Investment in SARS-CoV-2 sequencing in Africa over the past year has led to a major increase in the number of sequences generated, now exceeding 100,000 genomes, used to track the pandemic on the continent. Our results show an increase in the number of African countries able to sequence domestically, and highlight that local sequencing enables faster turnaround time and more regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and shed light on the distinct dispersal dynamics of Variants of Concern, particularly Alpha, Beta, Delta, and Omicron, on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve, while the continent faces many emerging and re-emerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century.

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BackgroundEstimates of influenza‐associated outpatient consultations and hospitalizations are severely limited in low‐ and middle‐income countries, especially in Africa.MethodsWe conducted active prospective surveillance for influenza‐like illness (ILI) and severe acute respiratory illness (SARI) at 5 healthcare facilities situated in Kinshasa Province during 2013‐2015. We tested upper respiratory tract samples for influenza viruses using a reverse transcription‐polymerase chain reaction assay. We estimated age‐specific numbers and rates of influenza‐associated ILI outpatient consultations and SARI hospitalizations for Kinshasa Province using a combination of administrative and influenza surveillance data. These estimates were extrapolated to each of the remaining 10 provinces accounting for provincial differences in prevalence of risk factors for pneumonia and healthcare‐seeking behavior. Rates were reported per 100 000 population.ResultsDuring 2013‐2015, the mean annual national number of influenza‐associated ILI outpatient consultations was 1 003 212 (95% Confidence Incidence [CI]: 719 335‐1 338 050 ‐ Rate: 1205.3; 95% CI: 864.2‐1607.5); 199 839 (95% CI: 153 563‐254 759 ‐ Rate: 1464.0; 95% CI: 1125.0‐1866.3) among children aged <5 years and 803 374 (95% CI: 567 772‐1 083 291 ‐ Rate: 1154.5; 95% CI: 813.1‐1556.8) among individuals aged ≥5 years. The mean annual national number of influenza‐associated SARI hospitalizations was 40 361 (95% CI: 24 014‐60 514 ‐ Rate: 48.5; 95% CI: 28.9‐72.7); 25 452 (95% CI: 19 146‐32 944 ‐ Rate: 186.5; 95% CI: 140.3‐241.3) among children aged <5 years and 14 909 (95% CI: 4868‐27 570 ‐ Rate: 21.4; 95% CI: 28.9‐72.7) among individuals aged ≥5 years.ConclusionsThe burden of influenza‐associated ILI outpatient consultations and SARI hospitalizations was substantial and was highest among hospitalized children aged <5 years.

BackgroundThe World Health Organization recommends periodic evaluations of influenza surveillance systems to identify areas for improvement and provide evidence of data reliability for policymaking. However, data about the performance of established influenza surveillance systems are limited in Africa, including in the Democratic Republic of Congo (DRC).MethodsWe used the Centers for Disease Control and Prevention guidelines to evaluate the performance of the influenza sentinel surveillance system (ISSS) in DRC during 2012–2015. The performance of the system was evaluated using eight surveillance attributes: (i) data quality and completeness for key variables, (ii) timeliness, (iii) representativeness, (iv) flexibility, (v) simplicity, (vi) acceptability, (vii) stability and (viii) utility. For each attribute, specific indicators were developed and described using quantitative and qualitative methods. Scores for each indicator were as follows: < 60% weak performance; 60–79% moderate performance; ≥80% good performance.ResultsDuring 2012–2015, we enrolled and tested 4339 patients with influenza-like illness (ILI) and 2869 patients with severe acute respiratory illness (SARI) from 11 sentinel sites situated in 5 of 11 provinces. Influenza viruses were detected in 446 (10.3%) samples from patients with ILI and in 151 (5.5%) samples from patients with SARI with higher detection during December–May. Data quality and completeness was > 90% for all evaluated indicators. Other strengths of the system were timeliness, simplicity, stability and utility that scored > 70% each. Representativeness, flexibility and acceptability had moderate performance. It was reported that the ISSS contributed to: (i) a better understanding of the epidemiology, circulating patterns and proportional contribution of influenza virus among patients with ILI or SARI; (ii) acquisition of new key competences related to influenza surveillance and diagnosis; and (iii) continuous education of surveillance staff and clinicians at sentinel sites about influenza. However, due to limited resources no actions were undertaken to mitigate the impact of seasonal influenza epidemics.ConclusionsThe system performed overall satisfactorily and provided reliable and timely data about influenza circulation in DRC. The simplicity of the system contributed to its stability. A better use of the available data could be made to inform and promote prevention interventions especially among the most vulnerable groups.

BackgroundWorldwide, the highest malaria mortality is due to Plasmodium falciparum infection. However, other species of Plasmodium (Plasmodium vivax, Plasmodium ovale, Plasmodium malariae, and Plasmodium knowlesi) can also cause malaria. Therefore, accurate identification of malaria species is crucial for patient management and epidemiological surveillance. This study aimed to determine the different Plasmodium species causing malaria in children under 5 years old in two provinces (Kinshasa and North Kivu) of the Democratic Republic of Congo (DRC).MethodsFrom October to December 2015, a health-facility based cross-sectional study was conducted in General Reference Hospitals in Kinshasa and North Kivu. Four hundred and seven blood samples were collected from febrile children aged ≤ 5 years. Nested polymerase chain reaction assays were performed for Plasmodium species identification.ResultsOut of 407 children, 142 (34.9%) were infected with Plasmodium spp. and P. falciparum was the most prevalent species (99.2%). Among those infected children, 124 had a mono infection with P. falciparum and one with P. malariae. Mixed infections with P. falciparum/P. malariae and P. falciparum/P. vivax were observed in 6 (1.5%) and 8 (2.0%) children, respectively. The prevalence of infection was higher in females (64.8%) than in males (35.2%), p < 0.001. The age-specific distribution of infection showed that children of less than 2 years old were less infected (18.4%) compared to those aged above 2 years (81.6%), p < 0.001.ConclusionAlthough this study showed clearly that the most prevalent species identified was P. falciparum, the findings demonstrate the existence of non-falciparum malaria, especially P. malariae and P. vivax among children aged ≤ 5 years living both Kinshasa and North Kivu Provinces in DRC.