17 research outputs found
DETECTION OF NON-INFLUENZA VIRUSES IN ACUTE RESPIRATORY INFECTIONS IN CHILDREN UNDER FIVE-YEAR-OLD IN COTE DâIVOIRE (JANUARY â DECEMBER 2013)
Background: Influenza sentinel surveillance in Cote dâIvoire showed that 70% of Acute Respiratory Infections (ARI)
cases remained without etiology. This work aims to describe the epidemiological, clinical, and virological pattern of
ARI that tested negative for influenza virus, in children under five years old.
Materials and Methods: one thousand and fifty nine samples of patients presenting influenza Like Illness (ILI) or
Severe Acute Respiratory Infections (SARI) symptoms were tested for other respiratory viruses using multiplex RTPCR
assays targeting 10 respiratory viruses.
Results: The following pathogens were detected as follows, hRV 31,92% (98/307), hRSV 24.4% (75/329), PIV 20.5%
(63/307), HCoV 229E 12,05% (37/307), hMPV 6.2% (19/307), HCoVOC43 1.0% (3/307) and EnV 1.0% (3/307).
Among the 1,059 specimens analyzed, 917 (86.6%) were ILI samples and 142 (23.4%) were SARI samples. The
proportion of children infected with at least one virus was 29.8% (273/917) in ILI cases and 23.9% (34/142) in SARI
cases. The most prevalent viruses, responsible for ILI cases were hRV with 35.89% (98/273) and hRSV in SARI cases
with 41.2% (14/34) of cases. Among the 1,059 patients, only 22 (2.1%) children presented risk factors related to the
severity of influenza virus infection.
Conclusion: This study showed that respiratory viruses play an important role in the etiology of ARI in children. For a
better understanding of the epidemiology of ARI and improved case management, it would be interesting in this
context to expand the surveillance of influenza to other respiratory viruses
Results from the second WHO external quality assessment for the molecular detection of respiratory syncytial virus, 2019-2020
BACKGROUND: External quality assessments (EQAs) for the molecular detection of human respiratory syncytial virus (RSV) are necessary to ensure the standardisation of reliable results. The Phase II, 2019-2020 World Health Organization (WHO) RSV EQA included 28 laboratories in 26 countries. The EQA panel evaluated performance in the molecular detection and subtyping of RSV-A and RSV-B. This manuscript describes the preparation, distribution, and analysis of the 2019-2020 WHO RSV EQA. METHODS: Panel isolates underwent whole genome sequencing and in silico primer matching. The final panel included nine contemporary, one historical virus and two negative controls. The EQA panel was manufactured and distributed by the UK National External Quality Assessment Service (UK NEQAS). National laboratories used WHO reference assays developed by the United States Centers for Disease Control and Prevention, an RSV subtyping assay developed by the Victorian Infectious Diseases Reference Laboratory (Australia), or other in-house or commercial assays already in use at their laboratories. RESULTS: An in silico analysis of isolates showed a good match to assay primer/probes. The panel was distributed to 28 laboratories. Isolates were correctly identified in 98% of samples for detection and 99.6% for subtyping. CONCLUSIONS: The WHO RSV EQA 2019-2020 showed that laboratories performed at high standards. Updating the composition of RSV molecular EQAs with contemporary strains to ensure representation of circulating strains, and ensuring primer matching with EQA panel viruses, is advantageous in assessing diagnostic competencies of laboratories. Ongoing EQAs are recommended because of continued evolution of mismatches between current circulating strains and existing primer sets
The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance.
Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern-particularly Alpha, Beta, Delta, and Omicron-on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century
The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance
INTRODUCTION
Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic.
RATIONALE
We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs).
RESULTS
Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants.
CONCLUSION
Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century
Epidemiological and virological characteristics of influenza B: results of the Global Influenza B Study
INTRODUCTION Literature on influenza focuses on influenza A,
despite influenza B having a large public health impact. The
Global Influenza B Study aims to collect information on global
epidemiology and burden of disease of influenza B since 2000.
METHODS Twenty-six countries in the Southern (n = 5) and
Northern (n = 7) hemispheres and intertropical belt (n = 14)
provided virological and epidemiological data. We calculated the
proportion of influenza cases due to type B and Victoria and
Yamagata lineages in each country and season; tested the correlation
between proportion of influenza B and maximum weekly influenzalike
illness (ILI) rate during the same season; determined the
frequency of vaccine mismatches; and described the age distribution
of cases by virus type.
RESULTS The database included 935 673 influenza cases (2000â
2013). Overall median proportion of influenza B was 22 6%, with no statistically significant differences across seasons. During seasons
where influenza B was dominant or co-circulated (>20% of total
detections), Victoria and Yamagata lineages predominated during
64% and 36% of seasons, respectively, and a vaccine mismatch was
observed in 25% of seasons. Proportion of influenza B was inversely
correlated with maximum ILI rate in the same season in the Northern
and (with borderline significance) Southern hemispheres. Patients
infected with influenza B were usually younger (5â17 years) than
patients infected with influenza A.
CONCLUSION Influenza B is a common disease with some
epidemiological differences from influenza A. This should be
considered when optimizing control/prevention strategies in different
regions and reducing the global burden of disease due to influenza.http://www.influenzajournal.comam201
Epidemiological and virological characteristics of influenza B: results of the Global Influenza B Study
Introduction Literature on influenza focuses on influenza A, despite influenza B having a large public health impact. The Global Influenza B Study aims to collect information on global epidemiology and burden of disease of influenza B since 2000
Temporal Patterns of Influenza A and B in Tropical and Temperate Countries: What Are the Lessons for Influenza Vaccination?
<div><p>Introduction</p><p>Determining the optimal time to vaccinate is important for influenza vaccination programmes. Here, we assessed the temporal characteristics of influenza epidemics in the Northern and Southern hemispheres and in the tropics, and discuss their implications for vaccination programmes.</p><p>Methods</p><p>This was a retrospective analysis of surveillance data between 2000 and 2014 from the Global Influenza B Study database. The seasonal peak of influenza was defined as the week with the most reported cases (overall, A, and B) in the season. The duration of seasonal activity was assessed using the maximum proportion of influenza cases during three consecutive months and the minimum number of months with â„80% of cases in the season. We also assessed whether co-circulation of A and B virus types affected the duration of influenza epidemics.</p><p>Results</p><p>212 influenza seasons and 571,907 cases were included from 30 countries. In tropical countries, the seasonal influenza activity lasted longer and the peaks of influenza A and B coincided less frequently than in temperate countries. Temporal characteristics of influenza epidemics were heterogeneous in the tropics, with distinct seasonal epidemics observed only in some countries. Seasons with co-circulation of influenza A and B were longer than influenza A seasons, especially in the tropics.</p><p>Discussion</p><p>Our findings show that influenza seasonality is less well defined in the tropics than in temperate regions. This has important implications for vaccination programmes in these countries. High-quality influenza surveillance systems are needed in the tropics to enable decisions about when to vaccinate.</p></div
Distribution of influenza virus types by age using case-based global surveillance data from twenty-nine countries, 1999-2014
Background: Influenza disease burden varies by age and this has important public health implications. We compared the proportional distribution of different influenza virus types within age strata using surveillance data from twenty-nine countries during 1999-2014 (N=358,796 influenza cases)
Distribution of influenza virus types by age using case-based global surveillance data from twenty-nine countries, 1999-2014
BACKGROUND : Influenza disease burden varies by age and this has important public health implications. We
compared the proportional distribution of different influenza virus types within age strata using surveillance data
from twenty-nine countries during 1999-2014 (N=358,796 influenza cases).
METHODS : For each virus, we calculated a Relative Illness Ratio (defined as the ratio of the percentage of cases in an
age group to the percentage of the country population in the same age group) for young children (0-4 years),
older children (5-17 years), young adults (18-39 years), older adults (40-64 years), and the elderly (65+ years). We
used random-effects meta-analysis models to obtain summary relative illness ratios (sRIRs), and conducted metaregression
and sub-group analyses to explore causes of between-estimates heterogeneity.
RESULTS : The influenza virus with highest sRIR was A(H1N1) for young children, B for older children, A(H1N1)
pdm2009 for adults, and (A(H3N2) for the elderly. As expected, considering the diverse nature of the national
surveillance datasets included in our analysis, between-estimates heterogeneity was high (I2>90%) for most sRIRs.
The variations of countriesâ geographic, demographic and economic characteristics and the proportion of
outpatients among reported influenza cases explained only part of the heterogeneity, suggesting that multiple
factors were at play.
CONCLUSIONS : These results highlight the importance of presenting burden of disease estimates by age group and
virus (sub)type.Table S1. Number of influenza cases caused by the
difference influenza viruses that were included in the analysis. The Global
Influenza B Study, 1999-2014.Figure S1. Forest plot of the Relative Illness Ratio for
patients aged 0-4 years infected with A(H1N1) influenza virus. The Global
Influenza B Study, 1999-2014. Figure S2. Forest plot of the Relative Illness
Ratio for patients aged 5-17 years infected with A(H1N1) influenza virus.
The Global Influenza B Study, 1999-2014. Figure S3. Forest plot of the
Relative Illness Ratio for patients aged 18-39 years infected with A(H1N1)
influenza virus. The Global Influenza B Study, 1999-2014. Figure S4. Forest
plot of the Relative Illness Ratio for patients aged 40-64 years infected
with A(H1N1) influenza virus. The Global Influenza B Study, 1999-2014.
Figure S5. Forest plot of the Relative Illness Ratio for patients aged 65+
years infected with A(H1N1) influenza virus. The Global Influenza B Study,
1999-2014.Table S2. Summary Relative Illness Ratio (sRIR), 95%
confidence intervals (95% CI) across age groups and influenza viruses by
categories of country ageing index. The Global Influenza B Study, 1999-
2014. Table S3. Summary Relative Illness Ratio (sRIR), 95% confidence
intervals (95% CI) across age groups and influenza viruses by percentage
of outpatients among cases reported to the influenza surveillance system.
The Global Influenza B Study, 1999-2014. Table S4. Summary Relative
Illness Ratio (sRIR), 95% confidence intervals (95% CI) across age groups
and influenza viruses by country latitude. The Global Influenza B Study,
1999-2014. Table S5. Summary Relative Illness Ratio (sRIR), 95%
confidence intervals (95% CI) across age groups and influenza viruses by
percentage of influenza cases caused by that influenza virus in the same
season. The Global Influenza B Study, 1999-2014. Table S6. Summary
Relative Illness Ratio (sRIR), 95% confidence intervals (95% CI) across age
groups and influenza viruses by percentage of influenza cases caused by
that influenza virus in the previous season. The Global Influenza B Study, 1999-2014. Table S7. Summary Relative Illness Ratio (sRIR), 95%
confidence intervals (95% CI) across age groups and influenza viruses
by categories of country gross domestic product (GDP) per capita. The
Global Influenza B Study, 1999-2014.The Global Influenza B Study is funded by an unrestricted research grant
from Sanofi Pasteur.https://bmcinfectdis.biomedcentral.comam2019Medical Virolog