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Lancet Reg Health Am . The clinical and genomic epidemiology of seasonal human coronaviruses in congregate homeless shelter settings: A repeated cross-sectional study

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  • Lancet Reg Health Am . The clinical and genomic epidemiology of seasonal human coronaviruses in congregate homeless shelter settings: A repeated cross-sectional study


    Lancet Reg Health Am


    . 2022 Nov;15:100348.
    doi: 10.1016/j.lana.2022.100348. Epub 2022 Aug 18.
    The clinical and genomic epidemiology of seasonal human coronaviruses in congregate homeless shelter settings: A repeated cross-sectional study


    Eric J Chow 1 , Amanda M Casto 1 2 , Julia H Rogers 1 3 , Pavitra Roychoudhury 2 4 , Peter D Han 5 6 , Hong Xie 4 , Margaret G Mills 4 , Tien V Nguyen 4 , Brian Pfau 5 6 , Sarah N Cox 1 3 , Caitlin R Wolf 1 , James P Hughes 2 7 , Timothy M Uyeki 8 , Melissa A Rolfes 8 , Emily Mosites 9 , M Mia Shim 10 11 , Jeffrey S Duchin 1 10 , Nancy Sugg 11 , Lea A Starita 2 4 , Janet A Englund 12 , Helen Y Chu 1



    Affiliations

    Abstract

    Background: The circulation of respiratory viruses poses a significant health risk among those residing in congregate settings. Data are limited on seasonal human coronavirus (HCoV) infections in homeless shelter settings.
    Methods: We analysed data from a clinical trial and SARS-CoV-2 surveillance study at 23 homeless shelter sites in King County, Washington between October 2019-May 2021. Eligible participants were shelter residents aged ≥3 months with acute respiratory illness. We collected enrolment data and nasal samples for respiratory virus testing using multiplex RT-PCR platform including HCoV. Beginning April 1, 2020, eligibility expanded to shelter residents and staff regardless of symptoms. HCoV species was determined by RT-PCR with species-specific primers, OpenArray assay or genomic sequencing for samples with an OpenArray relative cycle threshold <22.
    Findings: Of the 14,464 samples from 3281 participants between October 2019-May 2021, 107 were positive for HCoV from 90 participants (median age 40 years, range: 0·9-81 years, 38% female). HCoV-HKU1 was the most common species identified before and after community-wide mitigation. No HCoV-positive samples were identified between May 2020-December 2020. Adults aged ≥50 years had the highest detection of HCoV (11%) among virus-positive samples among all age-groups. Species and sequence data showed diversity between and within HCoV species over the study period.
    Interpretation: HCoV infections occurred in all congregate homeless shelter site age-groups with the greatest proportion among those aged ≥50 years. Species and sequencing data highlight the complexity of HCoV epidemiology within and between shelters sites.
    Funding: Gates Ventures, Centers for Disease Control and Prevention, National Institute of Health.

    Keywords: Homeless shelters; Homelessness; Human coronavirus; Respiratory viral infections.

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