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The Journal of hospital infection
Oct 24, 2020;

Clinical Utility of SARS-CoV-2 Whole Genome Sequencing in Deciphering Source of Infection.

Toshiki Takenouchi, Yuka W Iwasaki, Sei Harada, Hirotsugu Ishizu, Yoshifumi Uwamino, Shunsuke Uno, Asami Osada, Kodai Abe, Naoki Hasegawa, Mitsuru Murata, Toru Takebayashi, Koichi Fukunaga, Hideyuki Saya, Yuko Kitagawa, Masayuki Amagai, Haruhiko Siomi, Kenjiro Kosaki, Keio Donner Project
Author Information
  1. Toshiki Takenouchi: Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan.
  2. Yuka W Iwasaki: Department of Molecular Biology, Keio University School of Medicine, Tokyo, Japan.
  3. Sei Harada: Department of Preventive Medicine and Public Health, Keio University School of Medicine, Tokyo, Japan.
  4. Hirotsugu Ishizu: Department of Molecular Biology, Keio University School of Medicine, Tokyo, Japan.
  5. Yoshifumi Uwamino: Division of Infection Control, Keio University Hospital, Tokyo, Japan; Department of Infectious Diseases, Keio University School of Medicine, Tokyo, Japan.
  6. Shunsuke Uno: Division of Infection Control, Keio University Hospital, Tokyo, Japan; Department of Infectious Diseases, Keio University School of Medicine, Tokyo, Japan.
  7. Asami Osada: Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan.
  8. Kodai Abe: Department of Infectious Diseases, Keio University School of Medicine, Tokyo, Japan; Department of Surgery, Keio University School of Medicine, Tokyo, Japan.
  9. Naoki Hasegawa: Division of Infection Control, Keio University Hospital, Tokyo, Japan.
  10. Mitsuru Murata: Department of Surgery, Keio University School of Medicine, Tokyo, Japan; Department of Laboratory Medicine, Keio University School of Medicine, Tokyo, Japan.
  11. Toru Takebayashi: Department of Preventive Medicine and Public Health, Keio University School of Medicine, Tokyo, Japan.
  12. Koichi Fukunaga: Department of Laboratory Medicine, Keio University School of Medicine, Tokyo, Japan; Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan.
  13. Hideyuki Saya: Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan; Division of Gene Regulation, Institute for Advanced Medical Research, Keio University School of Medicine, Tokyo, Japan.
  14. Yuko Kitagawa: Department of Infectious Diseases, Keio University School of Medicine, Tokyo, Japan.
  15. Masayuki Amagai: Division of Gene Regulation, Institute for Advanced Medical Research, Keio University School of Medicine, Tokyo, Japan; Department of Dermatology, Keio University School of Medicine, Tokyo, Japan.
  16. Haruhiko Siomi: Department of Molecular Biology, Keio University School of Medicine, Tokyo, Japan. Electronic address: awa403@keio.jp.
  17. Kenjiro Kosaki: Department of Dermatology, Keio University School of Medicine, Tokyo, Japan; Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan. Electronic address: kkosaki@keio.jp.
PMID: 34756867 DOI: 10.1016/j.jhin.2020.10.014

Abstract

COVID-19 caused by SARS-CoV-2 is a worldwide problem. From the standpoint of hospital infection control, determining the source of infection is critical. We conducted the present study to evaluate the efficacy of using whole genome sequencing to determine the source of infection in hospitalized patients who do not have a clear infectious contact history. Recently, we encountered two seemingly separate COVID-19 clusters in a tertiary hospital. Whole viral genome sequencing distinguished the two clusters according to the viral haplotype. However, the source of infection was unclear in 14 patients with COVID-19 who were clinically unlinked to clusters #1 or #2. These patients, who had no clear history of infectious contact within the hospital ("undetermined source of infection"), had haplotypes similar to those in cluster #2 but did not have two of the mutations used to characterize cluster #2, suggesting that these 14 cases of "undetermined source of infection" were not derived from cluster #2. Whole viral genome sequencing can be useful for confirming that sporadic COVID-19 cases with an undetermined source of infection are indeed not part of clusters at the institutional level.

Keywords

COVID-19 Community infection Nosocomial infection SARS-CoV-2 Whole genome sequencing

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Journal Article
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