Host shifts result in parallel genetic changes when viruses evolve in closely related species

Ben Longdon; Jonathan P Day; Joel M Alves; Sophia CL Smith; Thomas M Houslay; John E McGonigle; Lucia Tagliaferri; Francis M Jiggins

To examine how viruses evolve in different host species we serially passaged DCV in 19 species of 73 Drosophilidae. In total we infected 22,095 adult flies and generated 173 independent replicate 74 . CC-BY-NC 4.0 International license author/funder. It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/226175 doi: bioRxiv preprint lineages (6-10 per host species). We deep sequenced the evolved virus genomes to generate over 75 740,000 300bp sequence reads from each viral lineage. Out of 8989 sites, 584 contained a SNP with 76 a derived allele frequency >0.05 in at least one viral lineage, and 84 of these were tri-allelic. None of 77 these variants were found at an appreciable frequency in five sequencing libraries produced from 78 the ancestral virus, indicating that they had spread though populations during the experiment 79 ( Figure 1 ). In multiple cases these variants had nearly reached fixation (Figure 1 ).