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Evidence of natural recombination within the S1 gene of infectious bronchitis virus
L Wang1, D Junker, E W Collisson
1Department of Veterinary Pathobiology, Texas A&M University, College Station 77843.
Abstract:
During an outbreak of severe respiratory disease, a field strain of infectious bronchitis virus (IBV), PP14, was isolated from a bird in a Texas flock that had been previously vaccinated with an attenuated Mass serotype virus. After cloning and sequencing the S1 gene from several IBV strains, it was found that the 5' end of the cDNA was 96% identical to the published sequences of Mass41 and 77% identical with Ark99. The following 402 bases which included the hypervariable regions (HVR) of the S1 gene were 94% homologous with Ark99 and only 69% with Mass41. In addition, the HVR in the 3' noncoding region of the genome, which is totally absent in Mass41, was 99% homologous with the Ark99 strain. This abrupt shift in identity of PP14 in the S1 strongly indicated that a recombination event had occurred about 98 bases from the beginning of the S1 gene between an Ark-like and a Mass-like virus. Downstream, 33 bases from the PP14 recombination junction, a second putative "cross-over" site was identified in the S1 of the SE17 strain where the 5'131 bases of the S1 gene of the Ark99 and SE17 were found to be 95% identical and the following 368 base sequence was only 78% homologous. In addition, a second shift in homology in the S1 of SE17 was identified between nucleotide 1112 and 1460 which shared 95% identity with Mass41. The putative recombination junctions which were downstream of the signal sequence and upstream of the S1 HVR may represent a "hot spot," but not an exclusive region, for exchanging genetic material between IBV strains. Genetic shifts are apparently not only common mechanisms for variation in nature, but vaccine strains may actually play a critical role in these events in the evolution of virulent strains of IBV.
Insights
Genetic recombination between infectious bronchitis virus (IBV) strains, potentially involving vaccine strains, leads to the evolution of new virulent IBV variants. This study identifies recombination "hot spots" in the S1 gene, crucial for understanding IBV genetic shifts.
Area of Science:
- Virology
- Molecular Biology
- Genetics
Background:
- Severe respiratory disease outbreaks caused by infectious bronchitis virus (IBV) pose significant challenges in poultry farming.
- Previous vaccination with attenuated strains, such as the Mass serotype, did not prevent infection with a novel field strain, PP14.
- Understanding the genetic mechanisms driving IBV evolution is critical for developing effective control strategies.
Purpose of the Study:
- To investigate the genetic makeup of the PP14 IBV field strain isolated from a vaccinated flock.
- To identify potential recombination events within the S1 gene of IBV strains.
- To explore the role of genetic recombination and vaccine strains in the emergence of virulent IBV.
Main Methods:
- Isolation and sequencing of the S1 gene from field and reference IBV strains (PP14, Mass41, Ark99, SE17).
- Comparative sequence analysis to identify regions of homology and divergence.
- Identification of putative recombination junctions based on abrupt shifts in sequence identity.
Main Results:
- The PP14 strain exhibited a distinct genetic profile, with high homology to Ark99 in hypervariable regions of the S1 gene and its 3' noncoding region, but similarity to Mass41 at the 5' end of the S1 gene.
- Evidence of a recombination event was detected in the S1 gene of PP14, approximately 98 bases from its beginning, between Ark-like and Mass-like viruses.
- A second putative recombination site was identified in the SE17 strain, with distinct homology shifts suggesting genetic exchange with both Ark99 and Mass41.
Conclusions:
- Recombination events, particularly within the S1 gene, are significant drivers of genetic variation in IBV.
- Specific regions in the S1 gene, such as near the signal sequence and upstream of the S1 HVR, may act as 'hot spots' for genetic exchange.
- Vaccine strains may play a crucial role in the evolution of virulent IBV strains through facilitating or participating in recombination events.