Rates of HIV-1 virological suppression and patterns of acquired drug resistance among fisherfolk on first-line antiretroviral therapy in Uganda

CRF08_BC subtype is more prone to ART failure and new-generation NNRTI-resistance under long-term first-line ART

OBJECTIVE

To investigate the characteristics of drug resistance mutations (DRMs) and their contextual influence on drug susceptibility in CRF07_BC and CRF_08BC subtypes.

METHODS

Patients with virological failure were genotyped using phylogenetic analysis. DRMs and susceptibility to antiretroviral drugs were analysed using the Stanford University HIV Drug Resistance Database.

RESULTS

Six HIV subtypes were identified among 1296 successfully amplified sequences, with the CRF07_BC subtype prevailing at a rate of 91.7%, followed by CRF08_BC. Overall, the CRF07_BC and CRF08_BC subtypes were similar in the distribution and frequency of DRMs, the most common DRMs were K103N and M184V. However, among patients with antiretroviral therapy duration of ≥3 y who developed resistance, CRF08_BC exhibited a higher mutation frequency at sites 184, 138, 221, and 188 (Chi-square test, P < 0.05), and compared with CRF07_BC, patients with CRF08_BC had higher prevalence of abacavir, emtricitabine, lamivudine, doravirine, etravirine, and rilpivirine resistance. Moreover, there was an increased prevalence of cross-resistance between efavirenz/nevirapine and new-generation NNRTIs in patients with CRF08_BC; doravirine (r = 1.0), rilpivirine (r = 0.93), and etravirine (r = 0.86) resistance highly correlated with efavirenz/nevirapine.

CONCLUSIONS

The present study provides valuable insights into the profile of DRMs and resistance patterns in patients with CRF07_BC and CRF08_BC experiencing treatment failure in Butuo. These findings have the potential to contribute to future strategies for HIV control and treatment.

HIV protease resistance mutations in patients receiving second-line antiretroviral therapy in Libreville, Gabon

INTRODUCTION

In 2022, the WHO reported that 29.8 million people around the world were living with HIV (PLHIV) and receiving antiretroviral treatment (ART), including 25‌ 375 people in Gabon (54% of all those living with HIV in the country). The literature reports a frequency of therapeutic failure with first-line antiretrovirals (ARVs) of between 20% and 82%. Unfortunately, data relating to the failure of second-line ARVs are scarce in Gabon. This study aims to determine the profiles of HIV drug resistance mutations related to protease inhibitors in Gabon.

METHODOLOGY

Plasma from 84 PLHIV receiving ARVs was collected from 2019 to 2021, followed by RNA extraction, amplification, and sequencing of the protease gene. ARV resistance profiles were generated using the Stanford interpretation algorithm version 8.9-1 ( https://hivdb.stanford.edu ) and statistical analyses were performed using EpiInfo software version 7.2.1.0 (CDC, USA).

RESULTS

Of 84 HIV plasma samples collected from 45 men and 39 women, 342 mutations were detected. Of these, 43.3% (148/342) were associated with nucleoside reverse transcriptase inhibitors (NRTIs), 30.4% (104/342) with non-nucleoside reverse transcriptase inhibitors (NNRTIs), and 26.3% (90/342) with protease inhibitors (PIs). Most NRTI mutations were associated with thymidine analogues (TAMs) (50.7%; 75/148), including T215F/V (14.9%; 22/148), D67DN/E/G/N/T (10.1%; 15/148), M41L (9.5%; 14/148), and K70E/KN/S/R (9.5%; 14/148). Resistance mutations related to non-TAM NRTIs (33.1%; 49/148) were M184V (29.1%; 43/148), and L74I/V (8.1%; 12/148). NNRTI mutations were predominantly K103N/S (32.7%; 34/104), V108I (10.6%; 11/104), A98G (10.6%; 11/104), and P225H (9.6%; 10/104). Minor mutations associated with PIs (60.0%; 54/90) were predominantly K20I (15.6%; 14/90) and L10F/I/V (14.5%; 13/90). The major mutations associated with PIs (40.0%; 36/90) were M41L (12.2%; 11/90), I84V (6.7%; 06/90), and V82A (6.7%; 06/90). The four most prescribed therapeutic regimens were TDF + 3TC + LPV/r (20.3%; 17/84), ABC + DDI + LPV/r (17.9%; 15/84), TDF + FTC + LPV/r (11.9%; 10/84), and ABC + 3TC + LPV/r (11.9%; 10/84).

CONCLUSION

This study revealed that HIV drug resistance mutations are common in Gabon. The major mutations associated with PIs were M41L, I84V, and V82A. There is a need for access to new NRTIs, NNRTIs, and PIs for a better therapeutic management of PLHIV in Gabon.

Virological non-suppression among adult males attending HIV care services in the fishing communities in Bulisa district, Uganda

BACKGROUND

Virological non-suppression is a critical factor in driving HIV transmission rates, yet there is limited data available on the determinants of this phenomenon, particularly in fishing communities where the incidence of HIV is disproportionately high. We aimed to determine the prevalence and determinants of virological non-suppression among adult males (≥15 years) attending HIV care services in the fishing communities of Bulisa district.

METHODS

We conducted a cross-sectional study among all adult males (≥15 years) living with HIV who were resident within the fishing communities, and in care for atleast 6 months at the six health facilities offering HIV services in the fishing communities in Bulisa district. To obtain data on patient and health facility characteristics, we reviewed patients' records and conducted face-to-face interviews with the participants. We conducted descriptive and regression analyses using modified Poisson regression, accounting for data correlation of observation at the facility level to obtain prevalence ratios (PR) with 95% confidence intervals in Stata version 14.0.

RESULTS

413 participants were studied and 379 (91.8%) were interviewed. The participant's average age (SD) was 40 (10.7) years and 70.5% (267/379) were engaged in the fishing business. The prevalence of virological non-suppression was 88/413-21.3% (95% CI: 18%-26%). Factors associated with higher odds of virological non-suppression included: Age 26-50 years (adj.PR = 1.53, 95%CI: 1.11-2.08) and 15-25 years (adj.PR = 2.99, 95%CI: 1.27-7.05) compared to age above 50 years; unemployment (adj.PR = 1.28, 95%CI: 1.10-1.49); hazardous use of alcohol (adj.PR = 1.34, 95%CI: 1.10-1.62); non-mobility between fish landing sites (adj.PR = 1.37, 95%CI: 1.003-1.87); distant HIV treatment services (adj.PR = 1.37, 95%CI: 1.11-1.69) and TB diagnosis (adj.PR = 1.87, 95%CI: 1.33-2.64).

CONCLUSION

Virological non-suppression among people living with HIV in fishing communities along the shores of Lake Albert is alarmingly high, exceeding the UNAIDS threshold of 10% by two-fold. Several key determinants were identified, including hazardous alcohol use, unemployment, and access barriers to HIV treatment services.

Development and validation of a scoring system for the prediction of HIV drug resistance in Hubei province, China

Objective

The present study aimed to build and validate a new nomogram-based scoring system for the prediction of HIV drug resistance (HIVDR).

Design and methods

Totally 618 patients with HIV/AIDS were included. The predictive model was created using a retrospective set (N = 427) and internally validated with the remaining cases (N = 191). Multivariable logistic regression analysis was carried out to fit a model using candidate variables selected by Least absolute shrinkage and selection operator (LASSO) regression. The predictive model was first presented as a nomogram, then transformed into a simple and convenient scoring system and tested in the internal validation set.

Results

The developed scoring system consisted of age (2 points), duration of ART (5 points), treatment adherence (4 points), CD4 T cells (1 point) and HIV viral load (1 point). With a cutoff value of 7.5 points, the AUC, sensitivity, specificity, PLR and NLR values were 0.812, 82.13%, 64.55%, 2.32 and 0.28, respectively, in the training set. The novel scoring system exhibited a favorable diagnostic performance in both the training and validation sets.

Conclusion

The novel scoring system can be used for individualized prediction of HIVDR patients. It has satisfactory accuracy and good calibration, which is beneficial for clinical practice.

Virologic status and pattern of drug resistance mutation among ART-experienced HIV-infected patients in Butuo County, China

OBJECTIVES

To assess the virological outcomes, prevalence of HIV drug resistance mutation (DRM), and correlates in Butuo County.

METHODS

We conducted a cross-sectional study. Virological failure (VF) was defined as HIV-1 RNA ≥1000 copies/mL and on antiretroviral therapy (ART) for ≥6 months. Genotypic drug resistance was performed among VF cases. Correlates of DRM were identified using multivariate logistic regression.

RESULTS

The overall virological suppression rate was 85.3%; DRM was detected in 42.6% (517/1215) VF cases and 6.2% of the sample patients. A total of 90.9% of patients were infected with HIV-1 CRF07_BC subtype. The prevalence of DRM to nucleoside reverse transcriptase inhibitor (NRTI) and non-nucleoside reverse transcriptase inhibitor (NNRTI) were 46.0% and 96.9%, respectively. The most prevalent mutation for NRTI was M184V (84.5%). Lamivudine (3TC), emtricitabine (FTC), and abacavir (ABC) had the highest resistance rates. For NNRTI, K103N (60.7%), nevirapine (NVP), and efavirenz (EFV) had the highest resistance rates and cross resistance to rilpivirine (RPV), doravirine (DOR), and etravirine (ETR). Ritonavir boosted lopinavir (LPV/r) resistance rate was extremely low. The occurrence of DRM was associated with age at ART ≤18 years, baseline CD4 count ≤200 cells/mL, NVP-based regimen, and ART duration >3 years.

CONCLUSION

A relatively high proportion of VF and broad DRM for NRTI and NNRTI were observed, causing high-level resistance to first-line NRTI, NNRTI, and next generation NNRTI. Our findings necessitate the implementation of scaling up virological monitoring, adherence support, and timely switching to an LPV/r-containing regimen when patients with VF to reduce the occurrence of DRM.

HIV-1 drug resistance genotyping success rates and correlates of Dried-blood spots and plasma specimen genotyping failure in a resource-limited setting

BACKGROUND

HIV-1 drug resistance genotyping is critical to the monitoring of antiretroviral treatment. Data on HIV-1 genotyping success rates of different laboratory specimen types from multiple sources is still scarce.

METHODS

In this cross-sectional study, we determined the laboratory genotyping success rates (GSR) and assessed the correlates of genotyping failure of 6837 unpaired dried blood spot (DBS) and plasma specimens. Specimens from multiple studies in a resource-constrained setting were analysed in our laboratory between 2016 and 2019.

RESULTS

We noted an overall GSR of 65.7% and specific overall GSR for DBS and plasma of 49.8% and 85.9% respectively. The correlates of genotyping failure were viral load (VL) < 10,000 copies/mL (aOR 0.3 95% CI: 0.24-0.38; p < 0.0001), lack of viral load testing prior to genotyping (OR 0.85 95% CI: 0.77-0.94; p = 0.002), use of DBS specimens (aOR 0.10 95% CI: 0.08-0.14; p < 0.0001) and specimens from routine clinical diagnosis (aOR 1.4 95% CI: 1.10-1.75; p = 0.005).

CONCLUSIONS

We report rapidly decreasing HIV-1 genotyping success rates between 2016 and 2019 with increased use of DBS specimens for genotyping and note decreasing median viral loads over the years. We recommend improvement in DBS handling, pre-genotyping viral load testing to screen samples to enhance genotyping success and the development of more sensitive assays with well-designed primers to genotype specimens with low or undetectable viral load, especially in this era where virological suppression rates are rising due to increased antiretroviral therapy roll-out.

Men missing from the HIV care continuum in sub-Saharan Africa: a meta-analysis and meta-synthesis

Introduction

Men are missing along the HIV care continuum. However, the estimated proportions of men in sub‐Saharan Africa meeting the UNAIDS 95‐95‐95 goals vary substantially between studies. We sought to estimate proportions of men meeting each of the 95‐95‐95 goals across studies in sub‐Saharan Africa, describe heterogeneity, and summarize qualitative evidence on factors influencing care engagement.

Methods

We systematically searched PubMed and Embase for peer‐reviewed articles published between 1 January 2014 and 16 October 2020. We included studies involving men ≥15 years old, with data from 2009 onward, reporting on at least one 95‐95‐95 goal in sub‐Saharan Africa. We estimated pooled proportions of men meeting these goals using DerSimonion‐Laird random effects models, stratifying by study population (e.g. studies focusing exclusively on men who have sex with men vs. studies that did not), facility setting (healthcare vs. community site), region (eastern/southern Africa vs. western/central Africa), outcome measurement (e.g. threshold for viral load suppression), median year of data collection (before vs. during or after 2017) and quality criteria. Data from qualitative studies exploring barriers to men's HIV care engagement were summarized using meta‐synthesis.

Results and discussion

We screened 14,896 studies and included 129 studies in the meta‐analysis, compiling data over the data collection period. Forty‐seven studies reported data on knowledge of serostatus, 43 studies reported on antiretroviral therapy use and 74 studies reported on viral suppression. Approximately half of men with HIV reported not knowing their status (0.49 [95% CI, 0.41–0.58; range, 0.09–0.97]) or not being on treatment (0.58 [95% CI, 0.51–0.65; range, 0.07–0.97]), while over three‐quarters of men achieved viral suppression on treatment (0.79 [95% CI, 0.77–0.81; range, 0.39–0.97]. Heterogeneity was high, with variation in estimates across study populations, settings and outcomes. The meta‐synthesis of 40 studies identified three primary domains in which men described risks associated with engagement in HIV care: perceived social norms, health system challenges and poverty.

Conclusions

Psychosocial and systems‐level interventions that change men's perceptions of social norms, improve trust in and accessibility of the health system, and address costs of accessing care are needed to better engage men, especially in HIV testing and treatment.

Analytical Assessment of the Vela Diagnostics NGS Assay for HIV Genotyping and Resistance Testing: The Apulian Experience

Drug-resistance monitoring is one of the hardest challenges in HIV management. Next-generation sequencing (NGS) technologies speed up the detection of drug resistance, allowing the adjustment of antiretroviral therapy and enhancing the quality of life of people living with HIV. Recently, the NGS Sentosa^® SQ HIV Genotyping Assay (Vela Diagnostics) received approval for in vitro diagnostics use. This work is the first Italian evaluation of the performance of the Vela Diagnostics NGS platform, assessed with 420 HIV-1 clinical samples. A comparison with Sanger sequencing performance is also reported, highlighting the advantages and disadvantages of the Sentosa^® NGS assay. The precision of the technology was studied with reference specimens, while intra- and inter-assay reproducibility were evaluated for selected clinical samples. Vela Diagnostics’ NGS assay reached an 87% success rate through 30 runs of analysis in a real-world clinical context. The concordance with Sanger sequencing outcomes was equal to 97.2%. Several detected mismatches were due to NGS’s superior sensitivity to low-frequency variants. A high accuracy was observed in testing reference samples. Repeatability and reproducibility assays highlighted the good performance of the NGS platform. Beyond a few technical issues that call for further optimization, the key improvement will be a better balance between costs and processing speed. Once these issues have been solved, the Sentosa^® SQ HIV Genotyping Assay will be the way forward for HIV resistance testing.

Prediction-driven pooled testing methods: Application to HIV treatment monitoring in Rakai, Uganda

Chronic medical conditions often necessitate regular testing for proper treatment. Regular testing of all afflicted individuals may not be feasible due to limited resources, as is true with HIV monitoring in resource-limited settings. Pooled testing methods have been developed in order to allow regular testing for all while reducing resource burden. However, the most commonly used methods do not make use of covariate information predictive of treatment failure, which could improve performance. We propose and evaluate four prediction-driven pooled testing methods that incorporate covariate information to improve pooled testing performance. We then compare these methods in the HIV treatment management setting to current methods with respect to testing efficiency, sensitivity, and number of testing rounds using simulated data and data collected in Rakai, Uganda. Results show that the prediction-driven methods increase efficiency by up to 20% compared with current methods while maintaining equivalent sensitivity and reducing number of testing rounds by up to 70%. When predictions were incorrect, the performance of prediction-based matrix methods remained robust. The best performing method using our motivating data from Rakai was a prediction-driven hybrid method, maintaining sensitivity over 96% and efficiency over 75% in likely scenarios. If these methods perform similarly in the field, they may contribute to improving mortality and reducing transmission in resource-limited settings. Although we evaluate our proposed pooling methods in the HIV treatment setting, they can be applied to any setting that necessitates testing of a quantitative biomarker for a threshold-based decision.

HIV-1 Drug Resistance and Genetic Transmission Networks Among MSM Failing Antiretroviral Therapy in South China 2014-2019

Background

Guangdong, located in South China, is one of the areas heavily affected by HIV-1 in China. The transmission of HIV-1 among men who have sex with men (MSM) has gradually been increasing in Guangdong.

Objective

To investigate the characteristics of the HIV-1 drug resistance, and genetic transmission networks in MSM with antiretroviral therapy (ART) failure from 2014 to 2019 in Guangdong.

Methods

HIV-1 pol gene sequences were amplified. An online subtyping tool was used to determine the genotype, and a maximum likelihood phylogenetic tree was reconstructed to confirm the genotype results. The Stanford University HIV Drug Resistance Database was used to analyse the sequences of drug resistance mutations (DRMs) and drug resistance profiles. A pairwise Tamura-Nei 93 genetic distance-based method was used to analyse the genetic transmission networks.

Results

Of 393 sequences isolated from HIV-infected MSM with ART failure, CRF01_AE (47.3%), CRF07_BC (21.4%) and CRF55_01B (21.4%) were the top three strains. 55.2% individuals harboured NRTI DRMs, whereas 67.4% carried NNRTI DRMs. 96.8% cases harboured mutations resistance to NRTIs or NNRTIs at high-level. The most common DRMs were M184I/V (42.2%), followed by V179D/E (37.9%) and K65R (27.2%). Of the subtype B sequences, no sequence fell into a cluster. Of the CRF01_AE, CRF55_01B, and CRF59_01B sequences, 14.5%, 61.9%, and 33.3% fell into clusters, respectively. Of the CRF07_BC sequences, 39.3% fell into clusters. The majority of MSM in transmission networks were concentrated at age below 35 years old, with multiple links. Moreover, approximately 54.8% of MSM had more than 2 potential transmission partners.

Conclusion

Drug resistance mutations more frequently occurred in NNRTIs among MSM with ART failure in Guangdong Province. Transmission network analysis revealed a complex transmission pattern, and more attention should be given to younger HIV-1-infected MSM with multiple links.

Virological Suppression and Its Associated Factors of Dolutegravir Based Regimen in a Resource-Limited Setting: An Observational Retrospective Study in Ethiopia

Background

Toxicity, treatment failure, and resistance to existing HIV treatment regimens have become a challenge in resource-limited settings. As a result, a dolutegravir based regimen has recently been utilized. However, there is a paucity of evidence in sub-Saharan countries regarding its virological suppression. Thus, this study aimed to assess virological suppression and associated factors of dolutegravir based regimen.

Methods

A retrospective follow-up study was conducted on 349 individuals. They were selected using a systematic random sampling technique among all treatment-experienced adult HIV patients who were on a dolutegravir based regimen. From this, 81.4% of them were virologically suppressed before the initiation of dolutegravir based regimen. The study was carried out at twelve months of therapy after shifting to dolutegravir based regimen (TDF-3TC-DTG) during the period May 2018–August 2020 at Debre Markos referral hospital. Retrospective data before and after dolutegravir based regimen initiation were collected from their medical records. The time on dolutegravir based regimen was one year. Bivariable and multivariable logistic regression was used to identify factors. Variables with p <0.05 were considered statistically significant.

Results

From a total of 359, 349 participated (97.2%) in the study, and the mean age of the participants was 40.28 ±11.6 years. Totally, 192 (55.0%) of them were female. The proportion of virological suppression was 92%. Good adherence (participants who reported an intake of ≥95% of the prescribed medication) (AOR=6.2, 95% CI: 1.93, 20.11) and overall duration of ART (AOR=1.02, 95% CI: 1.01, 1.04) were associated with virological suppression.

Conclusion

Dolutegravir based regimen maintains high virological suppression. Adherence and duration of ART were associated with virological suppression. Therefore, designing effective mechanisms to maintain virological suppression is important.

Linkage to intensive adherence counselling among HIV-positive persons on ART with detectable viral load in Gomba district, rural Uganda

BACKGROUND

Antiretroviral therapy (ART) adherence is a primary determinant of sustained viral suppression, HIV transmission risk, disease progression and death. The World Health Organization recommends that adherence support interventions be provided to people on ART, but implementation is suboptimal. We evaluated linkage to intensive adherence counselling (IAC) for persons on ART with detectable viral load (VL).

METHODS

Between January and December 2017, we conducted a retrospective chart review of HIV-positive persons on ART with detectable VL (> 1000 copies/ml), in Gomba district, rural Uganda. We abstracted records from eight HIV clinics; seven health center III's (facilities which provide basic preventive and curative care and are headed by clinical officers) and a health center IV (mini-hospital headed by a medical doctor). Linkage to IAC was defined as provision of IAC to ART clients with detectable VL within three months of receipt of results at the health facility. Descriptive statistics and multivariable logistic regression analyses were used to evaluate factors associated with linkage to IAC.

RESULTS

Of 4,100 HIV-positive persons on ART for at least 6 months, 411 (10%) had detectable VL. The median age was 32 years (interquartile range [IQR] 13-43) and 52% were female. The median duration on ART was 3.2 years (IQR 1.8-4.8). A total of 311 ART clients (81%) were linked to IAC. Receipt of ART at a Health Center level IV was associated with a two-fold higher odds of IAC linkage compared with Health Center level III (adjusted odds ratio [aOR] 1.78; 95% CI 1.00-3.16; p = 0.01). Age, gender, marital status and ART duration were not related to IAC linkage.

CONCLUSIONS

Linkage to IAC was high among persons with detectable VL in rural Uganda, with greater odds of linkage at a higher-level health facility. Strategies to optimize IAC linkage at lower-level health facilities for persons with suboptimal ART adherence are needed.

The misuse of antiretrovirals to boost pig and poultry productivity in Uganda and potential implications for public health

Background and Aim: Since 2015, local newspapers reported that pig and poultry farmers in Uganda use antiretroviral drugs (ARVs) to promote growth in animals and control diseases. This study was conducted to assess farmers' knowledge, attitude and perceptions about the use of antiretroviral drugs as boosters in pigs and poultry and the possibility of detecting the antiretroviral drugs in meat using available laboratory methods. Materials and Methods: In 2019, a cross-sectional study was conducted in ten districts in Uganda. In 20 focus group discussions with 100 pig and poultry farmers and 70 animal health service providers, we assessed the use of ARV in livestock enterprises. Subsequently, samples of chicken, pigs, and animal feeds were collected from volunteer participants, and screened for residues of saquinavir, lopinavir, nevirapine, and efavirenz using liquid chromatography-tandem mass spectrophotometer. Results: Participants in all ten districts were predominantly smallholder farmers supplying the local markets. All groups reported the use of ARVs in pigs and broiler birds but not in layer hens. In the absence of good quality feeds, the motivation for feeding ARVs was rapid animal weight gain, as well as the control of animal diseases, for which farmers have no alternative solutions. ARVs were obtained within the community for free, against cash, or in-kind payment. Residues of lopinavir were detected in four, and saquinavir in seven districts, and all three sample matrices. Conclusion: Our study findings confirm anecdotal news reports on ARV use in livestock. While our findings are not generalizable to the whole country, they call for a representative follow-up. As the drugs were detected in tissues destined for human consumption, the potential risk to human health warrants further investigation.

HIV epidemic in fishing communities in Uganda: A scoping review

Background

Fishing communities in many Sub-Saharan African countries are a high-risk population group disproportionately affected by the HIV epidemic. In Uganda, literature on HIV in fishing communities has grown extensively since the first country’s documented case of HIV in a fishing community in 1985. The current study describes the status of the HIV burden, prevention, and treatment in Ugandan fishing communities.

Method

This scoping review was conducted based on the York Framework outlined by Arksey and O’Malley. We searched the PubMed, Embase, and Web of Science databases to identify relevant quantitative and qualitative studies on HIV incidence, HIV prevalence, HIV-related risk factors, HIV testing, antiretroviral therapy coverage and adherence, and interventions to improve treatment outcomes and reduce HIV risk factors.

Results & conclusion

We identified 52 papers and 2 reports. Thirty-four were quantitative, 17 qualitative, and 3 had a mixed-methods design. Eleven studies reported on the prevalence of HIV and 8 on HIV incidence; 9 studies documented factors associated with HIV incidence or HIV positive status; 10 studies reported on HIV testing coverage and/or associated factors; 7 reported on antiretroviral therapy coverage/adherence/outcomes; and 1 study reported on the impact of combination HIV interventions in fishing communities. This scoping review revealed a significant lack of evidence in terms of what works in HIV prevention and for improving adherence to ART, in contrast to the relatively large amount of evidence from observational quantitative and qualitative studies on HIV prevalence, incidence and related risk factors in Ugandan fishing communities. Intervention studies are urgently needed to fill the current evidence gaps in HIV prevention and ART adherence.

High Levels of Acquired HIV Drug Resistance Following Virological Nonsuppression in HIV-Infected Women from a High-Risk Cohort in Uganda

HIV drug resistance (HIVDR) is of increasing health concern, especially among key populations. We investigated the prevalence of virological suppression (VS), prevalence and correlates of HIVDR in HIV-infected women, enrolled in a high-risk cohort. We enrolled 267 women initiated on first-line antiretroviral therapy (ART) between 2015 and 2018. Participants' plasma samples were analyzed for HIV RNA viral load (VL) and genotypic resistance testing was performed on those with VL nonsuppression (defined as VL ≥1,000 copies/mL). We used the Stanford HIVDR database-algorithm to assess HIVDR mutations and logistic regression to assess risk factors for VL nonsuppression and HIVDR. We observed an overall VS prevalence of 76.0% (203/267) and detected respective acquired drug resistance prevalence to non-nucleoside reverse transcriptase inhibitors (NNRTIs) and nucleoside reverse transcriptase inhibitors (NRTIs) of 81.3% [confidence interval (CI) 67.4-91.1] and 45.8% (CI 31.4-60.8) among the 48 successfully genotyped VL nonsuppressors. NNRTI mutations were observed in 81.3% (39/48) of the genotyped participants and 45.8% (22/48) had both NRTI and NNRTI mutations. The mutation K103N was detected in 62.5% (30/48) of participants, 41.7% (20/48) had M184V/I, 14.6% had K65R, and 12.5% (6/48) had thymidine analog mutations (TAMs). None of the analyzed potential risk factors, including age and duration on ART, was significantly correlated with VL nonsuppression or HIVDR. Although high levels of NNRTI mutations support the transition to dolutegravir, the presence of NRTI mutations, especially TAMs, may compromise dolutegravir-based regimens or other second-line ART options. The moderate VS prevalence and high HIVDR prevalence therefore call for timely ART switching and intensive adherence counseling.

Phylogenetic and Demographic Characterization of Directed HIV-1 Transmission Using Deep Sequences from High-Risk and General Population Cohorts/Groups in Uganda

Across sub-Saharan Africa, key populations with elevated HIV-1 incidence and/or prevalence have been identified, but their contribution to disease spread remains unclear. We performed viral deep-sequence phylogenetic analyses to quantify transmission dynamics between the general population (GP), fisherfolk communities (FF), and women at high risk of infection and their clients (WHR) in central and southwestern Uganda. Between August 2014 and August 2017, 6185 HIV-1 positive individuals were enrolled in 3 GP and 10 FF communities, 3 WHR enrollment sites. A total of 2531 antiretroviral therapy (ART) naïve participants with plasma viral load >1000 copies/mL were deep-sequenced. One hundred and twenty-three transmission networks were reconstructed, including 105 phylogenetically highly supported source–recipient pairs. Only one pair involved a WHR and male participant, suggesting that improved population sampling is needed to assess empirically the role of WHR to the transmission dynamics. More transmissions were observed from the GP communities to FF communities than vice versa, with an estimated flow ratio of 1.56 (95% CrI 0.68–3.72), indicating that fishing communities on Lake Victoria are not a net source of transmission flow to neighboring communities further inland. Men contributed disproportionally to HIV-1 transmission flow regardless of age, suggesting that prevention efforts need to better aid men to engage with and stay in care.