Circulation of classic and recombinant human astroviruses detected in South Africa : 2009 to 2014

BACKGROUND : Astroviruses (AstVs) are associated with diarrhoeal and extra-intestinal infections in human, animal and avian species. A prevalence of 7% was reported in selected regions in SA while AstVs detected from clinical stool specimens were almost identical phylogenetically to strains identified in environmental and water samples. This study investigated the molecular diversity of astroviruses circulating between 2009 and 2014 in South Africa (SA). METHODS : Astroviruses detected in stool specimens collected from hospitalised children were investigated retrospectively. Astroviruses were characterised using type-specific RT-PCR, partial nucleotide sequence analyses in ORF1 and ORF2 and whole genome sequencing. Different genotypes were compared with clinical features to investigate genotype-related associations. The Vesikari severity scale (VSS) was evaluated for scoring astrovirus diarrhoeal infections. RESULTS : Of 405 astroviruses detected, 49.9 % (202/405) were characterised into 32 genotypes comprising 66.3 % (134/202) putative-recombinants and 33.7 % (68/202) classic strains. No trends by year of collection, age or site were observed. Whole genome analysis in eight strains revealed that genotypes assigned by partial nucleotide sequence analyses to five astroviruses were incorrect. Bivariate analyses showed there were no significant associations between genotypes and clinical symptoms or severity of infection. A comparison of Vesikari parameters with astrovirus-positive proxy values demonstrated that Vesikari scores for duration of diarrhoea and admission temperatures would result in a milder infection rating in astrovirus-positive cases. CONCLUSIONS : Diverse genotypes co-circulated with putative-recombinants predominating. Astrovirus classification was complicated by the lack of a consistent characterisation system and reliable reference database. The VSS should be used cautiously to rate astrovirus diarrhoea. While surveillance in communities and out-patient clinics must be continued, screening for human astroviruses in alternate hosts is needed to determine the reservoir species.The Rotavirus Sentinel Surveillance program was funded by GlaxoSmithKline (E-Track 200238). Research was supported by a National Health Laboratory Service Research Grant and the Poliomyelitis Research Foundation.http://www.elsevier.com/locate/jcv2021-12-31hj2021Medical Virolog

A systematic review on mobile health applications for foodborne disease outbreak management

BACKGROUND : Foodborne disease outbreaks are common and notifiable in South Africa; however, they are rarely reported and poorly investigated. Surveillance data from the notification system is suboptimal and limited, and does not provide adequate information to guide public health action and inform policy. We performed a systematic review of published literature to identify mobile application-based outbreak response systems for managing foodborne disease outbreaks and to determine the elements that the system requires to generate foodborne disease data needed for public action. METHODS : Studies were identified through literature searches using online databases on PubMed/Medline, CINAHL, Academic Search Complete, Greenfile, Library, Information Science & Technology. Search was limited to studies published in English during the period January 1990 to November 2020. Search strategy included various terms in varying combinations with Boolean phrases “OR” and “AND”. Data were collected following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Statement. A standardised data collection tool was used to extract and summarise information from identified studies. We assessed qualities of mobile applications by looking at the operating system, system type, basic features and functionalities they offer for foodborne disease outbreak management. RESULTS : Five hundred and twenty-eight (528) publications were identified, of which 48 were duplicates. Of the remaining 480 studies, 2.9% (14/480) were assessed for eligibility. Only one of the 14 studies met the inclusion criteria and reported on one mobile health application named MyMAFI (My Mobile Apps for Field Investigation). There was lack of detailed information on the application characteristics. However, based on minimal information available, MyMAFI demonstrated the ability to generate line lists, reports and offered functionalities for outbreak verification and epidemiological investigation. Availability of other key components such as environmental and laboratory investigations were unknown. CONCLUSIONS : There is limited use of mobile applications on management of foodborne disease outbreaks. Efforts should be made to set up systems and develop applications that can improve data collection and quality of foodborne disease outbreak investigations.http://www.biomedcentral.com/bmcpublichealtham2022Medical VirologySchool of Health Systems and Public Health (SHSPH

Scalar meson dynamics in Chiral Perturbation Theory

A comparison of the linear sigma model (L$\sigma$M) and Chiral Perturbation Theory (ChPT) predictions for pion and kaon dynamics is presented. Lowest and next-to-leading order terms in the ChPT amplitudes are reproduced if one restricts to scalar resonance exchange. Some low energy constants of the order $p^4$ ChPT Lagrangian are fixed in terms of scalar meson masses. Present values of these low energy constants are compatible with the L$\sigma$M dynamics. We conclude that more accurate values would be most useful either to falsify the L$\sigma$M or to show its capability to shed some light on the controversial scalar physics.Comment: 9 pages, REVTeX 4.0. Final version accepted for publicatio

Molecular epidemiology of human bocavirus infection in hospitalized children with acute gastroenteritis in South Africa, 2009‐2015

Human bocavirus (HBoV) is known to be associated with a variety of clinical manifestation including acute gastroenteritis (AGE). Despite their global prevalence, no data is available on the epidemiology of HBoV associated with AGE in South Africa (SA). Between April 2009 and April 2015, 3765 stool specimens were collected from children less than 5 years of age hospitalized with diarrhea. Specimens were screened for selected enteric viruses by enzyme immunoassay and quantitative polymerase chain reaction, bacteria by culture and parasites by staining and microscopy. HBoV was detected in 5.63% (212 of 3765) of cases, the majority of which were children ≤2 years (92%, 195 of 212), and were common in the summer and autumn months (60%; 128 of 212). Further investigations of coinfections showed that bacteria (adjusted odds ratio [aOR] = 2.20; 95% confidence interval [CI], 1.41‐3.45; P = .001) and sapovirus (aOR = 2.05; 95% CI, 1.08‐3.86; P = .027) were significantly associated with HBoV in multivariate analysis. HBoV genotyping was successful in 191 of the 212 samples with HBoV‐1 being the most prevalent genotype observed (79.6%; 152 of 191) followed by HBoV‐3 (13.6%; 26 of 191), HBoV‐2 (5.2%; 10 of 191), and HBoV‐4 (1.6%; 3 of 191). The high prevalence of HBoV‐1, a virus known to be associated with respiratory infections, and the association between HBoV‐positive specimens and already established AGE agents, suggests that HBoV may play a limited role in the observed AGE cases in SA.The Rotavirus Sentinel Surveillance Program was funded by GlaxoSmithKline (E-Track 200238). Research was supported by a National Health Laboratory Service Research Grant (GRANT004_94519) (RN).http://wileyonlinelibrary.com/journal/jmv2020-11-22hj2020Medical VirologyPlant Production and Soil ScienceSchool of Health Systems and Public Health (SHSPH

Diagnostic testing practices for diarrhoeal cases in South African public hospitals

BACKGROUND : Stool samples submitted for diagnostic testing represent a proportion of diarrhoeal cases seeking healthcare, and an even smaller proportion of diarrhoeal cases in the community. Despite this, surveillance relies heavily on these laboratory results. This study described diarrhoeal diagnostic practices and aetiological agents of diarrhoea in patients admitted to three South African public hospitals in order to understand biases in surveillance data, and inform guidelines, diagnostic and laboratory practices to improve clinical management. METHODS : A doctors’ survey was conducted to determine sample submission, diarrhoeal treatment and barriers to submitting samples for testing. Results for all samples submitted for routine diagnostics were obtained from the NHLS Central Data Warehouse. An enhanced surveillance study enrolled patients with acute diarrhoea at the same hospitals over the same period. Differences between routine culture results and molecular testing from the surveillance study were described. RESULTS : Stool samples were seldom submitted for diagnostic testing (median of 10% of admitted cases). Current diagnostic guidelines were not useful, hence most doctors (75.1%) relied on their own clinical judgement or judgement of a senior clinician. Although most doctors (90.3%) agreed that diagnostics were helpful for clinical management, they reported patients being unwilling to provide samples and long laboratory turnaround times. Routine diagnostic data represent cases with chronic diarrhoea and dysentery since doctors are most likely to submit specimens for these cases. Pathogen yield (number of pathogens detected for samples tested for specific pathogens) was significantly higher in the surveillance study, which used molecular methods, than through routine diagnostic services (73.3% versus 8.2%, p < 0.001), including for viruses (48.9% versus 2.6%, p < 0.001), bacteria (40.1% versus 2.2%, p < 0.001) and parasites (16.2% versus 3.6%, p < 0.001). Despite viruses being commonly detected in the surveillance study, viral testing was seldom requested in routine diagnostic investigations. CONCLUSIONS : Comprehensive diagnostic and treatment guidelines are required for diarrhoeal diseases. These guidelines should be informed by local epidemiological data, where diagnostic testing is reserved for cases most likely to benefit from specific treatment. Optimisation of current diagnostic processes and methods are required for these cases, specifically in terms of minimising turnaround times while maximising diagnostic acumen.The ANDEMIA study was supported by the German Federal Ministry of Education and Research.http://www.biomedcentral.com/bmcinfectdisam2023Medical VirologyPaediatrics and Child Healt

Studying Kaon-pion S-wave scattering in K-matrix formalism

We generalize our previous work on \pi\pi scattering to K\pi scattering, and re-analyze the experiment data of K\pi scattering below 1.6 GeV. Without any free parameter, we explain K\pi I=3/2 S-wave phase shift very well by using t-channel rho and u-channel K^* meson exchange. With the t-channel and u-channel meson exchange fixed as the background term, we fit the K\pi I=1/2 S-wave data of the LASS experiment quite well by introducing one or two s-channel resonances. It is found that there is only one s-channel resonance between K\pi threshold and 1.6 GeV, i.e., K_0^*(1430) with a mass around 1438~1486 MeV and a width about 346 MeV, while the t-channel rho exchange gives a pole at (450-480i) MeV for the amplitude.Comment: REVTeX4 file, 11 pages and 3 figure

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

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

A search for ferromagnetism in transition-metal-doped piezoelectric ZnO

We present the results of a computational study of ZnO in the presence of Co and Mn substitutional impurities. The goal of our work is to identify potential ferromagnetic ground states within the (Zn,Co)O or (Zn,Mn)O material systems that are also good candidates for piezoelectricity. We find that, in contrast to previous results, robust ferromagnetism is not obtained by substitution of Co or Mn on the Zn site, unless additional carriers (holes) are also incorporated. We propose a practical scheme for achieving such $p$-type doping in ZnO