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

Using phylodynamics to inform and evaluate HIV public health interventions across three distinct epidemics

Over 40 years on, progress towards ending the HIV/AIDS pandemic is slowing rather than accelerating. HIV molecular epidemiology tools, including phylogenetic, phylodynamic, and phylogeographic analyses have proven increasingly useful in public health planning, including in advising public health authorities and evaluating interventions. In this thesis, I apply phylodynamic and phylogeographic analyses to assess the impact of HIV public health interventions and inform public health responses across three diverse settings: a generalised epidemic in sub-Saharan Africa, a national epidemic in Kazakhstan, and a localised outbreak in Glasgow, Scotland. In the first study I used HIV sequences obtained from dried blood spots to detect HIV transmission clusters within a universal test-and-treat trial in East Africa. Using partial gag and pol HIV-1 consensus sequences collected between 2013 and 2017 from 745 trial participants, I identified putative transmission clusters arising after the start of the trial with Bayesian time-calibrated phylogenies. The identification of trial-incident, within-community transmissions revealed the role of unsuppressed individuals in sustaining the epidemic in both arms of a universal test-and-treat trial setting, highlighting the need to improve delivery and adherence to up-to-date therapy recommendations to halt HIV transmission. In the second study I focused on the HIV epidemic in Kazakhstan, a middle-income country in Central Asia that is experiencing a rapidly growing HIV epidemic. I used 968 partial HIV-1 pol sequences collected between 2017 and 2020 from people living with HIV across all regions of Kazakhstan to characterise the epidemic. I quantified levels of drug resistance within the study sample, identified distinct frequencies of drug resistant mutations among the two main viral subtypes, A6 and CRF02_AG, and carried out phylodynamic and phylogeographic analyses to elucidate the evolutionary history of the HIV epidemic in Kazakhstan and infer the routes of introduction of the two HIV subtypes into the country. Phylodynamic analysis revealed similar growth dynamics for both subtypes despite differences in the timing of the introduction of each one. Phylogeographic analyses inferred differences in the introduction and spread of A6 and CRF02_AG into Kazakhstan, although uncertainty in the inferences was high and differed depending on the subsampling strategy employed, cautioning against the bias that can be introduced into phylogeographic analyses in this setting. In the third study I evaluated the impact of the COVID-19 pandemic on continued transmission of HIV subtype C among people who inject drugs in Glasgow, Scotland. Using partial HIV- 1 pol consensus sequences collected between 2005 and 2022 from the 217 individuals phylogenetically linked to the outbreak, and a subset of near full-length genomes, I performed a phylodynamic analysis to reconstruct the HIV effective population size among individuals linked to the outbreak before and after (a) the introduction of targeted interventions to control the outbreak and (b) the introduction of COVID-19 lockdown measures in the UK. Additionally, I inferred a transmission tree from the phylogeny to estimate the number of unsampled cases linked to the outbreak. Finally, I performed a continuous phylogeographic analysis to quantify the spatiotemporal diffusion of the outbreak, which is presented in this thesis in an anonymised, discretised manner to avoid risks of deductive disclosure. These results were used to directly support the understanding of the HIV outbreak by public health authorities, informing a focused public health response. Overall, this thesis provides three distinct examples of the use of molecular epidemiology tools applied to aiding HIV public health responses, highlighting differences in the state of the HIV/AIDS pandemic worldwide and the need for targeted public health interventions

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

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

Evaluation of a quality improvement intervention to reduce anastomotic leak following right colectomy (EAGLE): pragmatic, batched stepped-wedge, cluster-randomized trial in 64 countries

Background Anastomotic leak affects 8 per cent of patients after right colectomy with a 10-fold increased risk of postoperative death. The EAGLE study aimed to develop and test whether an international, standardized quality improvement intervention could reduce anastomotic leaks. Methods The internationally intended protocol, iteratively co-developed by a multistage Delphi process, comprised an online educational module introducing risk stratification, an intraoperative checklist, and harmonized surgical techniques. Clusters (hospital teams) were randomized to one of three arms with varied sequences of intervention/data collection by a derived stepped-wedge batch design (at least 18 hospital teams per batch). Patients were blinded to the study allocation. Low- and middle-income country enrolment was encouraged. The primary outcome (assessed by intention to treat) was anastomotic leak rate, and subgroup analyses by module completion (at least 80 per cent of surgeons, high engagement; less than 50 per cent, low engagement) were preplanned. Results A total 355 hospital teams registered, with 332 from 64 countries (39.2 per cent low and middle income) included in the final analysis. The online modules were completed by half of the surgeons (2143 of 4411). The primary analysis included 3039 of the 3268 patients recruited (206 patients had no anastomosis and 23 were lost to follow-up), with anastomotic leaks arising before and after the intervention in 10.1 and 9.6 per cent respectively (adjusted OR 0.87, 95 per cent c.i. 0.59 to 1.30; P = 0.498). The proportion of surgeons completing the educational modules was an influence: the leak rate decreased from 12.2 per cent (61 of 500) before intervention to 5.1 per cent (24 of 473) after intervention in high-engagement centres (adjusted OR 0.36, 0.20 to 0.64; P < 0.001), but this was not observed in low-engagement hospitals (8.3 per cent (59 of 714) and 13.8 per cent (61 of 443) respectively; adjusted OR 2.09, 1.31 to 3.31). Conclusion Completion of globally available digital training by engaged teams can alter anastomotic leak rates. Registration number: NCT04270721 (http://www.clinicaltrials.gov)