Evaluation of un-methylated DNA enrichment in sequencing of African swine fever virus complete genome

Pereira De Oliveira Rémi, Lucas Pierrick, Chastagner Amélie, De Boisseson Claire, Vial Laurence, Le Potier Marie-Frédérique, Blanchard Yannick. 2020. Evaluation of un-methylated DNA enrichment in sequencing of African swine fever virus complete genome. Journal of Virological Methods, 285:113959, 7 p.

https://doi.org/10.1016/j.jviromet.2020.113959

Article de revue ; Article de recherche ; Article de revue à facteur d'impact

Version publiée - Anglais
Accès réservé aux personnels Cirad
Utilisation soumise à autorisation de l'auteur ou du Cirad.
Pereira De Oliveira et al. - 2020 - Evaluation of un-methylated DNA enrichment in sequ.pdf
Télécharger (1MB) | Demander une copie

Prévisualisation

Version post-print - Anglais
Sous licence

.
ID596605.pdf
Télécharger (298kB) | Prévisualisation

Quartile : Q4, Sujet : BIOCHEMICAL RESEARCH METHODS / Quartile : Q4, Sujet : BIOTECHNOLOGY & APPLIED MICROBIOLOGY / Quartile : Q4, Sujet : VIROLOGY

Résumé : African swine fever is a febrile hemorrhagic fever disease that is caused by the African swine fever virus (ASFV) and is lethal for domestic pigs and wild boar. ASFV also infects soft ticks of the genus Ornithodoros, some species of which can act as a vector for ASFV. Whole genome sequencing of ASFV is a challenge because, due to the size difference of the host genome versus the viral genome, the higher proportion of host versus virus DNA fragments renders the virus sequencing poorly efficient. A novel approach of DNA enrichment, based on the separation of methylated and un-methylated DNA, has been reported but without an evaluation of its efficacy. In this study, the efficiency of the un-methylated DNA enrichment protocol was evaluated for pig and tick samples infected by ASFV. As expected, fewer reads corresponding to ASFV were found in the methylated fraction compared to the un-methylated fraction. However, the sequencing coverage of the un-methylated fraction was not improved compared to the untreated DNA. In our hands, the ASFV DNA enrichment was inefficient for tick samples and very limited for pig samples. This enrichment process represents extra work and cost without a significant improvement of ASFV genome coverage. The efficiency of this enrichment approach and the cost/benefit ratio are discussed.

Mots-clés Agrovoc : virus peste porcine africaine, méthylation, génome, séquence d'adn

Mots-clés libres : African swine fever virus, NGS, Enrichment, Methylation

Classification Agris : L73 - Maladies des animaux
L10 - Génétique et amélioration des animaux

Champ stratégique Cirad : CTS 4 (2019-) - Santé des plantes, des animaux et des écosystèmes

Agences de financement européennes : European Commission

Programme de financement européen : H2020

Projets sur financement : (EU) COllaborative Management Platform for detection and Analyses of (Re-)emerging and foodborne outbreaks in Europe

Auteurs et affiliations