Whole-genome sequencing of SARS-CoV-2 reveals diverse mutations in circulating Alpha and Delta variants during the first, second, and third waves of COVID-19 in South Kivu, east of the Democratic Republic of the Congo.

OBJECTIVES: We used whole-genome sequencing of SARS-CoV-2 to identify variants circulating in the Democratic Republic of the Congo and obtain molecular information useful for diagnosis, improving treatment, and general pandemic control strategies. METHODS: A total of 74 SARS-CoV-2 isolates were sequenced using Oxford Nanopore platforms. Generated reads were processed to obtain consensus genome sequences. Sequences with more than 80% genome coverage were used for variant calling, phylogenetic analysis, and classification using Pangolin lineage annotation nomenclature. RESULTS: Phylogenetic analysis based on Pangolin classification clustered South Kivu sequences into seven lineages (A.23.1, B.1.1.6, B.1.214, B.1.617.2, B.1.351, C.16, and P.1). The Delta (B.1.617.2) variant was the most dominant and responsible for outbreaks during the third wave. Based on the Wuhan reference genome, 289 distinct mutations were detected, including 141 missenses, 123 synonymous, and 25 insertions/deletions when our isolates were mapped to the Wuhan reference strain. Most of these point mutations were located within the coding sequences of the SARS-CoV-2 genome that includes spike, ORF1ab, ORF3, and nucleocapsid protein genes. The most common mutation was D614G (1841A>G) observed in 61 sequences, followed by L4715L (14143 C>T) found in 60 sequences. CONCLUSION: Our findings highlight multiple introductions of SARS-CoV-2 into South Kivu through different sources and subsequent circulation of variants in the province. These results emphasize the importance of timely monitoring of genetic variation and its effect on disease severity. This work set a foundation for the use of genomic surveillance as a tool for future global pandemic management and control.

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.