Non-invasive surveys of mammalian viruses using environmental DNA

Niccolo Alfano; Anisha Dayaram; Jan Axtner; Kyriakos Tsangaras; Marie-Louise Kampmann; Azlan Mohamed; Seth Timothy Wong; M. Thomas P. Gilbert; Andreas Wilting; Alex Daivd Greenwood

Viral contigs were assigned to viral families according to the best BLAST results. Comprehensive sets of representative sequences from these viral families were retrieved from GenBank and aligned with the contigs using MAFFT v7.450 [44] . Phylogenetic analysis was performed using the maximum-likelihood method based on the general time reversible substitution model with amongsite rate heterogeneity modelled by the Γ distribution and estimation of proportion of invariable sites available in RAxML v8 [45] , including 500 bootstrap replicates to determine node support. Phylogenetic analyses were performed only on viral contigs i) showing divergence from known viruses, i.e. with both BLAST identity and coverage to the best reference below 95%, to place them into a phylogenetic context, and ii) mapping to phylogenetically relevant genomic regions. Therefore, Circoviridae and Anelloviridae contigs were excluded as were those identified from water.