HIV transmission and source-sink dynamics in sub-Saharan Africa.
Ontology highlight
ABSTRACT:
SUBMITTER: Okano JT
PROVIDER: S-EPMC7259817 | biostudies-literature | 2020 Mar
REPOSITORIES: biostudies-literature
Publications
HIV transmission and source-sink dynamics in sub-Saharan Africa.
Okano Justin T JT Sharp Katie K Valdano Eugenio E Palk Laurence L Blower Sally S
The lancet. HIV 20200214 3
Multiple phylogenetic studies of HIV in sub-Saharan Africa have shown that mobility-driven transmission frequently occurs: many communities export and import strains. Mobility-driven transmission can result in source-sink dynamics: one community can sustain a micro-epidemic in another community in which transmission is too low to be self-sustaining. In epidemiology, the basic reproduction number (R<sub>0</sub>) is used to specify the sustainability threshold. R<sub>0</sub> represents the average ...[more]
Similar Datasets
Project description:Sub-Saharan Africa represents 69% of the total number of individuals living with HIV infection worldwide and 72% of AIDS deaths globally. Pulmonary infection is a common and frequently fatal complication, though little is known regarding the lower airway microbiome composition of this population. Our objectives were to characterize the lower airway microbiome of Ugandan HIV-infected patients with pneumonia, to determine relationships with demographic, clinical, immunological, and microbiological variables and to compare the composition and predicted metagenome of these communities to a comparable cohort of patients in the US (San Francisco). Bronchoalveolar lavage samples from a cohort of 60 Ugandan HIV-infected patients with acute pneumonia were collected. Amplified 16S ribosomal RNA was profiled and aforementioned relationships examined. Ugandan airway microbiome composition and predicted metagenomic function were compared to US HIV-infected pneumonia patients. Among the most common bacterial pulmonary pathogens, Pseudomonas aeruginosa was most prevalent in the Ugandan cohort. Patients with a richer and more diverse airway microbiome exhibited lower bacterial burden, enrichment of members of the Lachnospiraceae and sulfur-reducing bacteria and reduced expression of TNF-alpha and matrix metalloproteinase-9. Compared to San Franciscan patients, Ugandan airway microbiome were significantly richer, and compositionally distinct with predicted metagenomes that encoded a multitude of distinct pathogenic pathways e.g secretion systems. Ugandan pneumonia-associated airway microbiome is compositionally and functionally distinct from those detected in comparable patients in developed countries, a feature which may contribute to adverse outcomes in this population. Please note that the data from the comparable cohort of patients in the USUS data was published as supplemental material of PMID: 22760045 but not submitted to GEO The 'patient_info.txt' contains 12 clinical, 7 immunological and 3 microbiological variables for each patient.
2014-02-20 | GSE52791 | GEO
Project description:BackgroundThe cause of the high HIV prevalence in sub-Saharan Africa is incompletely understood, with heterosexual penile-vaginal transmission proposed as the main mechanism. Heterosexual HIV transmission has been estimated to have a very low probability; but effects of cofactors that vary in space and time may substantially alter this pattern.MethodsTo test the effect of individual variation in the HIV infectiousness generated by co-infection, we developed and analyzed a mathematical sexual network model that simulates the behavioral components of a population from Malawi, as well as the dynamics of HIV and the co-infection effect caused by other infectious diseases, including herpes simplex virus type-2, gonorrhea, syphilis and malaria.ResultsThe analysis shows that without the amplification effect caused by co-infection, no epidemic is generated, and HIV prevalence decreases to extinction. But the model indicates that an epidemic can be generated by the amplification effect on HIV transmission caused by co-infection.ConclusionThe simulated sexual network demonstrated that a single value for HIV infectivity fails to describe the dynamics of the epidemic. Regardless of the low probability of heterosexual transmission per sexual contact, the inclusion of individual variation generated by transient but repeated increases in HIV viral load associated with co-infections may provide a biological basis for the accelerated spread of HIV in sub-Saharan Africa. Moreover, our work raises the possibility that the natural history of HIV in sub-Saharan Africa cannot be fully understood if individual variation in infectiousness is neglected.
| S-EPMC3175213 | biostudies-literature
Project description:Sub-Saharan Africa represents 69% of the total number of individuals living with HIV infection worldwide and 72% of AIDS deaths globally. Pulmonary infection is a common and frequently fatal complication, though little is known regarding the lower airway microbiome composition of this population. Our objectives were to characterize the lower airway microbiome of Ugandan HIV-infected patients with pneumonia, to determine relationships with demographic, clinical, immunological, and microbiological variables and to compare the composition and predicted metagenome of these communities to a comparable cohort of patients in the US (San Francisco). Bronchoalveolar lavage samples from a cohort of 60 Ugandan HIV-infected patients with acute pneumonia were collected. Amplified 16S ribosomal RNA was profiled and aforementioned relationships examined. Ugandan airway microbiome composition and predicted metagenomic function were compared to US HIV-infected pneumonia patients. Among the most common bacterial pulmonary pathogens, Pseudomonas aeruginosa was most prevalent in the Ugandan cohort. Patients with a richer and more diverse airway microbiome exhibited lower bacterial burden, enrichment of members of the Lachnospiraceae and sulfur-reducing bacteria and reduced expression of TNF-alpha and matrix metalloproteinase-9. Compared to San Franciscan patients, Ugandan airway microbiome were significantly richer, and compositionally distinct with predicted metagenomes that encoded a multitude of distinct pathogenic pathways e.g secretion systems. Ugandan pneumonia-associated airway microbiome is compositionally and functionally distinct from those detected in comparable patients in developed countries, a feature which may contribute to adverse outcomes in this population. Please note that the data from the comparable cohort of patients in the USUS data was published as supplemental material of PMID: 22760045 but not submitted to GEO The 'patient_info.txt' contains 12 clinical, 7 immunological and 3 microbiological variables for each patient. The G2 PhyloChip microarray platform (commercially available from Second Genome, Inc.) was used to profile bacteria in lower airway samples from 60 subjects
2014-02-20 | E-GEOD-52791 | biostudies-arrayexpress
Project description:Numerous studies have suggested a role for natural killer (NK) cells in attenuation of HIV-1 disease progression via recognition by killer-cell immunoglobulin-like receptors (KIRs) of specific HLA class I molecules. The role of KIR and HLA class I has not been addressed in the context of maternal-infant HIV-1 transmission. KIR and HLA class I B and C genes from 224 HIV-1-infected mothers and 222 infants (72 infected and 150 uninfected) from South Africa were characterized. Although a number of significant associations were determined in both the total group and in the nevirapine (NVP) exposed group, the most significant findings involved KIR2DL2 and KIR2DL3 and HLA-C. KIR2DL2/KIR2DL3 was underrepresented in intrapartum (IP)-transmitting mothers compared to non-transmitting (NT) mothers (P?=?0.008) and remained significant (P?=?0.036) after correction for maternal viral load (MVL). Homozygosity for KIR2DL3 alone and in combination with HLA-C allotype heterozygosity (C1C2) was elevated in IP-transmitting mothers compared to NT mothers (P?=?0.034 and P?=?0.01 respectively), and after MVL correction (P?=?0.033 and P?=?0.027, respectively). In infants, KIR2DL3 in combination with its HLA-C1 ligand (C1) as well as homozygosity for KIR2DL3 with C1C2, were both found to be underrepresented in infected infants compared to exposed uninfected infants in the total group (P?=?0.06 and P?=?0.038, respectively) and in the sub-group of infants whose mothers received NVP (P?=?0.007 and P?=?0.03, respectively). These associations were stronger post MVL adjustment (total group: P?=?0.02 and P?=?0.009, respectively; NVP group: P?=?0.004 and P?=?0.02, respectively). Upon stratification according to low and high MVL, all significant associations fell within the low MVL group, suggesting that with low viral load, the effects of genotype can be more easily detected. In conclusion this study has identified a number of significant associations that suggest an important role for NK cells in maternal-to-infant HIV-1 transmission.
| S-EPMC3035631 | biostudies-literature
Project description:ObjectiveTo develop an analytical understanding of non-cohabiting sex partnering in sub-Saharan Africa (SSA) using nationally representative sexual behaviour data.MethodA non-homogenous Poisson stochastic process model was used to describe the dynamics of non-cohabiting sex. The model was applied to 25 countries in SSA and was fitted to Demographic and Health Survey data. The country-specific mean values and variances of the distributions of number of non-cohabiting partners were estimated.ResultsThe model yielded overall robust fits to the empirical distributions stratified by marital status and sex. The median across all country-specific mean values was highest for unmarried men at 0.574 non-cohabiting partners over the last 12 months, followed by that of unmarried women at 0.337, married men at 0.192 and married women at 0.038. The median of variances was highest for unmarried men at 0.127, followed by married men at 0.057, unmarried women at 0.003 and married women at 0.000. The largest variability in mean values across countries was for unmarried men (0.103-1.206), and the largest variability in variances was among unmarried women (0.000-1.994).ConclusionsNon-cohabiting sex appears to be a random 'opportunistic' phenomenon linked to situations that may facilitate it. The mean values and variances of number of partners in SSA show wide variation by country, marital status and sex. Unmarried individuals have larger mean values than their married counterparts, and men have larger mean values than women. Unmarried individuals appear to play a disproportionate role in driving heterogeneity in sexual networks and possibly epidemiology of sexually transmitted infections.
| S-EPMC4552955 | biostudies-literature
Project description:BackgroundThe proportion of heterosexual HIV transmission in sub-Saharan Africa that occurs within cohabiting partnerships, compared with that in single people or extra-couple relationships, is widely debated. We estimated the proportional contribution of different routes of transmission to new HIV infections. As plans to use antiretroviral drugs as a strategy for population-level prevention progress, understanding the importance of different transmission routes is crucial to target intervention efforts.MethodsWe built a mechanistic model of HIV transmission with data from Demographic and Health Surveys (DHS) for 2003-2011, of 27,201 cohabiting couples (men aged 15-59 years and women aged 15-49 years) from 18 sub-Saharan African countries with information about relationship duration, age at sexual debut, and HIV serostatus. We combined this model with estimates of HIV survival times and country-specific estimates of HIV prevalence and coverage of antiretroviral therapy (ART). We then estimated the proportion of recorded infections in surveyed cohabiting couples that occurred before couple formation, between couple members, and because of extra-couple intercourse.FindingsIn surveyed couples, we estimated that extra-couple transmission accounted for 27-61% of all HIV infections in men and 21-51% of all those in women, with ranges showing intercountry variation. We estimated that in 2011, extra-couple transmission accounted for 32-65% of new incident HIV infections in men in cohabiting couples, and 10-47% of new infections in women in such couples. Our findings suggest that transmission within couples occurs largely from men to women; however, the latter sex have a very high-risk period before couple formation.InterpretationBecause of the large contribution of extra-couple transmission to new HIV infections, interventions for HIV prevention should target the general sexually active population and not only serodiscordant couples.FundingUS National Institutes of Health, US National Science Foundation, and J S McDonnell Foundation.
| S-EPMC3703831 | biostudies-literature
Project description:To summarize recent developments for HIV-associated malignancies (HIVAM) in low-income and middle-income countries (LMIC) with particular focus on sub-Saharan Africa (SSA).Antiretroviral therapy (ART) scale-up is leading to epidemiologic transitions in LMIC similar to high-income countries, with aging and growth of HIV-infected populations, declining infectious deaths, increasing cancer deaths, and transitions from AIDS-defining cancers to non-AIDS defining cancers. Despite ART scale-up, the HIVAM burden remains high including an enormous AIDS-defining cancers burden in SSA. For Kaposi sarcoma, patients treated with ART and chemotherapy can experience good outcomes even in rural SSA, but Kaposi sarcoma heterogeneity remains insufficiently understood including virologic, immunologic, and inflammatory features that may be unique to LMIC. For cervical cancer, scale-up of prevention efforts including vaccination and screening is underway, with benefits already apparent despite continuing high disease burden. For non-Hodgkin lymphoma, curative treatment is possible in the ART era even in SSA, and multifaceted approaches can improve outcomes further. For many other prevalent HIVAM, care and research efforts are being established to guide treatment and prevention specifically in LMIC.Sustained investment for HIVAM in LMIC can help catalyze a cancer care and research agenda that benefits HIV-positive and HIV-negative patients worldwide.
| S-EPMC5241291 | biostudies-other
Project description:Konzo, a disease characterized by sudden, irreversible spastic paraparesis, affecting up to 10% of the population in some regions of Sub-Saharan Africa during outbreaks and is strongly associated with dietary exposure to cyanogenic bitter cassava. The molecular mechanisms underlying the development of konzo, remain largely unknown. Here, through an analysis of 16 individuals with konzo and matched healthy controls from the same outbreak zones, we identified 117 differentially methylated loci involved in numerous biological processes that may identify cyanogenic- sensitive regions of the genome, providing the first study of epigenomic alterations associated with sub-lethal cyanide exposure and a clinical phenotype.
2022-12-31 | GSE180119 | GEO
Project description:BackgroundIn 2015 around 15 million people living with HIV were receiving antiretroviral treatment (ART) in sub-Saharan Africa. Sustained provision of ART, though both prudent and necessary, creates substantial long-term fiscal obligations for countries affected by HIV/AIDS. As donor assistance for health remains constrained, novel financing mechanisms are needed to augment funding domestic sources. We explore how Innovative Financing has been used to co-finance domestic HIV/AIDS responses. Based on analysis of non-health sectors, we identify innovative financing instruments that could be used in the HIV response.MethodsWe undertook a systematic review to identify innovative financing instruments used for (1) domestic HIV/AIDS financing in sub-Saharan Africa (2) international health financing and (3) financing in non-health sectors. We analyzed peer-reviewed and grey literature published between 2002 and 2014. We examined the nature and volume of funds mobilized with innovative financing, then in consultation with leading experts, identified instruments that held potential for financing the HIV response.ResultsOur analysis revealed three innovative financing instruments in use: Zimbabwe's AIDS Trust Fund (a tax/levy-based instrument), Botswana's National HIV/AIDS Prevention Support (BNAPS) International Bank for Reconstruction and Development (IBRD) Buy-Down (a debt conversion instrument), and Côte d'Ivoire's Debt2Health Debt Swap Agreement (a debt conversion instrument). Zimbabwe's AIDS Trust Fund generated US$ 52.7 million between 2008 and 2011, Botswana's IBRD Buy-Down generated US$ 20 million, and Côte d'Ivoire's Debt2Health Debt Swap Agreement generated US$ 27 million, at least half of which was to be invested in HIV/AIDS programs. Four additional categories of innovative financing instruments met our criteria for future use: (1) remittances and diaspora bonds (2) social and development impact bonds (3) sovereign wealth funds (4) risk and credit guarantees.ConclusionA limited number of innovative financing instruments contributed a very modest share of funding toward domestic HIV/AIDS programs. Several innovative financing instruments successfully applied in other sectors could be used to augment domestic financing toward HIV/AIDS programmes.
| S-EPMC4871060 | biostudies-literature
Project description:Given the dual epidemics of HIV and tuberculosis in sub-Saharan Africa and evidence suggesting a disproportionate burden of these diseases among detainees in the region, we aimed to investigate the epidemiology of HIV and tuberculosis in prison populations, describe services available and challenges to service delivery, and identify priority areas for programmatically relevant research in sub-Saharan African prisons. To this end, we reviewed literature on HIV and tuberculosis in sub-Saharan African prisons published between 2011 and 2015, and identified data from only 24 of the 49 countries in the region. Where data were available, they were frequently of poor quality and rarely nationally representative. Prevalence of HIV infection ranged from 2·3% to 34·9%, and of tuberculosis from 0·4 to 16·3%; detainees nearly always had a higher prevalence of both diseases than did the non-incarcerated population in the same country. We identified barriers to prevention, treatment, and care services in published work and through five case studies of prison health policies and services in Zambia, South Africa, Malawi, Nigeria, and Benin. These barriers included severe financial and human-resource limitations and fragmented referral systems that prevent continuity of care when detainees cycle into and out of prison, or move between prisons. These challenges are set against the backdrop of weak health and criminal-justice systems, high rates of pre-trial detention, and overcrowding. A few examples of promising practices exist, including routine voluntary testing for HIV and screening for tuberculosis upon entry to South African and the largest Zambian prisons, reforms to pre-trial detention in South Africa, integration of mental health services into a health package in selected Malawian prisons, and task sharing to include detainees in care provision through peer-educator programmes in Rwanda, Zimbabwe, Zambia, and South Africa. However, substantial additional investments are required throughout sub-Saharan Africa to develop country-level policy guidance, build human-resource capacity, and strengthen prison health systems to ensure universal access to HIV and tuberculsosis prevention, treatment, and care of a standard that meets international goals and human rights obligations.
| S-EPMC6182190 | biostudies-literature