La 2ème réunion annuelle du réseau PhyloMAP s’est tenue le 19 Novembre 2021 à Paris (ISC-PIF, 113 rue nationale, Paris 13e). Nous avons eu le grand plaisir d’acceuillir et écouter comme orateurs: Claire Guinat, Benoît Moury, Arnaud Bataille, Laetitia Canini et Hélène Duault.
Vous trouverez ci-dessous les résumés des présentations ainsi que la possibilité de voir ou revoir les exposés!
Résumés des présentations et replay
Claire Guinat – Disentangling the role of poultry and wild birds in the spread of highly pathogenic avian influenza virus H5N8 in Europe
Recent outbreaks of highly pathogenic avian influenza H5N8 virus in Europe have caused severe damage to animal health, wildlife conservation and livestock economic sustainability. While epidemiological and phylogenetic studies have generated important clues about the virus spread in Europe, they remained opaque to the specific role of poultry farms and wild birds. Using a phylodynamic framework, we inferred the H5N8 virus transmission dynamics among poultry farms and wild birds in four severely affected countries and investigated drivers of spread between farms across borders during the 2016-17 epidemic. Based on existing genetic data, we showed that the virus was likely introduced into poultry farms during the autumn, in line with the timing of arrival of migratory wild birds. Then, transmission was mainly driven by farm-to-farm transmission in Germany, Hungary and Poland, suggesting that better understanding of how infected farms are connected in those countries would greatly help control efforts. In contrast, the epidemic was dominated by wild bird-to-farm transmission in Czech Republic, meaning that more sustainable prevention strategies should be developed to reduce virus exposure from wild birds. We inferred effective reproduction number Reestimates among poultry farms and wild birds. We expect those estimates being useful to parameterize predictive models of virus spread aiming at optimising control strategies. None of the investigated predictors related to live poultry trade, poultry census and geographic proximity were identified as supportive predictors of the viral spread between farms across borders, suggesting that other drivers should be considered in future studies.
Arnaud Bataille – Epidémiologie évolutive du virus de la peste des petits ruminants (genre : Morbillivirus)
La peste des petits ruminants (PPR) est une maladie très virulent affectant principalement les chèvres et les moutons, mais aussi d’autres Artiodactyles domestiques et sauvages en Afrique, Asie et Moyen-Orient. A cause de son impact sur la sécurité alimentaire et l’économie mondiale, la PPR est la cible d’une campagne mondiale d’éradication organisée par la FAO et l’OIE. Cette maladie est causée par un virus (PPRV) qui appartient au genre Morbillivirus, au même titre que les virus de la rougeole ou de la maladie de carré. Ces virus enveloppés à ARN simple brin négatif ont un taux de mutation assez élevé (~1x10-3 sub/site/an) à cause de l’incapacité de leur polymérase à corriger les erreurs lors de la réplication. L’étude du génome du PPRV, notamment par des analyses phylogénétiques, peut donc fournir des informations sur l’épidémiologie et l’évolution de ce virus à différentes échelles temporelles. Les questions de recherche principales dans ce domaine concernent l’histoire de l’apparition et de la propagation mondiale du PPRV, la dynamique de transmission du virus, ou encore sa capacité à s’adapter à de nouveaux hôtes. Ces études sont rendues difficiles par le manque de données génomiques existantes pour une maladie animale de faible intérêt pour le monde occidental, le caractère endémique de la maladie dans les zones atteintes, ou encore le manque de contrôle de la qualité des données génétiques publiées. Les recherches effectuées ces dernières années commencent à changer cet état des choses et à améliorer notre compréhension de l’épidémiologie évolutive du virus de la peste des petits ruminants.
Laetitia Canini – Deciphering the role of host species in Mycobacterium bovis SB0120 spoligotype circulation within a cattle-badger-wild boar multi-hosts system
Bovine tuberculosis (bTB) is a common disease affecting cattle and wildlife worldwide. The circulation of M. bovis in wildlife impedes the surveillance and control programs when implemented. Spoligotype SB0120 (BCG-like) is the most frequent in France and is widely spread across France but is mainly found in an area of South-West overlapping Dordogne, Haute-Vienne, Charente and Charente-Maritime départements and in the Côte-d’Or département in the East of France. The aim of our work was hence to investigate the role played by each species in M. bovis SB0120 circulation using genomic data. We used samples collected between 2010 and 2017 in two separate study areas in Côte-d’Or (CdO) and Dordogne/Haute-Vienne (DHV) from badger, wild boars and cattle. To study the impact of host species, we used the approximation of the structured coalescent as implemented in the Mascot package in BEAST2. From the sampled trees, we computed host species transition and persistence between two consecutive nodes and the average number of transition per tree. In total, 218 and 144 samples were collected respectively in CdO and DHV. For both study areas the best fitted model included a HKY substitution model and an uncorrelated lognormal molecular clock. In CdO, three host species migration rates stood out (>0.10 /host specie/yr): from cattle to badger, from badger to wild boar and from wild boar to cattle. In DHV an additional fourth migration rate was identified : from badger to cattle. However host transition remained a rare event (<2% in CdO and <13% in DHV). Although this approach do not allow us to quantify within-species transmission, our result shed light on the wild boar role, serving as an intermediary between badger and cattle in the circulation of M. bovis spoligotype SB0120 in two distinct study areas. Our results also highlight the differences between these two areas, suggesting that the transition pattern does not only depend on the host species.
Benoît Moury – Les apports de la phylodynamique à la compréhension de l’épidémiologie et de l’évolution des virus de plantes
En l’absence de fossiles ou d’échantillons anciens, l’origine (date, zone géographique) des principaux groupes de virus de plantes et leurs patrons de dispersion de l’échelle régionale jusqu’à l’échelle intercontinentale sont peu connus. Par ailleurs, l’analyse des facteurs impliqués dans le rythme de leur diversification au cours du temps et de leur vitesse de diffusion spatiale est rendue difficile par la diversité et la complexité de certaines propriétés biologiques telles que leur gamme d’hôte ou leurs modes de transmission multiples (vecteurs biologiques; transmission par contact, par la graine, le pollen ou des propagules et/ou diffusion anthropique). Les approches de phylodynamique récemment appliquées aux virus de plantes permettent de quantifier certains de ces processus et d’estimer la contribution de différents facteurs à leur diversification temporelle et leur diffusion spatiale. Cette synthèse des apports de la phylodynamique à l’étude de l’épidémiologie et de l’évolution des phytovirus montrera :
- la datation de l’origine de plusieurs groupes de ces virus et le rôle probable de l’agriculture dans leur diversification,
- la reconstitution de routes de dispersion de ces virus à différentes échelles et la détermination des dates d’introduction dans certaines zones géographiques,
- la reconstitution d’événements particuliers dans leur histoire évolutive (recombinaison, saut d’hôte)
- et l’analyse du rôle de facteurs écologiques dans leur vitesse de diffusion ou leur rythme de diversification.
Hélène Duault – Methods combining genomic and epidemiological data in the reconstruction of transmission trees: a systematic review
In order to better understand transmission dynamics and appropriately target control and preventive measures, studies have aimed to identify who-infected-whom in actual outbreaks. While transmission trees have been inferred from contact tracing and epidemiological data, genomic data are increasingly included in these approaches. Since numerous reconstruction methods exist, each with their own assumptions, type of data necessary to implement them and inference strategy, selecting a single method can be difficult. We were interested in discussing transmission tree reconstruction methods that used both epidemiological and genomic data. Following PRISMA guidelines, we systematically reviewed the literature for methods combing epidemiological and genomic data in transmission tree reconstruction. We selected 41 articles among which we identified 20 methods. We grouped these methods into three families according to how genomic data was handled: a non-phylogenetic family, a sequential phylogenetic family and a simultaneous phylogenetic family. We then compared these methods according to the epidemiological data necessary to implement them as well as the underlying transmission, case observation and evolutionary models. In the non-phylogenetic family consisting of 11 methods, pairwise genetic distances were calculated to determine transmission likelihoods. In the phylogenetic families, transmission trees were inferred from phylogenetic trees either simultaneously (4 methods) or sequentially (5 methods). While a majority of methods (17/20) modeled the transmission process, few (7/20) took into account the fact that not all infected cases are detected in an outbreak and modeled case observation. Depending on the epidemiological unit considered (an individual vs. group of individuals, e.g. a farm), within-host evolution describes either intra-individual pathogen dynamics or transmission dynamics between individuals of the same unit. Within-host evolution was generally (7/8) modeled as a coalescent process. These practical and theoretical considerations were highlighted in order to help select the appropriate reconstruction method for an outbreak.