Frequency of respiratory pathogens other than SARS-CoV-2 detected during COVID-19 testing

Boschiero, Matheus Negri; Duarte, Aires; Palamim, Camila Vantini Capasso; Alvarez, Alfonso Eduardo; Mauch, Renan Marrichi; Marson, Fernando Augusto Lima

The frequencies of 19 respiratory pathogens other than SARS-CoV-2 were assessed in 6,235 Brazilian individuals tested for COVID-19. Overall, only 83 individuals who tested positive for SARS-CoV-2 had co-detection of other pathogens. Individuals infected with Rhinovirus/Enterovirus, Human Coronavirus (HCoV)-HKU1, HCoV-NL63, HPIV-4, Influenza A (-H1N1 and other subtypes), Influenza B, Human Respiratory Syncytial Virus and Human Metapneumovirus were less likely to test positive for SARS-CoV-2. Infection with Streptococcys pyogenes, Chlamydophila pneumoniae, Mycoplasma pneumoniae and Bordetella pertussis were more frequent in individuals who tested negative for SARS-CoV-2, but without significancy. We found 150 individuals infected with ≥2 pathogens other than SARS-CoV-2, only three out of whom tested positive for COVID-19. The co-detection frequency was low in individuals diagnosed with COVID-19. Other viral infections may provide a cross-reactive, protective immune response against SARS-CoV-2. Screening for bacterial respiratory infections upon COVID-19 testing is important to drive suitable therapeutic approaches and avoid unnecessary antibiotic prescription.