Identification and characterization of viruses infecting soybean (glycine max. L) in KwaZulu-Natal, South Africa.

Masters Degree. University of KwaZulu-Natal, Pietermaritzburg.Soybean (Glycine max L.) is the world's most important seed legume, primarily used as an oil crop and protein source. Plant viruses are a major limiting factor to soybean production worldwide. Many destructive plant viruses have been discovered to infect soybean on a global scale. In South Africa, few viruses have been detected infecting soybean crops. The studies of viruses on soybean were undertaken several years ago and it is possible that the virus population structure may have evolved over time. The aim of the study was to identify and characterise viruses infecting some soybean cultivars grown in KwaZulu-Natal. Additionally, to determine the incidence of seed transmitted viruses. The first part of the study was undertaken to detect and identify viruses presently infecting soybean grown in the province of KwaZulu-Natal, South Africa and determine the incidence of any seed transmitted viruses. Fifty-four soybean leaf samples exhibiting virus-like symptoms were collected from breeding lines growing in a Plant Pathology disease garden and greenhouses at the University of KwaZulu-Natal during the 2018 - 2019 and 2019 - 2020 growing seasons. Mechanical inoculation using inoculum prepared from the soybean field samples was done on Nicotiana tabacum L. to propagate the viruses in the collected samples. Symptom development was monitored on inoculated N. tabacum plants for 2-3 weeks after inoculation. The field samples were also subjected to Reverse Transcription Polymerase Chain Reaction (RT-PCR) and PCR to detect viruses known to infect soybean worldwide. Generic and specific primers were used to target specific coding regions of the viruses tested. Antibodies specific to cucumber mosaic virus (CMV) and tobacco mosaic virus (TMV) were used to test for virus presence in the field samples using double antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA). The study also focused on determining the incidence of seed transmitted viruses by planting different soybean varieties/lines and testing for virus presence after the plants had germinated. Virus presence was based on symptoms exhibited by the germinated plants and by DAS-ELISA. Results of this study showed that the inoculated N. tabacum plants developed virus-like symptoms. Soybean mosaic virus (SMV), TMV, CMV, and hibiscus chlorotic ringspot virus (HCRSV) were identified in the field samples based on PCR results. Seed transmission assays did not demonstrate the presence of viruses based on symptomatology and DAS-ELISA tests. The second part of the study was undertaken by using Next Generation Sequencing (NGS) to analyse the complete genome sequence of HCRSV infecting soybean in the province of KwaZulu-Natal, South frica Total RNA extracted from soybean samples exhibiting virus-like symptoms was combined into one sample and used as template for NGS analysis. The sequence data generated was analysed using Genome Detective Virus Tool version 1.133. The HCRSV complete genome sequence obtained was compared with other HCRSV sequences from GenBank database using BLASTN. Pairwise and Multiple sequence alignments of the sequences were done using ClustalW tool available in MEGA X. Phylogenetic analysis was done using nine closely related HCRSV sequences including turnip crinkle virus (TCV) which was used as an outgroup. The open reading frames (ORFs) for the HCRSV genome were determined using ORF finder and protein sizes were measured using Protein Molecular Weight software. Recombination events were analysed using RDP4 software. NGS data analysis revealed that HCRSV, CMV and TMV were present in the infected soybean samples. Results from the phylogenetic analysis showed that the NdlovuNS_HCRSV-SA isolate from this study (Accession number: OK636421) was closely related to isolate XM from China with a bootstrap value of 99%. Genome organisation analysis of the NdlovuNS_HCRSV_SA isolate compared with other HCRSV isolates suggested high levels of similarity. The BLAST analysis correlated with the results from the genome organisation data, with the HCRSV isolates sharing 87.87% - 97.10% nucleotide identity. Recombination analyses showed a single event confirming that the NdlovuNS_HCRSV-SA isolate is a recombinant strain. Accurate detection and identification of viruses plays an important role in virus disease management. Undetected viruses many occur and cause severe losses in soybean production. In this study, molecular detection techniques were used to accurately detectand identify the viruses infecting soybean field samples. It is important to emphasize that accurate and early detection of viruses is crucial for application of proper and effective control measures. The findings of this study will contribute to the body of knowledge on viruses infecting soybean in South Africa and will help in developing effective control measures

Independent and combined effects of improved water, sanitation, and hygiene, and improved complementary feeding, on child stunting and anaemia in rural Zimbabwe: a cluster-randomised trial.

BACKGROUND: Child stunting reduces survival and impairs neurodevelopment. We tested the independent and combined effects of improved water, sanitation, and hygiene (WASH), and improved infant and young child feeding (IYCF) on stunting and anaemia in in Zimbabwe. METHODS: We did a cluster-randomised, community-based, 2 × 2 factorial trial in two rural districts in Zimbabwe. Clusters were defined as the catchment area of between one and four village health workers employed by the Zimbabwe Ministry of Health and Child Care. Women were eligible for inclusion if they permanently lived in clusters and were confirmed pregnant. Clusters were randomly assigned (1:1:1:1) to standard of care (52 clusters), IYCF (20 g of a small-quantity lipid-based nutrient supplement per day from age 6 to 18 months plus complementary feeding counselling; 53 clusters), WASH (construction of a ventilated improved pit latrine, provision of two handwashing stations, liquid soap, chlorine, and play space plus hygiene counselling; 53 clusters), or IYCF plus WASH (53 clusters). A constrained randomisation technique was used to achieve balance across the groups for 14 variables related to geography, demography, water access, and community-level sanitation coverage. Masking of participants and fieldworkers was not possible. The primary outcomes were infant length-for-age Z score and haemoglobin concentrations at 18 months of age among children born to mothers who were HIV negative during pregnancy. These outcomes were analysed in the intention-to-treat population. We estimated the effects of the interventions by comparing the two IYCF groups with the two non-IYCF groups and the two WASH groups with the two non-WASH groups, except for outcomes that had an important statistical interaction between the interventions. This trial is registered with ClinicalTrials.gov, number NCT01824940. FINDINGS: Between Nov 22, 2012, and March 27, 2015, 5280 pregnant women were enrolled from 211 clusters. 3686 children born to HIV-negative mothers were assessed at age 18 months (884 in the standard of care group from 52 clusters, 893 in the IYCF group from 53 clusters, 918 in the WASH group from 53 clusters, and 991 in the IYCF plus WASH group from 51 clusters). In the IYCF intervention groups, the mean length-for-age Z score was 0·16 (95% CI 0·08-0·23) higher and the mean haemoglobin concentration was 2·03 g/L (1·28-2·79) higher than those in the non-IYCF intervention groups. The IYCF intervention reduced the number of stunted children from 620 (35%) of 1792 to 514 (27%) of 1879, and the number of children with anaemia from 245 (13·9%) of 1759 to 193 (10·5%) of 1845. The WASH intervention had no effect on either primary outcome. Neither intervention reduced the prevalence of diarrhoea at 12 or 18 months. No trial-related serious adverse events, and only three trial-related adverse events, were reported. INTERPRETATION: Household-level elementary WASH interventions implemented in rural areas in low-income countries are unlikely to reduce stunting or anaemia and might not reduce diarrhoea. Implementation of these WASH interventions in combination with IYCF interventions is unlikely to reduce stunting or anaemia more than implementation of IYCF alone. FUNDING: Bill & Melinda Gates Foundation, UK Department for International Development, Wellcome Trust, Swiss Development Cooperation, UNICEF, and US National Institutes of Health.The SHINE trial is funded by the Bill & Melinda Gates Foundation (OPP1021542 and OPP113707); UK Department for International Development; Wellcome Trust, UK (093768/Z/10/Z, 108065/Z/15/Z and 203905/Z/16/Z); Swiss Agency for Development and Cooperation; US National Institutes of Health (2R01HD060338-06); and UNICEF (PCA-2017-0002)

The role of agency in the implementation of Isoniazid Preventive Therapy (IPT): Lessons from <i>oMakoti</i> in uMgungundlovu District, South Africa

<div><p>Introduction</p><p>In response to revisions in global and national policy in 2011, six-month isoniazid preventive therapy (IPT) became freely available as a preventive measure for people living with HIV in the uMgungundlovu District of KwaZulu-Natal province, South Africa. Given a difference in uptake and completion by sex, we sought to explore the reasons why Zulu women were more likely to accept and complete IPT compared to men in an effort to inform future implementation.</p><p>Methods</p><p>Utilising a community-based participatory research approach and ethnographic methods, we undertook 17 individual and group interviews, and met regularly with grassroots community advisory teams in three Zulu communities located in uMgungundlovu District between March 2012–December 2016.</p><p>Findings & discussion</p><p>Three categories described women’s willingness to initiate IPT: women are caregivers, women are obedient, and appearance is important. The findings suggest that the success of IPT implementation amongst clinic-utilising women of uMgungundlovu is related to the cultural gender norms of <i>uMakoti</i>, isiZulu for “the bride” or “the wife.” We invoke the cultural concept of <i>inhlonipho</i>, meaning “to show respect,” to discuss how the cultural values of <i>uMakoti</i> may conflict with biomedical expectations of adherence. Such conflict can result in misinterpretations by healthcare providers or patients, and lead some patients to fear the repercussions of asking questions or contemplating discontinuation with the provider, preferring instead to appear obedient. We propose a shift in emphasis from adherence-focussed strategies, characteristic of the current biomedical approach, to practices that promote patient agency in an effort to offer IPT more appropriately.</p><p>Implications</p><p>Building on existing tools, namely the harm reduction model and the use of mini-ethnography, we provide guidance on how to support women to participate as agents in the decision to initiate or continue IPT, decisions which may also impact the health and choices of the family.</p></div

Sources of data by method of enquiry.

<p>Sources of data by method of enquiry.</p

Computer-aided interpretation of chest radiography reveals the spectrum of tuberculosis in rural South Africa

AbstractComputer-aided digital chest radiograph interpretation (CAD) can facilitate high-throughput screening for tuberculosis (TB), but its use in population-based active case-finding programs has been limited. In an HIV-endemic area in rural South Africa, we used a CAD algorithm (CAD4TBv5) to interpret digital chest x-rays (CXR) as part of a mobile health screening effort. Participants with TB symptoms or CAD4TBv5 score above the triaging threshold were referred for microbiological sputum assessment. During an initial pilot phase, a low CAD4TBv5 triaging threshold of 25 was selected to maximize TB case finding. We report the performance of CAD4TBv5 in screening 9,914 participants, 99 (1.0%) of whom were found to have microbiologically proven TB. CAD4TBv5 was able to identify TB cases at the same sensitivity but lower specificity as a blinded radiologist, whereas the next generation of the algorithm (CAD4TBv6) achieved comparable sensitivity and specificity to the radiologist. The CXRs of people with microbiologically confirmed TB spanned a range of lung field abnormality, including 19 (19.2%) cases deemed normal by the radiologist. HIV serostatus did not impact CAD4TB’s performance. Notably, 78.8% of the TB cases identified during this population-based survey were asymptomatic and therefore triaged for sputum collection on the basis of CAD4TBv5 score alone. While CAD4TBv6 has the potential to replace radiologists for triaging CXRs in TB prevalence surveys, population-specific piloting is necessary to set the appropriate triaging thresholds. Further work on image analysis strategies is needed to identify radiologically subtle active TB.</jats:p