Evaluation of Viruses Associated With Acute Respiratory Infections in Long-Term Care Facilities Using a Novel Method: Wisconsin, 2016‒2019

Checovich, Mary M.; Barlow, Shari; Shult, Peter; Reisdorf, Erik; Temte, Jonathan L.

Residents of long-term care facilities (LCTFs) have high morbidity and mortality associated with acute respiratory infections (ARIs). Limited information exists on the virology of ARI in LTCFs, where virological testing is reactive. We report on findings of a surveillance feasibility substudy from a larger prospective trial of introducing rapid influenza diagnostic testing (RIDT) at 10 Wisconsin LTCFs. Any resident with symptoms consistent with ARI had a nasal swab specimen collected for RIDT by staff. Following RIDT, the residual swab was placed into viral transport medium and tested for influenza using Reverse transcription polymerase chain reaction, and for 20 pathogens using a multiplex polymerase chain reaction respiratory pathogen panel. Numbers of viruses in each of 7 categories (influenza A, influenza B, coronaviruses, human metapneumovirus, parainfluenza, respiratory syncytial virus, and rhinovirus/enterovirus) across the 3 years were compared using χ(2). Totals of 160, 215, and 122 specimens were collected during 2016‒2017, 2017‒2018, and 2018‒2019, respectively. Respiratory pathogen panel identified viruses in 54.8% of tested specimens. Influenza A (19.2%), influenza B (12.6%), respiratory syncytial virus (15.9%), and human metapneumovirus (20.9%) accounted for 69% of all detections, whereas coronaviruses (17.2%), rhinovirus/enterovirus (10.5%) and parainfluenza (3.8%) were less common. The distribution of viruses varied significantly across the 3 years (χ(2) = 71.663; df = 12; P < .001). Surveillance in LTCFs using nasal swabs collected for RIDT is highly feasible and yields high virus identification rates. Significant differences in virus composition occurred across the 3 study years. Simple approaches to surveillance may provide a more comprehensive assessment of respiratory viruses in LTCF settings.