128 research outputs found
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 âORâ and âANDâ. 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
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 (â11.5M) perspectives and versus BRV-PV 1-dose vial
from the societal perspective (â51,834, 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
Scalar meson dynamics in Chiral Perturbation Theory
A comparison of the linear sigma model (LM) 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
ChPT Lagrangian are fixed in terms of scalar meson masses. Present values
of these low energy constants are compatible with the LM dynamics. We
conclude that more accurate values would be most useful either to falsify the
LM 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, 2009â2015
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 â€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]â=â2.20; 95% confidence interval [CI], 1.41â3.45; Pâ=â.001) and sapovirus (aORâ=â2.05; 95% CI, 1.08â3.86; Pâ=â.027) were significantly associated with HBoV in multivariate analysis. HBoV genotyping was successful in 191 of the 212 samples with HBoVâ1 being the most prevalent genotype observed (79.6%; 152 of 191) followed by HBoVâ3 (13.6%; 26 of 191), HBoVâ2 (5.2%; 10 of 191), and HBoVâ4 (1.6%; 3 of 191). The high prevalence of HBoVâ1, a virus known to be associated with respiratory infections, and the association between HBoVâpositive 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 doctorsâ 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 hospitalâbased sentinel surveillance in South Africa, 2009â2014
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 caseâcomparisons were investigated; HAstVâpositive and HAstVânegative children, human immunodeficiency virus (HIV)âinfected and HIVâuninfected (HAstVâpositive) children and HIVâexposed and unexposed (HAstVâpositive HIVâuninfected) 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 6âmonth 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, 1.1â2.1; Pâ=â0.009]. Astroviruses were detected in 8.4% (67/799) of HIVâuninfected patients that were exposed to HIV compared with 5.9% (74/1257) of HIVâunexposed patients ( Pâ=â0.032).
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 diarrhoeaâfree control groups. Future HAstV surveillance should include communityâbased studies and children presenting at outpatient facilities.The Rotavirus Sentinel Surveillance Program was funded by GlaxoSmithKline (EâTrack 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
- âŠ