Genetic Analysis of the Complete S1 Gene in Japanese Infectious Bronchitis Virus Strains

Abstract

The complete nucleotide sequence of the S1 glycoprotein gene of the Japanese infectious bronchitis virus (IBV) strains was determined and genetically analyzed. A total of 61 Japanese IBV strains were classified into seven genotypes, namely GI-1, 3, 7, 13, 18, 19, and GVI-1 using the classification scheme that was proposed by Valastro et al, with three exceptions. These genotypes practically corresponded to those defined in Japan, namely Mass, Gray, JP-II, 4/91, JP-I, JP-III, and JP-IV, which have been identified through their partial nucleotide sequences containing hypervariable regions 1 and 2. In addition, three exceptive strains were considered to be derived from recombination within the S1 gene of IBV strains G1-13 and GI-19. By analyzing the amino acid polymorphism of the S1 glycoprotein among Japanese genotypes, a diversity was observed based on the genotype-specific amino acid residue, the proteolytic cleavage motif at the S1/S2 cleavage site, and the position of the potential N-glycosylation sites.

Keywords: S1 gene; genotype; infectious bronchitis virus; phylogeny.

Figure 1

Phylogenetic trees that are based on the complete (a) and partial (b) S1 glycoprotein gene of the infectious bronchitis virus (IBV), strain Beaudette (GI-1, GenBank Accession No. NC001451). For (a,b), nucleotides 20368–21978 (1632 bases) and nucleotides 20368–20988 (621 bases), respectively, were subjected to phylogenetic analysis. Subsequently, both trees were generated using the neighbor-joining method in MEGA 7 [15] with 1000 bootstrap replications. All tools were run with the default parameters unless otherwise specified. Then, horizontal distances were proportionally set to the minimum number of nucleotide differences that were required to join nodes and sequences. The IBV genotypes were defined as described previously [10].

Figure 1

Phylogenetic trees that are based on the complete (a) and partial (b) S1 glycoprotein gene of the infectious bronchitis virus (IBV), strain Beaudette (GI-1, GenBank Accession No. NC001451). For (a,b), nucleotides 20368–21978 (1632 bases) and nucleotides 20368–20988 (621 bases), respectively, were subjected to phylogenetic analysis. Subsequently, both trees were generated using the neighbor-joining method in MEGA 7 [15] with 1000 bootstrap replications. All tools were run with the default parameters unless otherwise specified. Then, horizontal distances were proportionally set to the minimum number of nucleotide differences that were required to join nodes and sequences. The IBV genotypes were defined as described previously [10].

Figure 2

Similarity analysis (a) and BootScan analysis (b) on the putative recombinant JP/Nagasaki/2013 strain. Reference strains JP/Wakayama/2003 (GI-13, green) and JP/Shimane/98 (GI-19, blue) strains were used as putative parental strains. Additionally, the M41 strain (G1-1, red) was used as an outlier sequence. The y-axis indicates the percentage of identity within a 200-bp wide sliding window centered on the plotted position, with a step size of 20 bp between plots.