenetic analysis; whole genome sequencing.