Separate trees for each host, protein and subtype

Phylogenetic trees in Newick format. For each protein there is a separate tree which has sequences from a single host and a single subtype. The nodes in the tree are marked with the top 5 rules for the respective protein.The nodes of the trees are accession IDs of the sequences used in the creation of the phylogenies followed by the rules numbers that are supported by the sequence. The sequences used were obtained from NCBI database. The trees were created using FastTree 2.1.8

Neighbor-Joining analysis of a 249-bp fragment of the 5′UTR sequences under Kimura 3-parameter model.

<p>The sequences are labelled with sample ID (-number of clone)/country or region of origin. AU, Australia; BR, Brazil; CA, Canada; CO, Colombia; DK, Denmark; DR, Dominican Republic; EU, European Union; FR, France; MX, Mexico; NI, not identified by supplier; NZ, New Zealand; SA, South American; US, USA; ZA, South Africa. Numbers are percentage of bootstrap values (1000 replicates) for major clades. Bar indicates changes per site. The GenBank accession numbers for reference strains are DQ075210, NC_001461, U97481, AF026781, AB359927, AF049221, AY363096 and FJ493479 for BVDV-1, AY763053 and NC_002032 for BVDV-2, and NC_012812 for BVDV-3.</p

The batches of foetal bovine serum tested by real-time RT-PCR.

a<p>Sequence has not been determined.</p

Separate alignments for each protein of subtypes H1N1 and H3N2 and for humans and avians hosts

Multiple alignments of each protein of both the H1N1 and H3N2 subtypes. A separate file for sequences coming from human and avian hosts is present. All the sequences were obtained from the NCBI database. These were used to create phylogenetic trees (Figure 3 and additional file 5 in the paper

Induction of FCoV-neutralizing antibodies after oronasal challenge of cats with the parent virus FIPV DF-2 (n = 4) and recombinant FCoVs PBFIPV-DF-2(n = 4) and PBFIPV-DF-2-R3i (n = 4).

<p>The means of groups are given. Error bars represent standard deviations.</p

FCoV viraemia of cats challenged oronasally with the parent virus FIPV DF-2 (n = 4) and recombinant FCoVs PBFIPV-DF-2(n = 4) and PBFIPV-DF-2-R3i (n = 4), as monitored with genomic qRT-PCR.

<p>The means of groups are given. Error bars represent standard deviations.</p

Combined phylogenetic trees for each protein

Phylogenetic trees in Newick format. For each protein there is a tree which has sequences from both the avian and human hosts and from from both H1N1 and H3N2 subtypes. The nodes are the accession IDs of the sequences followed by the host and subtype information. The original sequences were taken from NCBI database. The trees were created using FastTree 2.1.8

FCoV load of organs of cats challenged oronasally with the parent virus FIPV DF-2 (n = 4) and recombinant FCoVs PBFIPV-DF-2 (n = 4) and PBFIPV-DF-2-R3i (n = 4), as monitored with genomic qRT-PCR.

<p>The means of groups are given. Error bars represent standard deviations.</p

Fecal shedding of FCoV by cats challenged oronasally with the parent virus FIPV DF-2 and recombinant FCoVs PBFIPV-DF-2 (n = 4) and PBFIPV-DF-2-R3i (n = 4), as monitored with genomic qRT-PCR.

<p>The means of groups are given. Error bars represent standard deviations.</p

Combined alignment for each protein with data from all hosts and subtypes

Multiple alignments for all the protein. Each file has sequences coming from both human and avian hosts and both subtypes H1N1 and H3N2. All the sequences were obtained from the NCBI database. They were used to infer phylogenies (Figure 4 and additional file 6 in the paper)