de Guzman Betito Gina, Magleby Reed, Caoili Janice C, Caravas Jason, Lemuel Ybañez Mark, Moser Kara, Westercamp Matthew, Tarcela Gler Maria
Infection Prevention & Control Unit, Makati Medical Center, Makati, Philippines.
Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, US Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
Clin Infect Dis. 2025 Jul 18;80(6):1262-1268. doi: 10.1093/cid/ciaf057.
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.
2019年冠状病毒病（COVID-19）大流行凸显了基因组监测和全基因组测序（WGS）对于识别突变和支持流行病学调查的重要性。医护人员（HCWs）面临感染COVID-19的独特风险，这可能会加剧医疗机构（HCFs）内的疫情爆发。本报告详细介绍了利用WGS对菲律宾一家三级护理HCF中医护人员之间的COVID-19聚集性病例进行回顾性调查的情况。
HCF感染预防与控制（IPC）工作人员进行了流行病学调查。全球医疗保健网络行动（GAIHN）COVID-19变异特征项目对与该聚集性病例相关的选定医护人员和住院患者呼吸道标本进行回顾性WGS，这些标本的逆转录聚合酶链反应循环阈值≤32。使用Nextstrain进行系统发育分析。亚群由共享的严重急性呼吸综合征冠状病毒2（SARS-CoV-2）谱系和流行病学数据定义。
IPC工作人员的调查确定了2022年9月2日至9日期间在一个护理单元确诊感染COVID-19的19名医护人员。从其中8名医护人员以及2022年8月1日至9月30日期间确诊感染COVID-19的另外43名HCF工作人员和住院患者中采集了用于WGS的标本。系统发育分析确定了12个独特的SARS-CoV-2谱系和2个亚群：亚群A（BA.5.2谱系，n = 6）和亚群B（BA.5.10.1谱系，n = 7）。逐位点成对替换分析与流行病学数据相结合，为多个潜在传播事件提供了支持。
WGS识别出了与三级护理机构中医护人员高风险暴露环境相关的SARS-CoV-2亚群，为传播途径提供了重要见解，并证明了其在指导针对性IPC干预措施和改进疫情应对策略方面的潜力。
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