Use of an alignment-free method for the geographical discrimination of GTPVs based on the GPCR sequences

Chibssa Tesfaye Rufael, Liu Yang, Sombo Melaku, Kasiiti Lichoti Jacqueline, Erdenebaatar Janchivdorj, Boldbaatar Bazartseren, Grabherr Reingard, Settypalli Tirumala Bharani Kumar, Berguido Francisco J., Loitsch Angelika, Damena Delesa, Cattoli Giovanni, Diallo Adama, Lamien Charles Euloge. 2021. Use of an alignment-free method for the geographical discrimination of GTPVs based on the GPCR sequences. Microorganisms, 9 (4):855, 9 p.

Quartile : Q2, Sujet : MICROBIOLOGY

Résumé : Goatpox 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.

Mots-clés Agrovoc : séquence nucléotidique, capripoxvirus, caprin, ovin, virus de la variole caprine, phylogénie, virose, maladie nodulaire cutanée, maladie de la peau, identification

Mots-clés géographiques Agrovoc : Afrique, Asie, Éthiopie, Ghana, Kenya

Mots-clés libres : GTPV, Alignment-free algorithm, K-mer, G-protein-coupled chemokine receptor

Agences de financement hors UE : African Renaissance and International Cooperation Fund

Auteurs et affiliations

• Chibssa Tesfaye Rufael, IAEA (AUT)
• Liu Yang, IAEA (AUT)
• Sombo Melaku, NAHDIC (ETH)
• Kasiiti Lichoti Jacqueline, Ministry of Agriculture, Livestock and Fisheries (KEN) (KEN)
• Erdenebaatar Janchivdorj, Mongolian University of Life Sciences (MNG)
• Boldbaatar Bazartseren, Mongolian University of Life Sciences (MNG)
• Grabherr Reingard, BOKU (AUT)
• Settypalli Tirumala Bharani Kumar, IAEA (AUT)
• Berguido Francisco J., IAEA (AUT)
• Loitsch Angelika, Austrian Agency for Health and Food Safety (AUT)
• Damena Delesa, NAHDIC (ETH)
• Cattoli Giovanni, IAEA (AUT)
• Diallo Adama, CIRAD-BIOS-UMR ASTRE (SEN)
• Lamien Charles Euloge, IAEA (AUT) - auteur correspondant

Source : Cirad-Agritrop (https://agritrop.cirad.fr/613467/)

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