Repeated avian infectious bronchitis virus infections within a single chicken farm

Figures

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  Fig. 1.. Partial sequence of the S gene of IBV. Samples isolated from tracheas and kidneys of six chickens were amplified by RT-PCR either with the S1 primer pair (A) or S2 primer pair (B). DNA fragments read from both termini by the dideoxy-chain-termination method were aligned. Asterisks show the nucleotides that are identical among the samples. Blanks show the nucleotides that differ between tracheas and kidneys. The 653 bp-regions of S1 (A) and the 379 bp-regions of S2 (B) are shown. A: Open circles indicated on the nucleotides shows the minor nucleotide changes found in one of six chickens (A63G, T86C and C246T). B: Numbers (1–36) shown on the nucleotides in the blank space corresponds to those in Fig. 2.

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  Fig. 3.. Phylogenetic tree based on the partial S gene sequences. Phylogenetic tree analysis based on the nucleotide sequences of amplified S1 (A) and S2 (B) regions were performed using the unweighted pair group method with arithmetic mean (UPGMA) method. Naming of groups followed previous publications [9,10,11,12,13]. Sequences of representative IBV were either downloaded through NCBI, PubMed, Nucleotide-searching site, or obtained by our own sequencing.

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  Fig. 2.. Minor peaks in the S2 region of trachea samples. Representative nucleotide sequencing peaks of the S2 region of trachea samples are shown. Green, black, blue, and red lines show the four nucleotide bases, adenine, guanine, cytosine, and thymine, respectively. Thirty-six nucleotides that differed between the samples obtained from tracheas and kidneys are marked and boxed. Under the main nucleotide peak, a smaller peak is present, but its color is identical to that in the kidney sample.