Emergence of subtype strains of the Arkansas serotype of infectious bronchitis virus in Delmarva broiler chickens.

Infectious bronchitis virus (IBV) field isolates of the Arkansas (Ark) serotype were identified by reverse transcription-polymerase chain reaction (RT-PCR) as the most common serotype isolated from 1993 to 1997. These isolates were recovered from broiler flocks with respiratory disease raised on the Delmarva peninsula in spite of Ark vaccination in the region. For the purposes of investigating this apparently paradoxical finding, five RT-PCR Ark-positive field isolates recovered in 1995 and 1996 were selected for further characterization. The isolates were compared with Ark reference strains by reciprocal virus neutralization (VN) in embryonated eggs, S-1 gene sequence analysis, and challenge of immunity studies in specific-pathogen-free (SPF) chickens. Antigenic (VN) comparisons and S-1 gene analysis confirmed that the five RT-PCR Ark-positive field isolates were of the Ark serotype but also revealed that the viruses could be readily distinguished from Ark reference strains. Four of the isolates (Ark/213/96, Ark/15C/96, Ark/1529/95, Ark/1534/95) were found to have higher antigenic relatedness percentages to each other (95%-100%) than to Ark reference strains DPI (52%-72%) and Georgia variant (Georgia var) (53%-68%) by VN. Another isolate, Ark/1535/95, was found to differ antigenically from the other four RT-PCR Ark-positive field isolates (34%-61%), Ark DPI (44%), and Georgia var (43%) strains. The trends in the S-1 gene sequencing results were similar to those observed for the VN findings. Isolates Ark/213/96, Ark/15C/96, Ark/1529/95, and Ark/1534/95 demonstrated a higher degree of predicted S-1 amino acid similarity to each other (96.5%-98.7%) than to Ark DPI (92.4%-93.7%), Ark 99 (93.2%-94.7%), and Georgia var (89.3%-90.8%). Ark/1535/95 S-1 amino acid similarity values were lower compared with those of the other four RT-PCR Ark-positive field isolates (93.4%-94.8%), Ark DPI (91.9%), Ark 99 (93.0%), and Georgia var (88.7%). Furthermore, the isolates could be distinguished from the Ark reference strains by a characteristic sequence polymorphism, a six-nucleotide deletion encoding amino acids 57 (Asp) and 58 (Asp) in hypervariable region 1 of S-1. On the basis of the VN and sequencing findings, isolates Ark/213/96, Ark/15C/96, Ark/1529/95, and Ark/1534/95 were considered to be a single subtype of the Ark serotype. The fifth isolate, Ark/1535/95, may constitute another subtype of the Ark serotype. Vaccination of SPF chickens with a high-titering commercially available live vaccine containing the Ark DPI strain provided solid protection (>90%) against challenge with the RT-PCR Ark-positive field isolates. Immunization of SPF chickens with Ark/213/96 produced 100% protection against challenge with the homologous strain, as well as isolates Ark/1535/95 and Ark 99 but lower levels of protection against Ark DPI (58%) and Georgia var (55%). Primers for RT-PCR were designed to distinguish between the Ark subtypes and the Ark reference strains on the basis of the characteristic six-nucleotide deletion identified in the S-1 gene of the Ark subtypes. Retrospective analysis of RT-PCR Ark-positive isolates found that the Ark subtypes existed as early as 1992 in Delmarva broilers and became prevalent by 1995. With RT-PCR, restriction fragment length polymorphism analysis, and DNA sequencing techniques, the presence of Ark subtype viruses was demonstrated in two commercial Ark DPI strain vaccines and in our Ark DPI laboratory stocks that were the original source of the virus used for vaccine development. The demonstration of the Ark subtype and reference strains in the Ark DPI strain is evidence of the existence of IBV quasispecies. Factors possibly influencing the emergence of the Ark subtype in commercial broilers are discussed.

Identification of avian infectious bronchitis virus by direct automated cycle sequencing of the S-1 gene.

Direct automated cycle sequencing (DACS) of a reverse transcription-polymerase chain reaction (RT-PCR) product of the S-1 subunit of the spike peplomer gene was used to identify infectious bronchitis virus (IBV) serotypes. Degenerate primers CK4 and CK2, utilized previously in our laboratory, were selected for DACS because they successfully amplify a wide range of serotypes represented by various reference strains and field isolates and the resulting polymerase chain reaction (PCR) product contains diagnostically relevant S-1 sequences that can be used to identify the serotype of IBV. The S-1 nucleotide sequences generated by DACS were aligned and analyzed with commercial software to determine their relationship to the S-1 nucleotide sequences of IBV strains on deposit in the GenBank and EMBL databases. Reference strains Massachusetts (Mass) 41, Connecticut (Conn), Arkansas (Ark) DPI, JMK, and DE/072/92 were initially tested by DACS to establish the feasibility of the procedure. The DACS procedure was further evaluated with a panel of "unknowns" comprised of IBV reference strains, field isolates, and variant serotypes collected by our laboratory. The DACS procedure provided high-quality and reproducible S-1 sequence for all IBV serotypes tested, including variant serotypes that had not been sequenced previously. The S-1 nucleotide sequences for the amplified PCR products of reference strains Mass 41, Conn, Ark DPI, JMK, and DE/072/92 generated by DACS were highly homologous (>99% nucleotide identity) with their respective GenBank database sequences. In the unknown panel, the nucleotide identities of the DACS S-1 sequences of field isolates of serotypes previously identified by virus neutralization were also found to be very high (> or = 95.5%) after alignment with database sequences. In contrast, the nucleotide identities of S-1 sequences of variant serotypes 37, 3330, and PA/1220/98 and reference strain Clark 333, for which database sequences were not available, ranged from 27.7% to 73.8%, well below the identity values for a homologous serotype. With alignment software, the identities of strains in mixtures of RNAs of two different serotypes were not resolvable. DACS of IBV S-1 RT-PCR products will enable researchers to rapidly identify field strains, including new, previously unrecognized variant virus serotypes.