Molecular evidence of coinfection with acute respiratory viruses and high prevalence of SARS-CoV-2 among patients presenting flu-like illness in Bukavu city, Democratic Republic of Congo

The coronavirus 2019 (COVID-19) is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with clinical manifestation cases are almost similar to those of common respiratory viral infections. This study determined the prevalence of SARS-CoV-2 and other acute respiratory viruses among patients with flu-like symptoms in Bukavu city Democratic republic of Congo. We screened 1352 individuals with flu-like illnesses seeking treatment in 10 health facilities. Nasopharyngeal swabs specimens were collected to detect SARS-CoV-2 using real-time reverse transcription-polymerase chain reaction (RT-PCR) and 10 common respiratory viruses were detected by multiplex reverse transcription polymerase chain reaction assay. Overall, 13.9% (188/1352) patients were confirmed positive for SARS-CoV-2. Influenza A 5.6% (56/1352), and Influenza B 0.9% (12/1352) were the most common respiratory viruses detected. Overall more than two cases of the other acute respiratory viruses were detected. Frequently observed symptoms associated with SARS-CoV-2 positivity were shivering (47.8%; OR= 1.8; CI: 0.88-1.35), cough (89.6%; OR=6.5, CI: 2.16-28.2), myalgia and dizziness (59.7%; OR=2.7; CI: 1.36-5.85). Moreover, coinfection was observed in 12 (11.5%) specimens. SARS-CoV-2, and Influenza A were the most co-occurring infections, accounting for 33.3% of all positive cases. This study demonstrates cases of COVID-19 infections co-occurring with other acute respiratory infections in Bukavu city during the ongoing outbreak of COVID-19. These data emphasize the need for routine testing of multiple viral pathogens for better prevention and treatment plans.