Respiratory Pathogen Coinfections in SARS-CoV-2-Positive Patients in Southeastern Wisconsin: A Retrospective Analysis

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of coronavirus disease 2019 (COVID-19), has infected all age groups and disproportionately impacted vulnerable populations globally. Polymicrobial infections may play an important role in the development of SARS-CoV-2 infection in susceptible hosts. These coinfections may increase the risk of disease severity and pose challenges to the diagnosis, treatment, and prognosis of COVID-19. There have been limited SARS-CoV-2 coinfection studies. In this retrospective study, residual nucleic acid extracts from 796 laboratory-confirmed COVID-19-positive specimens, collected between March 2020 and February 2021, were analyzed using a Luminex NxTAG respiratory pathogen panel (RPP). Of these, 745 returned valid results and were used for analysis; 53 (7.1%) were positive for one or more additional pathogens. Six different respiratory viruses were detected among the 53 SARS-CoV-2-positive patient specimens, and 7 of those specimens tested positive for more than one additional respiratory virus. The most common pathogens include rhinovirus/enterovirus (RV/EV) (n = 22, 41.51%), human metapneumovirus (hMPV) (n = 18, 33.9%), and adenovirus (n = 12, 22.6%). Interestingly, there were no SARS-CoV-2 coinfections involving influenza A or influenza B in the study specimens. The median age of the SARS-CoV-2-positive patients with coinfections was 38 years; 53% identified as female, and 47% identified as male. Based on our retrospective analysis, respiratory coinfections associated with SARS-CoV-2-positive patients were more common in young children (≤9 years old), with white being the most common race. Our findings will likely prompt additional investigation of polymicrobial infection associated with SARS-CoV-2 during seasonal respiratory pathogen surveillance by public health laboratories. IMPORTANCE This examination of respiratory pathogen coinfections in SARS-CoV-2 patients will likely shed light on our understanding of polymicrobial infection associated with COVID-19. Our results should prompt public health authorities to improve seasonal respiratory pathogen surveillance practices and address the risk of disease severity.

Keywords: COVID-19; SARS-CoV-2; coinfections; polymicrobial infections; public health; respiratory pathogen panel.

FIG 1

Rate of SARS-CoV-2 and respiratory pathogen coinfections detected within age groups, including pathogen(s) detected. RV/EV, rhinovirus/enterovirus; hMPV, human metapneumovirus; CoV 229E, human coronavirus 229E; RSV A, respiratory syncytial virus A. Total number of valid specimens per group: ≤9 (n = 21), 10 to 19 (n = 73), 20 to 29 (n = 153), 30 to 39 (n = 111), 40 to 49 (n = 95), 50 to 59 (n = 97), 60 to 69 (n = 79), 70 to 79 (n = 55), 80 to 89 (n = 37), ≥90 (n = 24).

FIG 2

Distribution of positive SARS-CoV-2 samples received by submitter type, including coinfections detected. Submitter categories: Milwaukee Health Department (MHD) and other local health departments (LHDs), hospitals and reference laboratories, local universities, correctional facilities or other congregate living facilities (CLFs), long-term care facilities (LTCFs), medical examiners, and free clinics.

FIG 3

Rate of respiratory viruses detected in SARS-CoV-2-positive specimens. RV/EV, rhinovirus/enterovirus; hMPV, human metapneumovirus; CoV 229E, human coronavirus 229E; RSV A, respiratory syncytial virus A.