Clinical and Genomic Epidemiology of Coxsackievirus A21 and Enterovirus D68 in Homeless Shelters, King County, Washington, USA, 2019-2021

Abstract

Congregate homeless shelters are disproportionately affected by infectious disease outbreaks. We describe enterovirus epidemiology across 23 adult and family shelters in King County, Washington, USA, during October 2019-May 2021, by using repeated cross-sectional respiratory illness and environmental surveillance and viral genome sequencing. Among 3,281 participants >3 months of age, we identified coxsackievirus A21 (CVA21) in 39 adult residents (3.0% [95% CI 1.9%-4.8%] detection) across 7 shelters during October 2019-February 2020. We identified enterovirus D68 (EV-D68) in 5 adult residents in 2 shelters during October-November 2019. Of 812 environmental samples, 1 was EV-D68-positive and 5 were CVA21-positive. Other enteroviruses detected among residents, but not in environmental samples, included coxsackievirus A6/A4 in 3 children. No enteroviruses were detected during April 2020-May 2021. Phylogenetically clustered CVA21 and EV-D68 cases occurred in some shelters. Some shelters also hosted multiple CVA21 lineages.

Keywords: King County; United States; Washington; communicable diseases; congregate settings; coxsackievirus; cross-sectional studies; disease outbreaks; enterovirus; enterovirus A; enterovirus C; enterovirus D; genome; homeless; human; ill-housed persons; viral; viruses.

Figure 1

Nasal swab specimens (A) and enterovirus detection (B) in homeless shelters, King County, Washington, USA, October 2019–February 2020. Detection frequency represents a 7-day rolling average. No coxsackievirus A21-positive or enterovirus D68-positive specimens were detected during March 2020–May 2021.

Figure 2

Unique participants with coxsackievirus A21 infection, by homeless shelter site, King County, Washington, USA, October 2019–February 2020.

Figure 3

Signs or symptoms reported at specimen collection and effect on daily activity among adult homeless shelter residents with confirmed coxsackievirus A21 infection (n = 39), King County, Washington, USA, October 2019–January 2020. One person with coxsackievirus A21 infection was presymptomatic on initial encounter (first positive specimen collection) but symptomatic on subsequent encounter (second positive specimen collection).

Figure 4

Phylogenetic tree of sequenced enterovirus D68 specimens of homeless shelter residents, King County, Washington, USA, October 2019–November 2019. Tips representing study specimens are colored according to shelter. Light gray tips represent enterovirus D68 genomes downloaded from GenBank. Inset shows a detailed view of the relationship among the study genomes. The x-axis represents the number of nucleotide changes in the genome relative to an enterovirus D68 reference genome (GenBank accession no. NC_038308.1).

Figure 5

Phylogenetic trees of sequenced coxsackievirus A21 specimens of homeless shelter residents, King County, Washington, USA, October 2019–February 2020. A) Tree containing all shelter coxsackievirus A21 and all coxsackievirus A21 genomes deposited in GenBank. Tips representing study specimens are colored according to shelter. Light gray tips represent coxsackievirus A21 genomes downloaded from GenBank. The x-axis represents number of nucleotide changes in the genome relative to a coxsackievirus A21 reference genome (GenBank accession no. AF465515.1). B) Tree containing all shelter coxsackievirus A21 genomes. Internal nodes with >90% bootstrap support are labeled on tree. C) Tree containing all shelter coxsackievirus A21 genomes with x-axis corresponding to sample collection date.