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

• Main Authors: Eric J. Chow (Author), Amanda M. Casto (Author), Julia H. Rogers (Author), Pavitra Roychoudhury (Author), Peter D. Han (Author), Hong Xie (Author), Margaret G. Mills (Author), Tien V. Nguyen (Author), Brian Pfau (Author), Sarah N. Cox (Author), Caitlin R. Wolf (Author), James P. Hughes (Author), Timothy M. Uyeki (Author), Melissa A. Rolfes (Author), Emily Mosites (Author), M. Mia Shim (Author), Jeffrey S. Duchin (Author), Nancy Sugg (Author), Lea A. Starita (Author), Janet A. Englund (Author), Helen Y. Chu (Author)
• Format: Book
• Published: Elsevier, 2022-11-01T00:00:00Z.
• Subjects: article
• Online Access: Connect to this object online.
• Notes: 2667-193X; 10.1016/j.lana.2022.100348
• Keywords: Human coronavirus; Homeless shelters; Respiratory viral infections; Homelessness; Public aspects of medicine; RA1-1270
• Source: The Lancet Regional Health. Americas, Vol 15, Iss , Pp 100348- (2022)

Summary: 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.