Dataset Information

Identification and characterization of CRF02_AG, CRF06_cpx, and CRF09_cpx recombinant subtypes in Mali, West Africa.

ABSTRACT: Abstract Multiple HIV-1 subtypes and circulating recombinant forms (CRFs) are known to cocirculate in Africa. In West Africa, the high prevalence of CRF02_AG, and cocirculation of subtype A, CRF01_AE, CRF06_cpx, and other complex intersubtype recombinants has been well documented. Mali, situated in the heart of West Africa, is likely to be affected by the spread of recombinant subtypes. However, the dynamics of the spread of HIV-1 recombinant subtypes as well as nonrecombinant HIV-1 group M subtypes in this area have not been systematically assessed. Herein, we undertook genetic analyses on full-length env sequences derived from HIV-1-infected individuals living in the capital city of Mali, Bamako. Of 23 samples we examined, 16 were classified as CRF02_AG and three had a subsubtype A3. Among the remaining HIV-1 strains, CRF06_cpx and CRF09_cpx were each found in two patients. Comparison of phylogenies for six matched pol and full-length env sequences revealed that two strains had discordant subtype/CRF designations between the pol and env regions: one had A3(pol)CRF02_AG(env) and the other had CRF02_AG(pol)A3(env). Taken together, our study demonstrated the high prevalence of CRF02_AG and complexity of circulating HIV-1 strains in Mali. It also provided evidence of ongoing virus evolution of CRF02_AG, as illustrated by the emergence of more complex CRF02_AG/A3 intersubtype recombinants in this area.

SUBMITTER: Imamichi H

PROVIDER: S-EPMC2981380 | biostudies-literature | 2009 Jan

REPOSITORIES: biostudies-literature

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Identification and characterization of CRF02_AG, CRF06_cpx, and CRF09_cpx recombinant subtypes in Mali, West Africa.

Imamichi Hiromi H Koita Ousmane O Dabitao Djeneba D Dao Sounkalo S Ibrah Mahamadou M Sogoba Dramane D Dewar Robin L RL Berg Steve C SC Jiang Min-Kang MK Parta Mark M Washington Janice A JA Polis Michael A MA Lane H Clifford HC Tounkara Anatole A

AIDS research and human retroviruses 20090101 1

Abstract Multiple HIV-1 subtypes and circulating recombinant forms (CRFs) are known to cocirculate in Africa. In West Africa, the high prevalence of CRF02_AG, and cocirculation of subtype A, CRF01_AE, CRF06_cpx, and other complex intersubtype recombinants has been well documented. Mali, situated in the heart of West Africa, is likely to be affected by the spread of recombinant subtypes. However, the dynamics of the spread of HIV-1 recombinant subtypes as well as nonrecombinant HIV-1 group M subt ...[more]

PMID: 19182920

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Project description:BACKGROUND/OBJECTIVE:Patient-centred attitudes have been shown to decline during medical training in high-income countries, yet little is known about attitudes among West African medical students. We sought to measure student attitudes towards patient-centredness and examine validity of the 18-item Patient-Practitioner Orientation Scale (PPOS) in this context. PARTICIPANTS/SETTING:430 medical students in years 1, 3, 5 and 6 of a 6-year medical training programme in Bamako, Mali. DESIGN:We conducted a cross-sectional survey, compared the proportion of students who agreed with each PPOS item by gender and academic year, and calculated composite PPOS scores. To examine psychometrics of the PPOS and its two subscales ('sharing' and 'caring'), we calculated internal consistency (Cronbach's alpha) and performed confirmatory and exploratory factor analyses (CFA and EFA). RESULTS:In seven of the nine 'sharing' items, the majority of students held attitudes favouring a provider-dominant style. For five of the nine 'caring' items, the majority of student responded consistently with patient-centred attitudes, while in the other four, responses indicated a disease-centred orientation. In eight items, a greater proportion of fifth/sixth year students held patient-centred attitudes as compared with first year students; there were few gender differences. Average PPOS scores indicated students were moderately patient-centred, with more favourable attitudes towards the 'caring' aspect than 'sharing'. Internal consistency of the PPOS was inadequate for the full scale (?=0.58) and subscales ('sharing' ?=0.37; 'caring' ?=0.48). CFA did not support the original PPOS factors and EFA did not identify an improved structure. CONCLUSIONS:West African medical students training in Bamako are moderately patient-centred and do not show the same declines in patient-centred attitudes in higher academic years as seen in other settings. Medical students may benefit from training in shared power skills and in attending to patient lifestyle factors. Locally validated tools are needed to guide West African medical schools in fostering patient-centredness among students.

Project description:BackgroundSchistosomiasis is classically described as a rural disease that occurs in areas with poor sanitary conditions. However, over recent decades, there has been an expansion of schistosomiasis foci towards urban areas faced with a rapid and disordered urbanization. In Bamako, Mali, the impact of environmental change on vector-borne diseases such as schistosomiasis is not well known. This study sought to identify the presence of schistosomiasis transmission hotspots in Bamako. Using this perspective, we aimed to describe the risk factors of the endemization and maintenance of schistosomiasis.Materials and methodsA cross-sectional study was carried out in the six municipalities (communes) in Bamako. Environmental information was obtained from earth observation satellites in order to maximize ecological contrasts. Twenty-nine blocks of 200 m x 200 m were identified. We selected a school inside or nearest to each block for urine and stool samples examination. The study cohort was school children aged between eight and 15 years. The Kato-Katz technique and filtration were used for Schistosoma mansoni and S. haematobium ova research in stools and urine, respectively. The schools and snail breeding sites were georeferenced. Four malacological surveys were conducted between October 2011 and February 2012. Bivariate analysis was used to identify independent predictors of being infected with schistosomiasis.ResultsThe prevalence rate of S. haematobium was 14.7% (n?=?1,761) and that of S. mansoni 1.5% (n?=?1,491). Overall, the urinary form was endemic in 76.6% of schools. The infection significantly varied between the municipalities (p?<?0.001). It was also more prevalent on the left side of the Niger River than the right side (17.4% vs. 9.5% respectively; p?<?0.001). The vicinity to snail breeding sites (OR?=?3.677; 95% IC [2.765-4.889]; p?<?10 (-3) ) and parents' occupations (OR?=?7.647; 95% IC [2.406-24.305]; p?<?0.001) were the most important risk factors associated with S. haematobium infection exposure. Biomphalaria pfeifferi, Bulinus truncatus, and B. globosus were the intermediate hosts captured. The schistosome natural infection rates (SNIRs), which were low or nil in October and November, rose to 2.8% in January and 8.3% in February for B. pfeifferi and B. truncatus, respectively.ConclusionOur findings show that there is a high transmission risk for schistosomiasis in Bamako. Appropriate integrated control measures need to be introduced to control the transmission of this disease in the study area.

Project description:BACKGROUND:HIV-1 is one of the fastest evolving pathogens, and is distinguished by geographic and genetic variants that have been classified into different subtypes and circulating recombinant forms (CRFs). Early in infection the primary coreceptor is CCR5, but during disease course CXCR4-using HIV-1 populations may emerge. This has been correlated with accelerated disease progression in HIV-1 subtype B. Basic knowledge of HIV-1 coreceptor tropism is important due to the recent introduction of coreceptor antagonists in antiretroviral therapy, and subtype-specific differences regarding how frequently HIV-1 CXCR4-using populations appear in late-stage disease need to be further investigated. To study how frequently CXCR4-using populations appear in late-stage disease among HIV-1 subtype A and CRF02_AG, we evaluated the accuracy of a recombinant virus phenotypic assay for these subtypes, and used it to determine the HIV-1 coreceptor tropism of plasma samples collected during late-stage disease in Guinea-Bissau. We also performed a genotypic analysis and investigated subtype-specific differences in the appearance of CXCR4 tropism late in disease. RESULTS:We found that the recombinant virus phenotypic assay accurately predicted HIV-1 coreceptor tropism of subtype A and CRF02_AG. Over the study period (1997-2007), we found an increasing and generally high frequency of CXCR4 tropism (86%) in CRF02_AG. By sequence analysis of the V3 region of our samples we developed a novel genotypic rule for predicting CXCR4 tropism in CRF02_AG, based on the combined criteria of the total number of charged amino acids and net charge. This rule had higher sensitivity than previously described genotypic rules and may be useful for development of future genotypic tools for this CRF. Finally, we conducted a literature analysis, combining data of 498 individuals in late-stage disease, and found high amounts of CXCR4 tropism for all major HIV-1 subtypes (60-77%), except for subtype C (15%). CONCLUSIONS:The increase in CXCR4 tropism over time suggests an evolving epidemic of CRF02_AG. The results of the literature analysis demonstrate the need for further studies investigating subtype-specific emergence for CXCR4-tropism; this may be particularly important due to the introduction of CCR5-antagonists in HIV treatment regimens.

Dataset Information

Identification and characterization of CRF02_AG, CRF06_cpx, and CRF09_cpx recombinant subtypes in Mali, West Africa.

Publications

Identification and characterization of CRF02_AG, CRF06_cpx, and CRF09_cpx recombinant subtypes in Mali, West Africa.

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