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 disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), with clinical manifestation cases that 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 swab 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) of 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), and 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 cooccurring infections, accounting for 33.3% of all positive cases. This study demonstrates cases of COVID-19 infections cooccurring with other acute respiratory infections in Bukavu city during the ongoing outbreak of COVID-19. Therefore, testing for respiratory viruses should be performed in all patients with flu-like symptoms for effective surveillance of the transmission patterns in the COVID-19 affected areas for optimal treatment and effective disease management.