Abstract
The nucleotide sequences of a region including S1, S2, 3a, 3b and E genes of twenty-seven infectious bronchitis virus (IBV) isolates in Korea between 1990–2011 were determined and phylogenetic and computational recombination analyses were conducted. The sizes of coding regions of some genes varied among IBV isolates due to deletion or insertion of nucleotides; the nucleotide similarities of S1, S2, 3a, 3b and E genes among the 27 isolates were 75.9%–100.0%, 85%–100.0%, 64.0%–100.0%, 60.4%–100.0% and 83.1%–100.0%, respectively. According to phylogenetic analysis of S1 gene, the 27 isolates were divided into five genotypes, Mass, Korean-I (K-I), QX-like, KM91-like and New cluster 1. The phylogenetic trees based on the S2, 3a, 3b, E genes and S1-S2-3a-3b-E (S1-E) region nucleotide sequences did not closely follow the clustering based on the S1 sequence. The New cluster 1 prevalent during 2009 and 2010 was not found in 2011 but QX-like viruses became prevalent in 2011. The recombination analysis revealed two new S gene recombinants, 11036 and 11052 which might have been derived from recombinations between the New cluster 1 and QX-like viruses and between the K-I and H120 (vaccine) viruses, respectively. In conclusion, multiple IBV genotypes have co-circulated; QX-like viruses have recurred and new recombinants have emerged in Korea. This has enriched molecular epidemiology information of IBV and is useful for the control of IB in Korea.
Highlights
Infectious bronchitis virus (IBV), a member of genus Gammacoronavirus, subfamily Coronavirinae, family Coronaviridae, order Nidovirales [1] is the causative agent of infectious bronchitis (IB), an acute, highly infectious and contagious disease of chickens worldwide
The objective of the present study was to decipher the genetic features of S1, S2, 3a, 3b and E genes of 27 infectious bronchitis virus (IBV) circulating in Korea and identify recombinants, providing IBV molecular epidemiology information and laying a good foundation for the control of IB in Korea
Extraction and subsequent RT-PCR detection based on the S1 gene of IBV
Summary
Infectious bronchitis virus (IBV), a member of genus Gammacoronavirus, subfamily Coronavirinae, family Coronaviridae, order Nidovirales [1] is the causative agent of infectious bronchitis (IB), an acute, highly infectious and contagious disease of chickens worldwide. Different serotypes of IBVs confer little or no cross-protection against each other. The increasing number of new serotypes of IBV, which were caused by frequent gene mutation and recombination, are a major challenge for the prevention and control of IB [3,4,5]. Two-thirds of the genome encodes two polyproteins 1a and 1b and the remaining one-third, structural proteins and small nonstructural accessory proteins [7]. IBV encodes four essential structural proteins, the spike (S) glycoprotein, the membrane (M) glycoprotein, the nucleocapsid (N) protein and the envelope or small membrane (E) protein [8]. The S1 glycoprotein is most variable and contains hypervariable regions carrying epitopes for serotype-specific, virus-neutralizing and hemagglutination-inhibiting antibodies. The S2 glycoprotein contains two antigenic determinants and may affect the S1 specific antibody binding [9,10]
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