RNA-seq analysis of mixed viral/host reads with salmon
You provide Salmon with a transcriptome fasta... so merging the human transcriptome with the pox virus genome fasta file should work. You don't mention that in your post but the viral genome should exist as a fasta. You can extract the sequences from genbank or maybe you can find our virus here: https://www.ebi.ac.uk/genomes/virus.html

You can find the coding transcriptome at the link below in the cdna folder.
The non-coding transcriptome is in the ncrna. You should probably merge them:

ftp://ftp.ensembl.org/pub/release-95/fasta/homo_sapiens/