This report describes the MalariaGEN Pv4 dataset, a new release of curated genome variation data on 1,895 samples of Plasmodium vivax collected at 88 worldwide locations between 2001 and 2017. It includes 1,370 new samples contributed by MalariaGEN and VivaxGEN partner studies in addition to previously published samples from these and other sources. We provide genotype calls at over 4.5 million variable positions including over 3 million single nucleotide polymorphisms (SNPs), as well as short indels and tandem duplications. This enlarged dataset highlights major compartments of parasite population structure, with clear differentiation between Africa, Latin America, Oceania, Western Asia and different parts of Southeast Asia. Each sample has been classified for drug resistance to sulfadoxine, pyrimethamine and mefloquine based on known markers at the dhfr, dhps and mdr1 loci. The prevalence of all of these resistance markers was much higher in Southeast Asia and Oceania than elsewhere. This open resource of analysis-ready genome variation data from the MalariaGEN and VivaxGEN networks is driven by our collective goal to advance research into the complex biology of P. vivax and to accelerate genomic surveillance for malaria control and elimination.

Studies from high-income settings show that both food insecurity and common mental disorders (CMDs) are associated with lower quality of life among people living with HIV (PLHIV). However, there is limited research among PLHIV in sub-Saharan Africa. In this study we tested the hypothesis that food insecurity and CMDs would be associated with poorer quality of life of PLHIV in Ethiopia. A cross-sectional study was carried out with 348 PLHIV who were initiating antiretroviral therapy recruited from two primary care centers and a tertiary Hospital in southwest Ethiopia. Food insecurity, CMD, and quality of life were measured using instruments adapted and validated in Ethiopia (Household Food Insecurity Access Scale, Kessler-6, and WHOQOL-HIV-BREF-ETH, respectively). Multiple linear regression analysis was used to identify factors associated with quality of life after adjusting for confounders. The prevalence of severe household food insecurity among PLHIV was 38.7 %. After adjusting for confounders, severe food insecurity (β = -3.24, 95 % CI: -6.19; -0.29) and higher levels of CMD symptoms (β = -1.72 for each 1 point increase, 95 % CI: -1.94; -1.49) were associated with lower quality of life. Other factors associated with lower quality of life were advanced HIV disease (β = -3.80, 95 % CI: -6.18; -1.42), and being underweight (BMI = 17.0 – 18.5 kg/m2) (β = -3.45, 95 % CI: -6.18; -0.71). Owning more household assets was associated with higher quality of life (β = 0.99 for owning one more asset, 95 % CI: 0.09; 1.89). Poor mental health and food insecurity are associated with lower quality of life in PLHIV. There is a need for longitudinal studies to elucidate the pathways linking CMD, food insecurity and quality of life.

The ongoing scale-up of antiretroviral therapy (ART) in sub-Saharan Africa has prompted the interest in surveillance of transmitted and acquired HIV drug resistance. Resistance data on virological failure and mutations in HIV infected populations initiating treatment in sub-Saharan Africa is sparse.

Malnourished HIV-infected African adults are at high risk of early mortality after starting antiretroviral therapy (ART). We hypothesized that short-course, high-dose vitamin and mineral supplementation in lipid nutritional supplements would decrease mortality. The study was an individually-randomised phase III trial conducted in ART clinics in Mwanza, Tanzania, and Lusaka, Zambia. Participants were 1,815 ART-naïve non-pregnant adults with body mass index (BMI) <18.5 kg/m² who were referred for ART based on CD4 count <350 cells/μL or WHO stage 3 or 4 disease. The intervention was a lipid-based nutritional supplement either without (LNS) or with additional vitamins and minerals (LNS-VM), beginning prior to ART initiation; supplement amounts were 30 g/day (150 kcal) from recruitment until 2 weeks after starting ART and 250 g/day (1,400 kcal) from weeks 2 to 6 after starting ART. The primary outcome was mortality between recruitment and 12 weeks of ART. Secondary outcomes were serious adverse events (SAEs) and abnormal electrolytes throughout, and BMI and CD4 count at 12 weeks ART. Follow-up for the primary outcome was 91%. Median adherence was 66%. There were 181 deaths in the LNS group (83.7/100 person-years) and 184 (82.6/100 person-years) in the LNS-VM group (rate ratio (RR), 0.99; 95% CI, 0.80–1.21; P = 0.89). The intervention did not affect SAEs or BMI, but decreased the incidence of low serum phosphate (RR, 0.73; 95% CI, 0.55–0.97; P = 0.03) and increased the incidence of high serum potassium (RR, 1.60; 95% CI, 1.19–2.15; P = 0.002) and phosphate (RR, 1.23; 95% CI, 1.10–1.37; P <0.001). Mean CD4 count at 12 weeks post-ART was 25 cells/μL (95% CI, 4–46) higher in the LNS-VM compared to the LNS arm (P = 0.02). High-dose vitamin and mineral supplementation in LNS, compared to LNS alone, did not decrease mortality or clinical SAEs in malnourished African adults initiating ART, but improved CD4 count. The higher frequency of elevated serum potassium and phosphate levels suggests high-level electrolyte supplementation for all patients is inadvisable but the addition of micronutrient supplements to ART may provide clinical benefits in these patients. PACTR201106000300631 , registered on 1^st June 2011.

Objective: We assessed healthcare workers (HCWs) COVID‐19 vaccine acceptability in Ethiopia.Methods: We carried out a cross‐sectional survey from February to April 2021 in HCWs from five teaching hospitals. HCWs were selected using convenient sampling, and data were collected through a survey link. Descriptive analysis and mixed‐effect logistic regression were performed. A total of 1,314 HCWs participated in the study.Results: We found that 25.5% (n = 332) of the HCWs would not accept a COVID‐19 vaccine and 20.2% (n = 264) were not willing to recommend COVID‐19 vaccination to others. Factors associated with vaccine non‐acceptance were female sex (AOR = 1.8; 95% CI: 1.3–2.5), the perception that vaccines are unsafe (AOR = 15.0; 95% CI: 8.7–25.9), not considering COVID‐19 as health risk (AOR = 4.4; 95% CI: 2.0–9.5) and being unconcerned about contracting COVID‐19 at work (AOR = 3.5; 95% CI: 1.5–8.4). Physicians were more willing to accept vaccination than other HCWs. Higher vaccine acceptability was also noted with increasing age. Participants most often indicated safety concerns as the determining factor on their decision to get vaccinated or not.Conclusion: Overall, a quarter of HCWs would not accept a COVID‐19 vaccine. Communications and training should address vaccine safety concerns. Additionally, emphasis should be given to showing current and future impact of COVID‐19 on the personal, public and country level unless control efforts are improved. Interventions aimed to increase vaccine uptake should focus their efforts on younger and non‐physician HCWs.

Under-reporting of COVID-19 and the limited information about circulating SARS-CoV-2 variants remain major challenges for many African countries. We analyzed SARS-CoV-2 infection dynamics in Addis Ababa and Jimma, Ethiopia, focusing on reinfection, immunity, and vaccination effects. We conducted an antibody serology study spanning August 2020 to July 2022 with five rounds of data collection across a population of 4723, sequenced PCR-test positive samples, used available test positivity rates, and constructed two mathematical models integrating this data. A multivariant model explores variant dynamics identifying wildtype, alpha, delta, and omicron BA.4/5 as key variants in the study population, and cross-immunity between variants, revealing risk reductions between 24% and 69%. An antibody-level model predicts slow decay leading to sustained high antibody levels. Retrospectively, increased early vaccination might have substantially reduced infections during the delta and omicron waves in the considered group of individuals, though further vaccination now seems less impactful.