Scientific Publications

South African adolescents are at-risk for HIV infection due to engaging in high-risk sexual behaviours. Understanding the factors influencing sexual decision-making is crucial for developing effective HIV prevention strategies. We conducted a qualitative study with adolescents and caregivers in Rustenburg, South Africa to explore individual and interpersonal factors that influence adolescent sexual decision-making. Focus Group Discussions (FGDs) were conducted in English and Setswana with 17 adolescents (13 females and 4 males) and 19 caregivers (17 females and 2 males) between April and July 2018. Thematic analysis revealed that while adolescents had access to sexual education from various sources, this knowledge did not translate into healthy sexual decision-making. Lack of effective communication and support between caregivers and adolescents in discussing sexual behaviours are a contributing barrier. Although adolescents expressed a strong need to be understood and supported by caregivers regarding sexual behaviours, there was perceived distrust, judgemental attitude from caregivers, poor role models of a father figure, and the traditional taboo nature of having these discussions with caregivers. While female adolescents and female caregivers discussed sexual matters, this type of communication was limited with adolescent males. Male adolescents were uncomfortable communicating with either caregiver, fearing caregiver judgemental attitudes and being misunderstood. Female caregivers perceived male caregiver roles to be absent and non-engaging. Caregivers desired to support their children, yet they seemed to doubt their skills. Communication tools and guidance on how adolescents and caregivers could communicate about sexual matters could create enabling environments for adolescents to make informed, healthy decisions regarding their sexual behaviours. Further, future interventions could consider gain-framed messaging to address adolescents translating knowledge of sexual behaviours to making healthy sexual choices. Improving equitable male caregiver role at home, is of particular importance in supporting adolescent sexual decision-making, and should be prioritized.

The complex dynamics of protein expression in plasma during hyperacute HIV-1 infection and its relation to acute retroviral syndrome, viral control, and disease progression are largely unknown. Here, we quantify 1293 blood plasma proteins from 157 longitudinally linked plasma samples collected before, during, and after hyperacute HIV-1 infection of 54 participants from four sub-Saharan African countries. Six distinct longitudinal expression profiles are identified, of which four demonstrate a consistent decrease in protein levels following HIV-1 infection. Proteins involved in inflammatory responses, immune regulation, and cell motility are significantly altered during the transition from pre-infection to one month post-infection. Specifically, decreased ZYX and SCGB1A1 levels, and increased LILRA3 levels are associated with increased risk of acute retroviral syndrome; increased NAPA and RAN levels, and decreased ITIH4 levels with viral control; and increased HPN, PRKCB, and ITGB3 levels with increased risk of disease progression. Overall, this study provides insight into early host responses in hyperacute HIV-1 infection, and present potential biomarkers and mechanisms linked to HIV-1 disease progression and viral load.

Background
An HIV-1 vaccine is long overdue. Although vaccine research focuses on the induction of broadly neutralising antibodies, challenging infections such as HIV-1 could require parallel induction of protective T cells. It is important to recognise that not all T cells contribute to protection equally. Previously, we developed a T-cell immunogen-based bivalent mosaic vaccine, HIVconsvX, delivered by vaccine vectors ChAdOx1 and modified vaccinia Ankara. In this study, we tested the HIVconsvX vaccine regimen for the first time in humans. Other ongoing trials will assess the contribution of the vaccine-induced killer T cells to the control of HIV-1.

Methods
HIV-CORE 005.2 was an open-label, dose-escalation, first-in-human, phase 1 trial done at the Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Oxford, UK. Eligible participants were healthy volunteers aged 18-65 years living without HIV-1 and at a low likelihood of acquiring it. Because it was the first administration of ChAdOx1.tHIVconsv1 (C1) to humans, participants were assigned stepwise to two groups. Volunteer group 1 received a low dose of C1 on enrolment. Following a satisfactory safety review 7 days after vaccination, volunteer group 2 received a full dose of C1 boosted by vaccines MVA.tHIVconsv3 (M3) and MVA.tHIVconsv4 (M4) 4 weeks later in regimen C1-M3M4 and were followed up until day 140. Focusing on the full vaccine doses in group 2, the primary outcome was the local and systemic safety of the vaccine. The secondary outcome was the frequency and breadth of epitope recognition by vaccine-induced T cells determined by IFN-γ ELISPOT assay using peripheral blood mononuclear cells (PBMC) at peak (1 and 2 weeks after the M3M4 boost) and at the end of the study, assessed against volunteer's pre-vaccination levels. The HIV-CORE 005.2 trial is registered at ClinicalTrials.gov (NCT04586673) and is closed.

Findings
Between July 3, 2021, and Aug 3, 2022, 13 participants were recruited and assigned to group 1 (n=3) and group 2 (n=10). Low-dose C1 was safe and well tolerated in group 1, and all three vaccine components were well tolerated in volunteer group 2. There were no serious adverse events. Local and systemic reactogenicities were consistent with intramuscular needle administration of immunogenic substances. All volunteers responded, and their vaccine-elicited T-cell frequencies peaked at a median of 4433 (IQR 2750-5820) IFN-γ spot-forming units per 106 PBMC and recognised a median of 9 (IQR 9-10) peptide pools out of 10, indicating that the responses were broadly specific and each vaccine recipient targeted at least nine epitopes on HIV-1. These frequencies were 7·4 times lower by day 140 (ie, 3 months later). T cells proliferated upon antigen re-exposure and displayed multiple effector functions, recognised variant epitopes, and inhibited HIV-1 from the four major global clades A, B, C, and D.

Interpretation
These results inform and support a programme of clinical evaluations of the HIVconsvX T-cell vaccines together with other cutting-edge tools for HIV-1 cure and prevention such as latency reactivating agents, passively infused combinations of broadly neutralising antibodies, and active Env-based vaccines or immunomodulators.

Funding
EU Horizon 2020 Research and Innovation programme, Medical Research Council and Foreign Commonwealth and Development Office Concordat agreement, European and Developing Countries Clinical Trials Partnership, National Institute for Health Research Oxford Biomedical Research Centre, and IAVI.

Background
H56:IC31 is a candidate vaccine against tuberculosis (TB) with the potential to reduce TB recurrence rate. It is thus important for future clinical trials to demonstrate safety and immunogenicity of H56:IC31 in individuals treated for TB.

Methods
Twenty-two adults confirmed to be Mycobacterium tuberculosis negative (by 2 GeneXpert tests or 2 sputum cultures) after 4-5 months of TB treatment, and not more than 28 days after completion of TB treatment, were randomized to receive 2 doses of H56:IC31 (5 mg H56:500 nmol IC31; n = 16) or placebo (n = 6) 56 days apart. Participants were followed for 420 days for safety and immunogenicity.

Results
H56:IC31 vaccination was associated with an acceptable safety profile, consisting mostly of mild self-limited injection site reactions. No serious adverse events or vaccine-related severe adverse events were reported. H56:IC31 induced a CD4+ T-cell response for Ag85B and ESAT-6, with ESAT-6 being immunodominant, which persisted through 6 months after the last vaccination. There was some evidence of CD8+ T-cell responses for both Ag85B and ESAT-6, but to a lesser extent than CD4+ responses.

Conclusions
H56:IC31 was associated with an acceptable safety profile, and induced a predominant CD4+ T-cell response, in adults recently treated for drug-susceptible, uncomplicated pulmonary TB.

Introduction
Uganda´s fishing communities experience a high burden of sexually transmitted infections (STIs) including human immunodeficiency virus (HIV), with limited access to healthcare. Knowledge on healthcare use and treatment seeking will help identify unmet needs and facilitate appropriate allocation of resources.

Methods
between 2014-2015, a mixed methods cross-sectional survey was conducted in four fishing communities on Lake Victoria, Uganda, as part of preparedness for HIV trials. The goal was to understand health problems (having any illness, medical condition, or injury in the past 12 months), perceptions of healthcare, health services use, and factors associated with seeking STI care. Data were collected from participants aged 13-49 years; quantitatively using a structured questionnaire and qualitatively via focus group discussions (FGDs) and key informant interviews (KIIs). Information covered recent health problems, health services use, and healthcare perceptions. Multivariable logistic regression modeling was used to determine factors associated with seeking care for STIs.

Results
participants´ median (interquartile range) age was 29 (23-35) years, more than half (51.9%, 763/1,469), were females, and the majority (60.4%, 888/1,469) had up to seven years of formal education. Most participants reported having had health problems (76%, 1,117/1,469). The most frequently reported health issues were STI symptoms (52.6%, 587/1,117). Lack of health services was mentioned as one of the reasons for not seeking care during the FDGs and KIIs. Adolescents, 13-19 were less likely to seek care for STIs symptoms than adults of 20 or more years (aOR= 0.5 (95% CI 0.3-0.9)). Females were more likely to seek STI treatment (aOR= 1.4 (95% CI 1.0-2.1)), as were participants who worked mainly in bars, restaurants or lodges (aOR= 2.0 (95% CI 1.1-3.6)).

Conclusion
In these communities, adolescents have low treatment seeking for STIs symptoms.

The generation of broadly neutralizing antibodies (bnAbs) to conserved epitopes on HIV Envelope (Env) is one of the cornerstones of HIV vaccine research. The animal models commonly used for HIV do not reliably produce a potent broadly neutralizing serum antibody response, with the exception of cows. Cows have previously produced a CD4 binding site response by homologous prime and boosting with a native-like Env trimer. In small animal models, other engineered immunogens were shown to focus antibody responses to the bnAb V2-apex region of Env. Here, we immunized two groups of cows (n = 4) with two regimens of V2-apex focusing Env immunogens to investigate whether antibody responses could be generated to the V2-apex on Env. Group 1 was immunized with chimpanzee simian immunodeficiency virus (SIV)-Env trimer that shares its V2-apex with HIV, followed by immunization with C108, a V2-apex focusing immunogen, and finally boosted with a cross-clade native-like trimer cocktail. Group 2 was immunized with HIV C108 Env trimer followed by the same HIV trimer cocktail as Group 1. Longitudinal serum analysis showed that one cow in each group developed serum neutralizing antibody responses to the V2-apex. Eight and 11 bnAbs were isolated from Group 1 and Group 2 cows, respectively, and showed moderate breadth and potency. Potent and broad responses in this study developed much later than previous cow immunizations that elicited CD4bs bnAbs responses and required several different immunogens. All isolated bnAbs were derived from the ultralong CDRH3 repertoire. The finding that cow antibodies can target more than one broadly neutralizing epitope on the HIV surface reveals the generality of elongated structures for the recognition of highly glycosylated proteins. The exclusive isolation of ultralong CDRH3 bnAbs, despite only comprising a small percent of the cow repertoire, suggests these antibodies outcompete the long and short CDRH3 antibodies during the bnAb response.

Snake venoms are cocktails of biologically active molecules that have evolved to immobilize prey, but can also induce a severe pathology in humans that are bitten. While animal-derived polyclonal antivenoms are the primary treatment for snakebites, they often have limitations in efficacy and can cause severe adverse side effects. Building on recent efforts to develop improved antivenoms, notably through monoclonal antibodies, requires a comprehensive understanding of venom toxins. Among these toxins, snake venom metalloproteinases (SVMPs) play a pivotal role, particularly in viper envenomation, causing tissue damage, hemorrhage and coagulation disruption. One of the current challenges in the development of neutralizing monoclonal antibodies against SVMPs is the large size of the protein and the lack of existing knowledge of neutralizing epitopes. Here, we screened a synthetic human antibody library to isolate monoclonal antibodies against an SVMP from saw-scaled viper (genus Echis) venom. Upon characterization, several antibodies were identified that effectively blocked SVMP-mediated prothrombin activation. Cryo-electron microscopy revealed the structural basis of antibody-mediated neutralization, pinpointing the non-catalytic cysteine-rich domain of SVMPs as a crucial target. These findings emphasize the importance of understanding the molecular mechanisms of SVMPs to counter their toxic effects, thus advancing the development of more effective antivenoms.

Background
Recent outbreaks of Ebola virus disease (EVD) and Marburg virus disease (MVD) in sub-Saharan Africa illustrate the need to better understand animal reservoirs, burden of disease, and human transmission of filoviruses. This protocol outlines a systematic literature review to assess the prevalence of filoviruses that infect humans in sub-Saharan Africa. A secondary aim is to qualitatively describe and evaluate the assays used to assess prevalence.

Methods
The data sources for this systematic review include PubMed, Embase, and Web of Science. Titles, abstracts, and full texts will be reviewed for inclusion by a primary reviewer and then by a team of secondary reviewers, and data will be extracted using a pre-specified and piloted data extraction form. The review will include human cross-sectional studies, cohort studies, and randomized controlled trials conducted in sub-Saharan Africa up until March 13, 2024 that have been published in peer-reviewed scientific journals, with no language restrictions. Prevalence will be stratified by pathogen, population, assay, and sampling methodology and presented in forest plots with estimated prevalence and 95% confidence intervals. If there are enough studies within a stratum, I2 statistics will be calculated (using R statistical software), and data will be pooled if heterogeneity is low. In addition, assays used to detect infection will be evaluated. All studies included in the review will be assessed for quality and risk of bias using the JBI Prevalence Critical Appraisal Tool and for certainty using the GRADE certainty ratings.

Discussion
Accurately measuring the rate of exposure to filoviruses infecting humans in sub-Saharan Africa using prevalence provides an essential understanding of natural history, transmission, and the role of subclinical infection. This systematic review will identify research gaps and provide directions for future research seeking to improve our understanding of filovirus infections. Understanding the natural history, transmission, and the role of subclinical infection is critical for predicting the impact of an intervention on disease burden.

Systematic Review Registration
In accordance with the guidelines outlined in the PRISMA-P methodology, this protocol was registered with PROSPERO on April 7, 2023 (ID: CRD42023415358).

Supplementary Information
The online version contains supplementary material available at 10.1186/s13643-024-02626-w.

Adolescents face a higher risk for HIV, STIs, and unintended pregnancy than any other age group in sub–Saharan Africa, and have unique health care needs as they navigate this period of growth and developmental milestones. We conducted the Youth Friendly Services study among adolescents in Rustenburg, South Africa to address some of these concerns. Participants aged 12–19 were followed quarterly for 12 months, asked at baseline about demographics, their sexual behavior, and tested for HIV, STIs, and pregnancy (girls). Report of sexual activity was not a requirement for enrollment. Assent and parental consent were obtained for participants under 18. Some follow up visits fell during COVID-mandated shutdowns, and we worked with participants to reschedule and extend follow up as appropriate. Here we present data on reported behaviors, participant attrition, risk of HIV, other STI, and pregnancy. From May 2018 to August 2019, we enrolled 223 HIV-negative, non-pregnant adolescents (64% girls). The median age was 17 (IQR: 14–18). Among the 119 (53%) participants who reported being sexually active at baseline, the median age at first sex was 16 years (IQR: 15–17). During follow-up, an additional 16 (7%) participants reported having their first sexual encounter. Among the sexually active participants, the incidence of HIV was 1.5 cases / 100 person-years at risk (PYAR, 95% CI: 0.4–6.0), the incidence of chlamydia was 15.7 cases (95% CI: 10.1–24.4), gonorrhea was 4.7 cases (95% CI: 2.1–10.5), and HSV was 6.3 cases (95% CI: 3.1–12.6); we observed no cases of incident syphilis. The incidence of pregnancy among sexually active girls was 15.0 pregnancies / 100 PYAR (95% CI: 8.5–26.5). Despite small numbers, the incidence of most STIs was significantly higher in females compared to males. We also observed two pregnancies and 5 incident STIs among participants who reported never having had sex, these tended to be younger participants. From March to September 2020, the clinic was shut down for COVID-19, and 53 study visits were postponed. Follow up was concluded in November 2020, a total of 19 participants were lost to follow up, however only one participant dropped off-study during COVID-19 shutdowns. Retention at the final visit was 91.5%. We successfully completed a prospective study of adolescents to learn more about the risks they face as they navigate sexual debut in the context of a program of youth-friendly counseling and services. Among self-reported sexually active participants, we observed a high rate of HIV, STI and pregnancy, however we also observed pregnancy and STIs among those who reported no sexual activity.

Monoclonal antibodies (mAbs) are revolutionizing management of non-communicable diseases in high-income countries and are increasingly being advanced for a range of infectious diseases (IDs). However, access to existing mAbs is limited in low- and middle-income countries (LMICs), and investment in developing fit-for-purpose mAbs for IDs that disproportionately affect LMICs has been limited. Underlying these access barriers are systemic challenges, including a lack of commercial incentives to target LMIC markets and complexity in manufacturing and regulatory processes. Novel strategies are needed to overcome systemic access barriers for mAbs. We outline key areas where new approaches could address these barriers, based on a multistakeholder consultation in March 2023. Three disease-market archetypes are identified to guide thinking about business models tailored to different contexts. New business models are needed to incentivize development and manufacturing of ID mAbs and to ensure mAbs are optimized with a target product profile and cost of goods that enable use in diverse LMIC settings. Lessons can be applied from voluntary licensing strategies and product development partnerships that have shown success in catalysing development and affordable supply for a range of infectious diseases. Technology transfer will be key to expand LMIC research and manufacturing capacity and to enable sustainable and diversified supply. Improved market intelligence, demand aggregation mechanisms, and portfolio-based manufacturing models could be used to de-risk commercial investment and establish a sustainable manufacturing ecosystem for affordable mAbs. Novel regulatory approaches and robust technology transfer may reduce data requirements and timelines for biosimilar approvals. Trailblazer products, with coordinated “end-to-end” support from funders, can demonstrate proof of concept for pathways to accessible mAbs across a broader range of LMICs. Research funders; local, regional, global health agencies; and, private sector partners should commit to implementing innovative partnerships and end-to-end strategies that enable equitable access to mAbs for infectious diseases in LMICs.

A key barrier to the development of vaccines that induce broadly neutralizing antibodies (bnAbs) against human immunodeficiency virus (HIV) and other viruses of high antigenic diversity is the design of priming immunogens that induce rare bnAb-precursor B cells. The high neutralization breadth of the HIV bnAb 10E8 makes elicitation of 10E8-class bnAbs desirable; however, the recessed epitope within gp41 makes envelope trimers poor priming immunogens and requires that 10E8-class bnAbs possess a long heavy chain complementarity determining region 3 (HCDR3) with a specific binding motif. We developed germline-targeting epitope scaffolds with affinity for 10E8-class precursors and engineered nanoparticles for multivalent display. Scaffolds exhibited epitope structural mimicry and bound bnAb-precursor human naive B cells in ex vivo screens, protein nanoparticles induced bnAb-precursor responses in stringent mouse models and rhesus macaques, and mRNA-encoded nanoparticles triggered similar responses in mice. Thus, germline-targeting epitope scaffold nanoparticles can elicit rare bnAb-precursor B cells with predefined binding specificities and HCDR3 features.

Current prophylactic human immunodeficiency virus 1 (HIV-1) vaccine research aims to elicit broadly neutralizing antibodies (bnAbs). Membrane-proximal external region (MPER)-targeting bnAbs, such as 10E8, provide exceptionally broad neutralization, but some are autoreactive. Here, we generated humanized B cell antigen receptor knock-in mouse models to test whether a series of germline-targeting immunogens could drive MPER-specific precursors toward bnAbs. We found that recruitment of 10E8 precursors to germinal centers (GCs) required a minimum affinity for germline-targeting immunogens, but the GC residency of MPER precursors was brief due to displacement by higher-affinity endogenous B cell competitors. Higher-affinity germline-targeting immunogens extended the GC residency of MPER precursors, but robust long-term GC residency and maturation were only observed for MPER-HuGL18, an MPER precursor clonotype able to close the affinity gap with endogenous B cell competitors in the GC. Thus, germline-targeting immunogens could induce MPER-targeting antibodies, and B cell residency in the GC may be regulated by a precursor–competitor affinity gap.

Background
Novel HIV pre-exposure prophylaxis (PrEP) methods including a potential future HIV vaccine, will increase prevention options for adolescent girls and young women (AGYW) at high risk of HIV infection in Eastern and Southern Africa, yet data on AGYW’s preferences for various PrEP methods is limited. We investigated preferences for five biomedical PrEP methods (oral, injectable, vaginal ring, implant, HIV vaccine) among 14–24-years-old AGYW in Kampala, Uganda.

Methods
From January to December 2019, we conducted a mixed methods study including 265 high-risk AGYW. After receiving two education sessions on the five PrEP methods, participants were asked about their “most preferred PrEP method.” Multinomial logistic regression (oral PrEP as reference category) was used to determine participant characteristics associated with method preference. Results are presented as adjusted relative risk ratios (aRRR) with 95% confidence intervals (CI). In-depth interviews were conducted with 20 selected participants to examine reasons influencing PrEP preferences and suggestions for method improvements. Transcripts were analyzed thematically.

Results
Participants preferred methods were: HIV vaccine (34.7%), oral PrEP (25.7%), injectable PrEP (24.9%), PrEP implant (13.6%), and vaginal ring (1.1%). Preference for injectable PrEP increased with every year of age (aRRR 1.22; 95% CI 1.04–1.44) and among participants with chlamydia or gonorrhoea (aRRR 2.53; 95% CI 1.08–5.90), while it was lower among participants having sexual partner(s) living with HIV or of unknown HIV status (aRRR 0.30; 95% CI 0.10–0.91). Preference for PrEP implants also increased with age (aRRR 1.42; 95% CI 1.14–1.77) and was strong among participants having ≥10 sexual partners in the past 3 months (aRRR 3.14; 95% CI 1.16–8.55), while it was lower among those with sexual partner(s) living with HIV or of unknown HIV status (aRRR 0.25; 95% CI 0.07–0.92). PrEP method preference was influenced by product attributes and prior experiences with similar product forms commonly used in health care.

Conclusion
AGYW have varied preferences for biomedical PrEP method and those with higher sexual behavioral risk prefer long-acting methods. As we anticipate more available PrEP options, oral PrEP use should be supported among AGYW, especially for those with sexual partners living with HIV or of unknown HIV status.