Performance of rapid subtyping tools used for the classification of HIV type 1 recombinants isolated from selected countries in west and central Africa

HIV-1 genetic diversity in sub-Saharan Africa is broad and the AIDS epidemic is driven predominantly by recombinants in Central and West Africa. The classification of HIV-1 strains is therefore necessary to understand diagnostic efficiency, individual treatment responses as well as options for designing vaccines and antiretroviral (ARV) treatment guidelines. More so, accurate subtyping of a partial or full genome would represent the population dynamics of HIV and provide evidence for designing surveillance strategies within a geographic region. Evaluating the performance of rapid subtyping tools with options that incorporate phylogeny could be fast, more user-friendly and of high performance. A total of 570 HIV-1 partial sequences from Cameroon, Angola, Democratic Republic of Congo, Gabon and Senegal were obtained from the Los Alamos National Library (LANL) HIV Sequence Database. Phylogeny was performed using MEGA v6 and the results were used to evaluate the performance of eleven different rapid HIV-1 subtyping tools: REGA v2, REGA v3, NCBI, Stanford HIVDB, SUDI, Geno2Pheno, Euresist, STAR, jpHMM, COMET and SCUEAL. The performance of these subtyping tools differed among HIV-1 clades and across different viral genes. NCBI and SUDI showed the highest performance in subtyping. The discordance observed between the rapid subtyping tools and phylogeny implies that phylogenetic analysis is still the more suitable method for HIV-1 classification. However, the need to update the reference datasets of the subtyping tools, and validate algorithms for rapid subtyping and quality control is imperative as this information is relevant for clinical use and policymaking to the AIDS response.Keywords: HIV, phylogeny, performance, subtyping tools, algorith

Erratum to: Investigation of the association between the TCF7L2 rs7903146 (C/T) gene polymorphism and obesity in a Cameroonian population: a pilot study

Upon publication of the original article [1], it was noticed that the author\u2019s name \u201cJean Jacques Noubiap\u201d was incorrectly given as \u201cJean Jacques N. Noubiap\u201d. This has now been acknowledged and corrected in this erratum

Investigation of the association between the TCF7L2 rs7903146 (C/T) gene polymorphism and obesity in a Cameroonian population: a pilot study

Objective: This study aimed at investigating the association between the rs7903146 (C/T) polymorphism of the TCF7L2 gene with obesity in a Cameroonian population. Method: This was a case-control pilot study including 61 obese and 61 non-obese Cameroonian adults. Anthropometric indices of obesity, blood pressure, fasting blood glucose, and blood lipids were measured. The rs7903146 (C/T) polymorphism of the TCF7L2 gene was genotyped using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), and genotypes were correlated with clinical and biological parameters. Results: The T allele was predominant in the study population with a frequency of 93%. No statistically significant difference was however observed between the genotypic (p = 0.50) and allelic frequencies (p = 0.58) of obese and non-obese subjects. Comparison of clinical and biochemical parameters of C allele carriers (CX = CC + CT) with those of TT genotype showed that there was no significant difference between the lipid profile of these two groups. Conclusion: The rs7903146 (C/T) polymorphism of the TCF7L2 gene might not be associated with obesity in the Cameroonian population

Fasting insulin sensitivity indices are not better than routine clinical variables at predicting insulin sensitivity among Black Africans: a clamp study in sub-Saharan Africans

BACKGROUND: We aimed to evaluate the predictive utility of common fasting insulin sensitivity indices, and non-laboratory surrogates [BMI, waist circumference (WC) and waist-to-height ratio (WHtR)] in sub-Saharan Africans without diabetes. METHODS: We measured fasting glucose and insulin, and glucose uptake during 80/mU/m2/min euglycemic clamp in 87 Cameroonians (51 men) aged (SD) 34.6 (11.4) years. We derived insulin sensitivity indices including HOMA-IR, quantitative insulin sensitivity check index (QUICKI), fasting insulin resistance index (FIRI) and glucose-to-insulin ratio (GIR). Indices and clinical predictors were compared to clamp using correlation tests, robust linear regressions and agreement of classification by sex-specific thirds. RESULTS: The mean insulin sensitivity was M =10.5+/-3.2mg/kg/min. Classification across thirds of insulin sensitivity by clamp matched with non-laboratory surrogates in 30-48% of participants, and with fasting indices in 27-51%, with kappa statistics ranging from 0.10 to 0.26. Fasting indices correlated significantly with clamp (/r/=0.23-0.30), with GIR performing less well than fasting insulin and HOMA-IR (both p <0.02). BMI, WC and WHtR were equal or superior to fasting indices (/r/=0.38-0.43). Combinations of fasting indices and clinical predictors explained 25-27% of variation in clamp values. CONCLUSION: Fasting insulin sensitivity indices are modest predictors of insulin sensitivity measured by euglycemic clamp, and do not perform better than clinical surrogates in this population

Persistent organic pollutants as risk factors for type 2 diabetes

Type 2 diabetes mellitus (T2DM) is a major and fast growing public health problem. Although obesity is considered to be the main driver of the pandemic of T2DM, a possible contribution of some environmental contaminants, of which persistent organic pollutants (POPs) form a particular class, has been suggested. POPs are organic compounds that are resistant to environmental degradation through chemical, biological, and photolytic processes which enable them to persist in the environment, to be capable of long-range transport, bio accumulate in human and animal tissue, bio accumulate in food chains, and to have potential significant impacts on human health and the environment. Several epidemiological studies have reported an association between persistent organic pollutants and diabetes risk. These findings have been replicated in experimental studies both in human (in-vitro) and animals (in-vivo and in-vitro), and patho-physiological derangements through which these pollutants exercise their harmful effect on diabetes risk postulated. This review summarizes available studies, emphasises on limitations so as to enable subsequent studies to be centralized on possible pathways and bring out clearly the role of POPs on diabetes risk