Dataset Information

HIV-1 Genetic Diversity Among Incident Infections in Mbeya, Tanzania.

ABSTRACT: In preparation for vaccine trials, HIV-1 genetic diversity was surveyed between 2002 and 2006 through the Cohort Development study in the form of a retrospective and prospective observational study in and around the town of Mbeya in Tanzania's Southwest Highlands. This study describes the molecular epidemiology of HIV-1 strains obtained from 97 out of 106 incident HIV-1 infections identified in three subpopulations of participants (one rural, two urban) from the Mbeya area. Near full-genome or half-genome sequencing showed a subtype distribution of 40% C, 17% A1, 1% D, and 42% inter-subtype recombinants. Compared to viral subtyping results previously obtained from the retrospective phase of this study, the overall proportion of incident viral strains did not change greatly during the study course, suggesting maturity of the epidemic. A comparison to a current Phase I-II vaccine being tested in Africa shows ?17% amino acid sequence difference between the gp120 of the vaccine and subtype C incident strains. Phylogenetic and recombinant breakpoint analysis of the incident strains revealed the emergence of CRF41_CD and many unique recombinants, as well as the presence of six local transmission networks most of which were confined to the rural subpopulation. In the context of vaccine cohort selection, these results suggest distinct infection transmission dynamics within these three geographically close subpopulations. The diversity and genetic sequences of the HIV-1 strains obtained during this study will greatly contribute to the planning, immunogen selection, and analysis of vaccine-induced immune responses observed during HIV-1 vaccine trials in Tanzania and neighboring countries.

SUBMITTER: Billings E

PROVIDER: S-EPMC5372774 | biostudies-literature | 2017 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

HIV-1 Genetic Diversity Among Incident Infections in Mbeya, Tanzania.

Billings Erik E Sanders-Buell Eric E Bose Meera M Kijak Gustavo H GH Bradfield Andrea A Crossler Jacqueline J Arroyo Miguel A MA Maboko Leonard L Hoffmann Oliver O Geis Steffen S Birx Deborah L DL Kim Jerome H JH Michael Nelson L NL Robb Merlin L ML Hoelscher Michael M Tovanabutra Sodsai S

AIDS research and human retroviruses 20161219 4

In preparation for vaccine trials, HIV-1 genetic diversity was surveyed between 2002 and 2006 through the Cohort Development study in the form of a retrospective and prospective observational study in and around the town of Mbeya in Tanzania's Southwest Highlands. This study describes the molecular epidemiology of HIV-1 strains obtained from 97 out of 106 incident HIV-1 infections identified in three subpopulations of participants (one rural, two urban) from the Mbeya area. Near full-genome or h ...[more]

PMID: 27841669

Similar Datasets

Project description:BackgroundTaenia solium cysticercosis/taeniosis is emerging as a serious public health and economic problem in many developing countries. This study was conducted to determine prevalence and risk factors of human T. solium infections in Mbeya Region, Tanzania.Methods and findingsA cross-sectional survey was conducted in 13 villages of Mbozi district in 2009. Sera of 830 people (mean 37.9±11.3 years (SD); 43% females) were tested for circulating cysticerci antigen (Ag-ELISA) and antibody (Ab-ELISA). A subset of persons found seropositive by Ag-ELISA underwent computed tomography (CT) scan of the brain for evidence of neurocysticercosis. Stool samples from 820 of the same participants were tested for taeniosis by copro-antigens (copro-Ag-ELISA) and formol-ether concentration technique. Cases of T. solium taeniosis were confirmed serologically by EITB assay (rES38). A questionnaire was used for identification of risk factors. Active cysticercosis by positive Ag-ELISA was found in 139 (16.7%) persons while anti-cysticercal antibodies were detected in 376 (45.3%) persons by Ab-ELISA. Among 55 persons positive for Ag-ELISA undergoing CT scan, 30 (54.6%) were found to have structures in the brain suggestive of neurocysticercosis. Using faecal analysis, 43 (5.2%) stool samples tested positive for taeniosis by copro-Ag-ELISA while Taenia eggs were detected in 9 (1.1%) stool samples by routine coprology. Antibodies specifically against adult T. solium were detected in 34 copro-Ag-ELISA positive participants by EITB (rES38) indicating T. solium taeniosis prevalence of 4.1%. Increasing age and hand washing by dipping in contrast to using running water, were found associated with Ag-ELISA seropositivity by logistic regression. Gender (higher risk in females) and water source were risk factors associated with Ab-ELISA seropositivity. Reported symptoms of chronic severe headaches and history of epileptic seizures were found associated with positive Ag-ELISA (p?0.05).ConclusionThe present study indicates T. solium infection in humans is highly endemic in the southern highlands of Tanzania.

Project description:Transfusion-transmissible infections including HIV-1 continue to pose major risks for unsafe blood transfusions due to both window phase infections and divergent viruses that may not be detected by donor screening assays. Given the recent emergence of several HIV-1 circulating recombinant forms (CRFs) in high-risk populations in the Southeast Asia region, we investigated the genetic diversity of HIV-1 among the blood donors in Kuala Lumpur, Malaysia. A total of 211 HIV-positive plasma samples detected among 730,188 donations to the National Blood Centre between 2013 and 2014 were provided (90.5% male, median age: 27.0 years old). Recent or long-term infection status at the time of donation was determined using a limiting antigen avidity enzyme immunoassay (LAg-Avidity EIA). HIV-1 gag-pol genes were amplified and sequenced from residual plasma for 149 cases followed by genotype determination using phylogenetic and recombination analyses. Transmitted antiretroviral resistance mutations were not observed among the blood donors, among which 22.7% were classified as recent or incident infections. Major circulating HIV-1 genotypes determined by neighbour-joining phylogenetic inference included CRF01_AE at 40.9% (61/149), CRF33_01B at 21.5% (32/149), and subtype B at 10.1% (15/149). Newly-described CRFs including CRF54_01B circulated at 4.0%, CRF74_01B at 2.0%, and CRF53_01B and CRF48_01B at 0.7% each. Interestingly, unique HIV-1 genotypes including African subtype G (8.7%), CRF45_cpx (1.3%), CRF02_AG (0.7%) and CRF07_BC (0.7%) from China were detected for the first time in the country. A cluster of subtype G sequences formed a distinct founder sub-lineage within the African strains. In addition, 8.7% (13/149) of HIV-infected donors had unique recombinant forms (URFs) including CRF01_AE/B' (4.7%), B'/C (2.7%) and B'/G (1.3%) recombinants. Detailed analysis identified similar recombinant structures with shared parental strains among the B'/C and B'/G URFs, some of which were sequenced from recently infected individuals, indicating the possible emergence and on-going spread of foreign clades of CRF candidates among the local population. The findings demonstrate extensive molecular complexity of HIV-1 among the infected blood donors in Malaysia, driven in part by the increased spread of recently described CRFs and multiple introductions of previously unreported genotypes from highly prevalent countries.

Project description:BACKGROUND:In remote rural Tanzania, the rate of linkage into HIV care was estimated at 28% in 2014. This study explored facilitators and barriers to linkage to HIV care at individual/patient, health care provider, health system, and contextual levels to inform eventual design of interventions to improve linkage to HIV care. METHODS:We conducted a descriptive qualitative study nested in a cohort study of 1012 newly diagnosed HIV-positive individuals in Mbeya region between August 2014 and July 2015. We conducted 8 focus group discussions and 10 in-depth interviews with recently diagnosed HIV-positive individuals and 20 individual interviews with healthcare providers. Transcripts were analyzed inductively using thematic content analysis. The emergent themes were then deductively fitted into the four level ecological model. RESULTS:We identified multiple factors influencing linkage to care. HIV status disclosure, support from family/relatives and having symptoms of disease were reported to facilitate linkage at the individual level. Fear of stigma, lack of disclosure, denial and being asymptomatic, belief in witchcraft and spiritual beliefs were barriers identified at individual's level. At providers' level; support and good patient-staff relationship facilitated linkage, while negative attitudes and abusive language were reported barriers to successful linkage. Clear referral procedures and well-organized clinic procedures were system-level facilitators, whereas poorly organized clinic procedures and visit schedules, overcrowding, long waiting times and lack of resources were reported barriers. Distance and transport costs to HIV care centers were important contextual factors influencing linkage to care. CONCLUSION:Linkage to HIV care is an important step towards proper management of HIV. We found that access and linkage to care are influenced positively and negatively at all levels, however, the individual-level and health system-level factors were most prominent in this setting. Interventions must address issues around stigma, denial and inadequate awareness of the value of early linkage to care, and improve the capacity of HIV treatment/care clinics to implement quality care, particularly in light of adopting the 'Test and Treat' model of HIV treatment and care recommended by the World Health Organization.

Project description:BackgroundSexually transmitted infections (STIs) are common among young people in low- and middle-income countries and are associated with negative reproductive and pregnancy outcomes. Most of the studies have assessed HIV among adolescents and young adults, with limited information on occurrence of other STIs in this population. This study aimed to describe the prevalence of and risk factors associated with Herpes Simplex Virus-type 2 (HSV-2), Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG), Syphilis and HIV infection among young adults attending Higher Learning Institutions (HLIs) in Mbeya, Tanzania.MethodsWe conducted a cross-sectional study among students aged 18-24years attending HLIs in Mbeya-Tanzania, randomly selected using a computerized random number. Participants were tested for HSV-2, CT, NG, Syphilis and HIV infection. We used a self-administered questionnaire to collect information on sexual activity and risk factors to the tested STIs.ResultsWe enrolled 504 students from 5 HLIs, with mean age of 21.5 years (SD 1.7). 17% of the students had at least one STI; prevalence was higher among females than males (21.1% versus 14.1%). CT (11%) and HSV-2 (6.1%) were the most common STIs, while NG (1.1%) and HIV (0.7%) infection had the least occurrence. None of the participants was diagnosed with Syphilis. In univariate analysis, predictors for STIs were Sex, inconsistent condom use in the past 4weeks, report of oral sex, sexual orientation (bisexual/homosexual) and having a sexual partner with an age-difference of at least 5years (either older or younger); while in the multivariate analysis, Sex, inconsistent condom use in the past 4weeks and sexual orientation (bisexual/homosexual) remained significant.ConclusionSTIs such as Chlamydia and HSV-2 which are commonly asymptomatic are of concern among young adults attending HLIs. The latter is an important group that needs attention and recognition that is pivotal in transmission of STIs considering their risk. Information, Education and Communication (IEC) campaigns targeting young adults, especially those at HLIs, need to focus on exposure-risk minimization. Funding institutions that have invested heavily on HIV prevention campaigns should consider giving similar recognition to other STIs for a streamlined outcome.

Project description:BACKGROUND:Taenia solium taeniasis/cysticercosis is a disease of substantial economic and public health importance particularly in low-income countries. The disease was reported to be endemic in Mbeya Rural and Mbozi districts, in the southern highlands of Tanzania, the major pig production area in the country. In 2008, using B158/B60 antigen detection enzyme-linked immunosorbent assay (Ag-ELISA), porcine cysticercosis prevalence of up to 32% was reported in the districts. A number of interventions have been implemented in selected villages including an integrated approach consisting of improving pig confinement and selective treatment of pigs with oxfendazole. Mass drug administration with praziquantel targeting schistosomiasis, with an expected effect on T. solium, was also provided to school-age children in the area. This study aimed at providing an update on prevalence and intensities of porcine cysticercosis; and assessing farmers' knowledge, attitudes and practices which could be associated to disease transmission in the area. The study involved a questionnaire survey conducted using face-to-face household interviews with 890 consenting farmers; and carcass dissections performed on 282 pigs randomly selected from the surveyed households. RESULTS:Twenty-six pigs (9.2%) were infected with T. solium; of which two-thirds (65.4%) had light to moderate infection intensities (1-1000 cysticerci), and one-third (34.6%) had heavy intensities (>?1000 cysticerci). Questionnaire results showed that only 5.7% of the respondents perceived T. solium cysticercosis to be an important disease in pigs. About 18.5% of the respondents were aware of T. solium taeniasis, but 32% of them were unaware of how the infection is acquired. Half of the respondents had seen cysticerci in pork, of whom 61% were not aware that consumption of infected pork could cause taeniasis. Latrines were observed to often (90%) lack doors with 45% considered accessible to pigs. CONCLUSIONS:This study provided an evidence that the disease was still endemic in the area. Poor knowledge of farmers, attitudes, and risky practices responsible for disease perpetuation were also revealed. A One Health approach targeting the whole area incorporating improvement of farmer knowledge regarding disease transmission needs to be trialed as a feasible approach to control.

Project description:ObjectiveLinkage to care is the bridge between HIV testing and HIV treatment, care and support. In Tanzania, mobile testing aims to address historically low testing rates. Linkage to care was reported at 14% in 2009 and 28% in 2014. The study compares linkage to care of HIV-positive individuals tested at mobile/outreach versus public health facility-based services within the first 6 months of HIV diagnosis.SettingRural communities in four districts of Mbeya Region, Tanzania.ParticipantsA total of 1012 newly diagnosed HIV-positive adults from 16 testing facilities were enrolled into a two-armed cohort and followed for 6 months between August 2014 and July 2015. 840 (83%) participants completed the study.Main outcome measuresWe compared the ratios and time variance in linkage to care using the Kaplan-Meier estimator and Log rank tests. Cox proportional hazards regression models to evaluate factors associated with time variance in linkage.ResultsAt the end of 6 months, 78% of all respondents had linked into care, with differences across testing models. 84% (CI 81% to 87%, n=512) of individuals tested at facility-based site were linked to care compared to 69% (CI 65% to 74%, n=281) of individuals tested at mobile/outreach. The median time to linkage was 1 day (IQR: 1-7.5) for facility-based site and 6 days (IQR: 3-11) for mobile/outreach sites. Participants tested at facility-based site were 78% more likely to link than those tested at mobile/outreach when other variables were controlled (AHR=1.78; 95% CI 1.52 to 2.07). HIV status disclosure to family/relatives was significantly associated with linkage to care (AHR=2.64; 95% CI 2.05 to 3.39).ConclusionsLinkage to care after testing HIV positive in rural Tanzania has increased markedly since 2014, across testing models. Individuals tested at facility-based sites linked in significantly higher proportion and modestly sooner than mobile/outreach tested individuals. Mobile/outreach testing models bring HIV testing services closer to people. Strategies to improve linkage from mobile/outreach models are needed.

Dataset Information

HIV-1 Genetic Diversity Among Incident Infections in Mbeya, Tanzania.

Publications

HIV-1 Genetic Diversity Among Incident Infections in Mbeya, Tanzania.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets