The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times 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 illuminate 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 reemerging 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.

Field evaluation of SD BIOLINE HIV/Syphilis Duo assay among pregnant women attending routine antenatal care in Juba, South Sudan

The SD BIOLINE HIV/Syphilis Duo assay is the first World Health Organization prequalified dual rapid diagnostic test for simultaneous detection of HIV and Treponema pallidum antibodies in human blood. Prior to introducing the test into antenatal clinics across South Sudan, a field evaluation of its clinical performance in diagnosing both HIV and syphilis in pregnant women was conducted. SD Bioline test performance on venous blood samples was compared with (i) Vironostika HIV1/2 Uniform II Ag/Ab reference standard and Alere Determine HIV 1/2 non-reference standard for HIV diagnosis, and (ii) Treponema pallidum hemagglutination reference standard and Rapid plasma reagin non-reference standard for syphilis. Sensitivity, specificity, positive predictive value (PPN), negative predictive value (NPV) and kappa (κ) value were calculated for each component against the reference standards within 95% confidence intervals (CIs); agreements between Determine HIV 1/2 and SD Bioline HIV tests were also calculated. Of 442 pregnant women recruited, eight (1.8%) were HIV positive, 22 (5.0%) had evidence of syphilis exposure; 14 (3.2%) had active infection. For HIV diagnosis, the sensitivity, specificity, PPV and NPV were 100% (95% CI: 63.1–100), 100% (95% CI: 99.2–100), 100% (95% CI: 63.1–100) and 100% (95% CI: 99.2–100) respectively with κ value of 1 (95% CI: 0.992–1.000). Overall agreement of the Duo HIV component and Determine test was 99.1% (95% CI: 0.977–0.998) with 66.7% (95% CI: 34.9–90.1) positive and 100% (95% CI: 0.992–1.000) negative percent agreements. For syphilis, the Duo assay sensitivity was 86.4% (95% CI: 65.1–97.1) and specificity 100% (95% CI: 99.1–100) with PPV 100% (95% CI: 82.4–100), NPV 99.2% (95% CI: 97.9–99.9) and κ value 0.92 (95% CI: 0.980–0.999). Our findings suggest the SD Bioline HIV/Syphilis Duo Assay could be suitable for HIV and syphilis testing in women attending antenatal services across South Sudan. Women with positive syphilis results should receive treatment immediately, whereas HIV positive women should undergo confirmatory testing following national HIV testing guidelines.

Risk Factors for Sustained Cholera Transmission, Juba County, South Sudan, 2014

We conducted a case–control study to identify risk factors for the 2014 cholera outbreak in Juba County, South Sudan. Illness was associated with traveling or eating away from home; treating drinking water and receiving oral cholera vaccination were protective. Oral cholera vaccination should be used to complement cholera prevention efforts.