Characterization of Rotavirus Strains Detected in Windhoek, Namibia during 1998-1999

Background. Namibia, located on the southwestern coast of southern Africa, is characterized by vast deserts, limited fresh water, and low population density. Mortality estimates among children <5 of age are 63 deaths per 1000 live-births, with diarrheal diseases contributing to 3% of these deaths. Data on the burden of rotavirus disease and circulating serotypes in Namibia are currently not available. Materials and methods. From May 1998 through December 1999, 815 stool specimens were collected from children <5 years of age who attended the Windhoek State Hospital, Windhoek, Namibia, for diarrhea. Specimens were screened for the presence of rotavirus antigens. Rotavirus-positive specimens were further analyzed to determine electropherotype, subgroup (SG) specificity, and G and P genotypes. Results. Rotavirus was detected in 113 (13.8%) of 815 specimens, with the majority of infections occurring in children <18 months of age. Strains bearing 1 long electropherotype, SGII, and G1P[8] or G1P[6] specificity predominated during the 20-month study period. In addition to the typical winter rotavirus season, a peak in rotavirus infection was also observed during the summer. Conclusions. Serotypes G1P[8], G1P[6], G1P[4], and G2P[4] were found throughout the study period, predominantly in children <18 months of age. The observed summer rotavirus peak coincided with increased rainfall in Namibia and an increase in the diversity of detected serotypes. During the October to December 1999 peak, 2 G9P[6] strains and 1 G8P[4] strain were identified. Expanded and updated information on prevalence of rotavirus infection, circulating serotypes, and burden of disease will be required to enable local government to make decisions on the implementation of rotavirus vaccination in Namibi

Economic evaluation of rotavirus vaccination in children aged under five years in South Africa

DATA SHARING STATEMENT : The datasets generated during and/or analysed during the current study are available from the corresponding author on reasonable request.BACKGROUND AND OBJECTIVE Evidence on the economic value of rotavirus vaccines in middle-income countries is limited. We aimed to model the implementation of three vaccines (human rotavirus, live, attenuated, oral vaccine [HRV, 2 doses]; rotavirus vaccine, live, oral, pentavalent [HBRV, 3 doses] and rotavirus vaccine, live attenuated oral, freeze-dried [BRV-PV, 3 doses] presented in 1-dose and 2-dose vials) into the South African National Immunisation Programme. METHODS Cost and cost-effectiveness analyses were conducted to compare three rotavirus vaccines using a static, deterministic, population model in children aged <5 years in South Africa from country payer and societal perspectives. Deterministic and probabilistic sensitivity analyses were conducted to assess the impact of uncertainty in model inputs. RESULTS The human rotavirus, live, attenuated, oral vaccine (HRV) was associated with cost savings versus HBRV from both perspectives, and versus BRV-PV 1-dose vial from the societal perspective. In the cost-effectiveness analysis, HRV was estimated to avoid 1,107 home care rotavirus gastroenteritis (RVGE) events, 247 medical visits, 35 hospitalisations, and 4 RVGErelated deaths versus HBRV and BRV-PV. This translated to 73 quality-adjusted life years gained. HRV was associated with lower costs versus HBRV from both payer (−$3.9M) and societal (−$11.5M) perspectives and versus BRV-PV 1-dose vial from the societal perspective (−$3.8M), dominating those options. HRV was associated with higher costs versus BRV-PV 1-dose vial from the payer perspective and versus BRV-PV 2‑dose vial from both payer and societal perspectives (ICERs:$51,834, $121,171, and$16,717, respectively), exceeding the assumed cost-effectiveness threshold of 0.5 GDP per capita. CONCLUSION Vaccination with a 2-dose schedule of HRV may lead to better health outcomes for children in South Africa compared with the 3-dose schedule rotavirus vaccines.This study was sponsored by GlaxoSmithKline Biologicals SA (Study identifier VEO-000364). Support for third-party writing assistance for this article, provided by Megan Thomas, Costello Medical, UK was funded by GSK in accordance with Good Publication Practice (GPP 2022) guidelines (https://www.ismpp.org/gpp-2022).https://www.springer.com/journal/40261am2024Medical VirologySDG-03:Good heatlh and well-bein

Diverse sapovirus genotypes identified in children hospitalised with gastroenteritis in selected regions of South Africa

BACKGROUND : Sapoviruses (SaVs) are recognised as causative agents of gastroenteritis worldwide. How-ever, data on the genetic diversity of this virus in Africa are lacking, particularly in the form of currentlong-term studies. OBJECTIVE : To determine the genetic diversity of SaVs in children hospitalised with gastroenteritis in SouthAfrica (SA). STUDY DESIGN : From April 2009 to December 2013, SaVs were characterised from stool specimens fromchildren hospitalised with gastroenteritis in four provinces of SA.RESULTS : Fourteen different SaV genotypes were identified from the 221 strains that were characterised.Genogroup (G) IV predominated overall and was detected in 24% (53/221) of specimens. The other iden-tified genotypes included six belonging to GI (GI.1–GI.3, GI.5, GI.6, and GI.7) and seven belonging to GII(GII.1–GII.7). CONCLUSION : This study has provided the first comprehensive data on the genetic diversity of SaVs in aclinical setting in SA, contributing to the global knowledge of this virus.http://www.elsevier.com/locate/jcv2017-03-31hb2016Medical Virolog

Emergence and Characterization of Serotype G9 Rotavirus Strains from Africa

Serotype G9 strains have been detected sporadically and in localized outbreaks in various African countries, including South Africa, Botswana, Malawi, Kenya, Cameroon, Nigeria, Ghana, Guinea-Bissau, Libya, and Mauritius. Serotype G9 strains were analyzed to investigate genogroup characteristics, including subgroup specificity, electropherotype, and P and G genotypes. In addition, the antigenic composition of the South African G9 strains was assessed. African G9 strains were associated with both DS-1-like characteristics and Wa-like characteristics, indicating the predisposition of G9 strains to frequently reassort. Despite these reassortment events, serotype G9 strains appear to maintain antigenic character in the outer capsid protein, as evident with the reaction of the South African G9 strains with the G9-specific monoclonal antibody F45:1. Phylogenetic analysis clustered African G9 strains geographically, regardless of genogroup characteristics, into 1 lineage (IIId). Two groups of G9 strains, originating in India and Japan, were identified in this lineage. Continuous surveillance of circulating rotavirus strains in Africa is vital to prepare for future vaccine implementation on a continent that clearly needs such preventative medicine

Tomographic entropy and cosmology

The probability representation of quantum mechanics including propagators and tomograms of quantum states of the universe and its application to quantum gravity and cosmology are reviewed. The minisuperspaces modeled by oscillator, free pointlike particle and repulsive oscillator are considered. The notion of tomographic entropy and its properties are used to find some inequalities for the tomographic probability determining the quantum state of the universe. The sense of the inequality as a lower bound for the entropy is clarified.Comment: 19 page

Identifying gaps in hand hygiene practice to support tailored target audience messaging in Soweto : a cross-sectional community survey

Effective risk communication is essential for outbreak mitigation, as recently highlighted during the coronavirus disease 2019 (COVID-19) pandemic. Hand hygiene is one of the proposed public health interventions to protect against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) acquisition and transmission along with social distancing, improved ventilation, environmental cleaning, and wearing of masks. Improving hand hygiene practices in the community requires an understanding of the socio-behavioural context. This cross-sectional community survey in Soweto identified gaps in hand hygiene, which can inform appropriate messaging at the community level. Only 42% of survey respondents practiced adequate hand hygiene. Tailored educational messaging should be targeted at young adults in particular, and the importance of soap for hand hygiene must be emphasised for all age groups. Risk communication should expand to focus on preventing multiple infectious diseases during and beyond the COVID-19 pandemic.GlaxoSmithKline and the German Federal Ministry of Education and Research. The CHAMPS programme is funded by the Bill & Melinda Gates Foundation.https://sajid.co.za/index.php/sajiddm2022Medical Virolog

Epidemiology of human astroviruses among children younger than 5 years : prospective hospital‐based sentinel surveillance in South Africa, 2009‐2014

BACKGROUND : The epidemiology of human astroviruses (HAstVs) in hospitalised patients less than 5 years of age from selected sites in South Africa was investigated. Diarrheagenic stool specimens collected from April 2009 to May 2014 were screened retrospectively for selected viruses, bacteria and parasites. METHOD : Patient data were analysed to identify epidemiologic factors most frequently detected with HAstV infections. The following case‐comparisons were investigated; HAstV‐positive and HAstV‐negative children, human immunodeficiency virus (HIV)‐infected and HIV‐uninfected (HAstV‐positive) children and HIV‐exposed and unexposed (HAstV‐positive HIV‐uninfected) children. RESULTS : Astrovirus was identified in 7.0% (234/3340) of cases and most frequently in ages 7 to 12 months (9.2%; 90/975) compared with 5.8% to 6.6% in other 6‐month age groups. No seasonal trends were observed. More HAstVs were detected in children from homes that used outdoor water sources (7.6%) compared to indoor sources [5.7%; adjusted odds ratio (aOR), 1.5; 95% CI, 1.1‐2.1; P = 0.009]. Astroviruses were detected in 8.4% (67/799) of HIV‐uninfected patients that were exposed to HIV compared with 5.9% (74/1257) of HIV‐unexposed patients ( P = 0.032). CONCLUSION : Astroviruses were most prevalent in children aged 7 to 12 months and were detected throughout the study period. The study was limited as only hospitalised patients were investigated and no comparisons were made to diarrhoea‐free control groups. Future HAstV surveillance should include community‐based studies and children presenting at outpatient facilities.The Rotavirus Sentinel Surveillance Program was funded by GlaxoSmithKline (E‐Track 200238). Research was supported by a National Health Laboratory Service Research (004_94494) (SN) and the Poliomyelitis Research Foundation (15/22) (NAP).http://wileyonlinelibrary.com/journal/jmv2020-02-01hj2018Medical Virolog

Microorganisms detected in intussusception cases and controls in children <3 years in South Africa from 2013 to 2017

A matched case-control evaluated infectious etiologies in children <3 years in post-rotavirus vaccine intussusception surveillance. Adenovirus and adenovirus types C, A, and B were detected more frequently in cases versus controls at statistically significant values. Wild-type rotavirus, rotavirus vaccine strains, and human herpesvirus were not associated with intussusception.The Bill & Melinda Gates Foundation and an Emerging Global Leader Award from the Fogarty International Center of the NIH.https://academic.oup.com/ofidhj2024Medical VirologyNon

Enriched biodiversity data as a resource and service

Background: Recent years have seen a surge in projects that produce large volumes of structured, machine-readable biodiversity data. To make these data amenable to processing by generic, open source “data enrichment” workflows, they are increasingly being represented in a variety of standards-compliant interchange formats. Here, we report on an initiative in which software developers and taxonomists came together to address the challenges and highlight the opportunities in the enrichment of such biodiversity data by engaging in intensive, collaborative software development: The Biodiversity Data Enrichment Hackathon. Results: The hackathon brought together 37 participants (including developers and taxonomists, i.e. scientific professionals that gather, identify, name and classify species) from 10 countries: Belgium, Bulgaria, Canada, Finland, Germany, Italy, the Netherlands, New Zealand, the UK, and the US. The participants brought expertise in processing structured data, text mining, development of ontologies, digital identification keys, geographic information systems, niche modeling, natural language processing, provenance annotation, semantic integration, taxonomic name resolution, web service interfaces, workflow tools and visualisation. Most use cases and exemplar data were provided by taxonomists. One goal of the meeting was to facilitate re-use and enhancement of biodiversity knowledge by a broad range of stakeholders, such as taxonomists, systematists, ecologists, niche modelers, informaticians and ontologists. The suggested use cases resulted in nine breakout groups addressing three main themes: i) mobilising heritage biodiversity knowledge; ii) formalising and linking concepts; and iii) addressing interoperability between service platforms. Another goal was to further foster a community of experts in biodiversity informatics and to build human links between research projects and institutions, in response to recent calls to further such integration in this research domain. Conclusions: Beyond deriving prototype solutions for each use case, areas of inadequacy were discussed and are being pursued further. It was striking how many possible applications for biodiversity data there were and how quickly solutions could be put together when the normal constraints to collaboration were broken down for a week. Conversely, mobilising biodiversity knowledge from their silos in heritage literature and natural history collections will continue to require formalisation of the concepts (and the links between them) that define the research domain, as well as increased interoperability between the software platforms that operate on these concepts

Diarrhoeal diseases in Soweto, South Africa, 2020 : a cross-sectional community survey

BACKGROUND : In South Africa, there are limited data on the burden of diarrhoea at a community level, specifically in older children and adults. This community survey estimated rates of and factors associated with diarrhoea across all ages and determined the proportion of cases presenting to healthcare facilities. METHODS : Households were enrolled from an existing urban health and demographic surveillance site. A household representative was interviewed to determine associated factors and occurrence of diarrhoea in the household, for all household members, in the past 2 weeks (including symptoms and health seeking behaviour). Diarrhoeal rate of any severity was calculated for 15 years age groups. Factors associated with diarrhoea and health seeking behaviour were investigated using binomial logistic regression. RESULTS : Diarrhoeal rate among respondents (2.5 episodes/person-year (95% CI, 1.8–3.5)) was significantly higher than for other household members (1.0 episodes/person-year (95% CI, 0.8–1.4); IRR = 2.4 (95% CI, 1.5–3.7) p < 0.001). Diarrhoeal rates were similar between age groups, however younger children (< 5 years) were more likely to present to healthcare facilities than adults (OR = 5.9 (95% CI, 1.1–31.4), p = 0.039). Oral rehydration solution was used in 44.8% of cases. Having a child between 5 and 15 years in the household was associated with diarrhoea (OR = 2.3 (95% CI, 1.3–3.9), p = 0.003) and, while 26.4% of cases sought healthcare, only 4.6% were hospitalised and only 3.4% of cases had a stool specimen collected. While the majority of cases were mild, 13.8% of cases felt they required healthcare but were unable to access it. CONCLUSION : Diarrhoeal rate was high across all age groups in this community; however, older children and adults were less likely to present to healthcare, and are therefore underrepresented through facility-based clinical surveillance. Current diarrhoeal surveillance represents a fraction of the overall cases occurring in the community.SUPPLEMENTARY MATERIAL: FIGURE S1. Health seeking for reported diarrhoeal episodes. TABLE S1. Factors associated with ORS knowledge.This work was supported by GlaxoSmithKline [E-Track 200238] and the German Federal Ministry of Education and Research [grant number 81203616] to SLJ. The CHAMPS program is funded by the Bill & Melinda Gates Foundation (Grant OPP1126780).http://www.biomedcentral.com/bmcpublichealtham2022Medical Virolog