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.

BackgroundThe prevalence of hepatitis B virus (HBV) amongst South African infants and children has been reported in the pre-HIV era. Despite the reported high prevalence of HIV in the general population of South Africa, the rate of HIV/HBV co-infection amongst infants and children remains poorly reported.ObjectivesWe describe the prevalence of HBV infection amongst HIV-positive and HIV-negative infants by molecular methods of diagnosis using dried blood spot samples.MethodsThis retrospective cross-sectional study was conducted between July 2011 and December 2011 in an academic referral laboratory offering viral diagnostic services to the entire KwaZulu-Natal province of South Africa. A total of 322 study samples were collected from discarded residual dried blood spot samples following routine infant diagnosis of HIV. Equal proportions of HIV-positive and HIV-negative infant specimens were studied. Statistical differences in the prevalence of HBV between the HIV-positive and HIV-negative samples were calculated using the Pearson chi-square test, and a p-value < 0.05 was considered statistically significant. Further testing for HBV DNA using a nested polymerase chain reaction method was performed.ResultsThe overall prevalence of HBV was 10%. In the HIV-positive group, 21 of 161 infants tested positive for HBV compared with 12 of 161 HIV-negative infants who tested positive for HBV. The proportion of infants infected with HBV was marginally higher amongst HIV-positive infants (13.0%; 95% CI 6.8–19.9) compared with HIV-negative infants (7.5%; 95% CI 2.5–13.7; P = 0.098), though not statistically significant.ConclusionThe finding of a 10% HBV prevalence in this infant cohort is clinically significant. The non-statistically significant difference in HBV prevalence between the HIV-positive and HIV-negative infants suggests that high prevalence of HBV infection in children may be a problem independent of HIV.

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