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Health care workers (HCWs) represent a vulnerable population during epidemic periods. Our cohort study aimed to estimate the risk of infection and associated factors among HCWs during the first wave of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Madagascar.A prospective cohort study was carried out in three hospitals that oversaw the first cases of COVID-19. Monthly ELISA-based serological tests were conducted, and nasopharyngeal swabs were collected in the case of symptoms linked to COVID-19 for RT-PCR analysis. Survival analyses were used to determine factors associated with SARS-CoV-2 infection.The study lasted 7 months from May 2020. We included 122 HCWs, 61.5% of whom were women. The median age was 31.9 years (IQR: 26.4-42.3). In total, 42 (34.4%) had SARS-CoV-2 infections, of which 20 were asymptomatic (47.6%). The incidence of SARS-CoV-2 infection was 9.3% (95% CI [6.5-13.2]) person-months. Sixty-five HCWs presented symptoms, of which 19 were positive by RT-PCR. When adjusted for exposure to deceased cases, infection was more frequent in HCWs younger than 30 years of age (RR = 4.9, 95% CI [1.4-17.2]).Our results indicate a high incidence of infection with SARS-CoV-2 among HCWs, with a high proportion of asymptomatic cases. Young HCWs are more likely to be at risk than others. Greater awareness among young people is necessary to reduce the threat of infection among HCWs.

The genus Henipavirus (family Paramyxoviridae) is currently comprised of seven viruses, four of which have demonstrated prior evidence of zoonotic capacity. These include the biosafety level 4 agents Hendra (HeV) and Nipah (NiV) viruses, which circulate naturally in pteropodid fruit bats. Here, we describe and characterize Angavokely virus (AngV), a divergent henipavirus identified in urine samples from wild, Madagascar fruit bats. We report the near-complete 16,740 nt genome of AngV, which encodes the six major henipavirus structural proteins (nucleocapsid, phosphoprotein, matrix, fusion, glycoprotein, and L polymerase). Within the phosphoprotein (P) gene, we identify an alternative start codon encoding the AngV C protein and a putative mRNA editing site where the insertion of one or two guanine residues encodes, respectively, additional V and W proteins. In other paramyxovirus systems, C, V, and W are accessory proteins involved in antagonism of host immune responses during infection. Phylogenetic analysis suggests that AngV is ancestral to all four previously described bat henipaviruses—HeV, NiV, Cedar virus (CedV), and Ghanaian bat virus (GhV)—but evolved more recently than rodent- and shrew-derived henipaviruses, Mojiang (MojV), Gamak (GAKV), and Daeryong (DARV) viruses. Predictive structure-based alignments suggest that AngV is unlikely to bind ephrin receptors, which mediate cell entry for all other known bat henipaviruses. Identification of the AngV receptor is needed to clarify the virus’s potential host range. The presence of V and W proteins in the AngV genome suggest that the virus could be pathogenic following zoonotic spillover.ImportanceHenipaviruses include highly pathogenic emerging zoonotic viruses, derived from bat, rodent, and shrew reservoirs. Bat-borne Hendra (HeV) and Nipah (NiV) are the most well-known henipaviruses, for which no effective antivirals or vaccines for humans have been described. Here we report the discovery and characterization of a novel henipavirus, Angavokely virus (AngV), isolated from wild fruit bats in Madagascar. Genomic characterization of AngV reveals all major features associated with pathogenicity in other henipaviruses, suggesting that AngV could be pathogenic following spillover to human hosts. Our work suggests that AngV is an ancestral bat henipavirus which likely uses viral entry pathways distinct from those previously described for HeV and NiV. In Madagascar, bats are consumed as a source of human food, presenting opportunities for cross-species transmission. Characterization of novel henipaviruses and documentation of their pathogenic and zoonotic potential are essential to predicting and preventing the emergence of future zoonoses that cause pandemics.

To assess the genetic diversity of circulating dengue virus 2 (DENV-2) in Senegal, we analyzed nine newly generated complete genomes of strains isolated during the 2018 outbreaks and 06 sequences obtained in 2018 and 2019 from Thiès and Rosso, respectively. Phylogenetic analyses revealed that Senegalese strains belonged to the cosmopolitan genotype of DENV-2, but we observed intragenotype variability leading to a divergence in two clades associated with specific geographic distribution. We report two DENV-2 variants belonging to two distinct clades. Isolates from the "Northern clade" (n = 8) harbored three nonsynonymous mutations (V1183M, R1405K, P2266T) located respectively on NS2A, NS2B, and NS4A, while isolates from the "Western clade" (n = 7) had two nonsynonymous mutations (V1185E, V3214E) located respectively in the NS2A and NS5 genes. These findings call for phylogeographic analysis to investigate routes of introductions, dispersal patterns, and in-depth in vitro and functional study to elucidate the impact of observed mutations on viral fitness, spread, epidemiology, and pathology.

Background Poliomyelitis outbreaks due to pathogenic vaccine-derived polioviruses (VDPVs) are threatening and complicating the global polio eradication initiative. Most of these VDPVs are genetic recombinants with non-polio enteroviruses (NPEVs) of species C. Little is known about factors favoring this genetic macroevolution process. Since 2001, Madagascar has experienced several outbreaks of poliomyelitis due to VDPVs, and most of VDPVs were isolated in the south of the island. The current study explored some of the viral factors that can promote and explain the emergence of recombinant VDPVs in Madagascar. Methods Between May to August 2011, we collected stools from healthy children living in two southern and two northern regions of Madagascar. Virus isolation was done in RD, HEp-2c, and L20B cell lines, and enteroviruses were detected using a wide-spectrum 5ʹ-untranslated region RT-PCR assay. NPEVs were then sequenced for the VP1 gene used for viral genotyping. Results Overall, we collected 1309 stools, of which 351 NPEVs (26.8%) were identified. Sequencing revealed 33 types of viruses belonging to three different species: Enterovirus A (8.5%), Enterovirus B (EV-B, 40.2%), and Enterovirus C (EV-C, 51.3%). EV-C species included coxsackievirus A13, A17, and A20 previously described as putative recombination partners for poliovirus vaccine strains. Interestingly, the isolation rate was higher among stools originating from the South (30.3% vs. 23.6%, p-value = 0.009). EV-C were predominant in southern sites (65.7%) while EV-B predominated in northern sites (54.9%). The factors that explain the relative abundance of EV-C in the South are still unknown. Conclusions Whatever its causes, the relative abundance of EV-C in the South of Madagascar may have promoted the infections of children by EV-C, including the PV vaccine strains, and have favored the recombination events between PVs and NPEVs in co-infected children, thus leading to the recurrent emergence of recombinant VDPVs in this region of Madagascar.

International audience; Influenza virus types A and B are responsible for acute viral infections that affect annually 1 billion people, with 290,000 to 650,000 deaths worldwide. In this study, we investigated the circulation of influenza B viruses over a 10-year period (2010–2019). Specimens from patients suspected of influenza infection were collected. Influenza detection was performed following RNA extraction and real-time RT-PCR. Genes coding for hemagglutinin (HA) and neuraminidase (NA) of influenza B viruses were partially sequenced, and phylogenetic analyses were carried out subsequently. During the study period, we received and tested a total of 15,156 specimens. Influenza B virus was detected in 1322 (8.7%) specimens. The mean age of influenza B positive patients was 10.9 years. When compared to reference viruses, HA genes from Senegalese circulating viruses showed deletions in the HA1 region. Phylogenetic analysis highlighted the co-circulation of B/Victoria and B/Yamagata lineage viruses with reassortant viruses. We also noted a clear seasonal pattern of circulation of influenza B viruses in Senegal.

As the national reference laboratory for febrile illness in Madagascar, we processed samples from the first epidemic wave of COVID-19, between March and September 2020. We fit generalized additive models to cycle threshold (Ct) value data from our RT-qPCR platform, demonstrating a peak in high viral load, low-Ct value infections temporally coincident with peak epidemic growth rates estimated in real time from publicly-reported incidence data and retrospectively from our own laboratory testing data across three administrative regions. We additionally demonstrate a statistically significant effect of duration of time since infection onset on Ct value, suggesting that Ct value can be used as a biomarker of the stage at which an individual is sampled in the course of an infection trajectory. As an extension, the population-level Ct distribution at a given timepoint can be used to estimate population-level epidemiological dynamics. We illustrate this concept by adopting a recently-developed, nested modeling approach, embedding a within-host viral kinetics model within a population-level Susceptible-Exposed-Infectious-Recovered (SEIR) framework, to mechanistically estimate epidemic growth rates from cross-sectional Ct distributions across three regions in Madagascar. We find that Ct-derived epidemic growth estimates slightly precede those derived from incidence data across the first epidemic wave, suggesting delays in surveillance and case reporting. Our findings indicate that public reporting of Ct values could offer an important resource for epidemiological inference in low surveillance settings, enabling forecasts of impending incidence peaks in regions with limited case reporting.

International audience; The COVID-19 pandemic caused by the novel coronavirus SARS-CoV-2 continues to have a major impact on healthcare and social systems throughout the world. As the clinical and epidemiological features of COVID-19 have many parallels with influenza, it is important to ensure optimal management of both respiratory diseases as we anticipate their continued co-circulation. In particular, there is a need to ensure that effective surveillance and diagnostic capacities are in place to monitor these and other respiratory viruses, as this will underpin decisions on the appropriate clinical management of the respective diseases. As such, we propose a series of key recommendations for stakeholders, public health authorities, primary care physicians and surveillance bodies that will help mitigate the combined risks of concurrent influenza epidemics and the COVID-19 pandemic. We advocate the judicious use of influenza vaccines and antivirals, particularly among groups at high risk of complications, with healthcare workers also considered a priority for vaccination. It is likely that the increased use of emerging technologies such as telemedicine and contact tracing will permanently change our approach to managing infectious disease. The use of these technologies, alongside existing pharmaceutical strategies, will ensure that we achieve a holistic approach to the global public health measures needed to deal with the combined threat of influenza and COVID-19. Ensuring that this approach is optimal will be key as we move from a reactive pandemic response towards preparing for the long-term management of the remarkable clinical burden associated with these respiratory pathogens.

International audience; In late 2017, Madagascar experienced a large urban outbreak of pneumonic plague, the largest outbreak to date this century. During the outbreak, there were widespread reports of plague patients presenting with atypical symptoms, such as prolonged duration of illness and upper respiratory tract symptoms. Reported mortality among plague cases was also substantially lower than that reported in the literature (25% versus 50% in treated patients). A prospective multicenter observational study was carried out to investigate potential reasons for these atypical presentations. Few subjects among our cohort had confirmed or probable plague, suggesting that, in part, there was overdiagnosis of plague cases by clinicians. However, 35% subjects reported using an antibiotic with anti-plague activity before hospital admission, whereas 55% had antibiotics with anti-plague activity detected in their serum at admission. Although there may have been overdiagnosis of plague by clinicians during the outbreak, the high frequency of community antibiotic may partly explain the relatively few culture-positive sputum samples during the outbreak. Community antibiotic use may have also altered the clinical presentation of plague patients. These issues make accurate detection of patients and the development of clinical case definitions and triage algorithms in urban pneumonic plague outbreaks difficult.

International audience; We conducted a national human serologic study of a hantavirus detected in Madagascar rodents using a commercial kit and a new ELISA targeting the virus. Our results suggest a conservative estimate of 2.7% (46/1,680) IgG seroprevalence. A second single-district study using the new ELISA revealed a higher prevalence (7.2%; 10/139).

Bats are natural reservoirs for both Alpha- and Betacoronaviruses and the hypothesized original hosts of five of seven known zoonotic coronaviruses. To date, the vast majority of bat coronavirus research has been concentrated in Asia, though coronaviruses are globally distributed; indeed, SARS-CoV and SARS-CoV-2-related Betacoronaviruses in the subgenus Sarbecovirus have been identified circulating in Rhinolophid bats in both Africa and Europe, despite the relative dearth of surveillance in these regions. As part of a long-term study examining the dynamics of potentially zoonotic viruses in three species of endemic Madagascar fruit bat (Pteropus rufus, Eidolon dupreanum, Rousettus madagascariensis), we carried out metagenomic Next Generation Sequencing (mNGS) on urine, throat, and fecal samples obtained from wild-caught individuals. We report detection of RNA derived from Betacoronavirus subgenus Nobecovirus in fecal samples from all three species and describe full genome sequences of novel Nobecoviruses in P. rufus and R. madagascariensis. Phylogenetic analysis indicates the existence of five distinct Nobecovirus clades, one of which is defined by the highly divergent ancestral sequence reported here from P. rufus bats. Madagascar Nobecoviruses derived from P. rufus and R. madagascariensis demonstrate, respectively, Asian and African phylogeographic origins, mirroring those of their fruit bat hosts. Bootscan recombination analysis indicates significant selection has taken place in the spike, nucleocapsid, and NS7 accessory protein regions of the genome for viruses derived from both bat hosts. Madagascar offers a unique phylogeographic nexus of bats and viruses with both Asian and African phylogeographic origins, providing opportunities for unprecedented mixing of viral groups and, potentially, recombination. As fruit bats are handled and consumed widely across Madagascar for subsistence, understanding the landscape of potentially zoonotic coronavirus circulation is essential for mitigation of future zoonotic threats.

Despite the establishment of Rabies surveillance in animals and humans since 2008, there is a lack of data on its circulation, dynamic of transmission and real burden in Senegal. To better understand the molecular epidemiology of rabies virus in Senegal, we investigated the genetic diversity of 18 new characterized Senegalese rabies virus sequences collected over 14 years, including a honey-badger-related isolate. Phylogeographic analyses demonstrated that the Senegalese isolates belong to a monophyletic cluster into the Africa-2 clade and supported two RABV introductions in Senegal from West-African neighbour countries, 36-40 years ago. Our study is noteworthy for reporting on the first characterization of an African honey-badger-related rabies virus that did not have the N-glycosylation site NKT at position 338-G of the glycoprotein. The identified amino acid polymorphisms found in the Senegalese rabies virus sequences are worthy of further investigation. Although a strong multidisciplinary stepwise cooperation is important for the successful elimination of Rabies in dog populations in Senegal by 2030, the establishment of surveillance in wildlife could be necessary to avoid future re-introductions into domestic hosts.

The progression of the SARS-CoV-2 pandemic in Africa has so far been heterogeneous and the full impact is not yet well understood. Here, we describe the genomic epidemiology using a dataset of 8746 genomes from 33 African countries and two overseas territories. We show that the epidemics in most countries were initiated by importations, predominantly from Europe, which diminished following the early introduction of international travel restrictions. As the pandemic progressed, ongoing transmission in many countries and increasing mobility led to the emergence and spread within the continent of many variants of concern and interest, such as B.1.351, B.1.525, A.23.1 and C.1.1. Although distorted by low sampling numbers and blind-spots, the findings highlight that Africa must not be left behind in the global pandemic response, otherwise it could become a breeding ground for new variants.

Bats are natural reservoirs for both

International audience; BackgroundHouseholds are among the highest risk for the transmission of SARS-CoV-2. In sub-Saharan Africa, very few studies have described household transmission during the COVID-19 pandemic. Our work aimed to describe the epidemiologic parameters and analyze the secondary attack rate (SAR) in Antananarivo, Madagascar, following the introduction of SARS-CoV-2 in the country in March 2020.MethodsA prospective case-ascertained study of all identified close contacts of laboratory-confirmed COVID-19 infections was conducted in Antananarivo from March to June 2020. Cases and household contacts were followed for 21 days. We estimated epidemic parameters of disease transmission by fitting parametric distributions based on infector-infected paired data. We assessed factors influencing transmission risk by analyzing the SAR.FindingsOverall, we included 96 index cases and 179 household contacts. Adjusted with the best-fit normal distribution, the incubation period was 4.1 days (95% CI 0.7–7.5]). The serial interval was 6.0 days (95% CI [2.4–9.6]) after adjusting with the best-fit Weibull distribution. On average, each index case infected 1.6 family members (95%CI [0.9–2.3]). The mean SAR among close contacts was 38.8% (95% CI [19.5–58.2]) with the best-fit gamma distribution. Contacts older than 35 years old were more likely to be infected, and the highest SAR was found among them.ConclusionThe results of our study provide key insights into the epidemiology of the first wave of SARS-CoV-2 in Madagascar. High rates of household transmission were found in Antananarivo, emphasizing the need for preventive measures to reduce community transmission.

We thank the blood donors and RBTC staff who supported this work, importantly Drs Jocelyne Nirina ANDRIAMBELO (RBTC Toamasina), Léa Isabelle RAMANDIMBISOA (RBTC Toliara), Michael Marie Osé HARIOLY NIRINA (NRTC Antananarivo), Dr Danielle FITAHIANA (RBTC Fianarantsoa) and Pr Tahiry RABENANDRIANINA (RBTC Mahajanga).We thank the Immunology of Infectious Diseases unit staff for performing assays, as well as the 4 laboratories in Madagascar where RT-PCRs were run particularly the IPM virology unit.We express our gratitude to the National Institute of Statistics of Madagascar and its Director General Isaora Zefania ROMALAHY, for sharing with us the 2020 demographics of Madagascar; International audience; Background: The incidence of the 2020 COVID-19 epidemic in Africa seems to be different from that of the rest of the world, however its true extent is probably underestimated. Conducting population based sero-surveys during the epidemic has moreover been extremely challenging, driving our group and others to study blood donor samples.Methods: We collected regional epidemiological COVID-19 surveillance data, and simultaneously monitored anti-SARS-CoV-2 antibody seroprevalences monthly throughout the epidemic in 5 major Region-associated Blood Transfusion Centres of Madagascar over a period of 9 months.Findings: Soon after attaining the first epidemic peaks between May and August 2020, both crude and population-weighted test-performance-adjusted seroprevalences of anti-SARS-CoV-2 antibodies was in Malagasy blood donors rapidly increased up to over 40% positivity.Interpretation: These findings suggest a high cumulative incidence of infection and seroconversion, which may have contributed to the observed deceleration of infection rates, but was not sufficient to prevent the second epidemic wave that struck Madagascar in Spring 2021.

International audience; ObjectivesTo improve our understanding of the global epidemiology of common respiratory viruses by analysing their contemporaneous incidence at multiple sites.Methods2010–2015 incidence data for influenza A (IAV), influenza B (IBV), respiratory syncytial (RSV) and parainfluenza (PIV) virus infections were collected from 18 sites (14 countries), consisting of local (n = 6), regional (n = 9) and national (n = 3) laboratories using molecular diagnostic methods. Each site submitted monthly virus incidence data, together with details of their patient populations tested and diagnostic assays used.ResultsFor the Northern Hemisphere temperate countries, the IAV, IBV and RSV incidence peaks were 2–6 months out of phase with those in the Southern Hemisphere, with IAV having a sharp out-of-phase difference at 6 months, whereas IBV and RSV showed more variable out-of-phase differences of 2–6 months. The tropical sites Singapore and Kuala Lumpur showed fluctuating incidence of these viruses throughout the year, whereas subtropical sites such as Hong Kong, Brisbane and Sydney showed distinctive biannual peaks for IAV but not for RSV and PIV.ConclusionsThere was a notable pattern of synchrony of IAV, IBV and RSV incidence peaks globally, and within countries with multiple sampling sites (Canada, UK, Australia), despite significant distances between these sites.

International audience; BackgroundInfluenza and respiratory syncytial virus (RSV) infections are responsible for substantial global morbidity and mortality in young children and elderly individuals. Estimates of the burden of influenza- and RSV-associated hospitalization are limited in Africa.MethodsWe conducted hospital-based surveillance for laboratory-confirmed influenza- and RSV-associated severe acute respiratory illness (SARI) among patients of any age at one hospital and a retrospective review of SARI hospitalizations in five hospitals situated in Antananarivo during 2011-2016. We estimated age-specific rates (per 100 000 population) of influenza- and RSV-associated SARI hospitalizations for the Antananarivo region and then extrapolated these rates to the national level.ResultsOverall, the mean annual national number of influenza-associated SARI hospitalizations for all age groups was 6609 (95% CI: 5381-7835-rate: 30.0; 95% CI: 24.4-35.6), 4468 (95% CI: 3796-5102-rate: 127.6; 95% CI: 108.4-145.7), 2141 (95% CI: 1585-2734-rate: 11.6; 95% CI: 8.6-14.8), and 339 (95% CI: 224-459-rate: 50.0; 95% CI: 36.3-74.4) among individuals aged

Administration of many childhood vaccines requires that multiple doses be delivered within a narrow time window to provide adequate protection and reduce disease transmission. Accurately quantifying vaccination coverage is complicated by limited individual-level data and multiple vaccination mechanisms (routine and supplementary vaccination programs). We analyzed 12,541 vaccination cards from 6 districts across Madagascar for children born in 2015 and 2016. For 3 vaccines—pentavalent diphtheria-tetanus-pertussis-hepatitis B-Haemophilus influenzae type b vaccine (DTP-HB-Hib; 3 doses), 10-valent pneumococcal conjugate vaccine (PCV10; 3 doses), and rotavirus vaccine (2 doses)—we used dates of vaccination and birth to estimate coverage at 1 year of age and timeliness of delivery. Vaccination coverage at age 1 year for the first dose was consistently high, with decreases for subsequent doses (DTP-HB-Hib: 91%, 81%, and 72%; PCV10: 82%, 74%, and 64%; rotavirus: 73% and 63%). Coverage levels between urban districts and their rural counterparts did not differ consistently. For each dose of DTP-HB-Hib, the overall percentage of individuals receiving late doses was 29%, 7%, and 6%, respectively; estimates were similar for other vaccines. Supplementary vaccination weeks, held to help children who had missed routine care to catch up, did not appear to increase the likelihood of being vaccinated. Maintaining population-level immunity with multiple-dose vaccines requires a robust stand-alone routine immunization program.

Rift Valley fever virus (RVFV), an arbovirus belonging to the Phlebovirus genus of the Phenuiviridae family, causes the zoonotic and mosquito-borne RVF. The virus, which primarily affects livestock (ruminants and camels) and humans, is at the origin of recent major outbreaks across the African continent (Mauritania, Libya, Sudan), and in the South-Western Indian Ocean (SWIO) islands (Mayotte). In order to be better prepared for upcoming outbreaks, to predict its introduction in RVFV unscathed countries, and to run efficient surveillance programmes, the priority is harmonising and improving the diagnostic capacity of endemic countries and/or countries considered to be at risk of RVF. A serological inter-laboratory proficiency test (PT) was implemented to assess the capacity of veterinary laboratories to detect antibodies against RVFV. A total of 18 laboratories in 13 countries in the Middle East, North Africa, South Africa, and the Indian Ocean participated in the initiative. Two commercial kits and two in-house serological assays for the detection of RVFV specific IgG antibodies were tested. Sixteen of the 18 participating laboratories (88.9%) used commercial kits, the analytical performance of test sensitivity and specificity based on the seroneutralisation test considered as the reference was 100%. The results obtained by the laboratories which used the in-house assay were correct in only one of the two criteria (either sensitivity or specificity). In conclusion, most of the laboratories performed well in detecting RVFV specific IgG antibodies and can therefore be considered to be prepared. Three laboratories in three countries need to improve their detection capacities. Our study demonstrates the importance of conducting regular proficiency tests to evaluate the level of preparedness of countries and of building a network of competent laboratories in terms of laboratory diagnosis to better face future emerging diseases in emergency conditions.

Author(s): Randremanana, Rindra Vatosoa; Andriamandimby, Soa-Fy; Rakotondramanga, Jean Marius; Razanajatovo, Norosoa Harline; Mangahasimbola, Reziky Tiandraza; Randriambolamanantsoa, Tsiry Hasina; Ranaivoson, Hafaliana Christian; Rabemananjara, Harinirina Aina; Razanajatovo, Iony; Razafindratsimandresy, Richter; Rabarison, Joelinotahiana Hasina; Brook, Cara E; Rakotomanana, Fanjasoa; Rabetombosoa, Roger Mario; Razafimanjato, Helisoa; Ahyong, Vida; Raharinosy, Vololoniaina; Raharimanga, Vaomalala; Raharinantoanina, Sandratana Jonhson; Randrianarisoa, Mirella Malala; Bernardson, Barivola; Randrianasolo, Laurence; Randriamampionona, Lea Bricette Nirina; Tato, Cristina M; DeRisi, Joseph L; Dussart, Philippe; Vololoniaina, Manuela Christophere; Randriatsarafara, Fidiniaina Mamy; Randriamanantany, Zely Arivelo; Heraud, Jean-Michel | Abstract: BackgroundFollowing the first detection of SARS-CoV-2 in passengers arriving from Europe on 19 March 2020, Madagascar took several mitigation measures to limit the spread of the virus in the country.MethodsNasopharyngeal and/or oropharyngeal swabs were collected from travellers to Madagascar, suspected SARS-CoV-2 cases and contact of confirmed cases. Swabs were tested at the national reference laboratory using real-time RT-PCR. Data collected from patients were entered in an electronic database for subsequent statistical analysis. All distribution of laboratory-confirmed cases were mapped, and six genomes of viruses were fully sequenced.ResultsOverall, 26,415 individuals were tested for SARS-CoV-2 between 18 March and 18 September 2020, of whom 21.0% (5,553/26,145) returned positive. Among laboratory-confirmed SARS-CoV-2-positive patients, the median age was 39nyears (IQR: 28-52), and 56.6% (3,311/5,553) were asymptomatic at the time of sampling. The probability of testing positive increased with age with the highest adjusted odds ratio of 2.2 [95% CI: 1.9-2.5] for individuals aged 49nyears and more. Viral strains sequenced belong to clades 19A, 20A and 20B indicative of several independent introduction of viruses.ConclusionsOur study describes the first wave of the COVID-19 in Madagascar. Despite early strategies in place Madagascar could not avoid the introduction and spread of the virus. More studies are needed to estimate the true burden of disease and make public health recommendations for a better preparation to another wave.

Pertussis is a highly contagious infectious disease and remains an important cause of mortality and morbidity worldwide. Over the last decade, vaccination has greatly reduced the burden of pertussis. Yet, uncertainty in individual vaccination coverage and ineffective case surveillance systems make it difficult to estimate burden and the related quantity of population-level susceptibility, which determines population risk. These issues are more pronounced in low-income settings where coverage is often overestimated, and case numbers are under-reported. Serological data provide a direct characterisation of the landscape of susceptibility to infection; and can be combined with vaccination coverage and basic theory to estimate rates of exposure to natural infection. Here, we analysed cross-sectional data on seropositivity against pertussis to identify spatial and age patterns of susceptibility in children in Madagascar. A large proportion of individuals surveyed were seronegative; however, there were patterns suggestive of natural infection in all the regions analysed. Improvements in vaccination coverage are needed to help prevent additional burden of pertussis in the country.

International audience; BackgroundInfluenza surveillance helps time prevention and control interventions especially where complex seasonal patterns exist. We assessed influenza surveillance sustainability in Africa where influenza activity varies and external funds for surveillance have decreased.MethodsWe surveyed African Network for Influenza Surveillance and Epidemiology (ANISE) countries about 2011-2017 surveillance system characteristics. Data were summarized with descriptive statistics and analyzed with univariate and multivariable analyses to quantify sustained or expanded influenza surveillance capacity in Africa.ResultsEighteen (75%) of 24 ANISE members participated in the survey; their cumulative population of 710 751 471 represent 56% of Africa's total population. All 18 countries scored a mean 95% on WHO laboratory quality assurance panels. The number of samples collected from severe acute respiratory infection case-patients remained consistent between 2011 and 2017 (13 823 vs 13 674 respectively) but decreased by 12% for influenza-like illness case-patients (16 210 vs 14 477). Nine (50%) gained capacity to lineage-type influenza B. The number of countries reporting each week to WHO FluNet increased from 15 (83%) in 2011 to 17 (94%) in 2017.ConclusionsDespite declines in external surveillance funding, ANISE countries gained additional laboratory testing capacity and continued influenza testing and reporting to WHO. These gains represent important achievements toward sustainable surveillance and epidemic/pandemic preparedness.

Summary box Measles vaccination is often referred to as a ‘best buy’ in public health, because of the high case fatality rate associated with infection, alongside the existence of a safe and inexpensive vaccine. The current WHO recommendation is that all children have access to two doses of the measles vaccine.1 In 2011, countries in the WHO African region adopted a measles elimination goal to be reached by 2020. In the last decades, substantial gains have been made in numbers of cases and deaths averted. Yet, an important feature of measles epidemiology is that large outbreaks can occur following years of (apparently) successful control. This phenomenon is known as a ‘posthoneymoon period’ outbreak.2 The ‘honeymoon’ consists of the period following vaccine introduction where cases drop substantially. This ‘honeymoon’ is at …

International audience; Background: Respiratory syncytial virus is the main cause of acute respiratory infections leading to a considerable morbidity and mortality among under-5 years children. A comprehensive scheme of RSV virus evolution is of great value in implementing effective universal RSV vaccine. Objective: We investigated the clinical spectrum and molecular characteristics of detected RSV over a period of seven years (January 2011 to June 2017) in Antananarivo, the capital city of Madagascar. Study design: 671 nasopharyngeal samples taken from children aged less than 5 years suffered from ARI were screened for RSV by real-time PCR. Clinical data were retrieved from case report forms. Genotype identification was performed by reverse-transcription PCR and sequencing of the second hyper variable region (HVR2) of the G glycoprotein. Results: Amongst samples tested, 292 (43.5 %) were found positive for RSV. RSV A predominated during the study period which accounted for 62.3 % (182/292) of positive samples while RSV B represented 37.0 % (108/ 292). Phylogenetic analyses identified NA1 and ON1 genotypes among RSV A. Though NA1 widespread from 2011 to 2013, ON1 became prevalent during the following years. Among RSV B, THB, CB1 and BA9 genotypes were detected. A co-circulation of THB and CB1 strains occurred during the 2011 season that was substituted by the BA9 from 2012. Malagasy ON1 strains carried some characteristic amino acid substitutions that distinguish them from the worldwide ON1 strains. By analyzing clinical spectrum, ON1 and BA genotypes seemed to prevail in mild infections compared to NA1. Conclusion: Results obtained here will have its implication in predicting temporal evolution of RSV at the local level. Considering the insularity of the country, information obtained should help in comparative analysis with global RSV strains to optimize vaccine efficacy.

The database of the Global Influenza B Study was created by collecting surveillance datasets from each of the participating countries. These national datasets are owned by the participating countries, and thus cannot be shared publicly. Researchers interested in obtaining the country-specific datasets may contact the individuals listed below for further details regarding data access.Argentina (Santa Fe Province): Gabriela Kusznierz (labconi@yahoo.com.ar)Australia: Kate Pennington (kate.pennington@health.gov.au)Bhutan: Sonam Wangchuk (swangchuk@health.gov.bt)Brazil: Cláudio Maierovitch Pessanha Henriques (claudio.henriques@saude.gov.br)Cameroon: Guy Vernet (vernet@pasteur-yaounde.org)Chile: Rodrigo Fasce (rfasce@ispch.cl)China: Feng Luzhao (fenglz@chinacdc.cn)Costa Rica: Alexey W. Clara (wclara@cdc.gov)Ecuador: Alfredo Bruno (alfredobruno@yahoo.es)El Salvador: Alexey W. Clara (wclara@cdc.gov)England: Maria Zambon (maria.zambon@phe.gov.uk)Guatemala: Alexey W. Clara (wclara@cdc.gov)Honduras: Alexey W. Clara (wclara@cdc.gov)Indonesia: Herman Kosasih (hermaninarespond@gmail.com)Italy: Caterina Rizzo (caterina.rizzo@iss.it)Ivory Coast: Herve A. Kadjo (hervekadjo@pasteur.ci)Kazakhstan: Gulzhan Muratbayeva (hnv2@cdc.gov)Kenya: Joshua Mott (zud9@cdc.gov)Madagascar: Jean-Michel Heraud (jmheraud@pasteur.mg)Morocco: Amal Barakat (amal.barakat@yahoo.fr)New Zealand: Sue Huang (sue.huang@esr.cri.nz)Nicaragua: Alexey W. Clara (wclara@cdc.gov)Panama: Alexey W. Clara (wclara@cdc.gov)Portugal: Ana Paula Rodrigues (ana.rodrigues@insa.min-saude.pt)Singapore: Vernon Lee (vernonljm@hotmail.com)South Africa: Cheryl Cohen (cherylc@nicd.ac.za)Turkey: Meral Akcay Ciblak (ciblakm@yahoo.com)Ukraine: Alla Mironenko (miralla@ukr.net)Viet Nam: Le Thi Quinh Mai (lom9@hotmail.com); International audience; 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 meta-regression 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 countries' 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.

International audience

Evaluation of influenza surveillance systems is poor, especially in Africa.In 2007, the Institut Pasteur de Madagascar and the Malagasy Ministry of Public Health implemented a countrywide system for the prospective syndromic and virological surveillance of influenza-like illnesses. In assessing this system's performance, we identified gaps and ways to promote the best use of resources. We investigated acceptability, data quality, flexibility, representativeness, simplicity, stability, timeliness and usefulness and developed qualitative and/or quantitative indicators for each of these attributes.Until 2007, the influenza surveillance system in Madagascar was only operational in Antananarivo and the observations made could not be extrapolated to the entire country.By 2014, the system covered 34 sentinel sites across the country. At 12 sites, nasopharyngeal and/or oropharyngeal samples were collected and tested for influenza virus. Between 2009 and 2014, 177 718 fever cases were detected, 25 809 (14.5%) of these fever cases were classified as cases of influenza-like illness. Of the 9192 samples from patients with influenza-like illness that were tested for influenza viruses, 3573 (38.9%) tested positive. Data quality for all evaluated indicators was categorized as above 90% and the system also appeared to be strong in terms of its acceptability, simplicity and stability. However, sample collection needed improvement.The influenza surveillance system in Madagascar performed well and provided reliable and timely data for public health interventions. Given its flexibility and overall moderate cost, this system may become a useful platform for syndromic and laboratory-based surveillance in other low-resource settings.La evaluación de los sistemas de vigilancia de la gripe es escasa, sobre todo en África.En 2007, el Instituto Pasteur de Madagascar y el Ministerio de Salud Pública de Madagascar implementaron un sistema nacional para la futura vigilancia sindrómica y epidemiológica de enfermedades similares a la gripe. Al evaluar el rendimiento de este sistema, se identificaron lagunas y formas de fomentar el mejor uso de los recursos. Se investigaron la aceptación, la calidad de la información, la flexibilidad, la representación, la simplicidad, la estabilidad, el momento y la utilidad, y se desarrollaron indicadores cualitativos y/o cuantitativos para cada uno de estos atributos.Hasta 2007, el sistema de vigilancia de la gripe en Madagascar operaba únicamente en Antananarivo, y las observaciones realizadas no podían extrapolarse al resto del país.En 2014, el sistema abarcaba 34 sitios centinela en todo el país. En 12 sitios, se recogieron muestras nasofaríngeas y/o bucofaríngeas, que se sometieron a pruebas del virus de la gripe. Entre 2009 y 2014 se detectaron 177 718 casos de fiebre, 25 809 (14,5%) de los cuales se clasificaron como casos de enfermedades similares a la gripe. De las 9 192 muestras de pacientes con enfermedades similares a la gripe sometidos a pruebas del virus de la gripe, 3 573 (38,9%) resultaron positivas. La calidad de los datos para todos los indicadores evaluados se categorizó como superior al 90% y el sistema también parecía ser sólido en cuanto a su aceptación, simplicidad y estabilidad. No obstante, la recogida de muestras necesitaba mejorar.El sistema de vigilancia de la gripe en Madagascar obtuvo buenos resultados y ofreció información fiable y oportuna para las intervenciones de salud pública. Dada su flexibilidad y el coste moderado general, este sistema podría convertirse en una plataforma útil para la vigilancia sindrómica y en laboratorios en otros entornos con pocos recursos.ضعف تقييم نظم ترصد الإنفلونزا خاصةً في أفريقيا.نفذ كلاً منحتى عام 2007، تم تشغيل نظام رصد الأنفلونزا في مدغشقر في أنتاناناريفو فقط، وتعذر استقراء الملاحظات للبلد بأكمله.بحلول عام 2014، غطى النظام 34 موقعًا رصديًا في جميع أنحاء البلاد. وتم جمع عينات بلعومية و/أو فموية بلعومية واختبارها لاكتشاف فيروس الإنفلونزا في 12 موقعًا. تم اكتشاف 177,718 حالة حمى في الفترة ما بين عامي 2009 و2014، وتم تصنيف 25,809 (‏14.5‏%) حالة من هذه الحالات على أنها أمراض مماثلة للإنفلونزا. وكان من بين 9192 عينة من المرضى المصابين بأمراض مماثلة للإنفلونزا والتي تم اختبارها لاكتشاف فيروس الإنفلونزا، ثبتت إصابة 3573 (‏38.9‏%) حالة. أشار تصنيف جودة البيانات لجميع المؤشرات التي تم تقييمها إلى نسبة تتعدى 90‏‏%، كما ظهر النظام قويًا فيما يتعلق بالمقبولية والبساطة والاستقرار. ومع ذلك، يلزم إدخال التحسين على عملية جمع العينات.حقق نظام رصد الإنفلونزا في مدغشقر أداءً جيدًا وقدّم بيانات موثوقة وفي الوقت المناسب لإجراء تدخلات الصحة العامة. قد يكون هذا النظام منصة مفيدة لرصد المتلازمات المرضية وعمليات الرصد في المختبرات في المواقع الأخرى قليلة الموارد وذلك بسبب مرونة هذا النظام وتكاليفه المعقولة بشكل عام.对流感监测系统的评估不足，尤其是在非洲。.2007 年，在 2007 年以前，马达加斯加的流感监测系统仅在塔那那利佛运行，并且观察结果无法外推到整个国家。.截止 2014 年，该系统覆盖全国 34 个哨点。 我们在 12 个哨点采集了鼻咽和/或口咽样本并进行了流感病毒检测。 在 2009 年至 2014 年期间，我们发现了 177 718 宗发热病例，其中 25 809 (14.5%) 宗被归类为流感样疾病病例。 在进行流感病毒检测的 9192 个流感样疾病患者的样本中，3573 (38.9%) 个样本的检测结果呈阳性。 所有评估指标下的数据质量均超过 90%，并且系统在其可接受性、简单性和稳定性方面似乎也非常卓越。 然而，样本采集需要改进。.马达加斯加流感监测系统运行情况良好，并且为公共卫生干预提供可靠、及时的数据。 鉴于其灵活性和总体适中的成本，该系统可能会成为其他资源匮乏的地区进行综合征监测和实验室监测的有用平台。.Неудовлетворительная оценка систем эпиднадзора за гриппом, особенно в Африке.В 2007 году Институтом Пастера в Мадагаскаре (До 2007 года система эпиднадзора за гриппом на Мадагаскаре действовала только в Антананариву и полученные результаты наблюдений было невозможно экстраполировать на всю страну.К 2014 году система охватывала 34 поста наблюдения по всей стране. На 12 постах были отобраны и протестированы на наличие вируса гриппа мазки из носоглотки и/или ротоглотки. В период с 2009 по 2014 год было выявлено 177 718 случаев лихорадки, 25 809 (14,5%) из этих случаев были классифицированы как случаи гриппоподобных заболеваний. Из 9192 проб, взятых у пациентов с гриппоподобными заболеваниями и протестированных на наличие вирусов гриппа, 3573 (38,9%) дали положительный результат. Качество данных для всех оцениваемых показателей было классифицировано как превышающее 90%. Система продемонстрировала хорошие показатели с точки зрения своей приемлемости, простоты и стабильности. Тем не менее отбор проб нуждается в улучшении.Система эпиднадзора за гриппом в Мадагаскаре хорошо зарекомендовала себя и позволяла получать надежные и своевременные данные для мероприятий в области общественного здравоохранения. С учетом гибкости и умеренной стоимости этой системы она может стать полезной платформой для синдромного и лабораторного наблюдения в условиях ограниченности ресурсов.

International audience; Africa is one of the endemic regions of HBV infection. In particular, genotype E is highly endemic in most of sub-Saharan Africa such as West African countries where it represents more than 90% of total infections. Madagascar, which is classified as a high endemic area for HBV and where the most prevalent genotype is E, might play a relevant role in the dispersion of this genotype due to its crucial position in the Indian Ocean. The aim of this study was to investigate the origin, population dynamics, and circulation of HBV-E genotype in Madagascar through high-resolution phylogenetic and phylodynamic approaches. The phylogenetic tree indicated that Malagasy isolates were intermixed and closely related with sequences mostly from West African countries. The Bayesian tree highlighted three statistically supported clusters of Malagasy strains which dated back to the years 1981 (95% HPD: 1971-1992), 1986 (95% HPD: 1974-1996), and 1989 (95% HPD: 1974-2001). Population dynamics analysis showed an exponential increase in the number of HBV-E infections approximately from the year 1975 until 2000s. The migration analysis was also performed and a dynamic pattern of gene flow was identified. In conclusion, this study confirms previous observation of HBV-E circulation in Africa and expands these findings at Madagascar demonstrating its recent introduction, and highlighting the role of the African countries in the spread of HBV-E genotype. Further studies on molecular epidemiology of HBV genotype E are needed to clarify the evolutionary history of this genotype.

International audience; Bats are reservoirs for emerging human pathogens, including Hendra and Nipah henipaviruses and Ebola and Marburg filoviruses. These viruses demonstrate predictable patterns in seasonality and age structure across multiple systems; previous work suggests that they may circulate in Madagascar's endemic fruit bats, which are widely consumed as human food. We aimed to (a) document the extent of henipa- and filovirus exposure among Malagasy fruit bats, (b) explore seasonality in seroprevalence and serostatus in these bat populations and (c) compare mechanistic hypotheses for possible transmission dynamics underlying these data. To this end, we amassed and analysed a unique dataset documenting longitudinal serological henipa- and filovirus dynamics in three Madagascar fruit bat species. We uncovered serological evidence of exposure to Hendra-/Nipah-related henipaviruses in Eidolon dupreanum, Pteropus rufus and Rousettus madagascariensis, to Cedar-related henipaviruses in E. dupreanum and R. madagascariensis and to Ebola-related filoviruses in P. rufus and R. madagascariensis. We demonstrated significant seasonality in population-level seroprevalence and individual serostatus for multiple viruses across these species, linked to the female reproductive calendar. An age-structured subset of the data highlighted evidence of waning maternal antibodies in neonates, increasing seroprevalence in young and decreasing seroprevalence late in life. Comparison of mechanistic epidemiological models fit to these data offered support for transmission hypotheses permitting waning antibodies but retained immunity in adult-age bats. Our findings suggest that bats may seasonally modulate mechanisms of pathogen control, with consequences for population-level transmission. Additionally, we narrow the field of candidate transmission hypotheses by which bats are presumed to host and transmit potentially zoonotic viruses globally.

Background The increasing use of malaria diagnostic tests reveals a growing proportion of patients with fever but no malaria. Clinicians and health care workers in low-income countries have few tests to diagnose causes of fever other than malaria although several diseases share common symptoms. We propose here to assess etiologies of fever in Madagascar to ultimately improve management of febrile cases. Methodology Consenting febrile outpatients aged 6 months and older were recruited in 21 selected sentinel sites throughout Madagascar from April 2014 to September 2015. Standard clinical examinations were performed, and blood and upper respiratory specimens were taken for rapid diagnostic tests and molecular assays for 36 pathogens of interest for Madagascar in terms of public health, regardless of clinical status. Principal findings A total of 682 febrile patients were enrolled. We detected at least one pathogen in 40.5% (276/682) of patients and 6.2% (42/682) with co-infections. Among all tested patients, 26.5% (181/682) had at least one viral infection, 17.0% (116/682) had malaria and 1.0% (7/682) presented a bacterial or a mycobacterial infection. None or very few of the highly prevalent infectious agents in Eastern Africa and Asia were detected in this study, such as zoonotic bacteria or arboviral infections. Conclusions These results raise questions about etiologies of fever in Malagasy communities. Nevertheless, we noted that viral infections and malaria still represent a significant proportion of causes of febrile illnesses. Interestingly our study allowed the detection of pathogens of public health interest such as Rift Valley Fever Virus but also the first case of laboratory-confirmed leptospirosis infection in Madagascar., Author summary Febrile illnesses have many origins, but infectious agents are the most important cause. Pathogens such as viruses and bacteria can cause various diseases, but associated signs and symptoms are generally non-specific and can overlap between diseases. Treatments of infectious diseases rely on the diagnostic of the causative agent however laboratory capacities are often lacking in resources-limited settings. Thus, health care workers generally follow clinical management guidelines that are rarely supported by information on the prevalence of local infections. The main objective of our study was to describe the common causes of fever in individuals presenting at outpatient healthcare center in Madagascar. Respiratory viruses, malaria and viral infection in the blood were the main infectious agents detected. Implementation of new diagnostic tools such as bedside testing (Point of Care Testing) could help health care workers to improve diagnosis and care of febrile patients. Detection of other pathogens such as hepatitis B virus, human immunodeficiency virus (HIV) or agent responsible for tuberculosis enhances the need for extended prevention, surveillance and detection of these infections. Interestingly, our study reported cases of leptospirosis and Rift Valley Fever virus infection that are pathogens of high public health concern.

International audience; BACKGROUND:Hantavirus infection is a zoonotic disease that is associated with hemorrhagic fever with renal syndrome and cardiopulmonary syndrome in human. Anjozorobe virus, a representative virus of Thailand orthohantavirus (THAIV), was recently discovered from rodents in Anjozorobe-Angavo forest in Madagascar. To assess the circulation of hantavirus at the national level, we carried out a survey of small terrestrial mammals from representative regions of the island and identified environmental factors associated with hantavirus infection. As we were ultimately interested in the potential for human exposure, we focused our research in the peridomestic area.METHODS:Sampling was achieved in twenty districts of Madagascar, with a rural and urban zone in each district. Animals were trapped from a range of habitats and examined for hantavirus RNA by nested RT-PCR. We also investigated the relationship between hantavirus infection probability in rats and possible risk factors by using Generalized Linear Mixed Models.RESULTS:Overall, 1242 specimens from seven species were collected (Rattus rattus, Rattus norvegicus, Mus musculus, Suncus murinus, Setifer setosus, Tenrec ecaudatus, Hemicentetes semispinosus). Overall, 12.4% (111/897) of Rattus rattus and 1.6% (2/125) of Mus musculus were tested positive for THAIV. Rats captured within houses were less likely to be infected than rats captured in other habitats, whilst rats from sites characterized by high precipitation and relatively low seasonality were more likely to be infected than those from other areas. Older animals were more likely to be infected, with infection probability showing a strong increase with weight.CONCLUSIONS:We report widespread distribution of THAIV in the peridomestic rats of Madagascar, with highest prevalence for those living in humid areas. Although the potential risk of infection to human may also be widespread, our results provide a first indication of specific zone with high transmission. Gathered data will be helpful to implement policies for control and prevention of human risk infection.

International audience; BACKGROUND:Few comprehensive data exist regarding the epidemiology of severe acute respiratory infections (SARI) in low income countries. This study aimed at identifying etiologies and describing clinical features of SARI-associated hospitalization in Madagascar.METHODS:It is a prospective surveillance of SARI in 2 hospitals for 3 years. Nasopharyngeal swabs, sputum, and blood were collected from SARI patients enrolled and tested for viruses and bacteria. Epidemiological and clinical information were obtained from case report forms.RESULTS:Overall, 876 patients were enrolled in the study, of which 83.1% (728/876) were tested positive for at least one pathogen. Viral and bacterial infections occurred in 76.1% (667/876) and 35.8% (314/876) of tested samples, respectively. Among all detected viruses, respiratory syncytial virus (RSV) was the most common (37.7%; 348/924) followed by influenza virus A (FLUA, 18.4%; 170/924), rhinovirus (RV, 13.5%; 125/924), and adenovirus (ADV, 8.3%; 77/924). Among bacteria, Streptococcus pneumoniae (S. pneumoniae, 50.3%, 189/370) was the most detected followed by Haemophilus influenzae type b (Hib, 21.4%; 79/370), and Klebsiella (4.6%; 17/370). Other Streptococcus species were found in 8.1% (30/370) of samples. Compared to patients aged less than 5 years, older age groups were significantly less infected with RSV. On the other hand, patients aged more than 64 years (OR = 3.66) were at higher risk to be infected with FLUA, while those aged 15-29 years (OR = 3.22) and 30-64 years (OR = 2.39) were more likely to be infected with FLUB (influenza virus B).CONCLUSION:The frequency of influenza viruses detected among SARI patients aged 65 years and more highlights the need for health authorities to develop strategies to reduce morbidity amongst at-risk population through vaccine recommendation. Amongst young children, the demonstrated burden of RSV should guide clinicians for a better case management of children. These findings reveal the need to develop point-of-care tests to avoid overuse of antibiotics and to promote vaccine that could reduce drastically the RSV hospitalizations.

SummaryBackground Influenza immunization still poses a critical challenge globally and specifically for tropical regions due to their complex influenza circulation pattern. Tropical regions should select the WHO's Northern or Southern hemisphere recommended vaccine composition based on local surveillance. Analyses of influenza immunization effectiveness have neglected to account for the proportion of circulating viruses prevented from causing infection each year. We investigate this question for Madagascar, where influenza vaccines are not widely available. Methods 78 Malagasy influenza strains characterized from 2002 to 2014 were challenged with hypothetical scenarios in which the WHO's Northern and Southern hemisphere recommended vaccine compositions were provided to the population. Match between circulating and vaccine strains was determined by haemagglutination inhibition assays. Strain-specific positive matches were scored assuming 9 months of protection and scenarios incorporated vaccine delays from zero to five months. Results Malagasy influenza strains matched 54% and 44% respectively with the Northern and Southern hemisphere recommended vaccine strains when the vaccine was delivered as soon as available. The matching values further decreased when additional delivery and application delays were considered. Differences between recommended compositions were not statistically significant. Conclusion Our results showed matching with the Northern hemisphere vaccine barely above 50%, even in the more favourable scenario. This suggests that if implemented, routine influenza vaccines would not protect against half of the influenza strains circulating in any epidemic season of Madagascar. We suggest that this limitation in influenza vaccine efficacy deserves greater attention, and should be considered in cost/benefit analyses of national influenza immunization programs. This article is protected by copyright. All rights reserved.

Background WHO developed a global strategy to eliminate hepatitis B by 2030 and set target to treat 80% of people with chronic hepatitis B virus (HBV) infection eligible for antiviral treatment. As a first step to achieve this goal, it is essential to conduct a situation analysis that is fundamental to designing national hepatitis plans. We therefore estimated the prevalence of chronic HBV infection, and described the existing infrastructure for HBV diagnosis in Madagascar. Methods We conducted a stratified multi-stage serosurvey of hepatitis B surface antigen (HBsAg) in adults aged ≥18 years using 28 sentinel surveillance sites located throughout the country. We obtained the list of facilities performing HBV testing from the Ministry of Health, and contacted the person responsible at each facility. Results A total of 1778 adults were recruited from the 28 study areas. The overall weighted seroprevalence of HBsAg was 6.9% (95% CI: 5.6–8.6). Populations with a low socio-economic status and those living in rural areas had a significantly higher seroprevalence of HBsAg. The ratio of facilities equipped to perform HBsAg tests per 100,000 inhabitants was 1.02 in the capital city of Antananarivo and 0.21 outside the capital. There were no facilities with the capacity to perform HBV DNA testing or transient elastography to measure liver fibrosis. There are only five hepatologists in Madagascar. Conclusion Madagascar has a high-intermediate level of endemicity for HBV infection with a severely limited capacity for its diagnosis and treatment. Higher HBsAg prevalence in rural or underprivileged populations underlines the importance of a public health approach to decentralize the management of chronic HBV carriers in Madagascar by using simple and low-cost diagnostic tools. Electronic supplementary material The online version of this article (doi:10.1186/s12889-017-4630-z) contains supplementary material, which is available to authorized users.

International audience; The circulation of West Nile virus (WNV) in horses was investigated in the Southwest Indian ocean. In 2010, blood samples were collected from a total of 303 horses originating from Madagascar, Mauritius, Reunion and the Seychelles and tested for WNV-specific antibodies. An overall seroprevalence of 27.39% was detected in the Indian Ocean with the highest WNV antibody prevalence of 46.22% (95% CI: [37.4–55.2%]) in Madagascar. The age and origin of the horses were found to be associated with the WNV infection risk. This paper presents the first seroprevalence study investigating WN fever in horses in the Southwest Indian Ocean area and indicates a potential risk of infection for humans and animals. In order to gain a better understanding of WN transmission cycles, WNV surveillance needs to be implemented in each of the countries.

Free PMC article: https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/31513690/ We describe the epidemiological characteristics, pattern of circulation, and geographical distribution of influenza B viruses and its lineages using data from the Global Influenza B Study. We included over 1.8 million influenza cases occurred in thirty-one countries during 2000-2018. We calculated the proportion of cases caused by influenza B and its lineages; determined the timing of influenza A and B epidemics; compared the age distribution of B/Victoria and B/Yamagata cases; and evaluated the frequency of lineage-level mismatch for the trivalent vaccine. The median proportion of influenza cases caused by influenza B virus was 23.4%, with a tendency (borderline statistical significance, p = 0.060) to be higher in tropical vs. temperate countries. Influenza B was the dominant virus type in about one every seven seasons. In temperate countries, influenza B epidemics occurred on average three weeks later than influenza A epidemics; no consistent pattern emerged in the tropics. The two B lineages caused a comparable proportion of influenza B cases globally, however the B/Yamagata was more frequent in temperate countries, and the B/Victoria in the tropics (p = 0.048). B/Yamagata patients were significantly older than B/Victoria patients in almost all countries. A lineage-level vaccine mismatch was observed in over 40% of seasons in temperate countries and in 30% of seasons in the tropics. The type B virus caused a substantial proportion of influenza infections globally in the 21st century, and its two virus lineages differed in terms of age and geographical distribution of patients. These findings will help inform health policy decisions aiming to reduce disease burden associated with seasonal influenza. info:eu-repo/semantics/publishedVersion

Erratum in - Correction: Temporal Patterns of Influenza A and B in Tropical and Temperate Countries: What Are the Lessons for Influenza Vaccination? PLoS One. 2016 May 2;11(5):e0155089. doi: 10.1371/journal.pone.0155089. Introduction: 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. Methods: 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 80% of cases in the season. We also assessed whether co-circulation of A and B virus types affected the duration of influenza epidemics. Results: 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. Discussion: 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. The Global Influenza B Study is supported by an unrestricted research grant from Sanofi Pasteur. info:eu-repo/semantics/publishedVersion

International audience; The role of antibodies directed against the hyper variable envelope region V1 of human immunode-ficiency virus type 1 (HIV-1), has not been thoroughly studied. We show that a vaccine able to elicit strain-specific non-neutralizing antibodies to this region of gp120 is associated with control of highly pathogenic chimeric SHIV 89.6P replication in rhesus macaques. The vaccinated animal that had the highest titers of antibodies to the amino terminus portion of V1, prior to challenge, had secondary antibody responses that mediated cell killing by antibody-dependent cellular cytotoxicity (ADCC), as early as 2 weeks after infection and inhibited viral replication by antibody-dependent cell-mediated virus inhibition (ADCVI), by 4 weeks after infection. There was a significant inverse correlation between virus level and binding antibody titers to the envelope protein, (R = −0.83, p = 0.015), and ADCVI (R = −0.84 p = 0.044). Genotyping of plasma virus demonstrated in vivo selection of three SHIV 89.6P variants with changes in potential N-linked glycosylation sites in V1. We found a significant inverse correlation between virus levels and titers of antibodies that mediated ADCVI against all the identified V1 virus variants. A significant inverse correlation was also found between neutralizing antibody titers to SHIV 89.6 and virus levels (R = −0.72 p = 0.0050). However, passive inoculation of purified immunoglobulin from animal M316, the macaque that best controlled virus, to a naïve macaque, resulted in a low serum neutralizing antibodies and low ADCVI activity that failed to protect from SHIV 89.6P challenge. Collectively, while our data suggest that anti-envelope antibodies with neutralizing and non-neutralizing Fc(R-dependent activities may be important in the control of SHIV replication, they also demonstrate that low levels of these antibodies alone are not sufficient to protect from infection.

International audience; BACKGROUND:The seasonal drivers of influenza activity remain debated in tropical settings where epidemics are not clearly phased. Antananarivo is a particularly interesting case study because it is in Madagascar, an island situated in the tropics and with quantifiable connectivity levels to other countries.OBJECTIVES:We aimed at disentangling the role of environmental forcing and population fluxes on influenza seasonality in Madagascar.METHODS:We compiled weekly counts of laboratory-confirmed influenza-positive specimens for the period 2002 to 2012 collected in Antananarivo, with data available from sub-Saharan countries and countries contributing most foreign travelers to Madagascar. Daily climate indicators were compiled for the study period.RESULTS:Overall, influenza activity detected in Antananarivo predated that identified in temperate Northern Hemisphere locations. This activity presented poor temporal matching with viral activity in other countries from the African continent or countries highly connected to Madagascar excepted for A(H1N1)pdm09. Influenza detection in Antananarivo was not associated with travel activity and, although it was positively correlated with all climatic variables studied, such association was weak.CONCLUSIONS:The timing of influenza activity in Antananarivo is irregular, is not driven by climate, and does not align with that of countries in geographic proximity or highly connected to Madagascar. This work opens fresh questions regarding the drivers of influenza seasonality globally particularly in mid-latitude and less-connected regions to tailor vaccine strategies locally.

Item does not contain fulltext BACKGROUND: Data on causes of death due to respiratory illness in Africa are limited. METHODS: From January to April 2013, 28 African countries were invited to participate in a review of severe acute respiratory illness (SARI)-associated deaths identified from influenza surveillance during 2009-2012. RESULTS: Twenty-three countries (82%) responded, 11 (48%) collect mortality data, and 8 provided data. Data were collected from 37 714 SARI cases, and 3091 (8.2%; range by country, 5.1%-25.9%) tested positive for influenza virus. There were 1073 deaths (2.8%; range by country, 0.1%-5.3%) reported, among which influenza virus was detected in 57 (5.3%). Case-fatality proportion (CFP) was higher among countries with systematic death reporting than among those with sporadic reporting. The influenza-associated CFP was 1.8% (57 of 3091), compared with 2.9% (1016 of 34 623) for influenza virus-negative cases (P < .001). Among 834 deaths (77.7%) tested for other respiratory pathogens, rhinovirus (107 [12.8%]), adenovirus (64 [6.0%]), respiratory syncytial virus (60 [5.6%]), and Streptococcus pneumoniae (57 [5.3%]) were most commonly identified. Among 1073 deaths, 402 (37.5%) involved people aged 0-4 years, 462 (43.1%) involved people aged 5-49 years, and 209 (19.5%) involved people aged >/=50 years. CONCLUSIONS: Few African countries systematically collect data on outcomes of people hospitalized with respiratory illness. Stronger surveillance for deaths due to respiratory illness may identify risk groups for targeted vaccine use and other prevention strategies.

To the Editor: Poliomyelitis outbreaks caused by pathogenic vaccine-derived polioviruses (VDPVs) are primarily a result of low polio vaccine coverage. Low coverage enables interhuman circulation of polioviruses (PVs) from the oral polio vaccine (OPV), and it enables genetic drift of the viruses and their subsequent reversion to neurovirulent phenotypes (1). Polio outbreaks associated with type 2 or 3 VDPVs (VDPV2s or VDPV3s) were reported in 2001–2002 and 2005 in Toliara Province in southern Madagascar (2,3). These VDPVs were found in patients with acute flaccid paralysis (AFP) and in healthy children who were contacts of the patients with AFP (2,4). The genomes of these VDPVs belong to several independent, complex mosaic recombinant lineages composed of sequences derived from vaccine polioviruses and other co-circulating species C human enteroviruses (human EV-C) (4,5). The 2001–2002 and 2005 outbreaks in Toliara Province were stopped after rapid and efficient OPV vaccination campaigns. No polio cases have been detected in Madagascar since 2005. However, OPV coverage fluctuates in Toliara Province. In June 2011, to determine if VDPVs were circulating in the province, we collected fecal samples from 616 healthy residents 0.5% nt sequence divergence from the type 2 OPV strain (Sabin 2) and were thus identified as potentially pathogenic VDPV2s. Two of these VDPV2s carried numerous mutations in the VP1 region (903 bp): isolates MAD-2593–11 (30 nt mutations) and MAD-2642–11 (33 nt mutations). The third VDPV2, MAD-2675–11, carried 6 nt mutations. The nucleotide differences between Sabin 2 and MAD-2593–11 (3.3%) and MAD-2642–11 (3.6%) suggest that these VDPV2s had been multiplying or circulating for ≈3.0 years, and the differences between Sabin 2 and MAD-2675–11 suggest it had been multiplying or circulating for ≈0.5 year. Almost complete genomic sequencing, from nt 36 to nt 7,420 (Sabin 2 numbering), was subsequently performed (EMBL accession nos. {"type":"entrez-nucleotide-range","attrs":{"text":"HF913426-HF913428","start_term":"HF913426","end_term":"HF913428","start_term_id":"510934497","end_term_id":"510934501"}}HF913426-HF913428). Isolate MAD-2675–11 was shown to be a mutated Sabin 2 PV, but isolates MAD-2593–11 and MAD-2642–11 displayed mosaic recombinant genomes composed of sequences derived from Sabin 2 and other human EV-Cs. Both recombinants had the 5′–untranslated region (UTR), the nonstructural P2–P3 regions, and the 3′-UTR derived from non-PV human EV-C. The 2 recombination sites were similarly located in each of these recombinant genomes (approximately at nt 760 and nt 3,368) at the 2 extremities of the structural genomic P1 region. Although these recombinants appeared to be related, they had different non-PV human EV-C sequences in the P2–P3 region and the 3′-UTR (6.0%–20.0% nt sequence difference). The phylogenetic relationship of these isolates to the previous Madagascar VDPV2s was assessed: the 2011 isolates originated from 2 novel, independent events (Figure). The 2011 VDPVs had lost the major attenuating determinants in the 5′-UTR (guanine to adenine at nt 481) and VP1 region (isoleucine to threonine at codon 143) regions (8). This finding strongly suggests that the 2011 VDPVs had regained a degree of neurovirulence. Figure Phylogenetic trees showing genetic relationships between sequences of vaccine-derived poliovirus (VDPV) isolates. The trees are based on nucleotide sequence alignments of various subgenomic regions. Multiple sequence alignments were performed with CLC ... Although there is currently no evidence of AFP cases linked to these new VDPVs, their detection in 3 children and their genetic characteristics strongly suggest insufficient OPV coverage in Toliara Province. We could obtain proof of vaccination (vaccination card) for only 27% of the participants. To prevent a third poliomyelitis outbreak, the Ministry of Health of Madagascar organized house-to-house OPV vaccination campaigns within Toliara Province in October and December 2011 and in January 2012. No polio cases have been reported in the province since then, suggesting that VDPV circulation was limited or stopped by these campaigns. Massive OPV immunization campaigns worldwide have greatly decreased the frequency of poliomyelitis caused by wild-type PVs. However, after the disease has been eliminated in developing countries, low polio vaccine coverage frequently enables the emergence of VDPVs or the reintroduction of wild-type PV from disease-endemic countries; both scenarios threaten the success of the poliomyelitis eradication program (9,10). More than 640 polio cases caused by circulating VDPVs have been reported in 21 developing countries. We have shown that even in the absence of polio cases, potentially pathogenic circulating VDPVs can be detected in fecal samples collected from children living in areas with fluctuating and often low polio vaccine coverage. Thus, such sampling can help determine whether vaccine campaigns should be implemented in areas where polio could reemerge. In Madagascar, vaccination appears to have cleared emerging VDPVs and to have prevented polio cases in children.

International audience; Background: Crimean-Congo hemorrhagic fever (CCHF) is a zoonotic arboviral infection with hemorrhagic manifestation and often a fatal ending. Human become infected mainly through tick bite or by crushing infected tick, by contact with blood or tissues from viraemic livestock or patient. CCHF virus (CCHFV) has been isolated once in Madagascar but data on the epidemiology of the disease in the country are very scarce. Objectives: To investigate the circulation and the geographic distribution of CCHFV infection among at risk population in Madagascar. Study design: A national cross-sectional serologic survey was performed in 2008–2009 among slaughterhouse workers. Results: A total of 1995 workers were included. A recent CCHFV infection was detected in 1 of the 1995 participants (0.5‰; 95% confidence interval [CI]: 0–0.15%), and a past CCHFV infection was detected in 15 participants (0.75%; 95% CI: 0.37–1.13%). Conclusion: Overall, the percentage of CCHFV infection seen in Madagascar among at-risk professionals is very low compared to endemic countries. An assessment of the prevalence in livestock as a sensitive indicator of CCHFV activity must be considered in order to confirm the lack or the weak endemicity of CCHF in Madagascar.

International audience; Most circulating strains of Human enterovirus 71 (EV-A71) have been classified primarily into three genogroups (A to C) on the basis of genetic divergence between the 1D gene, which encodes the VP1 capsid protein. The aim of the present study was to provide further insights into the diversity of the EV-A71 genogroups following the recent description of highly divergent isolates, in particular those from African countries, including Madagascar. We classified recent EV-A71 isolates by a large comparison of 3,346 VP1 nucleotidic sequences collected from GenBank. Analysis of genetic distances and phylogenetic investigations indicated that some recently-reported isolates did not fall into the genogroups A-C and clustered into three additional genogroups, including one Indian genogroup (genogroup D) and 2 African ones (E and F). Our Bayesian phylogenetic analysis provided consistent data showing that the genogroup D isolates share a recent common ancestor with the members of genogroup E, while the isolates of genogroup F evolved from a recent common ancestor shared with the members of the genogroup B. Our results reveal the wide diversity that exists among EV-A71 isolates and suggest that the number of circulating genogroups is probably underestimated, particularly in developing countries where EV-A71 epidemiology has been poorly studied.

International audience; Until now, there was only serological evidence that hantaviruses were circulating in rodents and infecting humans from Madagascar. To assess the presence of a hantavirus on the island, between October, 2008, and March, 2010, we sampled 585 rodents belonging to seven species in the Anjozorobe-Angavo forest corridor, 70 km north from the capital city Antananarivo. A hantavirus was detected from organs of the ubiquist roof rat (Rattus rattus) and of the endemic Major's tufted-tailed rat (Eliurus majori). Amazingly, sequence analysis of the S (small), M (medium), and L (large) coding DNA sequence of this virus showed that the Anjozorobe strain (proposed name) was a new genetic variant of Thailand virus (THAIV) that comprises other variants found in Southeast Asia. Because THAIV is suspected of causing hemorrhagic fever with renal syndrome in humans, ongoing studies are addressing the risk of infection by this new variant in the Malagasy population.

The annual incidence of Q fever in French Guiana was found to have increased in 1996 and was 37/100,000 population over the last 4 years. Subsequent investigations in Cayenne and its suburbs indicated that a wild reservoir of the bacteria was responsible for the epidemiologic pattern. A case-control study showed that residence near a forest and occupations and activities that result in exposure to aerosols of dusts from the soil are risk factors for Q fever. By means of time-series analysis, a strong positive correlation between rainfall and the incidence of Q fever with a time lag of 1-3 months was found. The spatial distribution of the cases showed that transmission occurs widely throughout greater Cayenne, which is incompatible with a pinpoint source of contamination. Transmission from livestock and dissemination of the bacteria by the wind appeared to be unlikely, which strengthens the hypothesis that a wild reservoir is responsible for transmission.

Background Acute respiratory infections are a leading cause of infectious disease-related morbidity, hospitalisation and mortality among children worldwide, and particularly in developing countries. In these low-income countries, most patients with acute respiratory infection (ARI), whether it is mild or severe, are still treated empirically. The aim of the study was to evaluate the risk factors associated with the evolution and outcome of respiratory illnesses in patients aged under 5 years old. Materials and Methods We conducted a prospective study in a paediatric ward in Antananarivo from November 2010 to July 2012 including patients under 5 years old suffering from respiratory infections. We collected demographic, socio-economic, clinical and epidemiological data, and samples for laboratory analysis. Deaths, rapid progression to respiratory distress during hospitalisation, and hospitalisation for more than 10 days were considered as severe outcomes. We used multivariate analysis to study the effects of co-infections. Results From November 2010 to July 2012, a total of 290 patients were enrolled. Co-infection was found in 192 patients (70%). Co-infections were more frequent in children under 36 months, with a significant difference for the 19–24 month-old group (OR: 8.0). Sixty-nine percent (230/290) of the patients recovered fully and without any severe outcome during hospitalisation; the outcome was scored as severe for 60 children and nine patients (3%) died. Risk factors significantly associated with worsening evolution during hospitalisation (severe outcome) were admission at age under 6 months (OR = 5.3), comorbidity (OR = 4.6) and low household income (OR = 4.1). Conclusion Co-mordidity, low-income and age under 6 months increase the risk of severe outcome for children infected by numerous respiratory pathogens. These results highlight the need for implementation of targeted public health policy to reduce the contribution of respiratory diseases to childhood morbidity and mortality in low income countries.

International audience; In the context of the possible introduction of a preventive vaccine against rotaviruses in Madagascar, the G and P genotypes distribution of the rotaviruses circulating in the children in Madagascar was studied, and the presence of emerging genotypes and unusual strains were assessed. From February 2008 to May 2009, 1,679 stools specimens were collected from children ≤5 years old with diarrhea. ELISA was used for antigen detection, and molecular amplification of VP7 and VP4 gene fragments was used for genotyping. Rotavirus antigen was detected in 104 samples (6.2%). Partial sequences of VP7 and VP4 genes were obtained from 81 and 80 antigen-positive stools, respectively. The most frequent G and P types combinations detected were G9P[8] (n = 51; 64.6%), followed by G1P[8] (n = 15; 18.9%), and G1P[6] (n = 8; 10.1%). A few unusual G-P combinations, such as G4P[6] (n = 3; 3.8%), G9P[6] (n = 1; 1.3%), and G3P[9] reassortant feline human virus (n = 1; 1.3%) were identified. Both VP4 and VP7 sequences in one of the three G4P[6] isolates were closely related to those in porcine strains, and one was a reassortant human porcine virus. These findings give an overview of the strains circulating in Madagascar and should help public health authorities to define a vaccine strategy.

International audience; Hepatitis E virus (HEV) causes an orofecal disease transmitted through poor hygiene environments, contaminated food (mainly pork products), or by contacts with infected animals. Very little data are currently available regarding the disease in the Southwestern Indian Ocean Islands. We report the first sero- and viro-survey for HEV in human and swine in Madagascar. A seroprevalence rate of 14.1% (60 of 427) was measured in slaughterhouse workers. Seroprevalence to HEV in pigs was estimated to 71.2% (178 of 250), strongly suggesting the existence of a zoonotic cycle. Three out of 250 pig livers (1.2%) tested HEV RNA-positive by quantitative polymerase chain reaction. Phylogenetic analyses based on 1-kb sequences of the ORF 2-3 identified these viruses as HEV genotype 3. Sequences clustered in a distinct Malagasy sub-clade, possibly representative of a new sub-genotype, for which the date of emergence was estimated around 1989. Further studies are needed to confirm other transmission routes of HEV to humans, especially through non-zoonotic cycles.

Influenza is a well-documented cause of morbidity and mortality in high- and middle-income countries. In the past few decades and particularly during the recent influenza pandemic, numerous studies and surveillance reports in the United States, Europe, Australia, and parts of Asia have improved our understanding of the epidemiology and burden of influenza in those regions. In Africa, however, the picture is quite different. Until the latter half of the last decade minimal effort had been made to understand the epidemiology, burden, and seasonality of influenza in Africa, a continent where some of the poorest populations in the world reside; where human immunodeficiency virus (HIV) infection and AIDS, tuberculosis, and malaria have long ravaged residents; and where resources for health are scarce and often directed at securing basic healthcare and prevention measures. As a result, the impact of the disease in this region has been considered negligible [1].

International audience; BACKGROUND: In response to the potential threat of an influenza pandemic, several international institutions and governments, in partnership with African countries, invested in the development of epidemiologic and laboratory influenza surveillance capacity in Africa and the African Network of Influenza Surveillance and Epidemiology (ANISE) was formed. METHODS: We used a standardized form to collect information on influenza surveillance system characteristics, the number and percent of influenza-positive patients with influenza-like illness (ILI), or severe acute respiratory infection (SARI) and virologic data from countries participating in ANISE. RESULTS: Between 2006 and 2010, the number of ILI and SARI sites in 15 African countries increased from 21 to 127 and from 2 to 98, respectively. Children 0-4 years accounted for 48% of all ILI and SARI cases of which 22% and 10%, respectively, were positive for influenza. Influenza peaks were generally discernible in North and South Africa. Substantial cocirculation of influenza A and B occurred most years. CONCLUSIONS: Influenza is a major cause of respiratory illness in Africa, especially in children. Further strengthening influenza surveillance, along with conducting special studies on influenza burden, cost of illness, and role of other respiratory pathogens will help detect novel influenza viruses and inform and develop targeted influenza prevention policy decisions in the region.