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.

Investment in Africa over the past year with regards to SARS-CoV-2 genotyping has led to a massive increase in the number of sequences, exceeding 100,000 genomes generated to track the pandemic on the continent. Our results show an increase in the number of African countries able to sequence within their own borders, coupled with a decrease in sequencing turnaround time. Findings from this genomic surveillance underscores the heterogeneous nature of the pandemic but we observe repeated dissemination of SARS-CoV-2 variants within the continent. Sustained investment for genomic surveillance in Africa is needed as the virus continues to evolve, particularly in the low vaccination landscape. These investments are very crucial for preparedness and response for future pathogen outbreaks.One-Sentence SummaryExpanding Africa SARS-CoV-2 sequencing capacity in a fast evolving pandemic.

Rapid diagnostic tests (RDTs) are a key tool for the diagnosis of malaria infections among clinical and subclinical individuals. Low-density infections, and deletions of the P. falciparum hrp2/3 genes (encoding the HRP2 and HRP3 proteins detected by many RDTs) present challenges for RDT-based diagnosis. The novel Rapigen Biocredit three-band Plasmodium falciparum HRP2/LDH RDT was evaluated among 444 clinical and 468 subclinical individuals in a high transmission setting in Burundi. Results were compared to the AccessBio CareStart HRP2 RDT, and qPCR with a sensitivity of <0.3 parasites/μL blood. Sensitivity compared to qPCR among clinical patients for the Biocredit RDT was 79.9% (250/313, either of HRP2/LDH positive), compared to 73.2% (229/313) for CareStart (P = 0.048). Specificity of the Biocredit was 82.4% compared to 96.2% for CareStart. Among subclinical infections, sensitivity was 72.3% (162/224) compared to 58.5% (131/224) for CareStart (P = 0.003), and reached 88.3% (53/60) in children <15 years. Specificity was 84.4% for the Biocredit and 93.4% for the CareStart RDT. No (0/362) hrp2 and 2/366 hrp3 deletions were observed. In conclusion, the novel RDT showed improved sensitivity for the diagnosis of P. falciparum.

EPO and low Hb levels (ESA hyporesponsive) had significantly higher risk of mortality (aHR 2.42, 95% CI 1.41-4.19, p=0.001). The high ERI group also had 36% higher incidence of hospitalisation (IRR 1.36, 95% CI 1.20-1.54, p<0.001) compared to low ERI group. The independent predictors of high ERI were female gender, low albumin, high ferritin, low transferrin saturation %, low BMI, high KT/V, high acuity status and increased hospital admissions in the exposure period. Conclusions: High ERI levels are associated with increased risk of allcause mortality and hospitalisation in incident HD patients. Lack of data on inflammatory markers is a study limitation.

Background: Globally in 2017, Burundi was the 9th country with the highest population growth rate of 3.2% and a fertility rate of 5.5 children per woman. This probably suggested low uptake of Modern Contraceptive methods (MCM) in the country. Our analysis investigated factors associated with low uptake of MCM among women of reproductive age in Burundi. Methods: Cross sectional data of non-pregnant women aged 15-49 years was extracted from the Burundi Demographic and Health Survey (2016-2017). We analysed the data at univariate, bivariate and multivariate levels to assess factors influencing MCM uptake among these women using Epi-Info 7.2.2.6. Results: Of the 9,945 women, 2,372 (23.8%) were using MCM. Ngozi province had the highest prevalence of MCM users [284/691(37.7%)]. The most used MCM among respondents was injectable contraceptive (48.3%). As respondent’s age increases, the odds of using MCM decreases; 20-24 years (aOR=0.9, 95% CI [0.6-1.2]), 30-34 years (aOR=0.8, 95% CI [0.5-1.0]), 35-39 years (aOR=0.7, 95% CI [0.5-0.9]), 40-44 years (aOR=0.5, 95% CI [0.5-0.9]) and 45-49 years (aOR=0.4, 95% CI [0.2-0.5]) compared with those in the age group 15-19 years. Muslims (aOR=1.5, 95% CI [1.2-1.9]) and Jehovah witnesses (aOR=3.1, 95% CI [1.7-6.5]) were more likely to use MCM than Catholics. Conclusion: The prevalence of MCM remains low among women of reproductive age in Burundi, with injectables being the most used method. Factors such as respondent’s age and religion were significantly associated with MCM use. Enhanced access to family planning information and services targeting women who are 30 years or more and engaging religious leaders for their active participation is recommended.