351 research outputs found
Louse (Insecta : Phthiraptera) mitochondrial 12S rRNA secondary structure is highly variable
Lice are ectoparasitic insects hosted by birds and mammals. Mitochondrial 12S rRNA sequences obtained from lice show considerable length variation and are very difficult to align. We show that the louse 12S rRNA domain III secondary structure displays considerable variation compared to other insects, in both the shape and number of stems and loops. Phylogenetic trees constructed from tree edit distances between louse 12S rRNA structures do not closely resemble trees constructed from sequence data, suggesting that at least some of this structural variation has arisen independently in different louse lineages. Taken together with previous work on mitochondrial gene order and elevated rates of substitution in louse mitochondrial sequences, the structural variation in louse 12S rRNA confirms the highly distinctive nature of molecular evolution in these insects
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
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 (−11.5M) perspectives and versus BRV-PV 1-dose vial
from the societal perspective (−51,834, 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
A Monitor of Beam Polarization Profiles for the TRIUMF Parity Experiment
TRIUMF experiment E497 is a study of parity violation in pp scattering at an
energy where the leading term in the analyzing power is expected to vanish,
thus measuring a unique combination of weak-interaction flavour conserving
terms. It is desired to reach a level of sensitivity of 2x10^-8 in both
statistical and systematic errors. The leading systematic errors depend on
transverse polarization components and, at least, the first moment of
transverse polarization. A novel polarimeter that measures profiles of both
transverse components of polarization as a function of position is described.Comment: 19 pages LaTeX, 10 PostScript figures. To appear in Nuclear
Instruments and Methods in Physics Research, Section
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
Molecular epidemiology of group A Rotaviruses in water sources and selected raw vegetables in Southern Africa
Group A rotaviruses (RVs) are the most important cause of acute viral gastroenteritis in infants and young children. In this study raw and treated drinking water supplies at plants in two geographic areas, as well as selected irrigation water and corresponding raw vegetables in three regions of southern Africa, were screened for the presence of RVs using molecular techniques. Group A RVs were detected in 11.8% of partially treated and 1.7% of finally treated drinking water samples and in 14% of irrigation water samples and 1.7% of corresponding raw vegetable samples. Type-specific reverse transcriptase-PCR and sequence analysis revealed the presence of multiple types (G1, G2, G8, and G9) in irrigation water and single types (G1 or G3) in raw and treated drinking water. Group A RVs detected in all samples consisted of mixed P types (P[4], P[6], P[8], and P[9]), with P[6] predominating. The detection of types G8, G9, and P[6] reflects the emergence of these types in clinical infections. The similarity of environmental types to those in patients with clinical RV infections confirms the value of wastewater screening as a tool for assessing RVs circulating in communities, with the benefit of detecting types that cause both clinical and subclinical infections. The results provide new information on RV types in water and related environments and identify the potential risk of waterborne transmission. In addition, the presence of RVs in drinking water underlines shortcomings in quality specifications. These data provide valuable information regarding the prevalence of RVs in environmental sources, with important implications for vaccine development.This study was supported by grants from the Water Research Commission, the Poliomyelitis Research Foundation, and the Research Committee, School of Medicine, University of Pretoria. A postdoctoral fellowship for W.B.V.Z. from the South African Medical Research Council is also gratefully acknowledged
Parity Violation in Proton-Proton Scattering
Measurements of parity-violating longitudinal analyzing powers (normalized
asymmetries) in polarized proton-proton scattering provide a unique window on
the interplay between the weak and strong interactions between and within
hadrons. Several new proton-proton parity violation experiments are presently
either being performed or are being prepared for execution in the near future:
at TRIUMF at 221 MeV and 450 MeV and at COSY (Kernforschungsanlage Juelich) at
230 MeV and near 1.3 GeV. These experiments are intended to provide stringent
constraints on the set of six effective weak meson-nucleon coupling constants,
which characterize the weak interaction between hadrons in the energy domain
where meson exchange models provide an appropriate description. The 221 MeV is
unique in that it selects a single transition amplitude (3P2-1D2) and
consequently constrains the weak meson-nucleon coupling constant h_rho{pp}. The
TRIUMF 221 MeV proton-proton parity violation experiment is described in some
detail. A preliminary result for the longitudinal analyzing power is Az = (1.1
+/-0.4 +/-0.4) x 10^-7. Further proton-proton parity violation experiments are
commented on. The anomaly at 6 GeV/c requires that a new multi-GeV
proton-proton parity violation experiment be performed.Comment: 13 Pages LaTeX, 5 PostScript figures, uses espcrc1.sty. Invited talk
at QULEN97, International Conference on Quark Lepton Nuclear Physics --
Nonperturbative QCD Hadron Physics & Electroweak Nuclear Processes --, Osaka,
Japan May 20--23, 199
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