H3Africa is developing capacity for health-related genomics research in Africa

Acute diarrhoeal diseases remain a leading cause of global morbidity and mortality particularly among young children in resource-limited countries. Recent large studies utilizing case-control design, prospective sampling and more sensitive and broad diagnostic techniques have shed light on particular pathogens of importance and highlighted the previously under recognized impact of these infections on post-acute illness mortality and growth. Vaccination, particularly against rotavirus, has emerged as a key effective means of preventing significant morbidity and mortality from childhood diarrhoeal disease. Other candidate vaccines against leading diarrhoeal pathogens, such as enterotoxigenic and spp., also hold significant promise in further ameliorating the burden of enteric infections in children. Large studies are also currently underway evaluating novel and potential easy-to-implement water, sanitation and hygiene (WASH) preventive strategies. Given the ongoing global burden of this illness, the paucity of new advances in case management over the last several decades remains a challenge. The increasing recognition of post-acute illness mortality and growth impairment has highlighted the need for interventions that go beyond management of dehydration and electrolyte disturbances. The few trials of novel promising interventions such as probiotics have mainly been conducted in high-income settings. Trials of antimicrobials have also been primarily conducted in high-income settings or in travellers from high-income settings. Bloody diarrhoea has been shown to be a poor marker of potentially treatable bacterial enteritis, and rising antimicrobial resistance has also made empiric antimicrobial therapy more challenging in many settings. Novel effective and sustainable interventions and diagnostic strategies are clearly needed to help improve case management. Diarrhoeal disease and other enteric infections remain an unmet challenge in global child health. Most promising recent developments have been focused around preventive measures, in particular vaccination. Further advances in prevention and case management including the possible use of targeted antimicrobial treatment are also required to fully address this critical burden on child health and human potential.

To determine whether increased dietary iron could be a risk factor for active tuberculosis, dietary iron history and human immunodeficiency virus (HIV) status were studied in 98 patients with pulmonary tuberculosis and in 98 control subjects from rural Zimbabwe. Exposure to high levels of dietary iron in the form of traditional beer is associated with increased iron stores in rural Africans. HIV seropositivity was associated with a 17.3-fold increase in the estimated odds of developing active tuberculosis (95% confidence interval [95% CI], 7.4-40.6; P<.001), and increased dietary iron was associated with a 3.5-fold increase (95% CI, 1.4-8.9; P=.009). Among patients treated for tuberculosis, HIV seropositivity was associated with a 3.8-fold increase in the estimated hazard ratio of death (95% CI, 1.0-13.8; P=.046), and increased dietary iron was associated with a 1.3-fold increase (95% CI, 0.4-6.4; P=.2). These findings are consistent with the hypothesis that elevated dietary iron may increase the risk of active pulmonary tuberculosis.

The hepatitis B virus (HBV) is a global problem; however, the burden of HBV infection in pregnant women in Botswana is unknown. We sought to determine the prevalence of chronic and occult HBV infection in human immunodeficiency virus (HIV)-infected and -uninfected pregnant women in Botswana. Samples from 752 pregnant women were tested for hepatitis B surface antigen (HBsAg), and HBsAg-positive samples were tested for hepatitis B e antigen (HBeAg) and HBV DNA load. Samples that were HBsAg negative were screened for occult HBV infection by determining the HBV DNA load. HBV genotypes were determined based on a 415-base-pair fragment of the surface gene. Among the 752 women tested during pregnancy or early postpartum, 16 (2.1%) (95% confidence interval (CI): 2.0–2.2) were HBsAg-positive. The prevalence of chronic HBV infection was higher (3.1%) among HIV-infected (95% CI: 3.0–3.2) compared with HIV-uninfected women (1.1%) (95% CI: 1.07–1.1, p = 0.057). Among the 622 HBsAg-negative women, the prevalence of occult HBV infection was 6.6% (95% CI: 6.5–6.7). Three of thirteen HBsAg-positive participants were HBeAg-positive, and all were HIV-negative. Of the 11 maternal samples successfully genotyped, five (45.5%) were genotype D3, five (45.5%) were genotype A1, and one was genotype E (9%). Low and similar proportions of HIV-infected and -uninfected pregnant women in Botswana had occult or chronic HBV infection. We identified a subset of HIV-negative pregnant women who had high HBV DNA levels and were HBeAg-positive, and thus likely to transmit HBV to their infants.

Transferrin concentration and total iron binding capacity (TIBC) are currently used to assess iron status. Although correlation between TIBC and transferrin is generally considered as good, conversion factors between the two analytes found in literature show large differences. Although the price per test is lower for TIBC, there are a number of analytical advantages of serum transferrin. Due to binding of iron to other plasma proteins (mainly albumin), TIBC methods generally overestimate the iron binding capacity of transferrin. Moreover, no generic reference values are available for TIBC. In contrast to TIBC, internationally accepted interim reference ranges are available for serum transferrin. The introduction of the international CRM 470 protein standard material has lead to a significant reduction in interlaboratory variation for transferring measurements. In view of these observations, determination of transferrin concentration, rather than TIBC, is recommended. However, in non-European populations characterized by a marked genetic variation in transferrin (TF BC and TF CD variants), in certain cases, immunochemical determination of transferrin may lead to errors. In these populations, TIBC measurements may be preferred.

Any effect of Q248H in protecting against iron deficiency may be observable in children exposed to repeated inflammatory conditions. Further studies of iron status and ferroportin Q248H in African children are needed.

Large-scale, population-based genomic studies have provided a context for modern medical genetics. Among such studies, however, African populations have remained relatively underrepresented. The breadth of genetic diversity across the African continent argues for an exploration of local genomic context to facilitate burgeoning disease mapping studies in Africa. We sought to characterize genetic variation and to assess population substructure within a cohort of HIV-positive children from Botswana-a Southern African country that is regionally underrepresented in genomic databases. Using whole-exome sequencing data from 164 Batswana and comparisons with 150 similarly sequenced HIV-positive Ugandan children, we found that 13%-25% of variation observed among Batswana was not captured by public databases. Uncaptured variants were significantly enriched (p = 2.2 × 10) for coding variants with minor allele frequencies between 1% and 5% and included predicted-damaging non-synonymous variants. Among variants found in public databases, corresponding allele frequencies varied widely, with Botswana having significantly higher allele frequencies among rare (<1%) pathogenic and damaging variants. Batswana clustered with other Southern African populations, but distinctly from 1000 Genomes African populations, and had limited evidence for admixture with extra-continental ancestries. We also observed a surprising lack of genetic substructure in Botswana, despite multiple tribal ethnicities and language groups, alongside a higher degree of relatedness than purported founder populations from the 1000 Genomes project. Our observations reveal a complex, but distinct, ancestral history and genomic architecture among Batswana and suggest that disease mapping within similar Southern African populations will require a deeper repository of genetic variation and allelic dependencies than presently exists.

Cervical cancer remains a significant cause of morbidity and mortality in women worldwide and is the leading cause of cancer-related death in Botswana. It is well established that women with HIV have a higher risk of persistent HPV infection leading to cervical cancer. We assessed HPV prevalence and genotype distribution in 126 tissue specimens from confirmed invasive cervical cancer cases using Abbott real-time PCR assay. Overall, 88(69.8%) women were HIV-infected. Fifty-seven (64.8%) of the HIV-infected women had a baseline CD4 + count ≥ 350 cells/μl, and 82(93.2%) were on antiretroviral therapy at the time of cervical cancer diagnosis. The median age of HIV-infected patients was signficantly younger than that of HIV-uninfected patients (p < 0.001). HPV DNA was detected in all of 126(100%) of tissues analysed in our study. The HPV genotypes identfied included the HPV-16 (75.4%), HPV-18 (28.6%) and other high-risk (hr) HPV genotypes