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“Estudis de detecció, caracterització i evolució de virus emergents: de la vida salvatge als humans”
Title: Detection, characterization and evolutionary studies of emerging viruses: from wildlife human.

Estudi de la detecció, caracterització i evolució de virus emergents: de la vida salvatge als humans

Emerging viruses is a research field that has directly and greatly benefited from the rise of disruptive and cutting-edge technologies in molecular biology and genomics such as high throughput sequencing (HTS).

This talk will focus on two examples of studies that use next generation sequencing for i) detecting and characterizing the etiological agent of seasonal outbreaks of pediatric encephalitis in Vietnam (Acmong project) and for ii) estimating the evolutionary dynamics of SARS-CoV sister clade betacoronaviruses infecting bats in the western Palearctic (including France and Spain, EPICOREM project, see

i) Since the end of the 1990s, seasonal outbreaks of pediatric acute encephalitis syndrome (AES) coinciding with litchi harvesting (May to July) have been documented in the Bac Giang Province located in Northern Vietnam. A retrospective ecological analysis from 2004 to 2009, involving environmental, agronomical and climatic factors, demonstrated the association between the outbreaks and litchi harvesting. In order to investigate the etiology of the disease, samples were collected during each epidemic, from 2007 to 2012. Cerebro-spinal fluids (CSF) of patients matching the inclusion criteria were investigated for the presence of pathogens by both specific and a broad range approach aiming at detecting pathogen by coupling random amplification of nucleic acids with HTS. In association with appropriate epidemiological selection of patients and specific preparation of samples, HTS without a-priori was efficient to detect and allow characterising pathogens in CSF of patients suffering from orphan pathology.

ii) Elucidating the evolutionary relationships between viruses and their hosts remains one of the great challenges in infectious diseases ecology. Coronaviruses were considered minor pathogens for human before the emergence of SARS-CoV and MERS-CoV. These emergences triggered research on coronaviruses from wildlife and light was shed on the extreme diversity of coronaviruses in nature and especially in bats, thus considered as a shedding source of coronaviruses. Accounting for more than 1300 species, which represent 21% of actual mammals diversity, bats are social animals structured in meta-populations and offer excellent opportunities for coronaviruses to evolve and to speciate.

In order to enlighten the diversity, the circulation, the phylogenetic relationships and the evolutionary traits of wildlife coronaviruses in the Western Old World, we investigated whether bats from France and Spain harbored coronaviruses. Dynamics of seasonal circulation and in-host genetic evolution of coronaviruses populations in nature is currently unknown and this study explore s these aspects through temporal monitoring of the evolution of a SARS-CoV sister clade Betacoronavirus circulating in a greater horseshoe bat (Rhinolophus ferrumequinum) maternity colony.

Among more than 2,500 samples (12% coronavirus-positive), new coronaviruses were detected in bats in the Western Palearctic. One SARS-CoV related Betacoronavirus-b and dozen alphacoronaviruses were detected. Temporal follow-up (since 2014) by high throughput sequencing of this new Betacoronavirus, revealed a complex quasi-species cloud that contributes to genetic variation and complex evolution.

Alphacoronaviruses and a SARS-CoV sister-clade Betacoronavirus-b currently circulate in France and Western-Europe and exhibit complex phylogeography and rapid genetic evolution in nature. The natural history and genetic evolution of coronaviruses in bats, coupled with the ecology and phylogeny of their hosts are keys for the understanding of their actual range and of potential threat posed by coronaviruses to humans.

Meriadeg Le Gouil,
Current institution: Université de Normandie, Groupe de Recherche sur l'Adaptation Microbienne EA 2656 Unicaen / Unirouen, Caen, France. EPICOREM Consortium -
Previous institution: Institut Pasteur, Environnement et Risques Infectieux, Paris, France.

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