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

Research output: Contribution to journalArticlepeer-review

Abstract

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.

Original languageEnglish
Article numberofab120
JournalOpen Forum Infectious Diseases
Volume8
Issue number10
DOIs
StatePublished - 1 Oct 2021

Keywords

  • COVID-19
  • Epidemiology
  • Nosocomial
  • Outbreak
  • Sequencing

All Science Journal Classification (ASJC) codes

  • Clinical Neurology
  • Oncology

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