Dearth of full-length HIV-1 sequences obscures the true HIV-1 genetic subtypes distribution in sub-Saharan Africa

HIV infection is still a public health problem in sub-Saharan Africa. The broad diversity exhibited by HIV-1 may impact on transmission, disease progression, drug resistance and vaccine development. Most analyses of HIV-1 subtype distribution have been on partial HIV-1 gene sequences, which may not adequately reflect the circulating subtypes. The objective of this study was to estimate the HIV-1 subtype distribution in sub-Saharan Africa using only full-length genome sequences. Using available HIV-1 full-length genome sequences from sub-Saharan Africa, the HIV-1 distribution in the region was analysed and compared with a previous global analysis which was not based entirely on full-length sequences. A total of 934 HIV-1 full-length genome sequences were available from 27 sub-Saharan countries. There was a disproportionate distribution of HIV-1 subtypes among countries with Cameroon having all the four HIV-1 groups. The subtype C was the most available in addition to a large proportion of circulating and unique recombinant forms (CRFs/URFs) especially in Central and West African countries, with frequencies of 32.6 to 90%. There was decreased representation of subtypes A and G in regions where CRFs/URFs were common compared with previous analysis using partial sequences. There is a need for more HIV-1 full-length genome sequences from sub-Saharan Africa for the true distribution of HIV-1 subtypes to be known, as analysis of partial sequences is not truly representative of the circulating subtypes. Keywords: Africa, distribution, genetic diversity, HIV sequence variability, subtypes, recombinationAfrican Journal of Biotechnology, Vol 13(21), 2166-217

À propos Prevalence and determinants of occupational exposures to blood and body fluids among health workers in two tertiary hospitals in Nigeria

Background: Healthcare associated infections among health workers  commonly follow occupational exposures to pathogens infecting blood orbody fluids of patients. We evaluated the prevalence and determinants of occupational exposures to blood/body fluids among health workers in two tertiary hospitals in Nigeria.Methods: In a cross section study undertaken in two tertiary hospitals in North-central and South-south Nigeria in 2011, a structured  selfadministered questionnaire was used to obtain demographic data and occupational exposures to blood/body fluids in the previous year fromdoctors, nurses and laboratory scientists. Independent predictors of occupational exposures were determined in an unconditional logisticregression model.Results: Out of 290 health workers studied, 75.8%, 44.7%, 32.9%, 33.9% and 84.4% had skin contact with patient’s blood, needle stick injuries, cut by sharps, blood/body fluid splashes to mucous membranes and one or more type of exposures respectively. Ninety one percent, 86%, 71.1%,87.6%, 81.3%, and 84.4% of house officers, resident doctors, consultant doctors, staff nurses, principal/chief nursing officers and laboratory scientists, respectively had one or more type of exposures in the previous year (P>0.05). Professional group was found to be the only independentpredictor of cut by sharps. House officers and nurses had higher and more frequent occupational exposures than other professional groups.Conclusion: Our results suggest high rates of occupational exposures to blood/body fluid among health workers in Nigeria, especially among newly qualified medical doctors and nurses. Health facilities in Nigeria ought to strengthen infection prevention and control practices while targeting high risk health workers such as house officers and nurses.Key words: Prevalence, occupational exposures, needlestick injuries, sharps, healthcare workers, Nigeria

Intercompartmental Recombination of HIV-1 Contributes to env Intrahost Diversity and Modulates Viral Tropism and Sensitivity to Entry Inhibitors▿†‡

HIV-1 circulates within an infected host as a genetically heterogeneous viral population. Viral intrahost diversity is shaped by substitutional evolution and recombination. Although many studies have speculated that recombination could have a significant impact on viral phenotype, this has never been definitively demonstrated. We report here phylogenetic and subsequent phenotypic analyses of envelope genes obtained from HIV-1 populations present in different anatomical compartments. Assessment of env compartmentalization from immunologically discrete tissues was assessed utilizing a single genome amplification approach, minimizing in vitro-generated artifacts. Genetic compartmentalization of variants was frequently observed. In addition, multiple incidences of intercompartment recombination, presumably facilitated by low-level migration of virus or infected cells between different anatomic sites and coinfection of susceptible cells by genetically divergent strains, were identified. These analyses demonstrate that intercompartment recombination is a fundamental evolutionary mechanism that helps to shape HIV-1 env intrahost diversity in natural infection. Analysis of the phenotypic consequences of these recombination events showed that genetic compartmentalization often correlates with phenotypic compartmentalization and that intercompartment recombination results in phenotype modulation. This represents definitive proof that recombination can generate novel combinations of phenotypic traits which differ subtly from those of parental strains, an important phenomenon that may have an impact on antiviral therapy and contribute to HIV-1 persistence in vivo

Antimicrobial resistance in Africa: a systematic review

Background: Antimicrobial resistance (AMR) is widely acknowledged as a global problem, yet in many parts of the world its magnitude is still not well understood. This review, using a public health focused approach, aimed to understand and describe the current status of AMR in Africa in relation to common causes of infections and drugs recommended in WHO treatment guidelines. Methods: PubMed, EMBASE and other relevant databases were searched for recent articles (2013–2016) in accordance with the PRISMA guidelines. Article retrieval and screening were done using a structured search string and strict inclusion/exclusion criteria. Median and interquartile ranges of percent resistance were calculated for each antibiotic-bacterium combination. Results: AMR data was not available for 42.6% of the countries in the African continent. A total of 144 articles were included in the final analysis. 13 Gram negative and 5 Gram positive bacteria were tested against 37 different antibiotics. Penicillin resistance in Streptococcus pneumoniae was reported in 14/144studies (median resistance (MR): 26.7%). Further 18/53 (34.0%) of Haemophilus influenza isolates were resistant to amoxicillin. MR of Escherichia coli to amoxicillin, trimethoprim and gentamicin was 88.1%, 80.7% and 29.8% respectively. Ciprofloxacin resistance in Salmonella Typhi was rare. No documented ceftriaxone resistance in Neisseria gonorrhoeae was reported, while the MR for quinolone was 37.5%. Carbapenem resistance was common in Acinetobacter spp. and Pseudomonas aeruginosa but uncommon in Enterobacteriaceae. Conclusion: Our review highlights three important findings. First, recent AMR data is not available for more than 40% of the countries. Second, the level of resistance to commonly prescribed antibiotics was significant. Third, the quality of microbiological data is of serious concern. Our findings underline that to conserve our current arsenal of antibiotics it is imperative to address the gaps in AMR diagnostic standardization and reporting and use available information to optimize treatment guidelines.</p