Scientific Publications

Background
Recruitment and retention of participants in research studies conducted in fishing communities remain a challenge because of population mobility. Reliable and acceptable methods for identifying and tracking participants taking part in HIV prevention and treatment research are needed. The study aims to assess the acceptability, and technical feasibility of iris scans as a biometric identification method for research participants in fishing communities.

Methods
This was a cross-sectional study conducted in eight fishing communities in Kenya, Tanzania, and Uganda, with follow-up after one month in a randomly selected subset of participants. All consenting participants had their iris scanned and then responded to the survey.

Results
1,199 participants were recruited. The median age was 33 [Interquartile range (IQR) 24–42] years; 56% were women. The overall acceptability of iris scanning was 99%, and the success rate was 98%. Eighty one percent (n = 949) had a successful scan on first attempt, 116 (10%) on second and 113 (9%) after more than two attempts. A month later, 30% (n = 341) of participants were followed up. The acceptability of repeat iris scanning was 99% (n = 340). All participants who accepted repeat iris scanning had successful scans, with 307 (90%) scans succeeding on first attempt; 25 (7%) on second attempt, and 8 (2%) after several attempts. The main reason for refusing iris scanning was fear of possible side effects of the scan on the eyes or body.

Conclusion
The acceptability and applicability of biometric iris scan as a technique for unique identification of research participants is high in fishing communities. However, successful use of the iris scanning technology in research will require education regarding the safety of the procedure.

Background:
Tuberculosis is a leading infectious cause of death worldwide. Novel vaccines will be required to reach global targets and reverse setbacks resulting from the COVID-19 pandemic. We estimated the impact of novel tuberculosis vaccines in low-income and middle-income countries (LMICs) in several delivery scenarios.

Methods:
We calibrated a tuberculosis model to 105 LMICs (accounting for 93% of global incidence). Vaccine scenarios were implemented as the base-case (routine vaccination of those aged 9 years and one-off vaccination for those aged 10 years and older, with country-specific introduction between 2028 and 2047, and 5-year scale-up to target coverage); accelerated scale-up similar to the base-case, but with all countries introducing vaccines in 2025, with instant scale-up; and routine-only (similar to the base-case, but including routine vaccination only). Vaccines were assumed to protect against disease for 10 years, with 50% efficacy.

Findings:
The base-case scenario would prevent 44·0 million (95% uncertainty range 37·2-51·6) tuberculosis cases and 5·0 million (4·6-5·4) tuberculosis deaths before 2050, compared with equivalent estimates of cases and deaths that would be predicted to occur before 2050 with no new vaccine introduction (the baseline scenario). The accelerated scale-up scenario would prevent 65·5 million (55·6-76·0) cases and 7·9 million (7·3-8·5) deaths before 2050, relative to baseline. The routine-only scenario would prevent 8·8 million (95% uncertainty range 7·6-10·1) cases and 1·1 million (0·9-1·2) deaths before 2050, relative to baseline.

Interpretation:
Our results suggest novel tuberculosis vaccines could have substantial impact, which will vary depending on delivery strategy. Including a one-off vaccination campaign will be crucial for rapid impact. Accelerated introduction-at a pace similar to that seen for COVID-19 vaccines-would increase the number of lives saved before 2050 by around 60%. Investment is required to support vaccine development, manufacturing, prompt introduction, and scale-up.

Background:
The HIV epidemic remains a major public health problem. Critical to transmission control are HIV prevention strategies with new interventions continuing to be developed. Mathematical models are important for understanding the potential impact of these interventions and supporting policy decisions. This systematic review aims to answer the following question: when a new HIV prevention intervention is being considered or designed, what information regarding it is necessary to include in a compartmental model to provide useful insights to policy makers? The primary objective of this review is therefore to assess suitability of current compartmental HIV prevention models for informing policy development.

Methods:
Articles published in EMBASE, Medline, Econlit, and Global Health were screened. Included studies were identified using permutations of (i) HIV, (ii) pre-exposure prophylaxis (PrEP), circumcision (both voluntary male circumcision [VMMC] and early-infant male circumcision [EIMC]), and vaccination, and (iii) modelling. Data extraction focused on study design, model structure, and intervention incorporation into models. Article quality was assessed using the TRACE (TRAnsparent and Comprehensive Ecological modelling documentation) criteria for mathematical models.

Results:
Of 837 articles screened, 48 articles were included in the review, with 32 unique mathematical models identified. The substantial majority of studies included PrEP (83%), whilst fewer modelled circumcision (54%), and only a few focussed on vaccination (10%). Data evaluation, implementation verification, and model output corroboration were identified as areas of poorer model quality. Parameters commonly included in the mathematical models were intervention uptake and effectiveness, with additional intervention-specific common parameters identified. We identified key modelling gaps; critically, models insufficiently incorporate multiple interventions acting simultaneously. Additionally, population subgroups were generally poorly represented-with future models requiring improved incorporation of ethnicity and sexual risk group stratification-and many models contained inappropriate data in parameterisation which will affect output accuracy.

Conclusions:
This review identified gaps in compartmental models to date and suggests areas of improvement for models focusing on new prevention interventions. Resolution of such gaps within future models will ensure greater robustness and transparency, and enable more accurate assessment of the impact that new interventions may have, thereby providing more meaningful guidance to policy makers.

Understanding the quality of immune repertoire triggered during natural infection can provide vital clues that form the basis for development of a humoral immune response in some individuals capable of broadly neutralizing pan-SARS-CoV-2 variants. In the present study, we report variations in neutralization potential against Omicron variants of two novel neutralizing monoclonal antibodies (MAbs), THSC20.HVTR11 and THSC20.HVTR55, isolated from an unvaccinated convalescent individual that represent distinct B cell lineage origins and epitope specificity compared to five MAbs we previously reported that were isolated from the same individual. In addition, we observed neutralization of Omicron variants by plasma antibodies obtained from this particular individual postvaccination with increased magnitude. Interestingly, this observation was found to be comparable with six additional individuals who initially were also infected with ancestral SARS-CoV-2 and then received vaccines, indicating that hybrid immunity can provide robust humoral immunity likely by antibody affinity maturation. Development of a distinct antigen-specific B cell repertoire capable of producing polyclonal antibodies with distinct affinity and specificities offers the highest probability of protecting against evolving SARS-CoV-2 variants. IMPORTANCE Development of robust neutralizing antibodies in SARS-CoV-2 convalescent individuals is known; however, it varies at the population level. We isolated monoclonal antibodies from an individual infected with ancestral SARS-CoV-2 in early 2020 that not only varied in their B cell lineage origin but also varied in their capability and potency to neutralize all the known variants of concern (VOCs) and currently circulating Omicron variants. This indicated establishment of unique lineages that contributed in forming a B cell repertoire in this particular individual immediately following infection, giving rise to diverse antibody responses that could complement each other in providing a broadly neutralizing polyclonal antibody response. Individuals who were able to produce polyclonal antibody responses with higher magnitude have a higher chance of being protected from evolving SARS-CoV-2 variants.

There has been a surge in the emergence of HIV-1 drug resistance in Low and Middle-Income Countries (LMICs) due to poor drug-adherence and limited access to viral load testing, the current standard for treatment-monitoring. It is estimated that only 75% of people living with HIV (PLWH) worldwide have access to viral load testing. In LMICs, this figure is below 50%. In a recent WHO survey in mostly LMICs, 21 out of 30 countries surveyed found HIV-1 first-line pre-treatment drug resistance in over 10% of study participants. In the worst-affected regions, up to 68% of infants born to HIV-1 positive mothers were found to harbour first-line HIV-1 treatment resistance. This is a huge public health concern. Greater access to treatment-monitoring is required in LMICs if the UNAIDS “third 95” targets are to be achieved by 2030. Here, we review the current challenges of viral load testing and present the case for greater utilization of Laboratory-based assays that quantify intracellular HIV-1 RNA and/or DNA to provide broader worldwide access to HIV-1 surveillance, drug-resistance monitoring, and cure-research.

Pan-betacoronavirus neutralizing antibodies may hold the key to developing broadly protective vaccines against novel pandemic coronaviruses and to more effectively respond to SARS-CoV-2 variants. The emergence of Omicron and subvariants of SARS-CoV-2 illustrates the limitations of solely targeting the receptor-binding domain (RBD) of the spike (S) protein. Here, we isolated a large panel of broadly neutralizing antibodies (bnAbs) from SARS-CoV-2 recovered-vaccinated donors, which targets a conserved S2 region in the betacoronavirus spike fusion machinery. Select bnAbs showed broad in vivo protection against all three deadly betacoronaviruses, SARS-CoV-1, SARS-CoV-2, and MERS-CoV, which have spilled over into humans in the past two decades. Structural studies of these bnAbs delineated the molecular basis for their broad reactivity and revealed common antibody features targetable by broad vaccination strategies. These bnAbs provide new insights and opportunities for antibody-based interventions and for developing pan-betacoronavirus vaccines.

The ability to efficiently isolate antigen-specific B cells in high throughput will greatly accelerate the discovery of therapeutic monoclonal antibodies (mAbs) and catalyze rational vaccine development. Traditional mAb discovery is a costly and labor-intensive process, although recent advances in single-cell genomics using emulsion microfluidics allow simultaneous processing of thousands of individual cells. Here we present a streamlined method for isolation and analysis of large numbers of antigen-specific B cells, including next generation antigen barcoding and an integrated computational framework for B cell multi-omics. We demonstrate the power of this approach by recovering thousands of antigen-specific mAbs, including the efficient isolation of extremely rare precursors of VRC01-class and IOMA-class broadly neutralizing HIV mAbs.

An effective HIV vaccine will need to stimulate immune responses against the sequence diversity presented in circulating virus strains. In this study, we evaluate breadth and depth estimates of potential T-cell epitopes (PTEs) in transmitted founder virus sequence-derived cohort-specific peptide reagents against reagents representative of consensus and global sequences. CD8 T-cells from twenty-six HIV-1+ PBMC donor samples, obtained at 1-year post estimated date of infection, were evaluated. ELISpot assays compared responses to 15mer consensus (n = 121), multivalent-global (n = 320), and 10mer multivalent cohort-specific (n = 300) PTE peptides, all mapping to the Gag antigen. Responses to 38 consensus, 71 global, and 62 cohort-specific PTEs were confirmed, with sixty percent of common global and cohort-specific PTEs corresponding to consensus sequences. Both global and cohort-specific peptides exhibited broader epitope coverage compared to commonly used consensus reagents, with mean breadth estimates of 3.2 (global), 3.4 (cohort) and 2.2 (consensus) epitopes. Global or cohort peptides each identified unique epitope responses that would not be detected if these peptide pools were used alone. A peptide set designed around specific virologic and immunogenetic characteristics of a target cohort can expand the detection of CD8 T-cell responses to epitopes in circulating viruses, providing a novel way to better define the host response to HIV-1 with implications for vaccine development.

Background
Adolescent girls and young women (AGYW), aged 15–24 years, are disproportionately affected by HIV and other sexual and reproductive health (SRH) risks due to varying social, cultural, and economic factors that affect their choices and shape their knowledge, understanding, and practices with regard to their health. Socio‐Behavioral Change Communication (SBCC) interventions targeted at strengthening the capabilities of individuals and their networks have supported the demand and uptake of prevention services and participation in biomedical research. However, despite growing global recognition of the domain, high‐quality evidence on the effectiveness of SBCC remains scattered. This evidence and gap map (EGM) report characterizes the evidence base on SBCC interventions for strengthening HIV Prevention and Research among AGYW in low‐ and middle‐income countries (LMICs), identifying evidence gaps and outlining the scope of future research and program design.

Objectives
The objectives of the proposed EGM are to: (a) identify and map existing EGMs in the use of diverse SBCC strategies to strengthen the adoption of HIV prevention measures and participation in research among AGYW in LMICs and (b) identify areas where more interventions and evidence are needed to inform the design of future SBCC strategies and programs for AGYW engagement in HIV prevention and research.

Methods
This EGM is based on a comprehensive search of systematic reviews and impact evaluations corresponding to a range of interventions and outcomes—aimed at engaging AGYW in HIV prevention and research ‐ that were published in LMICs from January 2000 to April 2021. Based on guidance for producing a Campbell Collaboration EGM, the intervention and outcome framework was designed in consultation with a group of experts. These interventions were categorized across four broad intervention themes: mass‐media, community‐based, interpersonal, and Information Communication and Technology (ICT)/Digital Media‐based interventions. They were further sub‐categorized into 15 intervention categories. Included studies looked at 23 unique behavioral and health outcomes such as knowledge attitude and skills, relationship dynamics, household dynamics, health care services, and health outcomes and research engagement. The EGM is presented as a matrix in which the rows are intervention categories/sub‐categories, and the columns are outcome domains/subdomains. Each cell is mapped to an intervention targeted at outcomes. Additional filters like region, country, study design, age group, funding agency, influencers, population group, publication status, study confidence, setting, and year of publication have been added.

Selection Criteria
To be eligible, studies must have tested the effectiveness of SBCC interventions at engaging AGYW in LMICs in HIV prevention and research. The study sample must have consisted of AGYW between the ages of 15–24, as defined by UNAIDS. Both experimental (random assignment) and quasi‐experimental studies that included a comparison group were eligible. Relevant outcomes included those at the individual, influencer, and institutional levels, along with those targeting research engagement and prevention‐related outcomes.

Results
This EGM comprises 415 impact evaluations and 43 systematic reviews. Interventions like peer‐led interactions, counseling, and community dialogues were the most dominant intervention sub‐types. Despite increased digital penetration use of media and technology‐driven interventions are relatively less studied. Most of the interventions were delivered by peers, health care providers, and educators, largely in school‐based settings, and in many cases are part of sex‐education curricula. Evidence across geographies was mostly concentrated in Sub‐Saharan Africa (70%). Most measured outcomes focused on disease‐related knowledge dissemination and enhancing awareness of available prevention options/strategies. These included messaging around consistent condom use, limiting sexual partners, routine testing, and awareness. Very few studies were able to include psychographic, social, and contextual factors influencing AGYW health behaviors and decisions, especially those measuring the impact of social and gender norms, relationship dynamics, and household dynamics‐related outcomes. Outcomes related to engagement in the research were least studied.

Conclusion
This EGM highlights that evidence is heavily concentrated within the awareness‐intent spectrum of behavior change and gets lean for outcomes situated within the intent‐action and the action‐habit formation spectrum of the behavior change continuum. Most of the evidence was concentrated on increasing awareness, knowledge, and building risk perception around SRH domains, however, fewer studies focused on strengthening the agency and self‐efficacy of individuals. Similarly, evidence on extrinsic factors—such as strengthening social and community norms, relationships, and household dynamics—that determine individual thought and action such as negotiation and life skills were also found to be less populated. Few studies explore the effectiveness of these interventions across diverse AGYW identities, like pregnant women and new mothers, sex workers, and people living with HIV, leading to limited understanding of the use of these interventions across multiple user segments including key influencers such as young men, partners, families, religious leaders, and community elders was relatively low. There is a need for better quality evidence that accounts for the diversity of experiences within these populations to understand what interventions work, for whom, and toward what outcome. Further, the evidence for use of digital and mass‐media tools remains poorly populated. Given the increasing penetration of these tools and growing media literacy on one end, with widening gender‐based gaps on the other, it is imperative to gather more high‐quality evidence on their effectiveness. Timely evidence generation can help leverage these platforms appropriately and enable intervention designs that are responsive to changing communication ecologies of AGYW. SBCC can play a critical role in helping researchers meaningfully engage and collaborate with communities as equal stakeholders, however, this remains poorly evidenced and calls for investigation and investment. A full list of abbreviations and acronyms are available in Supporting Information: Appendix F.

A prophylactic vaccine is needed to slow the spread of HIV-1 infection. Optimization of the wild-type envelope glycoproteins to create immunogens that can elicit effective neutralizing antibodies is a high priority. Starting with ten genes encoding subtype B HIV-1 gp120 envelope glycoproteins and using in vitro homologous DNA recombination, we created chimeric gp120 variants that were screened for their ability to bind neutralizing monoclonal antibodies. Hundreds of variants were identified with novel antigenic phenotypes that exhibit considerable sequence diversity. Immunization of rabbits with these gp120 variants demonstrated that the majority can induce neutralizing antibodies to HIV-1. One novel variant, called ST-008, induced significantly improved neutralizing antibody responses when assayed against a large panel of primary HIV-1 isolates. Further study of various deletion constructs of ST-008 showed that the enhanced immunogenicity results from a combination of effective DNA priming, an enhanced V3-based response, and an improved response to the constant backbone sequences.

Background
Population mobility is a demonstrated barrier to reducing HIV incidence. A clear understanding of social networks and their influence on mobility among women in the fishing communities of Lake Victoria may contribute to tailoring effective interventions that suit the needs of these mobile women.

Methods
A cross-sectional qualitative methods study was conducted to understand mobility patterns among women resident and or working in fishing communities of Lake Victoria in Kenya, Tanzania, and Uganda. The study was conducted in six fishing communities from March 2018 to June 2019. The communities were purposively selected, based on population size (1000 people or more) and HIV prevalence of > 15% among women aged 18 years or older who had lived in the fishing community for at least six months. In-depth interviews were conducted with 24 key informants and 72 women from the sites in the three countries. Questions focused on women’s social networks and other factors that fuelled or facilitated women’s mobility as well as challenges they faced due to mobility. Data analysis followed a thematic framework approach.

Results
Different social groupings/networks existed among women in the fishing communities of Lake Victoria. These included female sex workers, women fish processors/traders, women bar workers/owners, restaurant workers, and family networks. Networks encouraged mobility, supporting finding work opportunities, but also increased sexual risks through partner changes. The benefits of networks included information sharing, financial support, and group protection, especially against violence.

Conclusion
Social networks and groupings among women in the fishing communities of Lake Victoria could be useful in tailoring HIV prevention and HIV care interventions to suit the needs of these highly mobile populations.

Antibody heavy chain (HC) and light chain (LC) variable region exons are assembled by V(D)J recombination. V(D)J junctional regions encode complementarity-determining-region 3 (CDR3), an antigen-contact region immensely diversified through nontemplated nucleotide additions (“N-regions”) by terminal deoxynucleotidyl transferase (TdT). HIV-1 vaccine strategies seek to elicit human HIV-1 broadly neutralizing antibodies (bnAbs), such as the potent CD4-binding site VRC01-class bnAbs. Mice with primary B cells that express receptors (BCRs) representing bnAb precursors are used as vaccination models. VRC01-class bnAbs uniformly use human HC VH1-2 and commonly use human LCs Vκ3-20 or Vκ1-33 associated with an exceptionally short 5-amino-acid (5-aa) CDR3. Prior VRC01-class models had nonphysiological precursor levels and/or limited precursor diversity. Here, we describe VRC01-class rearranging mice that generate more physiological primary VRC01-class BCR repertoires via rearrangement of VH1-2, as well as Vκ1-33 and/or Vκ3-20 in association with diverse CDR3s. Human-like TdT expression in mouse precursor B cells increased LC CDR3 length and diversity and also promoted the generation of shorter LC CDR3s via N-region suppression of dominant microhomology-mediated Vκ-to-Jκ joins. Priming immunization with eOD-GT8 60mer, which strongly engages VRC01 precursors, induced robust VRC01-class germinal center B cell responses. Vκ3-20-based responses were enhanced by N-region addition, which generates Vκ3-20-to-Jκ junctional sequence combinations that encode VRC01-class 5-aa CDR3s with a critical E residue. VRC01-class-rearranging models should facilitate further evaluation of VRC01-class prime and boost immunogens. These new VRC01-class mouse models establish a prototype for the generation of vaccine-testing mouse models for other HIV-1 bnAb lineages that employ different HC or LC Vs.

Objective
To assess the feasibility of conducting HIV prevention trials among key populations in Nairobi, Kenya.

Background
HIV prevention trials require the inclusion of those at high risk of HIV infection and their informed decision to take part and remain in the clinical trial to the end is crucial. In Kenya key populations including men who have sex with men (MSM) and female sex workers (FSW) are, disproportionately, at high risk of HIV infection when compared to the general population. Few trials testing biomedical prevention products against HIV have enrolled Kenyan FSW and MSM.

Methods
We performed simulated vaccine efficacy trial (SiVET) using licensed hepatitis B vaccines as substitutes for a HIV vaccine candidate and included randomization for those immune to hep B. The SiVET was an observational study designed to mimic the rigors of a clinical trial; we assessed HIV risk, provided risk counselling and prevention tools and performed HIV testing at baseline and periodically until the end of the trial. MSM and FSW were enrolled at a ratio of 4:1. Volunteers were assigned to either hepatitis B vaccine or placebo.

Results
Recruitment took approximately 24 months between Sep 2015 and Sep 2017. Of the 368 volunteers screened, 250 (200 MSM and 50 FSW) were enrolled. Reasons for exclusion at screening included: being positive for HIV (n = 7), hepatitis (n = 14), other pre-existing medical conditions (n = 41), eligible but chose not to enrol (n = 47). Most of the volunteers adhered to study procedures and attended their study visits within the study window. These include volunteers who received the second vaccination 244 (98%), the third vaccination 228 (91%) and, the final study visit 217 (87%). The reasons volunteers discontinued from the study early included: relocation and loss to follow up (n = 14). A total of 8 cases of HIV infection were observed in 174.5 Person Years at Risk (PYAR), all among MSM, including 5 seroconversions identified at the last study visit, for a HIV incidence of 4.58 cases/ 100 PYAR, among MSM enrolled in the study.

Conclusion
Our findings suggest that it is possible to conduct HIV prevention trials among key populations in Nairobi with a good adherence to a vaccine efficacy trial schedule. Despite HIV prevention efforts, we also noted a high incidence of HIV infection. This demonstrates the need for effective HIV prevention products in these populations.