Reference-free detection of isolated SNPs

International audienceDetecting Single Nucleotide Polymorphisms (SNPs) between genomes is becoming a routine task with Next Generation Sequencing. Generally, SNP detection methods use a reference genome. As non-model organisms are increasingly investigated, the need for reference-free methods has been amplified. Most of the existing reference-free methods have fundamental limitations: they can only call SNPs between exactly two datasets, and/or they require a prohibitive amount of computational resources. The method we propose, DISCOSNP, detects both heterozygous and homozygous isolated SNPs from any number of read datasets, without a reference genome, and with very low memory and time footprints (billions of reads can be analyzed with a standard desktop computer). To facilitate downstream genotyping analyses, DISCOSNP ranks predictions and outputs quality and coverage per allele. Compared to finding isolated SNPs using a state-of-the-art assembly and mapping approach, DISCOSNP requires significantly less computational resources, shows similar precision/recall values, and highly ranked predictions are less likely to be false positives. An experimental validation was conducted on an arthropod species (the tick Ixodes ricinus) on which de novo sequencing was performed. Among the predicted SNPs that were tested, 96% were successfully genotyped and truly exhibited polymorphism

Putative role of arthropod vectors in African swine fever virus transmission in relation to their bio-ecological properties

African swine fever (ASF) is one of the most important diseases in Suidae due to its significant health and socioeconomic consequences and represents a major threat to the European pig industry, especially in the absence of any available treatment or vaccine. In fact, with its high mortality rate and the subsequent trade restrictions imposed on affected countries, ASF can dramatically disrupt the pig industry in afflicted countries. In September 2018, ASF was unexpectedly identified in wild boars from southern Belgium in the province of Luxembourg, not far from the Franco-Belgian border. The French authorities rapidly commissioned an expert opinion on the risk of ASF introduction and dissemination into metropolitan France. In Europe, the main transmission routes of the virus comprise direct contact between infected and susceptible animals and indirect transmission through contaminated material or feed. However, the seasonality of the disease in some pig farms in Baltic countries, including outbreaks in farms with high biosecurity levels, have led to questions on the possible involvement of arthropods in the transmission of the virus. This review explores the current body of knowledge on the most common arthropod families present in metropolitan France. We examine their potential role in spreading ASF—by active biological or mechanical transmission or by passive transport or ingestion—in relation to their bio-ecological properties. It also highlights the existence of significant gaps in our knowledge on vector ecology in domestic and wild boar environments and in vector competence for ASFV transmission. Filling these gaps is essential to further understanding ASF transmission in order to thus implement appropriate management measures

AVIS de l'ANSES relatif à " l'évaluation du rapport bénéfice risque des pratiques de lutte anti-vectorielle habituellement mises en oeuvre pour lutter contre la dengue, dans le contexte actuel de confinement global "

Dans le contexte de la gestion de crise liée à l'épidémie de Covid-19 en France, l'Anses a été saisie en urgence le 14 avril 2020 par la Direction Générale de la Santé pour réaliser l'expertise suivante : " Évaluation du rapport bénéfice-risque des pratiques de lutte anti-vectorielle habituellement mises en oeuvre pour lutter contre la dengue, dans le contexte actuel de confinement global "

Adaptation of Paramecium caudatum to variable conditions of temperature stress

International audienceThe environment is rarely constant and organisms are exposed to spatial and temporal variation that will impact life-histories. It is important to understand how such variation affects the adaptation of organisms to their local environment. We compare the adaptation of populations of the ciliate Paramecium caudatum exposed to constant (23 °C or 35 °C) and temporally variable temperature environments (random daily fluctuations between 23 °C or 35 °C). Consistent with theory, our experiment shows the evolution of specialists when evolution proceeds in constant environments and generalists when the environment is temporally variable. In addition, we demonstrate costs for specialists of being locally adapted through reduced fitness in novel environments. Conversely, we do not find any costs for generalists, as all populations from variable environments had equal or superior performance to specialists in their own environment. The lack of a cost for generalists is emphasised by the presence of a super generalist that has the highest performance at both assay temperatures

Development of genomic resources for the tick Ixodes ricinus: isolation and characterization of Single Nucleotide Polymorphisms

epub ahead of printInternational audience: Assessing the genetic variability of the tick Ixodes ricinus - an important vector of pathogens in Europe - is an essential step for setting up anti-tick control methods. Here we report the first identification of a set of SNPs isolated from the genome of I. ricinus, by applying a reduction of genomic complexity, pyrosequencing and new bioinformatics tools. Almost 1.4 million of reads (average length: 528 nt) were generated with a full Roche 454 GS FLX run on two Reduced Representation Libraries of I. ricinus. A newly developed bioinformatics tool (Read2Snps), which isolates SNPs without requiring any reference genome, was used to obtain 321,088 putative SNPs. Stringent selection criteria were applied in a bioinformatics pipeline to select 1,768 SNPs for the development of specific primers. Among 384 randomly SNPs tested by Fluidigm genotyping technology on 464 individuals ticks, 368 SNPs loci (96%) exhibited the presence of the two expected alleles. Hardy-Weinberg equilibrium tests conducted on 6 natural populations of ticks have shown that from 26 to 46 of the 384 loci exhibited significant heterozygote deficiency. This article is protected by copyright. All rights reserved

Genetic influence on disease spread following arrival of infected carriers

International audienceEpidemiology in host meta-populations depends on parasite ability to disperse between, establish and persist in distinct sub-populations of hosts. We studied the genetic factors determining the short-term establishment, and long-term maintenance, of pathogens introduced by infected hosts (i.e. carriers) into recipient populations. We used experimental populations of the freshwater ciliate Paramecium caudatum and its bacterial parasite Holospora undulata. Parasite short-term spread (approximately one horizontal transmission cycle) was affected mainly by carrier genotype, and its interactions with parasite and recipient genotypes. By contrast, parasite longer term spread (2-3 horizontal transmission cycles) was mostly determined by parasite isolate. Importantly, measures of parasite short-term success (reproductive number, R) were not good predictors for longer term prevalence, probably because of the specific interactions between host and parasite genotypes. Analogous to variation in vectorial capacity and super-spreader occurrence, two crucial components of epidemiology, we show that carrier genotype can also affect disease spread within meta-populations

Revue systématique des arthropodes hématophages présents chez les bovins en France

The authors are also particularly grateful to the working group “Vecteurs” and the specialized expert committee on health and animal welfare: “Santé et Bien-Etre des Animaux” (SABA), both from ANSES and to Claire Garros (CIRAD, Montpellier), Nil Rahola (IRD, Montpellier), and Gérard Duvallet (Montpellier University) for sharing their knowledge and expertise on hematophagous arthropods.International audienceThe arrival of pathogens, whether zoonotic or not, can have a lasting effect on commercial livestock farms, with dramatic health, social and economic consequences. However, available data concerning the arthropod vectors present and circulating on livestock farms in France are still very imprecise, fragmentary, and scattered. In this context, we conducted a systematic review of the hematophagous arthropod species recorded on different types of cattle farms in mainland France (including Corsica). The used vector “groups” studied were biting flies, biting midges, black flies, fleas, horse flies, lice, louse flies, mosquitoes, sand flies, and ticks. A large number of documents were selected ( N = 9,225), read ( N = 1,047) and analyzed ( N = 290), allowing us to provide distribution and abundance maps of different species of medical and veterinary interest according to literature data. Despite the large number of documents collected and analyzed, there are few data provided on cattle farm characteristics. Moreover, data on all arthropod groups lack numerical detail and are based on limited data in time and/or space. Therefore, they are not generalizable nor comparable. There is still little information on many vectors (and their pathogens) and still many unknowns for most studied groups. It appears necessary to provide new, updated and standardized data, collected in different geographical and climatological areas. Finally, this work highlights the lack of entomologists, funding, training and government support, leading to an increased risk of uncontrolled disease emergence in cattle herds.L’arrivée d’agents pathogènes, même non zoonotiques, peut affecter durablement les élevages commerciaux, avec des conséquences sanitaires, sociales et économiques dramatiques. Cependant, les données disponibles concernant les arthropodes vecteurs présents et circulants dans les élevages français sont encore très imprécises, fragmentaires et dispersées. Dans ce contexte, nous avons réalisé une revue systématique des espèces d’arthropodes hématophages présentes dans différents types d’élevages bovins en France métropolitaine (Corse comprise). Les “groupes” de vecteurs retenus et étudiés étaient les mouches piqueuses, les culicoïdes, les simulies, les puces, les taons, les poux, les hippobosques, les moustiques, les phlébotomes et les tiques. Un grand nombre de documents ont été sélectionnés ( N = 9 225), lus ( N = 1 047) et analysés ( N = 290), ce qui nous a permis de fournir des cartes de distribution et d’abondance des différentes espèces d’intérêt médical et vétérinaire en fonction des données de la littérature. Malgré le grand nombre de documents collectés et analysés, peu de données sont fournies sur les caractéristiques des élevages bovins. En outre, les données sur tous les groupes d’arthropodes manquent de détails numériques et sont basées sur des informations limitées dans le temps et/ou l’espace. Elles ne sont donc ni généralisables ni comparables. Il existe encore peu d’informations sur de nombreux vecteurs (et leurs agents pathogènes) et de multiples inconnues subsistent pour les groupes les plus étudiés. Il apparaît nécessaire de collecter de nouvelles données, actualisées et standardisées dans différentes zones géographiques et climatiques. Enfin, ce travail met en évidence le manque d’entomologistes, de financements, de formations et de soutien gouvernemental, ce qui accroît le risque d’émergence non contrôlée de maladies dans les troupeaux de bovins