Geometagenomics illuminates the impact of agriculture on the distribution and prevalence of plant viruses at the ecosystem scale

Disease emergence events regularly result from human activities such as agriculture, which frequently brings large populations of genetically uniform hosts into contact with potential pathogens. Although viruses cause nearly 50% of emerging plant diseases, there is little systematic information about virus distribution across agro-ecological interfaces and large gaps in understanding of virus diversity in nature. Here we applied a novel landscape-scale geometagenomics approach to examine relationships between agricultural land use and distributions of plantassociated viruses in two Mediterranean-climate biodiversity hotspots (Western Cape region of South Africa and Rhône river delta region of France). In total, we analysed 1725 geo-referenced plant samples collected over two years from 4.5 × 4.5 km2 grids spanning farmlands and adjacent uncultivated vegetation. We found substantial virus prevalence (25.8–35.7%) in all ecosystems, but prevalence and identified family-level virus diversity were greatest in cultivated areas, with some virus families displaying strong agricultural associations. Our survey revealed 94 previously unknown virus species, primarily from uncultivated plants. This is the first effort to systematically evaluate plant-associated viromes across broad agro-ecological interfaces. Our findings indicate that agriculture substantially influences plant virus distributions and highlight the extent of current ignorance about the diversity and roles of viruses in nature

Infection a VIH de l’enfant en milieu rural au Togo

Objectif: Analyser les particularités de l’infection à VIH chez l’enfant en milieu rural au Togo.Matériels et méthode: il s’agit d’une étude rétrospective descriptive, menée du 1er Janvier 2007 au 31 décembre 2011 sur 45 dossiers d’enfants de moins de 15 ans infectés par le VIH suivis dans l’USP Kolowaré.Résultats: Les enfants représentaient 8,8% des PvVIH en 2011 dont 33 % résidaient dans la ville de Tchamba. La sex-ratio était de 0,9. L’âge moyen était de 38,6 mois. Les mères n’ont souvent bénéficié d’aucune mesure de PTME (96,2 %). Le VIH-1 était responsable de l’infection dans tous les cas. Les stades cliniques OMS IV et le stade III étaient majoritaires (85,4 %). La malnutrition aiguë (38,5 %), la candidose digestive (26,9 %) et les pneumonies (23,1 %) ont été les affections opportunistes les plus fréquentes. Près de 65,5 % de nos patients avaient un déficit immunitaire modérée ou sévère. Quarante-deux enfants (93,3 %) ont été mis sous Stavudine /Lamivudine/ Névirapine. Le taux de létalité lié au VIH de l’enfant était de 26,9 % avant ou après le début du traitement antirétroviral.Conclusion: Le diagnostic de l’infection à VIH de l’enfant demeure tardif, particulièrement en milieu rural. La proposition du dépistage systématique du VIH chez l'enfant dans nos formations sanitaires et les prestations de PTME s’avèrent fondamentales.Mots clés: Enfant, VIH/Sida, traitement antirétroviral, milieu ruralEnglish Title: Features of HIV infected children in a rural area of TogoEnglish AbstractObjectives: To analyse HIV infected children features in a rural area of Togo.Materials and method: In a retrospective study, 45 medical files of infected children under 15 years were examinated at Koloware hospital in the Central Region of Togo from 1st January 2007 to 31st December 2011.Results: Proportion of infected children was 8.8% in 2011. Most of them (33%) were living in Tchamba. Sex-ratio was 0.9. The mean age was 38.6 month. Mother having PMCTC were rare (96.2%). VIH-1 was responsible of 100% of cases. The WHO clinical stages IV and III were frequent (85.4%). Wasting (38.5%), candida fungus infection (26.9 %) and respiratory lungs infections (23.1%) were the most frequent opportunistic diseases. Almost 65.5 % of patients were suffering from a moderate or severe immunodepression. Stavudine /Lamivudine/ Nevirapine (93.3%) was the main ART protocol in first line. Letality rate was 26.9% avant ou après le début du traitement antirétroviral.Conclusion: Early diagnosis of HIV infection is late, especially in the rural area. PMCTC is to be promoted.Keywords: children, HIV, rural, Tog

Two novel Alphaflexiviridae members revealed by deep sequencing of the Vanilla (Orchidaceae) virome.

The genomes of two novel viruses were assembled from 454 pyrosequencing data obtained from vanilla leaves from La Réunion. Based on genome organization and homologies, one agent was unambiguously classified as a member of the genus Potexvirus and named vanilla virus X (VVX). The second one, vanilla latent virus (VLV), is phylogenetically close to three unclassified members of the family Alphaflexiviridae with similarity to allexiviruses, and despite the presence of an additional 8-kDa open reading frame, we propose to include VLV as a new member of the genus Allexivirus. Both VVX and VLV were mechanically transmitted to vanilla plants, resulting in asymptomatic infections