Mapping of HIV-1C Transmission Networks Reveals Extensive Spread of Viral Lineages Across Villages in Botswana Treatment-as-Prevention Trial

Evidence from HIV sequencing for blood-borne transmission in Africa

Background

The consensus view that heterosexual transmission dominates human immunodeficiency viruses (HIV) epidemics in sub-Saharan Africa survives side-by-side with surveys and studies reporting infections in children with HIV-negative mothers, in virgins, and in adolescents and adults who claim no possible sexual exposure to HIV.

Aim

In this scoping review, we aim to show what phylogenetic analyses of HIV sequences say about the possible contribution of blood-borne transmission to HIV epidemics.

Setting

The focus was on sub-Saharan Africa.

Method

The authors conducted a search on PubMed and other platforms for studies reporting phylogenetic analyses of HIV in blood samples collected from at least 100 infected adults through community-based surveys in sub-Saharan Africa. They focussed on identifying information pertinent to assessing blood-borne transmission.

Results

Sixteen reports met the search criteria and provided information to assess blood-borne transmission. In five studies, similar HIV sequences from (reported or assumed) household couples identified a likely heterosexual source for 0.3% - 7.5% of community adults with sequenced HIV. In 10 studies, a median of 43% of sequence pairs linked two people of the same sex. Two studies report clusters of recent infections too large to be easily explained by sexual transmission.

Conclusion

Evidence from sequencing agrees with much other evidence that blood-borne HIV transmission is not rare in sub-Saharan Africa. Evidence also allows that blood-borne transmission could be making a major contribution to Africa's HIV epidemics.

Contribution

Evidence of harm is sufficient to stimulate discussions about what more could be done to address this continuing problem.

Pretreatment HIV-1 Drug Resistance Among Newly Diagnosed People in Eastern Ethiopia

Background and Aims

In Ethiopia, HIV-1 pretreatment drug resistance (PDR) data are limited owing to a lack of routine genotyping resistance tests. This study aimed to determine the prevalence of HIV-1 PDR mutations and genetic diversity among newly diagnosed people with HIV in eastern Ethiopia.

Methods

HIV RNA was extracted using Abbott m2000sp. HIV-1 partial pol genes were amplified and sequenced using the Sanger dideoxy method. DRM profiles were examined and interpreted according to the calibrated population resistance (CPR) and Stanford University HIV drug resistance algorithms. A maximum likelihood phylogenetic tree was constructed using PhyML version 3.0 and visualized using the iTOL tool. Bivariable and multivariable logistic regression models were used to identify baseline factors associated with outcomes at a p value of < 0.05.

Results

Among newly diagnosed individuals with baseline viral load (≥ 1000 copies/mL) and amplifications were successful, the genotyping success rate was 78.4%. Among the isolates successfully sequenced, three HIV-1 strains were detected, of which 97.1% had HIV-1 subtype C, 1.4% A1C, and 1.4% CF1 recombinant. According to the Stanford HIVDR algorithm, 21.7% of people had at least one drug associated PDR mutation, whereas CPR reported 14.5% DRMs. NNRTIs had the highest PDR mutation rate (13.0%), followed by NRTIs (7.2%) and PIs (2.9%). The most commonly observed major DRMs were: NNRTIs (K103N and G190A), NRTIs (D67G and L210W), and PIs (L90M and I54S). Patients who were bedridden at enrollment were more likely to harbor PDR mutations (AOR: 5.4; 95% CI: 1.53-30.7).

Conclusions

High PDR levels, predominantly for NNRTIs, are observed. During clinical follow-up, special attention should be given to bedridden functional status patients. Further surveillance studies are needed to evaluate the long-term effects of prolonged accumulation of resistance and its transmission on current ART regimens and to design appropriate interventions to halt the HIV epidemic.

Low prevalence of archived integrase strand transfer inhibitors resistance associated mutations in Botswana before the roll out of dolutegravir based first line antiretroviral therapy

Background

We evaluated the prevalence of archived proviral drug resistance mutations (DRMs) associated with resistance to integrase strand transfer inhibitors (INSTIs) shortly before Botswana transitioned in 2016 to using dolutegravir (DTG)-based antiretroviral treatment in first-line regimens.

Methods

We used the Stanford University HIV drug resistance database to analyze INSTI-resistance associated mutations (RAMs) in a large representative population-based cohort of adults recruited in 30 geographically dispersed communities as part of the Botswana Combination Prevention Project (BCPP) cohort from 2013 to 2018. A total of 5,144 HIV-1 proviral DNA sequences were included in our analysis; 1,281 sequences were from antiretroviral therapy (ART)-naïve individuals and 3,863 sequences were from non-nucleoside reverse transcriptase inhibitor (NNRTI) ART-experienced individuals. None of the sequences were from DTG-ART experienced participants.

Results

The overall prevalence of major INSTIs DRMs was 1.11% (95% CI 0.82-1.39%). The prevalence of INSTI DRMs in ART-naïve individuals was 1.64% (21/1,281) and 0.93% (36/3,863) in ART-experienced individuals. Major INSTI-RAMs detected in ART-naïve individuals were E138K (2/1,281; 0.16%), G140R (8/1,281;0.62%), E92G (2/1,281;0.16%), R263K (5/1,281; 0.4%), N155H (1/1,281; 0.08%), P145S (1/1,281;0.008%). Among the ART-experienced individuals, major INSTI RAMs detected were E138K (4/3,863; 0.10%), G140R (25/3,863;0.65%), G118R (2/3,863, 0.05%), R263K (4/3,863, 0.10%), T66I (1/3,863;0.03%), E138K + G140R (1/3,863, 0.03%|), G140R + R263K (1/3,863, 0.03%). High-level resistance to cabotegravir (CAB), elvitegravir (EVG), and raltegravir (RAL) was detected in 0.70, 0.16 and 0.06% of the individuals, respectively. Notably, bictegravir (BIC) and dolutegravir (DTG) showed no high-level resistance.

Conclusion

The overall prevalence of archived INSTI RAMs in Botswana was low prior to transitioning to first-line DTG-based ART regimens, and did not differ between ART-naïve and ART-experienced individuals. Ongoing surveillance of INSTI DRMs in Botswana will allow for re-assessment of INSTI resistance risk following nationwide DTG rollout.

Phylodynamic Structure in the Botswana HIV Epidemic

Background

Studying viral sequences can provide insights into the structure of host contact networks through which the virus is transmitted. Uncovering the population structure of the HIV-1 epidemic in Botswana will help optimise public health interventions and may identify hidden sub-epidemics. We sought to determine the phylodynamic structure of the Botswana HIV-1 epidemic from viral sequence genetic data.

Methods

The Botswana Combination Prevention Project (BCPP) randomly sampled 20% of households in 30 villages in Botswana between 2013-2018 and tested for HIV-1. Extensive demographic data were collected from all participants and next-generation full-genome HIV-1 sequences were generated from HIV-1 positive participants (n = 4,164), 78% of whom were on antiretroviral treatment (ART). We inferred the stage of infection (< or > 1 year) among HIV-1 cases based on nucleotide diversity and clinical data using a previously trained machine learning model. We then reconstructed time-resolved gag and pol phylogenies from sequences, other Botswana cohorts and publicly available sequences that were genetically close to those from Botswana. We statistically explored phylogenies for partitions with diverging patterns of coalescence, indicating sub-epidemics, and estimated viral effective population size through time, a measure of viral incidence, for each partition. Finally, we compared the demographic makeup, clinical and geographic characteristics across partitions using χ2, ANOVA tests and Tukey analysis.

Results

We identified three partitions of time-resolved gag and pol phylogenies, revealing divergent patterns of coalescence and HIV-1 transmission. In both gag and pol phylogenies, partitions with persistent growth and transmission were characterised by lower treatment coverage and more recent infections when compared to other partitions. The Southern and South East regions of Botswana were over-represented in the fast-growing partitions.

Conclusion

Our findings suggest that transmission is slowing in segments of the population that have high ART coverage. However, recent infections are over-represented in ongoing sub-epidemics. The phylodynamic structure suggests that there are districts with higher growth and prioritising these in the deployment of public health interventions might curb new infections. Nonetheless the high mobility of Botswana residents should be taken into consideration in implementing effective interventions to combat HIV-1.

Fostemsavir resistance-associated polymorphisms in HIV-1 subtype C in a large cohort of treatment-naïve and treatment-experienced individuals in Botswana

IMPORTANCE

Fostemsavir (FTR) is a newly licensed antiretroviral drug that has been shown to have activity against HIV-1. The mechanism of action of FTR is different from all currently available antiretrovirals (ARVs), and as such, it offers hope for HIV-1 suppression in those people with HIV (PWH) who harbor HIV-1 variants with drug resistance mutations to currently used ARVs. Using 6,030 HIV-1 sequences covering the HIV-1 envelope from PWH in Botswana who are antiretroviral therapy (ART) naïve as well as those who are failing ART, we explored the sequences for FTR resistance-associated polymorphisms. We found the prevalence of FTR polymorphisms to be similar in both ART-naïve and ART-experienced individuals with VF in this setting, with no prior FTR exposure. Further studies on the phenotypic impact of these polymorphisms are warranted to guide how to monitor for FTR resistance.

Longitudinal population-level HIV epidemiologic and genomic surveillance highlights growing gender disparity of HIV transmission in Uganda

HIV incidence in eastern and southern Africa has historically been concentrated among girls and women aged 15-24 years. As new cases decline with HIV interventions, population-level infection dynamics may shift by age and gender. Here, we integrated population-based surveillance of 38,749 participants in the Rakai Community Cohort Study and longitudinal deep sequence viral phylogenetics to assess how HIV incidence and population groups driving transmission have changed from 2003 to 2018 in Uganda. We observed 1,117 individuals in the incidence cohort and 1,978 individuals in the transmission cohort. HIV viral suppression increased more rapidly in women than men, however incidence declined more slowly in women than men. We found that age-specific transmission flows shifted, while HIV transmission to girls and women (aged 15-24 years) from older men declined by about one third, transmission to women (aged 25-34 years) from men that were 0-6 years older increased by half in 2003 to 2018. Based on changes in transmission flows, we estimated that closing the gender gap in viral suppression could have reduced HIV incidence in women by half in 2018. This study suggests that HIV programs to increase HIV suppression in men are critical to reduce incidence in women, close gender gaps in infection burden and improve men's health in Africa.

The role of migration networks in the development of Botswana's generalized HIV epidemic

The majority of people with HIV live in sub-Saharan Africa, where epidemics are generalized. For these epidemics to develop, populations need to be mobile. However, the role of population-level mobility in the development of generalized HIV epidemics has not been studied. Here we do so by studying historical migration data from Botswana, which has one of the most severe generalized HIV epidemics worldwide; HIV prevalence was 21% in 2021. The country reported its first AIDS case in 1985 when it began to rapidly urbanize. We hypothesize that, during the development of Botswana's epidemic, the population was extremely mobile and the country was highly connected by substantial migratory flows. We test this mobility hypothesis by conducting a network analysis using a historical time series (1981-2011) of micro-census data from Botswana. Our results support our hypothesis. We found complex migration networks with very high rates of rural-to-urban, and urban-to-rural, migration: 10% of the population moved annually. Mining towns (where AIDS cases were first reported, and risk behavior was high) were important in-flow and out-flow migration hubs, suggesting that they functioned as 'core groups' for HIV transmission and dissemination. Migration networks could have dispersed HIV throughout Botswana and generated the current hyperendemic epidemic.

Population mobility and the development of Botswana's generalized HIV epidemic: a network analysis

The majority of people with HIV live in sub-Saharan Africa, where HIV epidemics are generalized. For these epidemics to develop, populations need to be mobile. However, population-level mobility has not yet been studied in the context of the development of generalized HIV epidemics. Here we do so by studying historical migration data from Botswana which has one of the most severe generalized HIV epidemics worldwide; in 2021, HIV prevalence was 21%. The country reported its first AIDS case in 1985 when it began to rapidly urbanize. We hypothesize that, during the development of Botswana's epidemic, the population was highly mobile and there were substantial urban-to-rural and rural-to-urban migratory flows. We test this hypothesis by conducting a network analysis using a historical time series (1981 to 2011) of micro-census data from Botswana. We found 10% of the population moved their residency annually, complex migration networks connected urban with rural areas, and there were very high rates of rural-to-urban migration. Notably, we also found mining towns were both important in-flow and out-flow migration hubs; consequently, there was a very high turnover of residents in towns. Our results support our hypothesis, and together, provide one explanation for the development of Botswana's generalized epidemic.

HIV Incidence in Botswana Rural Communities With High Antiretroviral Treatment Coverage: Results From the Botswana Combination Prevention Project, 2013-2017

BACKGROUND AND SETTING

The Botswana Combination Prevention Project demonstrated a 30% reduction in community HIV incidence through expanded HIV testing, enhanced linkage to care, and universal antiretroviral treatment and exceeded the Joint United Nations Programme on HIV/AIDS 90-90-90 targets. We report rates and characteristics of incident HIV infections.

METHODS

The Botswana Combination Prevention Project was a community-randomized controlled trial conducted in 30 rural/periurban Botswana communities from 2013 to 2017. Home-based and mobile HIV-testing campaigns were conducted in 15 intervention communities, with 39% of participants testing at least twice. We assessed the HIV incidence rate [IR; number of new HIV infections per 100 person-years (py) at risk] among repeat testers and risk factors with a Cox proportional hazards regression model.

RESULTS

During 27,517 py, 195 (women: 79%) of 18,597 became HIV-infected (0.71/100 py). Women had a higher IR (1.01/100 py; 95% confidence interval: 0.99 to 1.02) than men (0.34/100 py; 95% confidence interval: 0.33 to 0.35). The highest IRs were among women aged 16-24 years (1.87/100 py) and men aged 25-34 years (0.56/100 py). The lowest IRs were among those aged 35-64 years (women: 0.41/100 py; men: 0.20/100 py). The hazard of incident infection was the highest among women aged 16-24 years (hazard ratio = 7.05). Sex and age were significantly associated with incidence (both P < 0.0001).

CONCLUSIONS

Despite an overall reduction in HIV incidence and approaching the United Nations Programme on HIV/AIDS 95-95-95 targets, high HIV incidence was observed in adolescent girls and young women. These findings highlight the need for additional prevention services (pre-exposure prophylaxis and DREAMS) to achieve epidemic control in this subpopulation and increased efforts with men with undiagnosed HIV.

Detection of HIV-1 Transmission Clusters from Dried Blood Spots within a Universal Test-and-Treat Trial in East Africa

The Sustainable East Africa Research in Community Health (SEARCH) trial was a universal test-and-treat (UTT) trial in rural Uganda and Kenya, aiming to lower regional HIV-1 incidence. Here, we quantify breakthrough HIV-1 transmissions occurring during the trial from population-based, dried blood spot samples. Between 2013 and 2017, we obtained 549 gag and 488 pol HIV-1 consensus sequences from 745 participants: 469 participants infected prior to trial commencement and 276 SEARCH-incident infections. Putative transmission clusters, with a 1.5% pairwise genetic distance threshold, were inferred from maximum likelihood phylogenies; clusters arising after the start of SEARCH were identified with Bayesian time-calibrated phylogenies. Our phylodynamic approach identified nine clusters arising after the SEARCH start date: eight pairs and one triplet, representing mostly opposite-gender linked (6/9), within-community transmissions (7/9). Two clusters contained individuals with non-nucleoside reverse transcriptase inhibitor (NNRTI) resistance, both linked to intervention communities. The identification of SEARCH-incident, within-community transmissions reveals the role of unsuppressed individuals in sustaining the epidemic in both arms of a UTT trial setting. The presence of transmitted NNRTI resistance, implying treatment failure to the efavirenz-based antiretroviral therapy (ART) used during SEARCH, highlights the need to improve delivery and adherence to up-to-date ART recommendations, to halt HIV-1 transmission.

The Role of Phylogenetics in Discerning HIV-1 Mixing among Vulnerable Populations and Geographic Regions in Sub-Saharan Africa: A Systematic Review

To reduce global HIV-1 incidence, there is a need to understand and disentangle HIV-1 transmission dynamics and to determine the geographic areas and populations that act as hubs or drivers of HIV-1 spread. In Sub-Saharan Africa (sSA), the region with the highest HIV-1 burden, information about such transmission dynamics is sparse. Phylogenetic inference is a powerful method for the study of HIV-1 transmission networks and source attribution. In this review, we assessed available phylogenetic data on mixing between HIV-1 hotspots (geographic areas and populations with high HIV-1 incidence and prevalence) and areas or populations with lower HIV-1 burden in sSA. We searched PubMed and identified and reviewed 64 studies on HIV-1 transmission dynamics within and between risk groups and geographic locations in sSA (published 1995-2021). We describe HIV-1 transmission from both a geographic and a risk group perspective in sSA. Finally, we discuss the challenges facing phylogenetic inference in mixed epidemics in sSA and offer our perspectives and potential solutions to the identified challenges.

Using mobile phone data to reveal risk flow networks underlying the HIV epidemic in Namibia

Twenty-six million people are living with HIV in sub-Saharan Africa; epidemics are widely dispersed, due to high levels of mobility. However, global elimination strategies do not consider mobility. We use Call Detail Records from 9 billion calls/texts to model mobility in Namibia; we quantify the epidemic-level impact by using a mathematical framework based on spatial networks. We find complex networks of risk flows dispersed risk countrywide: increasing the risk of acquiring HIV in some areas, decreasing it in others. Overall, 40% of risk was mobility-driven. Networks contained multiple risk hubs. All constituencies (administrative units) imported and exported risk, to varying degrees. A few exported very high levels of risk: their residents infected many residents of other constituencies. Notably, prevalence in the constituency exporting the most risk was below average. Large-scale networks of mobility-driven risk flows underlie generalized HIV epidemics in sub-Saharan Africa. In order to eliminate HIV, it is likely to become increasingly important to implement innovative control strategies that focus on disrupting risk flows.

HIV incidence after pre-exposure prophylaxis initiation among women and men at elevated HIV risk: A population-based study in rural Kenya and Uganda

BACKGROUND

Oral pre-exposure prophylaxis (PrEP) is highly effective for HIV prevention, but data are limited on HIV incidence among PrEP users in generalized epidemic settings, particularly outside of selected risk groups. We performed a population-based PrEP study in rural Kenya and Uganda and sought to evaluate both changes in HIV incidence and clinical and virologic outcomes following seroconversion on PrEP.

METHODS AND FINDINGS

During population-level HIV testing of individuals ≥15 years in 16 communities in the Sustainable East Africa Research in Community Health (SEARCH) study (NCT01864603), we offered universal access to PrEP with enhanced counseling for persons at elevated HIV risk (based on serodifferent partnership, machine learning-based risk score, or self-identified HIV risk). We offered rapid or same-day PrEP initiation and flexible service delivery with follow-up visits at facilities or community-based sites at 4, 12, and every 12 weeks up to week 144. Among participants with incident HIV infection after PrEP initiation, we offered same-day antiretroviral therapy (ART) initiation and analyzed HIV RNA, tenofovir hair concentrations, drug resistance, and viral suppression (<1,000 c/ml based on available assays) after ART start. Using Poisson regression with cluster-robust standard errors, we compared HIV incidence among PrEP initiators to incidence among propensity score-matched recent historical controls (from the year before PrEP availability) in 8 of the 16 communities, adjusted for risk group. Among 74,541 individuals who tested negative for HIV, 15,632/74,541 (21%) were assessed to be at elevated HIV risk; 5,447/15,632 (35%) initiated PrEP (49% female; 29% 15-24 years; 19% in serodifferent partnerships), of whom 79% engaged in ≥1 follow-up visit and 61% self-reported PrEP adherence at ≥1 visit. Over 7,150 person-years of follow-up, HIV incidence was 0.35 per 100 person-years (95% confidence interval [CI] 0.22-0.49) among PrEP initiators. Among matched controls, HIV incidence was 0.92 per 100 person-years (95% CI 0.49-1.41), corresponding to 74% lower incidence among PrEP initiators compared to matched controls (adjusted incidence rate ratio [aIRR] 0.26, 95% CI 0.09-0.75; p = 0.013). Among women, HIV incidence was 76% lower among PrEP initiators versus matched controls (aIRR 0.24, 95% CI 0.07-0.79; p = 0.019); among men, HIV incidence was 40% lower, but not significantly so (aIRR 0.60, 95% CI 0.12-3.05; p = 0.54). Of 25 participants with incident HIV infection (68% women), 7/25 (28%) reported taking PrEP ≤30 days before HIV diagnosis, and 24/25 (96%) started ART. Of those with repeat HIV RNA after ART start, 18/19 (95%) had <1,000 c/ml. One participant with viral non-suppression was found to have transmitted viral resistance, as well as emtricitabine resistance possibly related to PrEP use. Limitations include the lack of contemporaneous controls to assess HIV incidence without PrEP and that plasma samples were not archived to assess for baseline acute infection.

CONCLUSIONS

Population-level offer of PrEP with rapid start and flexible service delivery was associated with 74% lower HIV incidence among PrEP initiators compared to matched recent controls prior to PrEP availability. HIV infections were significantly lower among women who started PrEP. Universal HIV testing with linkage to treatment and prevention, including PrEP, is a promising approach to accelerate reductions in new infections in generalized epidemic settings.

TRIAL REGISTRATION

ClinicalTrials.gov NCT01864603.