@article{3166f4da71104a45a5d227e7ae34fc29,
title = "Clinical utility of SARS-CoV-2 whole genome sequencing in deciphering source of infection",
abstract = "Coronavirus disease 2019 (COVID-19) caused by human severe acute respiratory syndrome coronavirus 2 (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 ({\textquoteleft}undetermined source of infection{\textquoteright}), 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 {\textquoteleft}undetermined source of infection{\textquoteright} 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",
author = "{Keio Donner Project} and T. Takenouchi and Iwasaki, {Y. W.} and S. Harada and H. Ishizu and Y. Uwamino and S. Uno and A. Osada and K. Abe and N. Hasegawa and M. Murata and T. Takebayashi and K. Fukunaga and H. Saya and Y. Kitagawa and M. Amagai and H. Siomi and K. Kosaki",
note = "Funding Information: We downloaded the full nucleotide sequences of the SARS-CoV-2 genomes from the GISAID database (https://www.gisaid.org/). We uploaded the full nucleotide sequences of our cohort to the GISAID database. A table of the contributors is available in Supplementary Table S1. We thank all the patients and healthcare workers who have fought against COVID-19. The Keio Donner Project is devoted to the late Professor S. Kitasato, the founder of The Keio University School of Medicine.This work was supported by Keio Gijuku Academic Development Funds and by AMED under Grant Number JP20he0622043. Funding Information: This work was supported by Keio Gijuku Academic Development Funds and by AMED under Grant Number JP20he0622043. Publisher Copyright: {\textcopyright} 2020",
year = "2021",
month = jan,
doi = "10.1016/j.jhin.2020.10.014",
language = "English",
volume = "107",
pages = "40--44",
journal = "Journal of Hospital Infection",
issn = "0195-6701",
publisher = "W.B. Saunders Ltd",
}