Genomic and Phylogenetic Dissection of SARS-CoV-2 Transmission Networks in Healthcare Workers

Understanding how SARS-CoV-2 circulates among healthcare workers (HCWs) is critical for maintaining safe hospitals and protecting communities. We retrospectively examined 93 archived nasopharyngeal swabs collected from SARS-CoV-2 positive HCWs and their close contacts at a Turkish university hospital between March 2020 and November 2021. Viral RNA was confirmed by RT-PCR and sequenced with the QIAseq DIRECT SARS-CoV-2 workflow on an Illumina platform; genomes were aligned to the Wuhan-H1 reference and analyzed with maximum-likelihood phylogenetics. Sixty-three individuals formed 20 epidemiologically defined clusters (40 HCWs, 23 contacts; mean age ≈ 34 years), most experiencing only mild or moderate illness. Sequencing quality improved as RT-PCR cycle threshold values fell, and nearly 98% of each genome was covered at 10 × depth. Fourteen viral lineages were detected, yet samples from the same cluster differed by no more than two single-nucleotide changes, indicating recent person-to-person spread. Phylogenetic reconstruction suggested single-source introduction in three-quarters of clusters, with the remainder reflecting multiple introductions. Observational data linked transmission events to inconsistent use of personal protective equipment and inadequate physical distancing in break rooms, shared offices, and household settings. By combining genomic and field evidence, this study clarifies the paths by which SARS-CoV-2 moved through a healthcare workforce, highlights the value of whole-genome sequencing for outbreak resolution, and reinforces the continuing need for rigorous infection-control practices even when overall case severity appears low to prevent future clusters and maintain healthcare resilience.