Description of viral cross-species transmission
The project 'C THE LIGER' has studied how gammaretroviruses transmitted across different species using genomics, bioinformatics and viral molecular evolution. Training activities to improve research skills included the areas of molecular evolution of ERVs, data-mining, bioinformatics, genome analyses, software programming and advanced statistics. To begin with, project members built two reference libraries using sequences from GenBank. One was a partial pol sequence library from all available ERV families and XRV (exogenous RV) species. The other, a full-length genome library of all available gammaretroviruses and class-I families, was used to construct alignments. Pol sequences are the most conserved part of the genomes and were therefore selected for data-mining. All possible ERVs were located from the available mammalian genomes and used to optimise the data-mining algorithms. C THE LIGER devised algorithms to measure the genetic integrity, replicating techniques, shared deletions and functionality of the envelope gene in Class-I ERV elements. Noteworthy is the algorithm to measure cross-species transmission based on an approach called maximum parsimony. Project outcomes resulted in four publications. The data and algorithms produced during the project will prove useful in future research endeavours on this topic. Describing the ability of viruses to cross the species barrier could eventually help understand zoonotic viral transmissions and design preventative measures.
