H3ABioNet, a sustainable pan-African bioinformatics network for human heredity and health in Africa.

The application of genomics technologies to medicine and biomedical research is increasing in popularity, made possible by new high-throughput genotyping and sequencing technologies and improved data analysis capabilities. Some of the greatest genetic diversity among humans, animals, plants, and microbiota occurs in Africa, yet genomic research outputs from the continent are limited. The Human Heredity and Health in Africa (H3Africa) initiative was established to drive the development of genomic research for human health in Africa, and through recognition of the critical role of bioinformatics in this process, spurred the establishment of H3ABioNet, a pan-African bioinformatics network for H3Africa. The limitations in bioinformatics capacity on the continent have been a major contributory factor to the lack of notable outputs in high-throughput biology research. Although pockets of high-quality bioinformatics teams have existed previously, the majority of research institutions lack experienced faculty who can train and supervise bioinformatics students. H3ABioNet aims to address this dire need, specifically in the area of human genetics and genomics, but knock-on effects are ensuring this extends to other areas of bioinformatics. Here, we describe the emergence of genomics research and the development of bioinformatics in Africa through H3ABioNet.

Efficacy of artesunate-amodiaquine, dihydroartemisinin-piperaquine and artemether-lumefantrine for the treatment of uncomplicated Plasmodium falciparum malaria in Maradi, Niger.

BACKGROUND: Malaria endemic countries need to assess efficacy of anti-malarial treatments on a regular basis. Moreover, resistance to artemisinin that is established across mainland South-East Asia represents today a major threat to global health. Monitoring the efficacy of artemisinin-based combination therapies is of paramount importance to detect as early as possible the emergence of resistance in African countries that toll the highest burden of malaria morbidity and mortality. METHODS: A WHO standard protocol was used to assess efficacy of the combinations artesunate-amodiaquine (AS-AQ Winthrop®), dihydroartemisinin-piperaquine (DHA-PPQ, Eurartesim®) and artemether-lumefantrine (AM-LM, Coartem®) taken under supervision and respecting pharmaceutical recommendations. The study enrolled for each treatment arm 212 children aged 6-59 months living in Maradi (Niger) and suffering with uncomplicated falciparum malaria. The Kaplan-Meier 42-day PCR-adjusted cure rate was the primary outcome. A standardized parasite clearance estimator was used to assess delayed parasite clearance as surrogate maker of suspected artemisinin resistance. RESULTS: No early treatment failures were found in any of the study treatment arms. The day-42 PCR-adjusted cure rate estimates were 99.5, 98.4 and 99.0% in the AS-AQ, DHA-PPQ and AM-LM arms, respectively. The reinfection rate (expressed also as Kaplan-Meier estimates) was higher in the AM-LM arm (32.4%) than in the AS-AQ (13.8%) and the DHA-PPQ arm (24.9%). The parasite clearance rate constant was 0.27, 0.26 and 0.25 per hour for AS-AQ, DHA-PPQ and AM-LM, respectively. CONCLUSIONS: All the three treatments evaluated largely meet WHO criteria (at least 95% efficacy). AS-AQ and AL-LM may continue to be used and DHA-PPQ may be also recommended as first-line treatment for uncomplicated falciparum malaria in Maradi. The parasite clearance rate were consistent with reference values indicating no suspected artemisinin resistance. Nevertheless, the monitoring of anti-malarial drug efficacy should continue. Trial registration details Registry number at ClinicalTrial.gov: NCT01755559.

Regulation of genomic and biobanking research in Africa: a content analysis of ethics guidelines, policies and procedures from 22 African countries.

BACKGROUND: The introduction of genomics and biobanking methodologies to the African research context has also introduced novel ways of doing science, based on values of sharing and reuse of data and samples. This shift raises ethical challenges that need to be considered when research is reviewed by ethics committees, relating for instance to broad consent, the feedback of individual genetic findings, and regulation of secondary sample access and use. Yet existing ethics guidelines and regulations in Africa do not successfully regulate research based on sharing, causing confusion about what is allowed, where and when. METHODS: In order to understand better the ethics regulatory landscape around genomic research and biobanking, we conducted a comprehensive analysis of existing ethics guidelines, policies and other similar sources. We sourced 30 ethics regulatory documents from 22 African countries. We used software that assists with qualitative data analysis to conduct a thematic analysis of these documents. RESULTS: Surprisingly considering how contentious broad consent is in Africa, we found that most countries allow the use of this consent model, with its use banned in only three of the countries we investigated. In a likely response to fears about exploitation, the export of samples outside of the continent is strictly regulated, sometimes in conjunction with regulations around international collaboration. We also found that whilst an essential and critical component of ensuring ethical best practice in genomics research relates to the governance framework that accompanies sample and data sharing, this was most sparingly covered in the guidelines. CONCLUSIONS: There is a need for ethics guidelines in African countries to be adapted to the changing science policy landscape, which increasingly supports principles of openness, storage, sharing and secondary use. Current guidelines are not pertinent to the ethical challenges that such a new orientation raises, and therefore fail to provide accurate guidance to ethics committees and researchers.

Obtaining informed consent for genomics research in Africa: analysis of H3Africa consent documents.

BACKGROUND: The rise in genomic and biobanking research worldwide has led to the development of different informed consent models for use in such research. This study analyses consent documents used by investigators in the H3Africa (Human Heredity and Health in Africa) Consortium. METHODS: A qualitative method for text analysis was used to analyse consent documents used in the collection of samples and data in H3Africa projects. Thematic domains included type of consent model, explanations of genetics/genomics, data sharing and feedback of test results. RESULTS: Informed consent documents for 13 of the 19 H3Africa projects were analysed. Seven projects used broad consent, five projects used tiered consent and one used specific consent. Genetics was mostly explained in terms of inherited characteristics, heredity and health, genes and disease causation, or disease susceptibility. Only one project made provisions for the feedback of individual genetic results. CONCLUSION: H3Africa research makes use of three consent models-specific, tiered and broad consent. We outlined different strategies used by H3Africa investigators to explain concepts in genomics to potential research participants. To further ensure that the decision to participate in genomic research is informed and meaningful, we recommend that innovative approaches to the informed consent process be developed, preferably in consultation with research participants, research ethics committees and researchers in Africa.

Small is beautiful: demystifying and simplifying standard operating procedures: a model from the ethics review and consultancy committee of the Cameroon Bioethics Initiative.

BACKGROUND: Research ethics review is a critical aspect of the research governance framework for human subjects research. This usually requires that research protocols be submitted to a research ethics committee (REC) for review and approval. This has led to very rapid developments in the domain of research ethics, as RECs proliferate all over the globe in rhyme with the explosion in human subjects research. The work of RECs has increasingly become elaborate, complex, and in many cases urgent, necessitating supporting rules and procedures of operation. Guidelines for elaborating standard operating procedures (SOPs) for the functioning of RECs have also been proposed. The SOPs of well-placed and well-resourced RECs have tended to pay much attention to details, resulting, as a consequence, in generally long, elaborate, intricate and complex SOPs; a model that can hardly be replicated by other committees, equally under ethics review pressures, but working under much more constraining conditions in resource-destitute environments. METHODS: In this paper, we looked at the content and length of SOPs from African RECs and compared them to the World Health Organization (WHO)'s guidelines as the gold standard. We also looked at the SOPs from the Ethics Review and Consultancy Committee (ERCC) of the Cameroon Bioethics Initiative that we elaborated in a simplified way in 2013, and compared them to the WHO's guidelines and to the other SOPs. RESULTS: Sixteen SOPs from 14 African countries were collected from various sources. Their average length was of 30 pages. By comparison to the guidance of the WHO, only six of them were found acceptable with more than 70 % of the criteria from the gold standard that were fully described. Among those six, two of them were very long and detailed (65 and 102 pages), while the four remaining SOPs ranged from 16 to 24 pages. The ERCC SOPs are seven pages long but maintain all that is of essence for the rigorous, efficient and timely review of protocols. CONCLUSIONS: We are convinced that, because of their brevity, simplicity, clarity and user-friendliness, the ERCC SOPs recommend themselves as a model template to, at least, committees similarly situated and/or circumstanced as the ERCC of the Cameroon Bioethics Initiative is. In fact, brevity, clarity, simplicity and user-friendliness are recognized values. Whatever is brief and clear is better than what is not and saves time. What is simple and user-friendly is better than what is not even though the two have the same aims because it saves both time and mental energy. And if this be true in general, it is even truer of the context and its peculiar constraints that we are addressing.

A perpetual source of DNA or something really different: ethical issues in the creation of cell lines for African genomics research.

BACKGROUND: The rise of genomic studies in Africa - not least due to projects funded under H3Africa - is associated with the development of a small number of biorepositories across Africa. For the ultimate success of these biorepositories, the creation of cell lines including those from selected H3Africa samples would be beneficial. In this paper, we map ethical challenges in the creation of cell lines. DISCUSSION: The first challenge we identified relates to the moral status of cells living in culture. There is no doubt that cells in culture are alive, and the question is how this characteristic is relevant to ethical decision-making. The second challenge relates to the fact that cells in culture are a source of cell products and mitochondrial DNA. In combination with other technologies, cells in culture could also be used to grow human tissue. Whilst on the one hand, this feature increases the potential utility of the sample and promotes science, on the other it also enables further scientific work that may not have been specifically consented to or approved. The third challenge relates to ownership over samples, particularly in cases where cell lines are created by a biobank, and in a different country than where samples were collected. Relevant questions here concern the export of samples, approval of secondary use and the acceptability of commercialisation. A fourth challenge relates to perceptions of blood and bodily integrity, which may be particularly relevant for African research participants from certain cultures or backgrounds. Finally, we discuss challenges around informed consent and ethical review. SUMMARY: In this paper, we sought to map the myriad of ethical challenges that need to be considered prior to making cell line creation a reality in the H3Africa project. Considering the relative novelty of this practice in Africa, such challenges will need to be considered, discussed and potentially be resolved before cell line creation in Africa becomes financially feasible and sustainable. We suggest that discussions need to be undertaken between stakeholders internationally, considering the international character of the H3Africa project. We also map out avenues for empirical research.

Are students kidding with health research ethics? The case of HIV/AIDS research in Cameroon.

BACKGROUND: Universities in Cameroon are playing an active part in HIV/AIDS research and much of this research is carried out by students, usually for the purpose of a dissertation/thesis. Student theses/dissertations present research findings in a much more comprehensive manner and have been described as the stepping-stone of a budding scientist's potential in becoming an independent researcher. It is therefore important to verify how students handle issues of research ethics. METHOD: Theses/dissertations on HIV/AIDS that described research studies involving the use of human research participants were screened to verify if research ethics approval and informed consent were obtained and documented. The contents of the consent forms were also qualitatively analyzed. RESULTS: Of 174 theses/dissertations on HIV, ethics approval was documented in 17 (9.77%) and informed consent in 77 (47.83%). Research ethics approval was first mentioned at all in 2002 and highly reported in the year 2007. Evidence of ethics approval was found for the first time in 2005 and informed consent first observed and evidenced in 1997. Ethics approval was mostly reported by students studying for an MD (14.01%) and was not reported in any Bachelors' degree dissertation. Informed consent was also highly reported in MD theses (64.58%) followed by undergraduate theses (31.58%). Voluntary participation and potential benefits of the study were some of the common aspects dealt with in most of the consent forms. The right to discontinue participation in the study and management of residual samples were scarcely ever mentioned. CONCLUSIONS: Overall, and given the current state of the art of research ethics around the world, student-scientists in Cameroon would seem to be merely kidding with research ethics. It is thus essential that training in health research ethics (HRE) be incorporated in the curriculum of universities in Cameroon in order that the next generation of scientists may be better equipped with thorough knowledge and practice of HRE. This, we believe, would be one way of fighting the occurrence of research scandals, which have not yet abated significantly, especially those arising from negligence or inexcusable ignorance.

Ethics of human genetic studies in sub-saharan Africa: the case of Cameroon through a bibliometric analysis.

UNLABELLED: Many ethical concerns surrounding human genetics studies remain unresolved. We report here the situation in Cameroon. OBJECTIVES: To describe the profile of human genetic studies that used Cameroonian DNA samples, with specific focus on i) the research centres that were involved, ii) authorship, iii) population studied, iv) research topics and v) ethics disclosure, with the aim of raising ethical issues that emerged from these studies. METHOD: Bibliometric Studies; we conducted a PubMed-based systematic review of all the studies on human genetics that used Cameroonian DNA samples from 1989 to 2009. RESULTS AND DISCUSSION: Fifty articles were identified, involving predominantly research centres from Europe (64%) and America (32%). Only 7 (14%) Cameroonian institutions and 14 (28%) Cameroonian authors were associated with these publications. At least 52% of publications were devoted to population genetics (variation/migration patterns) amongst 30 Cameroonian ethnic groups. Very few studies concerned public health related genetic issues and only 5 (10%) references were found for hemoglobinopathies like sickle cell anaemia. Almost all DNA samples are 'banked' outside of the African continent. Capacity building, rights to the genetic information and benefits to the individuals, communities and populations who contribute to these studies are addressed. CONCLUSIONS: 1) Our data suggests the need for a wider debate towards building capacity and addressing ethical issues related to human genomic research in sub-Saharan Africa and specifically in Cameroon; 2) National ethical guidelines and regulations concerning the collection, use and storage of human DNA are urgently needed in Cameroon.

Cytoadherence and genotype of Plasmodium falciparum strains from symptomatic children in Franceville, southeastern Gabon.

BACKGROUND: Plasmodium falciparum causes severe clinical manifestations by sequestering parasitized red blood cells (PRBC) in the microvasculature of major organs such as the brain. This sequestration results from PRBC adherence to vascular endothelial cells via erythrocyte membrane protein 1, a variant parasite surface antigen. OBJECTIVE: To determine whether P. falciparum multiple genotype infection (MGI) is associated with stronger PRBC cytoadherence and greater clinical severity. METHODS: Nested polymerase chain reaction was used to genotype P. falciparum isolates from symptomatic children and to distinguish between single genotype infection (SGI) and MGI. PRBC cytoadhesion was studied with cultured human lung endothelial cells. RESULTS: Analysis of two highly polymorphic regions of the merozoite surface antigen (MSP)-1 and MSP-2 genes and a dimorphic region of the erythrocyte binding antigen-175 gene showed that 21.4% and 78.6% of the 42 children had SGI and MGI, respectively. It also showed that 37 (89%) of the 42 PRBC samples expressed MSP-1 allelic family K1. Cytoadherence values ranged from 58 to 1811 PRBC/mm(2) of human lung endothelial cells monolayer in SGI and from 5 to 5744 PRBC/mm(2) in MGI. MGI was not associated with higher cytoadherence values or with more severe malaria. CONCLUSIONS: These results suggested that infection of the same individual by multiple clones of P. falciparum does not significantly influence PRBC cytoadherence or disease severity and confirmed the predominance of the MSP-1 K1 genotype in southeastern Gabon.

Serogroup-Specific Characteristics of Localized Meningococcal Meningitis Epidemics in Niger 2002-2012 and 2015: Analysis of Health Center Level Surveillance Data.

To compare dynamics of localized meningitis epidemics (LE) by meningococcal (Nm) serogroup, we analyzed a surveillance database of suspected and laboratory-confirmed Nm cases from 373 health areas (HA) of three regions in Niger during 2002-2012 and one region concerned by NmC epidemics during 2015. We defined LE as HA weekly incidence rates of ≥20 suspected cases per 100,000 during ≥2 weeks and assigned the predominant serogroup based on polymerase chain reaction testing of cerebrospinal fluid. Among the 175 LE, median peak weekly incidence rate in LE due to NmA, W, X and C were 54, 39, 109 and 46 per 100,000, respectively. These differences impacted ability of the epidemic to be detected at the district level. While this analysis is limited by the small number of LE due to NmX (N = 4) and NmW (N = 5), further research should explore whether strategies for prevention and response to meningitis epidemics need to be adapted according to predominant meningococcal serogroups.

Implementation of HIV early infant diagnosis and HIV type 1 RNA viral load determination on dried blood spots in Cameroon: challenges and propositions.

The testing of dried blood spots (DBSs) for human immunodeficiency type 1 (HIV-1) proviral DNA by PCR is a technology that has proven to be particularly valuable in diagnosing exposed infants. We implemented this technology for HIV-1 early infant diagnosis (EID) and HIV-1 RNA viral load determination in infants born of HIV-1-seropositive mothers from remote areas in Cameroon. The samples were collected between December 2007 and September 2010. Fourteen thousand seven hundred and sixty-three (14,763) DBS samples from infants born of HIV-positive mothers in 108 sites nationwide were tested for HIV. Of these, 1452 were positive on first PCR analyses (PCR1), giving an overall infection rate of 12.30%. We received only 475 DBS specimen for a second PCR testing (PCR2); out of these, 145 were positive. The median HIV-1 RNA viral load for 169 infant DBS samples tested was 6.85 log copies/ml, with values ranging from 3.37 to 8 log copies/ml. The determination of the viral load on the same DBS as that used for PCR1 allowed us to bypass the PCR2. The viral load values were high and tend to decrease with age but with a weak slope. The high values of viral load among these infants call for early and effective administration of antiretroviral therapy (ART). The findings from this study indicate that the use of DBS provides a powerful tool for perinatal screening programs, improvement on the testing algorithm, and follow-up during treatment, and thus should be scaled up to the entire nation.

How often are ethics approval and informed consent reported in publications on health research in Cameroon? A five-year review.

We assessed the extent of research ethics approval and informed consent reporting in publications emanating from Cameroon and indexed in PubMed from 2005-2009. In our review of 219 full-length articles, we found that 57.53% reported ethics approval, 70.78% informed consent, and 50.68% both ethics approval and informed consent. Reporting these procedures was more common in randomized clinical trials than in other study designs. Also, 59.52% of the articles on vulnerable populations documented ethics approval and 76.19% documented informed consent. This study also identified some structures for ethics review and recommends some next steps for research on the quality of ethics review in Cameroon.

Reference values of lymphocyte subsets in healthy, HIV-negative children in Cameroon.

Lymphocyte subset reference values used to monitor infectious diseases, including HIV/AIDS, tuberculosis, malaria, or other immunological disorders in healthy children in Cameroon, are lacking. Values for Caucasian cohorts are already being utilized for clinical decisions but could be inappropriate for African populations. We report here the immunological profile for children aged from birth through 6 years in Cameroon and also compare our values to data from other African and Caucasian populations. In a cohort of 352 healthy children, aged 0 to 6 years, the relative and absolute numbers of T-cell subsets, B cells, and NK lymphocytes were determined from peripheral blood collected in EDTA tubes. Samples were stained with BD Multitest reagents in Trucount tubes and analyzed by using CellQuest-Pro and FlowJo software. We evaluated about 23 different lymphocyte subsets in which the absolute number and percentage values differed significantly (P < 0.05) with age and peaked between 6 and 12 months. B-cell values were higher compared to reported values from developed countries. Differences in activated and differentiated T cells were observed in subjects between 1 and 6 years of age. The absolute CD8(+) T-cell count and the CD4(+)/CD8(+) ratio seem to depend on gender. Normal lymphocyte subsets values among children from Cameroon differ from reported values in Caucasian and some African populations. The differences observed could be due to genetic and environmental factors coupled with the methodology used. These values could be used as initial national reference guidelines as more data are assembled.

Hepatitis C virus infection may lead to slower emergence of P. falciparum in blood.

BACKGROUND: Areas endemic for Plasmodium falciparum, hepatitis B virus (HBV) and hepatitis C virus (HCV) overlap in many parts of sub-Saharan Africa. HBV and HCV infections develop in the liver, where takes place the first development stage of P. falciparum before its further spread in blood. The complex mechanisms involved in the development of hepatitis may potentially influence the development of the liver stage of malaria parasites. Understanding the molecular mechanisms of these interactions could provide new pathophysiological insights for treatment strategies in Malaria. METHODOLOGY: We studied a cohort of 319 individuals living in a village where the three infections are prevalent. The patients were initially given a curative antimalarial treatment and were then monitored for the emergence of asexual P. falciparum forms in blood, fortnightly for one year, by microscopy and polymerase chain reaction. PRINCIPAL FINDINGS: At inclusion, 65 (20.4%) subjects had detectable malaria parasites in blood, 36 (11.3%) were HBV chronic carriers, and 61 (18.9%) were HCV chronic carriers. During follow-up, asexual P. falciparum forms were detected in the blood of 203 patients. The median time to P. falciparum emergence in blood was respectively 140 and 120 days in HBV- and HBV+ individuals, and 135 and 224 days in HCV- and HCV+ individuals. HCV carriage was associated with delayed emergence of asexual P. falciparum forms in blood relative to patients without HCV infection. CONCLUSIONS: This pilot study represents first tentative evidence of a potential epidemiological interaction between HBV, HCV and P. falciparum infections. Age is an important confounding factor in this setting however multivariate analysis points to an interaction between P. falciparum and HCV at the hepatic level with a slower emergence of P. falciparum in HCV chronic carriers. More in depth analysis are necessary to unravel the basis of hepatic interactions between these two pathogens, which could help in identifying new therapeutic approaches against malaria.

Whole-transcriptome analysis of Plasmodium falciparum field isolates: identification of new pathogenicity factors.

BACKGROUND: Severe malaria and one of its most important pathogenic processes, cerebral malaria, involves the sequestration of parasitized red blood cells (pRBCs) in brain postcapillary venules. Although the pathogenic mechanisms underlying malaria remain poorly characterized, it has been established that adhesion of pRBCs to endothelial cells (ECs) can result in cell apoptosis, which in turn may lead to disruption of the blood-brain barrier. The nature of the parasite molecules involved in the pathogenesis of severe malaria remains elusive. METHODS: Whole-transcriptome profiling of nonapoptogenic versus apoptogenic parasite field isolates obtained from Gabonese children was performed with pan-genomic Plasmodium falciparum DNA microarrays; radiolabeled instead of fluorescent cDNAs were used to improve the sensitivity of signal detection. RESULTS: Our methods allowed the identification of 59 genes putatively associated with the induction of EC apoptosis. Silencing of Plasmodium gene expression with specific double-stranded RNA was performed on 8 selected genes; 5 of these, named "Plasmodium apoptosis-linked pathogenicity factors" (PALPFs), were found to be linked to parasite apoptogenicity. Of these genes, 2 might act via parasite cytoadherence. CONCLUSION: This is the first attempt to identify genes involved in parasite pathogenic mechanisms against human ECs. The finding of PALPFs illuminates perspectives for novel therapeutic strategies against cerebral complications of malaria.

Fetal ultrasonography: biometric data from four African primate species.

BACKGROUND: Nonhuman primates are raised in large numbers in research centers and zoos. Reproductive monitoring is required to improve breeding performances. Ultrasonography is a safe method to determine gestational age and to estimate the date of parturition. However only few data are available in nonhuman primates. METHODS: Fetal biometric data were obtained throughout pregnancy on four African primate species, namely chimpanzee, gorilla, mandrill and patas monkey. Measurements included biparietal diameter, transverse abdominal diameter, femur and humerus length, external interorbital diameter, and fetal heart rate. Curves established from these data were compared with previously published data in chimpanzees and gorillas and with those for humans and other closely related primate species. RESULTS: The curves for the different hominids were very similar, while those for mandrills more closely resembled baboons and data for patas monkeys were comparable to those for macaques. CONCLUSIONS: These data, by providing a tool to evaluate precise gestational age, will be useful for centers raising these four primate species.

Submicroscopic Plasmodium falciparum infections before and after sulfadoxine-pyrimethamine and artesunate association treatment in Dienga, Southeastern Gabon.

BACKGROUND: It has been shown that Plasmodium falciparum submicroscopic infections (SMI) can contribute to malaria-associated anemia as well as to cerebral malaria. Polymerase chain reaction (PCR) assays are usually used as an alternative to microscopy in detecting subpatently infected individuals. OBJECTIVES: The main objective of this study was to investigate the occurrence of SMI before and after a suppressive antimalarial treatment in the population of the village of Dienga in Gabon. METHODS: Nested PCR was used to detect SMI and to determine genotypes. RESULTS: The prevalence rates of SMI were 13.67% (38/278) at day 0 and 8.99% (25/278) at day 14 after sulfadoxine-pyrimethamine-artesunate treatment. Genotype analysis of two polymorphic regions of the merozoite surface protein (MSP)-1 block 2, MSP-2 and a dimorphic region of the erythrocyte binding antigen (EBA-175) revealed that as many as 88% (22/25) of SMI detected after treatment were completely new alleles, indicating either previously sequestered parasites or newly acquired infections. CONCLUSION: These results demonstrate the usefulness of sulfadoxine-pyrimethamine-artesunate association treatment in the population of Dienga and confirmed early parasite genotype change after a suppressive antimalarial treatment in endemic areas.