Unraveling a Nosocomial Outbreak of COVID-19: The Role of Whole Genome Sequence Analysis

Meijer, Suzy E; Harel, Noam; Ben-Ami, Ronen; Nahari, Meital; Yakubovsky, Michal; Oster, Howard S; Kolomansky, Albert; Halutz, Ora; Laskar, Orly; Henig, Oryan; Stern, Adi; Paran, Yael

BACKGROUND: The COVID-19 pandemic poses many epidemiological challenges. The investigation of nosocomial transmission is usually performed via thorough investigation of an index case and subsequent contact tracing. Notably, this approach has a subjective component and there is accumulating evidence that whole genome sequencing of the virus may provide a more objective insight. METHODS: We report a large nosocomial outbreak in one of the medicine departments in our institution. Following intensive epidemiological investigation, we discovered that one of the patients involved was suffering from persistent COVID-19 while initially thought to be a recovering patient. She was therefore deemed to be the most likely source of the outbreak. We then performed whole genome sequencing of the virus of fourteen infected individuals involved in the outbreak. RESULTS: Surprisingly, the results of whole genome sequencing refuted our initial hypothesis. A phylogenetic tree of the samples showed multiple introductions of the virus into the ward, one of which led to a cluster of ten of the infected individuals. Importantly, the results pointed in the direction of a specific index patient that was different from the one that arose from our initial investigation. CONCLUSIONS: These results underscore the important added value of using whole genome sequencing in epidemiological investigations as it may reveal unexpected connections between cases and aid in understanding transmission dynamics, especially in the setting of a pandemic where multiple possible index cases exist simultaneously.