Detection and Characterization of Homologues of Human Hepatitis Viruses and Pegiviruses in Rodents and Bats in Vietnam

Van Nguyen, Dung; Van Nguyen, Cuong; Bonsall, David; Ngo, Tue Tri; Carrique-Mas, Juan; Pham, Anh Hong; Bryant, Juliet E.; Thwaites, Guy; Baker, Stephen; Woolhouse, Mark; Simmonds, Peter

For rodent hepacivirus, HEV and pegivirus genomes, extracted RNA from representative positive samples was subjected to deep sequencing using an Illumina platform. Libraries were prepared from total extracted RNA using the NEBNext Ultra Directional Sequencing Kit (New England Biolabs, Hitchin, UK) with omission of actinomycin D, then pooled and sequenced on a HiSeq 4000 instrument (Illumina, Nr Saffron Walden, UK). Quality control and trimming of reads were performed before genome mapping using CLC Genomics Workbench (Qiagen Bioinformatics, Redwood City, CA, USA) with the default affine gap cost parameters. The closest related virus genomes (Genbank numbers KC815310, JX120573 and KJ950934 for hepacivirus, HEV and pegivirus, respectively) were used as templates for genome mapping. Additional primers were designed using the obtained contigs for gap fillings.