key: cord-355672-egjdy7o0 authors: Castillo, Edward M.; Coyne, Christopher J.; Brennan, Jesse J.; Tomaszewski, Christian A. title: Rates of coinfection with other respiratory pathogens in patients positive for coronavirus disease 2019 (COVID‐19) date: 2020-07-02 journal: J Am Coll Emerg Physicians Open DOI: 10.1002/emp2.12172 sha: doc_id: 355672 cord_uid: egjdy7o0 OBJECTIVES: The purpose of this study was to assess coinfection rates of coronavirus disease 2019 (COVID‐19) with other respiratory infections on presentation. METHODS: This is a retrospective analysis of data from a 2 hospital academic medical centers and 2 urgent care centers during the initial 2 weeks of testing for severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) , March 10, 2020 to March 23, 2020. Testing was targeted toward high‐risk patients following US Centers for Disease Control and Prevention guidelines. Demographics include age group and sex. Laboratory test results included SARS‐CoV‐2, rapid influenza A/B, and upper respiratory pathogen nucleic acid detection. Patient demographics and coinfections are presented overall and by test results with descriptive statistics. RESULTS: Complete laboratory results from the first 2 weeks of testing were available for 471 emergency department patients and 117 urgent care center patients who were tested for SARS‐CoV. A total of 51 (8.7%) patients tested positive for COVID‐19 with only 1 of these patients also testing positive for another respiratory infection. One of the patients positive for COVID‐19 also tested positive for influenza A. Among the 537 patients who were screened and tested negative for COVID‐19, there were 33 (6.1%) patients who tested positive in the upper respiratory pathogen nucleic acid detection test. CONCLUSION: In our study investigating coinfections among 51 patients testing positive for COVID‐19, 1 patient also tested positive for influenza A. Although we found limited coinfections in our emergency department and urgent care center patient populations, further research is needed to assess potential coinfection in patients with COVID‐19. On March 10, 2020, the World Health Organization declared a global pandemic due to widespread infection with novel coronavirus COVID-19 (coronavirus disease 2019) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Initial testing protocols from the US Centers for Disease Control and Prevention (CDC) for COVID-19 for detection in patients with possible infection recommend that samples also should be first sent for influenza viruses along with respiratory panels for detection of parainfluenza virus, adenovirus, human rhinovirus, respiratory syncytial virus, Bordetella pertussis, Chlamydia pneumoniae, and Mycoplasma pneumoniae. 1 The problem with testing for coinfections in suspected patients is that the presence of a positive upper respiratory pathogen nucleic acid detection (RPNA) test for viruses other than SARS-CoV-2 may suggest to the clinicians alternate explanations for the patients' symptoms. The CDC continues to strongly encourage to test for other causes of respiratory illness. 1 Therefore, a positive RPNA test could potentially lead to failure to test for COVID-19, thereby increasing exposure risks if a patient has a coinfection. Initial investigations of patients with COVID-19 in Wuhan, China, showed a low to non-existent rate of coinfection with other respiratory viral pathogens. 2,3 However, a more recent study, in presumably cooler climates, have shown an increasing presence of coinfections (up to 50%), typically influenza or rhinovirus. 4 Because of the large variations in data, and the lack of experience with comprehensive testing for COVID-19 along with other respiratory pathogens, we elected to look retrospectively at our own experience with testing. Such data could help in weighing the pros and cons of strategies or algorithms that involve respiratory pathogen panels or flu testing as a decision point for COVID-19 testing. This study is a retrospective analysis of data from an academic medical center with 2 hospitals and 2 urgent care centers in San Diego, California, during the initial 2 weeks of SARS-CoV-2 testing, March 10, 2020 COVID-19 testing was targeted toward high-risk patients with the following known criteria as per the CDC guidelines that were consistent during the study period: patients presenting with symptoms concerning for COVID-19 infection (fever and cough or shortness of breath), Data were queried from the shared electronic medical record (EPIC) using standard structured query language (SQL) queries. Data col- A flow diagram of virology testing for patients during the first 2 weeks of COVID-19 testing is presented in Figure 1 . The main limitation of our study is the small sample size and lack of Also, a simple detection of a virus on a pharyngeal swab does not necessarily imply active infection with that virus. COVID-19 initially causes non-specific symptoms with most being mild with cough, myalgia, and fever. 3 In published series so far, for adults, influenza is the most common coinfection seen in SARS-CoV-2-positive patients, as was seen in our single case. A recent series of 116 SARS-CoV-2-positive samples from Northern California showed an astounding rate of 7.5% (24) with 1 or more non-SARS-CoV-2 pathogens. 8 is not surprising that that SARS-CoV-2 is being added to the next iteration of the diagnostic testing assay for respiratory pathogens, which will prove most useful as this pandemic unfolds. Therefore, based on our experience and review of the literature in patients with respiratory illness who need testing for SARS-CoV-2 or another respiratory virus, one should consider testing for both SARS-CoV-2, regardless of preliminary testing, if done, and for flu or other respiratory pathogens. As this new virus continues to be a common cause of respiratory infection, any patient with cough, dyspnea, and/or fever should be suspect for COVID-19 regardless of the preliminary testing results for other respiratory pathogens. Center for Disease Control and Prevention. Criteria to guide evaluation and laboratory testing for COVID-19 Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Clinical features of patients infected with 2019 novel coronavirus in Wuhan Precautions are needed for COVID-19 patients with coinfection of common respiratory pathogens Human coronavirus alone or in co-infection with rhinovirus C is a risk factor for severe respiratory disease and admission to the pediatric intensive care unit: a one-year study in Southeast Brazil The prevalence of respiratory pathogens in adults with community-acquired pneumonia in an outpatient cohort COVID-19 and mycoplasma pneumoniae coinfection Rates of co-infection between SARS-CoV-2 and other respiratory pathogens Clinical and CT features in pediatric patients with COVID-19 infection: different points from adults PhD, MPH, is a Professor in the Department of Emergency Medicine at the University of California Rates of coinfection with other respiratory pathogens in patients positive for coronavirus disease 2019 (COVID-19) The authors declare no conflicts of interest. Edward M. Castillo, Christopher J. Coyne, and Christian A.Tomaszewski contributed to conception and design of the study.