Viral and bacterial etiology of severe acute respiratory illness among children < 5 years of age without influenza in Niger.

International audienceGlobally, pneumonia is the leading cause of morbidity and mortality in children, with the highest burden experienced in sub-Saharan Africa and Asia. However, there is a dearth of information on the etiology of severe acute respiratory illness (SARI) in Africa, including Niger. We implemented a retrospective study as part of national influenza sentinel surveillance in Niger. We randomly selected a sample of nasopharyngeal specimens collected from children <5 years of age hospitalized with SARI from January 2010 through December 2012 in Niger. The samples were selected from individuals that tested negative by real-time reverse transcription polymerase chain reaction (rRT-PCR) for influenza A and B virus. The samples were analyzed using the Fast Track Diagnostic Respiratory Pathogens 21plus Kit (BioMérieux, Luxemburg), which detects 23 respiratory pathogens including 18 viral and 5 bacterial agents. Among the 160 samples tested, 138 (86%) tested positive for at least one viral or bacterial pathogen; in 22 (16%) sample, only one pathogen was detected. We detected at least one respiratory virus in 126 (78%) samples and at least one bacterium in 102 (64%) samples. Respiratory syncytial virus (56/160; 35%), rhinovirus (47/160; 29%) and parainfluenza virus (39/160; 24%) were the most common viral pathogens detected. Among bacterial pathogens, Streptococcus pneumoniae (90/160; 56%) and Haemophilus influenzae type b (20/160; 12%) predominated. The high prevalence of certain viral and bacterial pathogens among children <5 years of age with SARI highlights the need for continued and expanded surveillance in Niger

Brucellosis knowledge, attitudes and practices of a South African communal cattle keeper group

Brucellosis remains an animal and public health concern in South Africa, given the intensity and widespread distribution of outbreaks in cattle. We conducted a cross-sectional survey among cattle keepers in the Whittlesea community of the Eastern Cape Province of South Africa, which utilises communal grazing. Individual cattle keepers (N = 227) who attended prearranged meetings in selected villages were interviewed using a structured questionnaire to assess their knowledge, attitude and practices (KAP) regarding bovine brucellosis. We compared KAP scores between previous brucellosis-affected villages and unaffected villages. We compared attitude and practices scores between those who had heard of brucellosis and those who had not and between those above the 75th percentile knowledge score and those below. The KAP for the study population were described using frequency tables. Scores of different groups were compared using the Welch t-test or the Wilcoxon rank-sum test. Knowledge scores of those who had heard of brucellosis (60%) showed a bimodal distribution with a 0/18 primary peak and 5–6/18 secondary peak. Attitude scores showed a median of 7/14 (interquartile range [IQR] 6–9), with 98% requesting more information on brucellosis. Practices scores showed a median of 6/18 (IQR 3–8), with high-risk practices identified that could facilitate brucellosis transmission. There were significant differences in attitude and practices scores between the groups above and below the 75th percentile knowledge score. The community showed poor knowledge, poor to average practices and average to good attitude. Identified high-risk practices highlight the risk of potential introduction and transmission of brucellosis between cattle and zoonotic transmission to humans

Risk mapping of Rinderpest sero-prevalence in Central and Southern Somalia based on spatial and network risk factors

The Somali livestock production system is oriented towards domestic trade and export with seasonal movement patterns of herds/flocks in search of water and pasture and towards export points. The objective of the study is to develop a predictive spatial model of presence of rinderpest.Habka loo diyaariyo xoola soomaliyeed ee loogu talagalay in lagu iibiyo dalka gudihiisa ama dibaddiisa, iyagoo xoolahaas loo kaxaynaayo hadba meeshi biyo iyo baad leh iyo goobtii laga dhoofinayaba. Qasdiga daraasaadkaani wuxuu yahay sidii loo hormarin lahaa habka looga hortegi lahaa cudurrada faafa ee lo'da.Il sistema di produzione di bestiame somalo è orientato verso il commercio interno e l'esportazione con movimenti stagionali delle mandrie/greggi in cerca di acqua e pascoli e verso i luoghi di esportazione. L'obiettivo dello studio è quello di sviluppare un modello spaziale predittivo della presenza di peste bovina

Evaluation of influenza vaccine effectiveness and description of circulating strains in outpatient settings in South Africa, 2014

The effectiveness of the trivalent seasonal influenza vaccine during the 2014 season in South Africa was assessed using a test-negative case–control study design including 472 cases and 362 controls. Influenza A(H3N2) was the dominant strain circulating. The overall vaccine effectiveness estimate, adjusted for age and underlying conditions, was43.1% (95% CI: 26.8-74.5). 2014 H3N2 viruses from South Africa were mainly in sublineage 3C.3 with accumulation of amino acid changes that differentiate them from the vaccine strain in 3C.1

Evaluation of influenza vaccine effectiveness and description of circulating strains in outpatient settings in South Africa, 2014

The effectiveness of the trivalent seasonal influenza vaccine during the 2014 season in South Africa was assessed using a test-negative case–control study design including 472 cases and 362 controls. Influenza A(H3N2) was the dominant strain circulating. The overall vaccine effectiveness estimate, adjusted for age and underlying conditions, was43.1% (95% CI: 26.8-74.5). 2014 H3N2 viruses from South Africa were mainly in sublineage 3C.3 with accumulation of amino acid changes that differentiate them from the vaccine strain in 3C.1

Rift Valley fever virus exposure amongst farmers, farm workers, and veterinary professionals in central South Africa

Rift Valley fever (RVF) is a re-emerging arboviral disease of public health and veterinary importance in Africa and the Arabian Peninsula. Major RVF epidemics were documented in South Africa in 1950–1951, 1974–1975, and 2010–2011. The number of individuals infected during these outbreaks has, however, not been accurately estimated. A total of 823 people in close occupational contact with livestock were interviewed and sampled over a six-month period in 2015–2016 within a 40,000 km2 study area encompassing parts of the Free State and Northern Cape provinces that were affected during the 2010–2011 outbreak. Seroprevalence of RVF virus (RVFV) was 9.1% (95% Confidence Interval (CI95%): 7.2–11.5%) in people working or residing on livestock or game farms and 8.0% in veterinary professionals. The highest seroprevalence (SP = 15.4%; CI95%: 11.4–20.3%) was detected in older age groups ( 40 years old) that had experienced more than one known large epidemic compared to the younger participants (SP = 4.3%; CI95%: 2.6–7.3%). The highest seroprevalence was in addition found in people who injected animals, collected blood samples (Odds ratio (OR) = 2.3; CI95%: 1.0–5.3), slaughtered animals (OR = 3.9; CI95%: 1.2–12.9) and consumed meat from an animal found dead (OR = 3.1; CI95%: 1.5–6.6), or worked on farms with dams for water storage (OR = 2.7; CI95%: 1.0–6.9). We estimated the number of historical RVFV infections of farm staff in the study area to be most likely 3849 and 95% credible interval between 2635 and 5374 based on seroprevalence of 9.1% and national census data. We conclude that human RVF cases were highly underdiagnosed and heterogeneously distributed. Improving precautions during injection, sample collection, slaughtering, and meat processing for consumption, and using personal protective equipment during outbreaks, could lower the risk of RVFV infection.U.S. Department of Defense, Defense Threat Reduction Agencyhttps://www.mdpi.com/journal/virusespm2020Animal and Wildlife Science

Estimating household contact matrices structure from easily collectable metadata

Contact matrices are a commonly adopted data representation, used to develop compartmental models for epidemic spreading, accounting for the contact heterogeneities across age groups. Their estimation, however, is generally time and effort consuming and model-driven strategies to quantify the contacts are often needed. In this article we focus on household contact matrices, describing the contacts among the members of a family and develop a parametric model to describe them. This model combines demographic and easily quantifiable survey-based data and is tested on high resolution proximity data collected in two sites in South Africa. Given its simplicity and interpretability, we expect our method to be easily applied to other contexts as well and we identify relevant questions that need to be addressed during the data collection procedure

Imputing direct and indirect vaccine effectiveness of childhood pneumococcal conjugate vaccine against invasive disease by surveying temporal changes in nasopharyngeal pneumococcal colonization

The limited capabilities in most low-middle income countries to study the benefit of pneumococcal conjugate vaccine (PCV) against invasive pneumococcal disease (IPD), calls for alternate strategies to assess this. We used a mathematical model, to predict the direct and indirect effectiveness of PCV by analyzing serotype specific colonization prevalence and IPD incidence prior to and following childhood PCV immunization in South Africa. We analyzed IPD incidence from 2005-2012 and colonization studies undertaken in HIV-uninfected and HIV-infected child-mother dyads from 2007-2009 (pre-PCV era), in 2010 (7-valent PCV era) and 2012 (13-valent PCV era). We compared the model-predicted to observed changes in IPD incidence, stratified by HIV-status in children >3 months to 5 years and also in women aged >18-45 years. We observed reductions in vaccine-serotype colonization and IPD due to vaccine serotypes among children and women after PCV introduction. Using the changes in vaccine-serotype colonization data, the model-predicted changes in vaccine-serotype IPD incidence rates were similar to the observed changes in PCV-unvaccinated children and adults, but not among children <24 months. Surveillance of colonization prior and following PCV use can be used to impute PCVs' indirect associations in unvaccinated age groups, including in high HIV-prevalence settings

Modeling the impact of COVID-19 nonpharmaceutical interventions on respiratory syncytial virus transmission in South Africa

Background: The South African government employed various nonpharmaceutical interventions (NPIs) to reduce the spread of SARS-CoV-2. Surveillance data from South Africa indicates reduced circulation of respiratory syncytial virus (RSV) throughout the 2020–2021 seasons. Here, we use a mechanistic transmission model to project the rebound of RSV in the two subsequent seasons. Methods: We fit an age-structured epidemiological model to hospitalization data from national RSV surveillance in South Africa, allowing for time-varying reduction in RSV transmission during periods of COVID-19 circulation. We apply the model to project the rebound of RSV in the 2022 and 2023 seasons. Results: We projected an early and intense outbreak of RSV in April 2022, with an age shift to older infants (6–23 months old) experiencing a larger portion of severe disease burden than typical. In March 2022, government alerts were issued to prepare the hospital system for this potentially intense outbreak. We then assess the 2022 predictions and project the 2023 season. Model predictions for 2023 indicate that RSV activity has not fully returned to normal, with a projected early and moderately intense wave. We estimate that NPIs reduced RSV transmission between 15% and 50% during periods of COVID-19 circulation. Conclusions: A wide range of NPIs impacted the dynamics of the RSV outbreaks throughout 2020–2023 in regard to timing, magnitude, and age structure, with important implications in a low- and middle-income countries (LMICs) setting where RSV interventions remain limited. More efforts should focus on adapting RSV models to LMIC data to project the impact of upcoming medical interventions for this disease.</p

A cost-effectiveness analysis of South Africa’s seasonal influenza vaccination programme

Background: Seasonal influenza imposes a significant health and economic burden in South Africa, particularly in populations vulnerable to severe consequences of influenza. This study assesses the cost-effectiveness of South Africa’s seasonal influenza vaccination strategy, which involves vaccinating vulnerable populations with trivalent inactivated influenza vaccine (TIV) during routine facility visits. Vulnerable populations included in our analysis are persons aged ≥ 65 years; pregnant women; persons living with HIV/AIDS (PLWHA), persons of any age with underlying medical conditions (UMC) and children aged 6–59 months. Method: We employed the World Health Organisation’s (WHO) Cost Effectiveness Tool for Seasonal Influenza Vaccination (CETSIV), a decision tree model, to evaluate the 2018 seasonal influenza vaccination campaign from a public healthcare provider and societal perspective. CETSIV was populated with existing country-specific demographic, epidemiologic and coverage data to estimate incremental cost-effectiveness ratios (ICERs) by comparing costs and benefits of the influenza vaccination programme to no vaccination. Results: The highest number of clinical events (influenza cases, outpatient visits, hospitalisation and deaths) were averted in PLWHA and persons with other UMCs. Using a cost-effectiveness threshold of US$3 400 per quality-adjusted life year (QALY), our findings suggest that the vaccination programme is cost-effective for all vulnerable populations except for children aged 6–59 months. ICERs ranged from ~US$ 1 750 /QALY in PLWHA to ~US$ 7 500/QALY in children. In probabilistic sensitivity analyses, the vaccination programme was cost-effective in pregnant women, PLWHA, persons with UMCs and persons aged ≥65 years in &gt;80% of simulations. These findings were robust to changes in many model inputs but were most sensitive to uncertainty in estimates of influenza-associated illness burden. Conclusion: South Africa's seasonal influenza vaccination strategy of opportunistically targeting vulnerable populations during routine visits is cost-effective. A budget impact analysis will be useful for supporting future expansions of the programme