Identification of pathogens from the upper respiratory tract of adult emergency department patients at high risk for influenza complications in a pre-Sars-CoV-2 environment

Diagn Microbiol Infect Dis. 2021 Jun;100(2):115352. doi: 10.1016/j.diagmicrobio.2021.115352. Epub 2021 Feb 17.


The emergence of SARS-CoV-2 and subsequent COVID-19 pandemic highlights the morbidity and potential disease severity caused by respiratory viruses. To elucidate pathogen prevalence, etiology of coinfections and URIs from symptomatic adult Emergency department patients in a pre-SARS-CoV-2 environment, we evaluated specimens from four geographically diverse Emergency departments in the United States from 2013-2014 utilizing ePlex RP RUO cartridges (Genmark Diagnostics). The overall positivity was 30.1% (241/799), with 6.6% (16/241) coinfections. Noninfluenza pathogens from most to least common were rhinovirus/enterovirus, coronavirus, human metapneumovirus and RSV, respectively. Broad differences in disease prevalence and pathogen distributions were observed across geographic regions; the site with the highest detection rate (for both mono and coinfections) demonstrated the greatest pathogen diversity. A variety of respiratory pathogens and geographic variations in disease prevalence and copathogen type were observed. Further research is required to evaluate the clinical relevance of these findings, especially considering the SARS-CoV-2 pandemic and related questions regarding SARS-CoV-2 disease severity and the presence of co-infections.

Keywords: Coinfections; Emergency department; Influenza; Multiplex diagnostics; Respiratory infections.

MeSH terms

  • Adolescent
  • Adult
  • Aged
  • Aged, 80 and over
  • Coinfection / virology*
  • Coronavirus Infections / complications
  • Coronavirus Infections / virology
  • Emergency Service, Hospital* / statistics & numerical data
  • Enterovirus Infections / complications
  • Enterovirus Infections / virology
  • Female
  • Humans
  • Influenza, Human / complications*
  • Influenza, Human / virology
  • Male
  • Metapneumovirus
  • Middle Aged
  • Paramyxoviridae Infections / complications
  • Paramyxoviridae Infections / virology
  • Picornaviridae Infections / complications
  • Picornaviridae Infections / virology
  • Prevalence
  • Respiratory Tract Infections / complications
  • Respiratory Tract Infections / virology*
  • Rhinovirus
  • Risk Factors
  • United States / epidemiology
  • Young Adult