Unraveling a Nosocomial Outbreak of COVID-19: The Role of Whole-Genome Sequence Analysis.
Suzy E Meijer, Noam Harel, Ronen Ben-Ami, Meital Nahari, Michal Yakubovsky, Howard S Oster, Albert Kolomansky, Ora Halutz, Orly Laskar, Oryan Henig, Adi Stern, Yael Paran
Author Information
Suzy E Meijer: Department of Infectious Diseases and Epidemiology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.
Noam Harel: The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv, Israel.
Ronen Ben-Ami: Department of Infectious Diseases and Epidemiology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.
Meital Nahari: Department of Infectious Diseases and Epidemiology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.
Michal Yakubovsky: Department of Infectious Diseases and Epidemiology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.
Howard S Oster: Department of Internal Medicine, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.
Albert Kolomansky: Department of Internal Medicine, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.
Ora Halutz: Laboratory of Microbiology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.
Orly Laskar: The Department of Infectious Diseases, Israel Institute for Biological Research, Ness-Ziona, Israel.
Oryan Henig: Department of Infectious Diseases and Epidemiology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.
Adi Stern: The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv, Israel. ORCID
Yael Paran: Department of Infectious Diseases and Epidemiology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel. ORCID
BACKGROUND: The coronavirus disease 2019 (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 more objective insight. METHODS: We report a large nosocomial outbreak in 1 of the medicine departments in our institution. Following intensive epidemiological investigation, we discovered that 1 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 14 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, 1 of which led to a cluster of 10 of the infected individuals. Importantly, the results pointed in the direction of a specific index patient that was different from the 1 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.
