Table 1.
Sequences were obtained from the following reference strains.
Fig 1.
Single nucleotide polymorphisms (SNPs) for Ark viruses.
Red box = recombination of MDL-Ark-DPI-15-5519 with DMV/1639 (24 SNPs in the first 110nt), and the Blue boxes = recombination of 6 Ark strains with Mass vaccine type virus.
Fig 2.
Phylogenetic tree created by the Maximum-likelihood algorithm for the S1 gene of IBV Ark type viruses.
Red is pathogenic Ark/Ark-DPI/81, blue is vaccine virus, green is viruses from DELMARVA and yellow is viruses from Georgia. Blue box = recombined with DMV/1639/14 and red box = recombined with Mass type virus.
Fig 3.
Median-joining phylogenetic network of Ark type viruses.
The median-joining network was constructed from the S1-encoding gene. The network included the most parsimonious trees linking the sequences. Viruses with identified recombination sequences to DMV/1639 or Mass-type viruses were not included in the analysis. Each unique sequence is represented by a circle whose size reflects the frequency of the sequence in the data set. Branch length is proportional to the number of mutations. Isolates are colored according to their origin as follows: blue = vaccine, green = DELMARVA, yellow = Georgia and red = pathogenic reference strain.
Fig 4.
Phylogenetic tree created by the Maximum-likelihood algorithm for the S1 gene of IBV Mass type viruses.
Fig 5.
Median-joining phylogenetic network of Mass-type viruses.
The median-joining network was constructed from the S1-encoding gene. The network included the most parsimonious trees linking the sequences. Each unique sequence is represented by a circle whose size reflects the frequency of the sequence in the data set. Branch length is proportional to the number of mutations. Isolates are colored according to their origin as follows: blue = vaccine, orange = DELMARVA, purple = Georgia.
Fig 6.
Phylogenetic tree created by the Maximum-likelihood algorithm for the S1 gene of IBV DMV/1639 type viruses.
Fig 7.
Median-joining phylogenetic network of DMV/1639 viruses.
The median-joining network was constructed from the S1-encoding gene. The network included the most parsimonious trees linking the sequences. Each unique sequence is represented by a circle whose size reflects the frequency of the sequence in the data set. Branch length is proportional to the number of mutations. Sequences with a rectangle around them are from nephropathogenicity cases. Sequences with an oval around them are from cases with respiratory signs only. All other sequences were from cases where the disease presentation was not known. All of the viruses are from DELMARVA.
Table 2.
Selection profiles of the S1 spike protein.