SARS-CoV-2 and co-infections: A detailed survey of viral and bacterial respiratory pathogens

The SARS-CoV-2 virus has created an unprecedented challenge to our healthcare system. Our understanding of the disease epidemiology and the causal organism is rapidly advancing with each passing day. Secondary and concurrent bacterial and viral co-infections are well documented for other viral respiratory pathogens, however our knowledge regarding co-infections with SARS-CoV-2 remains limited. The present study encompasses concurrent testing of 50,419 individual samples for the presence of SARS-CoV-2 and other bacterial and viral respiratory pathogens between March and August 2020. A total of 4,259 (8.4%) samples tested positive for SARS-CoV-2. Overall a lower rate of viral co-infection was observed in the SARS-CoV-2 positive population when compared to the population testing negative for the virus. Significant levels of EBV co-infections were detected in the SARS-CoV-2 positive population. Similar levels of bacterial pathogens were detected in both the viral positive and negative populations with significant co-infections of S. pneumoniae, H. influenzae and S. aureus. This is one of the largest surveys looking into the co-infection patterns of SARS-CoV-2 infection. Data from the present study will enhance our understanding of the current crisis.