PCR cycle sequencing is used by our lab to identify new IBV S1 genotypes. General (= universal) degenerate primers are used to amplify hypervariable regions that are used to identify field isolates from commercial poultry flocks. PCR products approximately 600 bp in length are then sequenced and aligned with sequences of known reference strains. Sequence analysis yields phylogenetic tree (= dendogram) and nucleotide and protein similarity values (%) for the included genotypes. The phylogenetic tree below illustrates the relationship between selected genotypes from a variety of geographic locations. The primers and procedures for IBV PCR cycle sequencing are described in Kingham, B. F., C. L. Keeler, Jr., W. A. Nix, B. S. Ladman, and J. Gelb, Jr. Identification of avian infectious bronchitis virus by direct automated cycle sequencing of the S-1 gene. Avian Diseases. 44:325-335 (2000).
S1 phylogeny of representative avian infectious bronchitis virus
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