Use of an Alignment-Free Method for the Geographical Discrimination of GTPVs Based on the GPCR Sequences
2021
Chibssa, Tesfaye, Rufael | Liu, Yang | Sombo, Melaku | Lichoti, Jacqueline, Kasiiti | Erdenebaatar, Janchivdorj | Boldbaatar, Bazartseren | Grabherr, Reingard | Settypalli, Tirumala, Bharani K | Berguido, Francisco, J | Loitsch, Angelika | Damena, Delesa | Cattoli, Giovanni | Diallo, Adama | Lamien, Charles, Euloge | Joint FAO/IAEA Programme - Nuclear Techniques in Food and Agriculture ; Food and Agriculture Organization of the United Nations [Rome, Italie] (FAO)-International Atomic Energy Agency [Vienna] (IAEA) | National Animal Health Diagnostic and Investigation Center (NAHDIC) | Universität für Bodenkultur Wien = University of Natural Resources and Life Sciences [Vienne, Autriche] (BOKU) | Ministry of Agriculture, Livestock and Fisheries [Kenya] | Mongolian University of Life Sciences | Austrian Agency for Health and Food Safety (AGES) | Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE) ; Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) | Département Systèmes Biologiques (Cirad-BIOS) ; Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad) | This study was supported by the VETLAB network initiative of the Joint FAO/IAEA Division, funded through the African Renaissance and International Cooperation Fund of South Africa and the Peaceful Uses Initiatives (PUI) funded by Japan and the United States of America.
International audience
显示更多 [+] 显示较少 [-]英语. This article is an oGoatpox virus (GTPV) belongs to the genus Capripoxvirus, together with sheeppox virus (SPPV) and lumpy skin disease virus (LSDV). GTPV primarily affects sheep, goats and some wild ruminants. Although GTPV is only present in Africa and Asia, the recent spread of LSDV in Europe and Asia shows capripoxviruses could escape their traditional geographical regions to cause severe outbreaks in new areas. Therefore, it is crucial to develop effective source tracing of capripoxvirus infections. Earlier, conventional phylogenetic methods, based on limited samples, identified three different nucleotide sequence profiles in the G-protein-coupled chemokine receptor (GPCR) gene of GTPVs. However, this method did not differentiate GTPV strains by their geographical origins. We have sequenced the GPCR gene of additional GTPVs and analyzed them with publicly available sequences, using conventional alignment-based methods and an alignment-free approach exploiting k-mer frequencies. Using the alignment-free method, we can now classify GTPVs based on their geographical origin: African GTPVs and Asian GTPVs, which further split into Western and Central Asian (WCA) GTPVs and Eastern and Southern Asian (ESA) GTPVs. This approach will help determine the source of introduction in GTPV emergence in disease-free regions and detect the importation of additional strains in disease-endemic areas
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