Sub-consensus variant detection and quasispecies reconstruction of two FMDV serotype A variants with differential virulence.

CACCIABUE M.; KÖNIG G.; GISMONDI M.I.

Utrecht

Congreso; 2nd Annual Meeting of the EVBC; 2018

European Virus Bioinformatics Center

Different animal models have been used to study FMDV biology and host susceptibility to viral infection. In the laboratory, we identified two FMDV viruses of serotype A/Arg/01 displaying differential virulence in adult mice: a non-lethal variant (A01NL) caused a mild disease, whereas a lethal variant (A01L) caused death within 24-48 hpi, independently of the dose used (10exp3-10exp6 pfu/mouse). Sanger sequencing of whole viral genomes suggested higher variability of A01L virus.In this work, we used an NGS approach to determine the viral complexity of A01NL and A01L viruses. Total RNA was isolated from supernatants of infected BHK-21 cells, cDNA was synthesized and two PCR fragments encompassing 94% of the whole viral genome were amplified and used for library preparation and sequencing in an Illumina MiSeq apparattus. Programs Lofreq and Qure were used to interrogate quasispecies variability and to reconstruct viral haplotypes, respectively.Viruses A01L and A01NL showed different levels of variability, which might be related with the differential virulence displayed by both viruses.