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Rhizobia is a group of gram-negative soil-borne bacteria with several beneficial strains for biological nitrogen fixation in legume crops. Rhizobium strains are found native in the soil but where they are absent, commercial strains are inoculated on crops. We assessed the availability of native rhizobia in chickpea fields at two sites, with contrasting soil types, in NE South Africa. Serial dilutions were used to identify bacteria from soil samples and chickpea nodules sampled before sowing and at flowering, respectively. Our results indicated the absence of rhizobia strains at both sites. Burkholderia cenocepacia, Klebsiella variicola, Bacillus subtilis and Ochrobactrum spp, which are not important in agriculture but are often reported in clinical environments, were identified. Therefore, inoculating chickpea with compatible rhizobia strains may be necessary in some soils in this region. [ABSTRACT FROM AUTHOR]

Lablab purpureus is a multipurpose legume with potential as a vegetable, pulse or forage crop for smallholder farming systems of southern Africa. Its use in the region is limited because the long-season forage types available result in unreliable seed set. In the first of three field evaluations conducted in Limpopo province, South Africa, 33 introduced accessions and three local varieties were evaluated. Days to 50% flowering and to maturity ranged from 51 to >150 days after planting (DAP) and from 90 to 197 DAP, respectively. Most accessions produced <5 000 kg ha-1 biomass at 87 DAP. The highest seed yields were between 500 and 600 kg ha-1 produced generally by the earliest flowering lines. The second evaluation repeated these measurements for 24 of the earliest flowering accessions and from these eight were selected for a third evaluation. Five accessions (CPI52552, CPI60795, CPI81364, CQ3620 and Q6990B) were found to be consistently early flowering (range 43 to 70 DAP), high seed yielding (331 to 1 233 kg ha-1) and are recommended for further evaluation. Further work should be in partnership with farmers to test desirable eating qualities and there is need for seed multiplication for future commercial release. [ABSTRACT FROM AUTHOR]

Due to global climate change, droughts are likely to become more frequent and more severe in many regions such as in South Africa. In Limpopo, observed high climate variability and projected future climate change will likely increase future maize production risks. This paper evaluates drought patterns in Limpopo at two representative sites. We studied how drought patterns are projected to change under future climatic conditions as an important step in identifying adaptation measures (e.g., breeding maize ideotypes resilient to future conditions). Thirty-year time horizons were analyzed, considering three emission scenarios and five global climate models. We applied the WOFOST crop model to simulate maize crop growth and yield formation over South Africa's summer season. We considered three different crop emergence dates. Drought indices indicated that mainly in the scenario SSP5-8.5 (2051-2080), Univen and Syferkuil will experience worsened drought conditions (DC) in the future. Maize yield tends to decline and future changes in the emergence date seem to impact yield significantly. A possible alternative is to delay sowing date to November or December to reduce the potential yield losses. The grain filling period tends to decrease in the future, and a decrease in the duration of the growth cycle is very likely. Combinations of changed sowing time with more drought tolerant maize cultivars having a longer post-anthesis phase will likely reduce the potential negative impact of climate change on maize., (© 2022. The Author(s).)

Background: We aimed to assess the effectiveness of a single dose of the Ad26.COV2.S vaccine (Johnson & Johnson) in health-care workers in South Africa during two waves of the South African COVID-19 epidemic., Methods: In the single-arm, open-label, phase 3B implementation Sisonke study, health-care workers aged 18 years and older were invited for vaccination at one of 122 vaccination sites nationally. Participants received a single dose of 5 × 10 10 viral particles of the Ad26.COV2.S vaccine. Vaccinated participants were linked with their person-level data from one of two national medical insurance schemes (scheme A and scheme B) and matched for COVID-19 risk with an unvaccinated member of the general population. The primary outcome was vaccine effectiveness against severe COVID-19, defined as COVID-19-related admission to hospital, hospitalisation requiring critical or intensive care, or death, in health-care workers compared with the general population, ascertained 28 days or more after vaccination or matching, up to data cutoff. This study is registered with the South African National Clinical Trial Registry, DOH-27-022021-6844, ClinicalTrials.gov, NCT04838795, and the Pan African Clinical Trials Registry, PACTR202102855526180, and is closed to accrual., Findings: Between Feb 17 and May 17, 2021, 477 102 health-care workers were enrolled and vaccinated, of whom 357 401 (74·9%) were female and 119 701 (25·1%) were male, with a median age of 42·0 years (33·0-51·0). 215 813 vaccinated individuals were matched with 215 813 unvaccinated individuals. As of data cutoff (July 17, 2021), vaccine effectiveness derived from the total matched cohort was 83% (95% CI 75-89) to prevent COVID-19-related deaths, 75% (69-82) to prevent COVID-19-related hospital admissions requiring critical or intensive care, and 67% (62-71) to prevent COVID-19-related hospitalisations. The vaccine effectiveness for all three outcomes were consistent across scheme A and scheme B. The vaccine effectiveness was maintained in older health-care workers and those with comorbidities including HIV infection. During the course of the study, the beta (B.1.351) and then the delta (B.1.617.2) SARS-CoV-2 variants of concerns were dominant, and vaccine effectiveness remained consistent (for scheme A plus B vaccine effectiveness against COVID-19-related hospital admission during beta wave was 62% [95% CI 42-76] and during delta wave was 67% [62-71], and vaccine effectiveness against COVID-19-related death during beta wave was 86% [57-100] and during delta wave was 82% [74-89])., Interpretation: The single-dose Ad26.COV2.S vaccine shows effectiveness against severe COVID-19 disease and COVID-19-related death after vaccination, and against both beta and delta variants, providing real-world evidence for its use globally., Funding: National Treasury of South Africa, the National Department of Health, Solidarity Response Fund NPC, The Michael & Susan Dell Foundation, The Elma Vaccines and Immunization Foundation, and the Bill & Melinda Gates Foundation., Competing Interests: Declaration of interests L-GB declares honoraria for advisory roles from MSD, ViiV Health Care, and Gilead. RJL declares Department of Science and Innovation and South African Medical Research Council (SAMRC) funding to the KwaZulu-Natal Research Innovation and Sequencing Platform at the University of KwaZulu-Natal for the Network for Genomic Surveillance South Africa, which supported the genomic sequencing for this study; and committee membership of the Ministerial Advisory Committee on COVID-19 Vaccines (a committee that makes recommendations to the Minister of South Africa on the national COVID-19 vaccine programme. CC declares grants or contracts from CDC, PATH, the Bill & Melinda Gates Foundation, SAMRC, Wellcome Trust, and Sanofi Pasteur in the past 36 months. MG reports grants from SAMRC during the conduct of the study, and grants from the Bill & Melinda Gates Foundation outside of the submitted work. DBa reports grants from US National Institutes of Health (NIH) and Janssen during the conduct of the study; grants from Defense Advanced Research projects Agency, Massachusetts Consortium on Pathogen Readiness, Ragon Institute, the Bill & Melinda Gates Foundation, SAMRC, Henry Jackson Foundation, Musk Foundation, Gilead, Legend Bio, CureVac, Sanofi, Intima Bio, Alkermes, and Zentalis; and personal fees from SZQ Bio, Pfizer, Celsion, Avidea, Laronde, Meissa, and Vector Sciences outside of the submitted work DBr has three patents (63/121,482; 63/133,969; 63/135,182) licensed to Janssen. All other authors declare no competing interests., (Copyright © 2022 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY 4.0 license. Published by Elsevier Ltd.. All rights reserved.)

Sisonke is a multicentre, open-label, single-arm phase 3B vaccine implementation study of healthcare workers (HCWs) in South Africa, with prospective surveillance for 2 years. The primary endpoint is the rate of severe COVID‑19, including hospitalisations and deaths. The  Sisonke study enrolled and vaccinated participants nationally at potential vaccination roll-out sites between 17 February and 26 May 2021. After May 2021, additional HCWs were vaccinated as part of a sub-study at selected clinical research sites. We discuss 10 lessons learnt to strengthen national and global vaccination strategies:(i) consistently advocate for vaccination to reduce public hesitancy; (ii) an electronic vaccination data system (EVDS) is critical; (iii) facilitate access to a choice of vaccination sites, such as religious and community centres, schools, shopping malls and drive-through centres; (iv) let digitally literate people help elderly and marginalised people to register for vaccination; (v) develop clear 'how to' guides for vaccine storage, pharmacy staff and vaccinators; (vi) leverage instant messaging platforms, such as WhatsApp, for quick communication among staff at vaccination centres; (vii) safety is paramount - rapid health assessments are needed at vaccination centres to identify people at high risk of serious adverse events, including anaphylaxis or thrombosis with thrombocytopenia syndrome. Be transparent about adverse events and contextualise vaccination benefits, while acknowledging the small risks; (viii) provide real-time, responsive support to vaccinees post vaccination and implement an accessible national vaccine adverse events surveillance system; (ix) develop efficient systems to monitor and investigate COVID‑19 breakthrough infections; and (x) flexibility and teamwork are essential in vaccination centres across national, provincial and district levels and between public and private sectors.

Background: FEM-PrEP-a clinical trial of daily, oral emtricitabine/tenofovir disoproxil fumarate for HIV prevention among women in sub-Saharan Africa-did not show a reduction in HIV acquisition because of low adherence to the study pill. We conducted a follow-up study to identify reasons for nonadherence., Methods: Qualitative, semistructured interviews (n = 88) and quantitative, audio computer-assisted self-interviews (n = 224) were conducted with former FEM-PrEP participants in Bondo, Kenya, and Pretoria, South Africa. Thematic analysis was used to analyze the qualitative data, and descriptive statistics were used to describe audio computer-assisted self-interviews responses. Data are presented within the 5 categories of Ickovics' and Meisler's conceptual framework on adherence: (1) the individual, (2) trial characteristics and study pill regimen, (3) patient-provider relationship, (4) clinical setting, and (5) the disease., Results: Participants' explanations for nonadherence were primarily situated within 3 of the framework's 5 categories: (1) the individual, (2) trial characteristics and study pill regimen, and (3) the disease. Concerns about the investigational nature of the drug being tested and side effects were the prominent reasons reported for nonadherence. Participants also described being discouraged from taking the study pill by members of the community, their sexual partners, and other participants, primarily because of these same concerns. Limited acceptability of the pill's attributes influenced nonadherence for some participants as did concerns about HIV-related stigma. In addition, many participants reported that others continued in FEM-PrEP while not taking the study pill because of the trial's ancillary benefits and visit reimbursement-factors related to the clinical setting. Negative patient-provider relationships were infrequently reported as a factor that influenced nonadherence., Conclusions: Despite substantial study staff engagement with participants and communities, concerns about the study pill and discouragement from others seemed to have influenced nonadherence considerably. Alternative study designs or procedures and enhanced community engagement paradigms may be needed in future studies.

Introduction: Several clinical trials have demonstrated the efficacy of pre-exposure prophylaxis (PrEP) in reducing HIV risk. One concern with introducing PrEP is whether users will engage in riskier sexual behaviors., Methods: We assessed the effect that PrEP may have on sexual risk behaviors by administering a survey to 799 women in Bondo, Kenya, and Pretoria, South Africa. Participants were asked about their sexual behavior intentions twice--once as if they were taking PrEP and once as if they were not taking PrEP--within four risk situations (vignettes). They responded using a 5-point ordinal scale. We used a series of linear mixed effects models with an unstructured residual covariance matrix to estimate the between- and within-subject differences in the mean likelihood of engaging in risky sexual behavior across the PrEP and non-PrEP contexts. We also calculated the total percentage of participants who reported a greater likelihood of engaging in risky sexual behavior if taking PrEP than if not taking PrEP, by vignette., Results: We found statistically significant differences in the mean likelihood of engaging in risky sexual behavior with the between-subject comparison (-0.17, p < 0.01) and with the within-subject comparison (-0.31, p < 0.001). Depending on the vignette, 27% to 40% of participants reported a greater likelihood of engaging in risky sexual behavior if taking PrEP than if not taking PrEP., Conclusions: Our findings indicate that modest increases in risky sexual behavior could occur with PrEP. Although responses from the majority of participants suggest they would not be more likely to engage in risky sexual behavior if they took PrEP, a substantial proportion might. Programs rolling out PrEP should be prepared to assist similar women in making informed choices about reducing their risk of HIV and about their sexual health beyond HIV prevention.

Background: FEM-PrEP was unable to determine whether once-daily, oral emtricitabine/tenofovir disoproxil fumarate reduces the risk of HIV acquisition among women because of low adherence. Self-reported adherence was high, and pill-count data suggested good adherence. Yet, drug concentrations revealed limited pill use. We conducted a follow-up study with former participants in Bondo, Kenya, and Pretoria, South Africa, to understand factors that had influenced overreporting of adherence and to learn the whereabouts of unused pills., Methods: Qualitative, semistructured interviews were conducted with 88 participants, and quantitative, audio computer-assisted self-interviews were conducted with 224 participants. We used thematic analysis and descriptive statistics to analyze the qualitative and quantitative data, respectively., Results: In audio computer-assisted self-interviews, 31% (n = 70) said they had overreported adherence; the main reason was the belief that nonadherence would result in trial termination (69%, n = 48). A considerable percentage (35%, n = 78) acknowledged discarding unused pills. Few acknowledged giving their pills to someone else (4%, n = 10), and even fewer acknowledged giving them to someone with HIV (2%, n = 5). Many participants in the semistructured interviews said other participants had counted and removed pills from their bottles to appear adherent., Conclusions: Despite repeated messages that nonadherence would not upset staff, participants acknowledged several perceived negative consequences of reporting nonadherence, which made it difficult to report accurately. Uneasiness continued in the follow-up study, as many said they had not overreported during the trial. Efforts to improve self-reported measures should include identifying alternative methods for creating supportive environments that allow participants to feel comfortable reporting actual adherence.

Background: Incidence rates in the FEM-PrEP and VOICE trials demonstrate that women from diverse sub-Saharan African communities continue to be at substantial HIV risk., Objective: To describe and compare the sexual risk context of the study population from two FEM-PrEP trial sites-Bondo, Kenya, and Pretoria, South Africa., Methods: At baseline we collected information about demographics, sexual behaviors, and partnership beliefs through quantitative questionnaires with all participants (Bondo, n = 720; Pretoria, n = 750). To explore the sexual risk context, we also conducted qualitative, semi-structured interviews with HIV-negative participants randomly selected at several time points (Bondo, n = 111; Pretoria, n = 69)., Results: Demographics, sexual behavior, and partnership beliefs varied significantly between the sites. Bondo participants were generally older, had fewer years of schooling, and were more likely to be employed and married compared to Pretoria participants. Bondo participants were more likely to report multiple partners and not knowing whether their partner had HIV than Pretoria participants. A significantly higher percentage of Bondo participants reported engaging in sex without a condom with their primary and other partners compared to Pretoria participants. We found a borderline association between participants who reported not using condoms in the 4 weeks prior to baseline and lower risk of HIV infection, and no association between having more than one sexual partner at baseline and HIV infection., Discussion: Despite significantly different demographics, sexual behaviors, and partnership beliefs, many women in the FEM-PrEP trial were at risk of acquiring HIV as demonstrated by the sites' high HIV incidence. Though gender dynamics differed between the populations, they appear to play a critical role in women's sexual practices. The findings highlight different ways women from diverse contexts may be at-risk for HIV and the importance of providing HIV prevention options that are both effective and feasible given personal and social circumstances.

Introduction: Risk perception is a core construct in many behaviour change theories in public health. Individuals who believe they are at risk of acquiring an illness may be more likely to engage in behaviours to reduce that risk; those who do not feel at risk may be unlikely to engage in risk reduction behaviours. Among participants who seroconverted in two FEM-PrEP sites - Bondo, Kenya, and Pretoria, South Africa - we explored perceived HIV risk and worry about acquiring HIV prior to HIV infection., Methods: FEM-PrEP was a phase III clinical trial of once-daily, oral emtricitabine and tenofovir disoproxil fumarate for HIV prevention among women in sub-Saharan Africa. We asked all participants about their perceived HIV risk in the next four weeks, prior to HIV testing, during a quantitative face-to-face interview at enrolment and at quarterly follow-up visits. Among participants who seroconverted, we calculated the frequencies of their responses from the visit conducted closest to, but before, HIV acquisition. Also among women who seroconverted, we conducted qualitative, semi-structured interviews (SSIs) at weeks 1, 4 and 8 after participants' HIV diagnosis visit to retrospectively explore feelings of HIV worry. Applied thematic analysis was used to analyse the SSI data., Results: Among participants who seroconverted in Bondo and Pretoria, 52% reported in the quantitative interview that they had no chance of acquiring HIV in the next four weeks. We identified four processes of risk rationalization from the SSI narratives. In "protective behaviour," participants described at least one risk reduction behaviour they used to reduce their HIV risk; these actions made them feel not vulnerable to HIV, and therefore they did not worry about acquiring the virus. In "protective reasoning," participants considered their HIV risk but rationalized, based on certain events or beliefs, that they were not vulnerable and therefore did not worry about getting HIV. In "recognition of vulnerability," participants described reasons for being worried about getting HIV but said no or limited action was taken to reduce their perceived vulnerability. Participants with "no rationalization or action" did not describe any HIV worry or did not engage in HIV risk reduction behaviours., Conclusions: Women who are at substantial risk of acquiring HIV may underestimate their actual risk. Yet, others who accurately understand their HIV risk may be unable to act on their concerns. Perceived HIV risk and risk rationalization are important concepts to explore in risk reduction counselling to increase the use of HIV prevention strategies among women at risk of HIV.

The early bactericidal activities (EBAs) of 300 mg isoniazid, 18.5 mg isoniazid, 600 mg rifampicin and 800 mg ofloxacin given daily to 262 patients with newly diagnosed pulmonary tuberculosis in Cape Town, Nairobi, Madras and Hong Kong were measured by counting cfu and total acid-fast bacilli in sputum collections taken pre-treatment (S1), at 2 days (S3) and at 5 days (S6). In Cape Town, Nairobi and Madras, the cfu findings suggested that isoniazid produced a massive kill, perhaps of actively growing organisms, during the first 2 days (mean S1-S3 EBAs of 0.636-1.006) but was almost inactive thereafter (mean S3-S6 EBAs of 0.000-0.081), whereas rifampicin maintained moderate activity against slowly growing organisms throughout the 5 days (mean S3-S6 EBAs of 0.242-0.305). This finding suggests that EBAs measured during the 2-5 day interval might be able to assess the sterilizing activity of drugs. Ofloxacin had moderately high mean S1-S3 EBAs of 0.130-0.391. However, in Hong Kong rifampicin appeared to be the most bactericidal drug from the start, possibly because patients had more chronic disease. A method of adjusting the cfu EBAs using total counts was devised which decreased the variability between patients within a treatment group without altering the mean cfu EBA. This resulted in a large gain in precision in Hong Kong, suggesting that their estimates were greatly affected by type II variation, due to dilution of pus by saliva and bronchial secretions, whereas small or no gains were obtained in the other three centres, suggesting that the main cause of variability was type I, due to other factors.