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Hunting of wild animals for meat and habitat loss are the main drivers of wildlife population decline around the world, and in tropical regions in particular. While Madagascar is a hotspot for biodiversity, hunting is widespread, mostly in form of subsistence hunting, while hunting for the pet trade is less often reported. We studied hunting of the Critically Endangered black-and-white ruffed lemur (Varecia variegata) in northeastern Madagascar. Using lemur surveys (102.7 km survey effort) and 54 semi-structured and seven key informant interviews, we assessed the local knowledge, hunting pressure, and the perceived and actual abundances of V. variegata in two hunting and two non-hunting villages. V. variegata was well known (> 83%) by the respondents but abundance estimates differed significantly between hunting and non-hunting villages, with 26% and 77% of respondents, respectively, estimating a high abundance of ruffed lemurs in the adjacent forests of the villages. Actual observations of V. variegata also differed strongly, in accordance to perceived abundances. Hunting was either done by trapping animals or by pursuit hunts. In both hunting villages, adult lemurs were used for direct meat consumption and juveniles for rearing for the later trade. Hand-raised V. variegata were reported to be sold for 38–71 USD on regional markets or 'delivered' directly to buyers. While wildlife hunting has been widely reported from all over Madagascar, commercial hunting, hand-rearing and trading adds a new dimension of threat towards these Critically Endangered lemurs. As such, the extent of the trade is a priority for future studies. [ABSTRACT FROM AUTHOR]

To assess circulation of the Sabin 2 poliovirus vaccine strain in Madagascar after its withdrawal from the oral polio vaccine in April 2016, a reinforced poliovirus surveillance was implemented in three regions of Madagascar from January 2016 to December 2017. Environmental samples and stool specimens from healthy children were screened using the Global Polio Laboratory Network algorithm to detect the presence of polioviruses. Detected polioviruses were molecularly typed and their genomes fully sequenced. Polioviruses were detected during all but 4 months of the study period. All isolates were related to the vaccine strains and no wild poliovirus was detected. The majority of isolates belong to the serotype 3. The last detection of Sabin 2 occurred in July 2016, 3 months after its withdrawal. No vaccine‐derived poliovirus of any serotype was observed during the study. Only few poliovirus isolates contained sequences from non‐polio origin. The genetic characterization of all the poliovirus isolates did not identify isolates that were highly divergent compared to the vaccine strains. This observation is in favor of a good vaccine coverage that efficiently prevented long‐lasting transmission chains between unvaccinated persons. This study underlines that high commitment in the fight against polioviruses can succeed in stopping their circulation even in countries where poor sanitation remains a hurdle. [ABSTRACT FROM AUTHOR]

Surveillance and detection of polioviruses (PV) remain crucial to monitoring eradication progress. Intratypic differentiation (ITD) using the real-time RT-PCR kit is key to the surveillance workflow, where viruses are screened after cell culture isolation before a subset are verified by sequencing. The ITD kit is a series of real-time RT-PCR assays that screens cytopathic effect (CPE)-positive cell cultures using the standard WHO method for virus isolation. Because ITD screening is a critical procedure in the poliovirus identification workflow, validation of performance of real-time PCR platforms is a core requirement for the detection of poliovirus using the ITD kit. In addition, the continual update and improvement of the ITD assays to simplify interpretation in all platforms is necessary to ensure that all real-time machines are capable of detecting positive real-time signals. Four platforms (ABI7500 real-time systems, Bio-Rad CFX96, Stratagene MX3000P, and the Qiagen Rotor-Gene Q) were validated with the ITD kit and a redesigned poliovirus probe. The poliovirus probe in the real-time RT-PCR pan-poliovirus (PanPV) assay was re-designed with a double-quencher (Zen™) to reduce background fluorescence and potential false negatives. The updated PanPV probe was evaluated with a panel consisting of 184 polioviruses and non-polio enteroviruses. To further validate the updated PanPV probe, the new assay was pilot tested in five Global Polio Laboratory Network (GPLN) laboratories (Madagascar, India, Philippines, Pakistan, and Democratic Republic of Congo). The updated PanPV probe performance was shown to reduce background fluorescence and decrease the number of false positives compared to the standard PanPV probe. [ABSTRACT FROM AUTHOR]

Background: Following 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. Methods: Nasopharyngeal 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. Results: Overall, 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 39 years (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 49 years and more. Viral strains sequenced belong to clades 19A, 20A and 20B indicative of several independent introduction of viruses. Conclusions: Our 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. [ABSTRACT FROM AUTHOR]

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Human enteroviruses of species A (EV-A) are the leading cause of hand-foot-and-mouth disease (HFMD). EV-A71 is frequently implicated in HFMD outbreaks and can also cause severe neurological manifestations. We investigated the molecular epidemiological processes at work and the contribution of genetic recombination to the evolutionary history of EV-A in Madagascar, focusing on the recently described EV-A71 genogroup F in particular. Twenty-three EV-A isolates, mostly collected in 2011 from healthy children living in various districts of Madagascar, were characterised by whole-genome sequencing. Eight different types were identified, highlighting the local circulation and diversity of EV-A. Comparative genome analysis revealed evidence of frequent recent intra- and intertypic genetic exchanges between the non-capsid sequences of Madagascan EV-A isolates. The three EV-A71 isolates had different evolutionary histories in terms of recombination, with one isolate displaying a mosaic genome resulting from recent genetic exchanges with Madagascan coxsackieviruses A7 and possibly -A5 and -A10 or common ancestors. The engineering and characterisation of recombinants generated from progenitors belonging to different EV-A types or EV-A71 genogroups with distantly related non-structural sequences indicated a high level of permissiveness for intertypic genetic exchange in EV-A. This permissiveness suggests that the primary viral functions associated with the non-structural sequences have been highly conserved, through the diversification and evolution of the EV-A species. No outbreak of disease due to EV-A has yet been reported in Madagascar, but the diversity, circulation and evolution of these viruses justify surveillance of EV-A circulation and HFMD cases, to prevent possible outbreaks due to emerging strains. [ABSTRACT FROM AUTHOR]

Madagascar reports few measles cases annually and high vaccination campaign coverage. However, the underlying age profile of immunity and risk of a measles outbreak is unknown. We conducted a nested serological survey, testing 1,005 serum samples (collected between November 2013 and December 2015 via Madagascar's febrile rash surveillance system) for measles immunoglobulin G antibody titers. We directly estimated the age profile of immunity and compared these estimates with indirect estimates based on a birth cohort model of vaccination coverage and natural infection. Combining these estimates of the age profile of immunity in the population with an age-structured model of transmission, we further predicted the risk of a measles outbreak and the impact of mitigation strategies designed around supplementary immunization activities. The direct and indirect estimates of age-specific seroprevalence show that current measles susceptibility is over 10%, and modeling suggests that Madagascar may be at risk of a major measles epidemic. [ABSTRACT FROM AUTHOR]

Background: Acute diarrhea is a major cause of childhood morbidity and mortality worldwide. Its microbiological causes and clinico-epidemiological aspects were examined during the rainy seasons from 2008 to 2009 in 14 districts in Madagascar. Methods: Stool specimens of 2196 children with acute diarrhea and 496 healthy children were collected in a community setting. Microscopy and bacteria diagnosed intestinal parasites by culturing methods. Rota-, astro and adenoviruses were identified using commercially available ELISA kits and rotaviruses were confirmed using reverse transcriptase polymerase chain reaction (RT-PCR). Results: Intestinal microorganisms were isolated from 54.6% of diarrheal patients and 45.9% of healthy subjects (p =<0.01). The most common pathogens in diarrheic patients were intestinal parasites (36.5%). Campylobacter spp. and Rotavirus were detected in 9.7% and 6.7% of diarrheic patients. The detection rates of Entamoeba histolytica, Trichomonas intestinalis and Giardia lamblia were much greater in diarrheal patients than in non-diarrheal subjects (odds ratios of 5.1, 3.2, 1.7 respectively). The abundance of other enteropathogens among the non-diarrheal group may indicate prolonged excretion or limited pathogenicity. Conclusion: In developing countries, where the lack of laboratory capacities is great, cross sectional studies of enteropathogens and their spatial distribution, including diarrheal and non diarrheal subjects, are interesting tools in order to advise regional policies on treatment and diarrheic patient management. [ABSTRACT FROM AUTHOR]

Background. Five cases of poliomyelitis due to type 2 or 3 recombinant vaccine-derived polioviruses (VDPVs) were reported in the Toliara province of Madagascar in 2005. Methods. We sequenced the genome of the VDPVs isolated from the patients and from 12 healthy children and characterized phenotypic aspects, including pathogenicity, in mice transgenic for the poliovirus receptor. Results. We identified 6 highly complex mosaic recombinant lineages composed of sequences derived from different vaccine polioviruses and other species C human enteroviruses (HEV-Cs). Most had some recombinant genome features in common and contained nucleotide sequences closely related to certain cocirculating coxsackie A virus isolates. However, they differed in terms of their recombinant characteristics or nucleotide substitutions and phenotypic features. All VDPVs were neurovirulent in mice. Conclusions. This study confirms the genetic relationship between type 2 and 3 VDPVs, indicating that both types can be involved in a single outbreak of disease. Our results highlight the various ways in which a vaccinederived poliovirus may become pathogenic in complex viral ecosystems, through frequent recombination events and mutations. Intertypic recombination between cocirculating HEV-Cs (including polioviruses) appears to be a common mechanism of genetic plasticity underlying transverse genetic variability. [ABSTRACT FROM AUTHOR]

Recombination events between human enteroviruses (HEV) are known to occur frequently and to participate in the evolution of these viruses. In a previous study, we reported the isolation of a panel of viruses belonging to the Human enterovirus species C (HEV-C) that had been cocirculating in a small geographic area of Madagascar in 2002. This panel included type 2 vaccine-derived polioviruses (PV) that had caused several cases of acute flaccid paralysis in humans. Previous partial sequencing of the genome of these HEV-C isolates revealed considerable genetic diversity, mostly due to recombination. In the work presented herein, we carried out a more detailed characterization of the genomes of viruses from this collection. First, we determined the full VP1 sequence of 41 of these isolates of different types. These sequences were compared with those of HEV-C isolates obtained from other countries or in other contexts. The sequences of the Madagascan isolates of a given type formed specific clusters clearly differentiated from those formed by other strains of the same type isolated elsewhere. Second, we sequenced the entire genome of 10 viruses representing most of the lineages present in this panel. All but one of the genomes appeared to be mosaic assemblies of different genomic fragments generated by intra- and intertypic recombination. The location of the breakpoints suggested potential preferred genomic regions for recombination. Our results also suggest that recombination between type HEV-99 and other HEV-C may be quite rare. This first exhaustive genomic analysis of a panel of non-PV HEV-C cocirculating in a small human population highlights the high frequency of inter and intra-typic genetic recombination, constituting a widespread mechanism of genetic plasticity and continually shifting the HEV-C biodiversity. [ABSTRACT FROM AUTHOR]

Background: The risk factors for the transmission of HCV vary substantially between countries and geographic regions. The overall prevalence in south and east Africa region has been estimated to be 1.6% but limited information about the epidemiology of HCV infection in Madagascar is available Methods: A cross-sectional survey for hepatitis C antibodies was conducted in 2,169 subjects of the general population of Antananarivo to determine seroprevalence of hepatitis C and associated risk factors. Results: The overall seroprevalence was 1.2% (25/2,169). The prevalence did not differ significantly according to gender but it increased with age (Chi2 tendency test, p < 10-5). The variable history of hospitalization, previous therapeutic injections, dental treatment, intravenous drug use, and abnormal ALT and AST were statistically significantly related with the presence of HCV antibodies. No relationship with past history of blood transfusion was observed. Conclusion: HCV prevalence in Madagascar seems to be similar to that in most other east African countries. Age appears to be an important risk factor. Iatrogenic causes of HCV transmission need to be further evaluated because all HCV cases had a history of receiving therapeutic injections and data suggested a cumulative effect in relation with therapeutic injections. [ABSTRACT FROM AUTHOR]

The prevalence of hepatitis C virus (HCV) genotypes in Madagascar is not well known. Serum samples were obtained from 2,169 individuals selected by random sampling in the population living in Antananarivo city. Using HCV antibody test (Monolisa anti‐HCV Plus version 2), 36 (1.7%) of the 2,169 samples were positive. The presence of HCV RNA was determined by using reverse transcription polymerase chain reaction amplifying the 5′‐untranslated region (UTR): HCV RNA was detected in 17 of the 36 HCV antibodies positive samples. The genotype was determined using BLAST tool with another 5′‐UTR fragment. The phylogenetic analysis of the polymerase (NS5b) and envelope (E1/E2) fragment sequences showed a low level of diversity compared to the high diversity in other African countries: subtype 1b (nine cases, 52.9%) and genotype 2 (eight cases, 47.1%) including subtype 2b (six cases), subtype 2k (one case), and one unclassified subtype. BLAST search with the 5′‐UTR fragment sequence of this unclassified subtype identified that strain as subtype 2a. J. Med. Virol. 79: 1082–1088, 2007. © 2007 Wiley‐Liss, Inc. [ABSTRACT FROM AUTHOR]

Presents an ecological and economic analysis of watershed protection in eastern Madagascar. Flooding alleviation benefits, resulting from the protection of upland forests; History of deforestation in the Mantadia area; Changes in flooding pattern; Change in agricultural production; Relationship between deforestation and flooding.

This article focuses on a study conducted to determine if vaccine-derived polioviruses (VDPV) were circulating in Toliara Province, Madagascar in June 2011. Researchers collected fecal samples from 616 healthy children aged five years or younger. They found no evidence of acute flaccid paralysis (AFP) cases linked to VDPV. The detection of VDPV in children and their genetic characteristics suggest insufficient oral polio vaccine (OPV) coverage in the province.

Focuses on the reported cases of acute flaccid paralysis associated with vaccine-derived poliovirus type 2 isolates in the southern province of the Republic of Madagascar between October 2001 and April 2002. Information on the patients afflicted by the disease; Laboratory examinations conducted on the patients; Action taken by the Madagascar authorities to the outbreak of the disease.

Introduction: in October 4th, 2018, a measles outbreak was declared in Madagascar. This study describes the epidemiology of the outbreak and determines public health implications for measles elimination in Madagascar. Methods: data have been collected using line list developed for the outbreak. Serum samples were collected within 30 days of rash onset for laboratory testing; confirmation was made by detection of measles immunoglobulin M (IgM) antibody. Results: a total of 2,930 samples were analysed in the laboratory among which 1,086 (37%) were laboratory confirmed. Measles cases age ranged from a minimum of 1 month to a maximum of 88 years. The median and the mean were 7 years and 9 years respectively. Children between 1 to 9 years accounted for 50.6% of measles cases. Attack rate (39,014 per 1,000,000 inhabitants) and case fatality rate (1.2%) were highest among children aged 9-11 months. A total of 67.2% cases were unvaccinated. As of March 14th, 2019, all the 22 regions and 105 (92%) health districts out of 114 were affected by the measles outbreak in Madagascar. Conclusion: measles outbreak in Madagascar showed that the country is not on the track to achieve the goal of measles elimination by 2020. [ABSTRACT FROM AUTHOR]

• Ecoacoustics can increase time and cost efficiency in biodiversity assessments. • We applied four acoustic indices to recordings from an agricultural landscape in Madagascar. • Three acoustic indices showed systematic variation among predominant land-use types. • We found a positive correlation of acoustic indices and bird species richness. • High indices in structurally diverse vanilla agroforests suggest a high value for conservation. New technologies like ecoacoustic surveys promise time and cost efficiency for biodiversity assessments, serve as a basis for effective conservation policies, and are particularly appealing for remote and highly diverse tropical areas. Acoustic indices facilitate the analysis of large acoustic datasets but no consensus on their performance has been reached yet. We evaluated the efficacy of four acoustic indices (Acoustic Complexity Index, Acoustic Diversity Index, Acoustic Evenness Index, Acoustic Entropy) for sound data analysis and biodiversity assessments inside a national park and the agricultural mosaic landscape of north-eastern Madagascar, a global biodiversity hotspot. We used self-built sound recorders to continuously record soundscapes on 80 plots across seven land-use types (old-growth forest, forest fragment, forest–derived and fallow-derived vanilla agroforest, herbaceous and woody fallow, rice paddy) and compared index values between land–use types, assessed the correlation with bird species richness as measured by point counts, and related the acoustic indices to plot- and landscape-scale parameters. The Acoustic Diversity Index, Acoustic Evenness Index (inverse) and Acoustic Entropy were highest in old-growth forest and lowest for rice paddies and fallow land. Index values for structurally similar land-use types did not differ significantly from each other. The correlation of the three acoustic indices with bird species richness was strongest during daytime (R 2 ≥ 0.30). Differences in the index values were best explained by land-use type and vegetation density. Our results showed that all investigated indices except the Acoustic Complexity Index were suitable biodiversity indicators for a tropical, agricultural landscape. Soundscape diversity was positively affected by plot-scale vegetation structure, emphasizing the importance of forests and particularly old-growth forest for conservation. We demonstrated that acoustic indices and sound recordings are a useful tool for assessing biodiversity in tropical agricultural mosaic landscapes. To realize the full potential of ecoacoustics in conservation, sampling guidelines and user-friendly analysis packages will be key to facilitate a wider implementation. [ABSTRACT FROM AUTHOR]