Evaluating South African Weather Service information on Idai tropical cyclone and KwaZulu-Natal flood events

Severe weather events associated with strong winds and flooding can cause fatalities, injuries and damage to property. Detailed and accurate weather forecasts that are issued and communicated timeously, and actioned upon, can reduce the impact of these events. The responsibility to provide such forecasts usually lies with government departments or state-owned entities; in South Africa that responsibility lies with the South African Weather Service (SAWS). SAWS is also a regional specialised meteorological centre and therefore provides weather information to meteorological services within the Southern African Development Community (SADC). We evaluated SAWS weather information using near real-time observations and models on the nowcasting to short-range forecasting timescales during two extreme events. These are the Idai tropical cyclone in March 2019 which impacted Mozambique, Zimbabwe and Malawi resulting in over 1000 deaths, and the floods over the KwaZulu-Natal (KZN) province in April 2019 that caused over 70 deaths. Our results show that weather models gave an indication of these systems in advance, with warnings issued at least 2 days in advance in the case of Idai and 1 day in advance for the KZN floods. Nowcasting systems were also in place for detailed warnings to be provided as events progressed. Shortcomings in model simulations were shown, in particular on locating the KZN flood event properly and over/-underestimation of the event. The impacts experienced during the two events indicate that more needs to be done to increase weather awareness, and build disaster risk management systems, including disaster preparedness and risk reduction.Significance: This paper is relevant for all South Africans and the SADC region at large because it provides information on: the weather forecasting processes followed at the South African Weather Service, available early warning products in South Africa and for the SADC region made possible through the public purse, the performance of nowcasting and modelling systems in the case of predicting two extreme weather events that had adverse impacts on southern African society, and the dissemination of warnings of future extreme weather events

Conducting sexualities research: An outline of emergent issues and case studies from ten wellcome-funded projects [version 1; peer review: 3 approved]

© 2019 Kneale D et al. This letter seeks to synthesise methodological challenges encountered in a cohort of Wellcome Trust-funded research projects focusing on sexualities and health. The ten Wellcome Trust projects span a diversity of gender and sexual orientations and identities, settings; institutional and non-institutional contexts, lifecourse stages, and explore a range of health-related interventions. As researchers, we originate from a breadth of disciplinary traditions, use a variety of research methods and data sources. Despite this breadth, four common themes are found across the projects: (i) inclusivity representations and representativeness, (ii) lumping together of diverse groups, (iii) institutions and closed settings (iv) ethical and governance barriers

Conducting sexualities research: an outline of emergent issues and case studies from ten Wellcome-funded projects [version 1; peer review: awaiting peer review]

This letter seeks to synthesise methodological challenges encountered in a cohort of Wellcome Trust-funded research projects focusing on sexualities and health. The ten Wellcome Trust projects span a diversity of gender and sexual orientations and identities, settings; institutional and non-institutional contexts, lifecourse stages, and explore a range of health-related interventions.  As researchers, we originate from a breadth of disciplinary traditions, use a variety of research methods and data sources. Despite this breadth, four common themes are found across the projects: (i) inclusivity, representations and representativeness, (ii) lumping together of diverse groups, (iii) institutions and closed settings (iv) ethical and governance barriers

Comparative genomics of Cluster O mycobacteriophages

Mycobacteriophages - viruses of mycobacterial hosts - are genetically diverse but morphologically are all classified in the Caudovirales with double-stranded DNA and tails. We describe here a group of five closely related mycobacteriophages - Corndog, Catdawg, Dylan, Firecracker, and YungJamal - designated as Cluster O with long flexible tails but with unusual prolate capsids. Proteomic analysis of phage Corndog particles, Catdawg particles, and Corndog-infected cells confirms expression of half of the predicted gene products and indicates a non-canonical mechanism for translation of the Corndog tape measure protein. Bioinformatic analysis identifies 8-9 strongly predicted SigA promoters and all five Cluster O genomes contain more than 30 copies of a 17 bp repeat sequence with dyad symmetry located throughout the genomes. Comparison of the Cluster O phages provides insights into phage genome evolution including the processes of gene flux by horizontal genetic exchange

Immunodominant HIV-1 Cd4+ T Cell Epitopes in Chronic Untreated Clade C HIV-1 Infection

Background: A dominance of Gag-specific CD8+ T cell responses is significantly associated with a lower viral load in individuals with chronic, untreated clade C human immunodeficiency virus type 1 (HIV-1) infection. This association has not been investigated in terms of Gag-specific CD4+ T cell responses, nor have clade C HIV-1–specific CD4+ T cell epitopes, likely a vital component of an effective global HIV-1 vaccine, been identified. Methodology/Principal Findings: Intracellular cytokine staining was conducted on 373 subjects with chronic, untreated clade C infection to assess interferon-gamma (IFN-γ) responses by CD4+ T cells to pooled Gag peptides and to determine their association with viral load and CD4 count. Gag-specific IFN-γ–producing CD4+ T cell responses were detected in 261/373 (70%) subjects, with the Gag responders having a significantly lower viral load and higher CD4 count than those with no detectable Gag response (p<0.0001 for both parameters). To identify individual peptides targeted by HIV-1–specific CD4+ T cells, separate ELISPOT screening was conducted on CD8-depleted PBMCs from 32 chronically infected untreated subjects, using pools of overlapping peptides that spanned the entire HIV-1 clade C consensus sequence, and reconfirmed by flow cytometry to be CD4+ mediated. The ELISPOT screening identified 33 CD4+ peptides targeted by 18/32 patients (56%), with 27 of the 33 peptides located in the Gag region. Although the breadth of the CD4+ responses correlated inversely with viral load (p = 0.015), the magnitude of the response was not significantly associated with viral load. Conclusions/Significance: These data indicate that in chronic untreated clade C HIV-1 infection, IFN-γ–secreting Gag-specific CD4+ T cell responses are immunodominant, directed at multiple distinct epitopes, and associated with viral control

Examining oral pre-exposure prophylaxis (PrEP) literacy among participants in an HIV vaccine trial preparedness cohort study

Background: PrEP literacy is influenced by many factors including the types of information available and how it is interpreted. The level of PrEP literacy may influence acceptability and uptake. Methods: We conducted 25 in-depth interviews in a HIV vaccine trial preparedness cohort study. We explored what participants knew about PrEP, sources of PrEP knowledge and how much they know about PrEP. We used the framework approach to generate themes for analysis guided by the Social Ecological Model and examined levels of PrEP literacy using the individual and interpersonal constructs of the SEM. Results: We found that PrEP awareness is strongly influenced by external factors such as social media and how much participants know about HIV treatment and prevention in the local community. However, while participants highlighted the importance of the internet/social media as a source of information about PrEP they talked of low PrEP literacy in their communities. Participants indicated that their own knowledge came as a result of joining the HIV vaccine trial preparedness study. However, some expressed doubts about the effectiveness of the drug and worried about side effects. Participants commented that at the community level PrEP was associated with being sexually active, because it was used to prevent the sexual transmission of HIV. As a result, some participants commented that one could feel judged by the health workers for asking for PrEP at health facilities in the community. Conclusion: The information collected in this study provided an understanding of the different layers of influence around individuals that are important to address to improve PrEP acceptability and uptake. Our findings can inform strategies to address the barriers to PrEP uptake, particularly at structural and community levels. Trial registration: https://clinicaltrials.gov/ct2/show/NCT04066881

Effects of conversion of native cerrado vegetation to pasture on soil hydro-physical properties, evapotranspiration and streamflow on the Amazonian agricultural frontier

Understanding the impacts of land-use change on landscape-hydrological dynamics is one of the main challenges in the Northern Brazilian Cerrado biome, where the Amazon agricultural frontier is located. Motivated by the gap in literature assessing these impacts, we characterized the soil hydro-physical properties and quantified surface water fluxes from catchments under contrasting land-use in this region. We used data from field measurements in two headwater micro-catchments with similar physical characteristics and different land use, i.e. cerrado sensu stricto vegetation and pasture for extensive cattle ranching. We determined hydraulic and physical properties of the soils, applied ground-based remote sensing techniques to estimate evapotranspiration, and monitored streamflow from October 2012 to September 2014. Our results show significant differences in soil hydro-physical properties between the catchments, with greater bulk density and smaller total porosity in the pasture catchment. We found that evapotranspiration is smaller in the pasture (639 ± 31% mm yr-1) than in the cerrado catchment (1,004 ± 24% mm yr-1), and that streamflow from the pasture catchment is greater with runoff coefficients of 0.40 for the pasture and 0.27 for the cerrado catchment. Overall, our results confirm that conversion of cerrado vegetation to pasture causes soil hydro-physical properties deterioration, reduction in evapotranspiration reduction, and increased streamflow

Teenage pregnancy rates and associations with other health risk behaviours: a threewave cross-sectional study among South African school-going adolescents

BACKGROUND: Teenage pregnancy still remains high in low and middle-income countries (LMIC), as well as in highincome countries (HIC). It is a major contributor to maternal and child morbidity and mortality rates. Furthermore, it has social consequences, such as perpetuating the cycle of poverty including early school dropout by the pregnant adolescent, especially in sub-Saharan Africa (SSA). Few studies in SSA have investigated the trends in teenage pregnancy and the associated factors, while this is critical in fully understanding teenage pregnancy and for promotion of reproductive health among adolescents at large in SSA. METHODS: To examine the trends in teenage pregnancy and to identify associations with other health risk behaviours in South Africa (SA), a total of 31 816 South African school-going adolescents between 11 to 19 years of age were interviewed in three cross-sectional surveys. Data from the first (2002, n = 10 549), second (2008, n = 10 270) and the third (2011, n = 10 997) nationally representative South African youth risk behaviour surveys (YRBS) were used for this study. RESULTS: The overall prevalence of having ever been pregnant among the combined 3-survey sample was selfreported to be 11.0 % and stable across the three surveys. Sexual intercourse among adolescents in SA has decreased from 41.9 % in 2002 to 36.9 % in 2011. However, pregnancy among girls who ever had sex increased from 17.3 % (95 % CI: 0.16–0.19) in 2002, to 23.6 % (95 % CI: 0.21–0.26) in 2008 and decreased to 21.3 % (95 % CI: 0.19–0.23) in 2011. The odds for ever been pregnant were higher for girls who had 2 or more sexual partners (OR: 1.250, 95 % CI: 1.039–1.503), girls who ever used alcohol before sex (OR: 1.373, 95 % CI: 1.004–1.878), practised binge-drinking during the last month (OR: 0.624, 95 % CI: 0.503–0.774), and girls who used mandrax (OR: 1.968, 95 % CI: 1,243–3.117). The odds for never been pregnant were lower for those who used condoms (OR: 0.462, 95 % CI: 0.309–0.691). CONCLUSIONS: Girls continue to become pregnant at unacceptably high rates in SA. Sexual intercourse among adolescents in SA has decreased slightly. However, among those who are sexually active pregnancy prevalence rates have increased. More over, this is in the context of high prevalence of HIV and other STI. There is a need to address adolescents’ sexual and reproductive health, and several health risk behaviours, including substance use, that are associated with teenage pregnancy in SA.IS