Classification of IBV S1 Genotypes by Direct Reverse Transcriptase-Polymerase Chain Reaction (RT-PCR) and Relationship between Serotypes and Genotypes of Strains Isolated between 1998 and 2008 in Japan

Abstract

ABSTRACT. In this study, we attempted to establish a simple detection method for classification of IBV S1 genotypes by direct reverse transcriptase-polymerase chain reaction (RT-PCR). Then, to evaluate the usefulness of the S1 genotype-specific RT-PCR, we examined the relationship between S1 genotypes and serotypes of IBV in Japan. Sequencing of the S1 genes of IBV and phylogenetic tree analysis were conducted. On the basis of the sequencing data of the S1 genotype samples, we determined primer sets specific for each genotype. Five vaccine strains in Japan as reference strains and 46 field isolates were classified into different genetic clusters by phylogenetic tree analysis (JP-1, JP-II, JP-III, Mass and 4/91) and were matched to the results of S1 genotype-specific RT-PCR. A cross virus-neutralizing test showed that the five vaccine strains in Japan exhibited different serotypes from each other. The concordance rate of the 46 field isolates between the S1 genotypes and serotypes was 65.2%. The present study indicates that genotype-specific RT-PCR could be a convenient and useful tool for determining IBV serotypes and could contribute to the control of IBV outbreaks in Japan.

S1 gene-based phylogeny of infectious bronchitis virus: An attempt to harmonize virus classification

“…In Europe, numerous reports described QX-like strains following the Chinese index case (Abro et al, 2011;Beato et al, 2005;de Wit et al, 2011b;Gough et al, 2008;Monne et al, 2008;Valastro et al, 2010;Worthington et al, 2008). At the same time, the first QX-like strains were identified in Japan (Ariyoshi et al, 2010;Mase et al, 2004) and Korea (Lee et al, 2008). Thereafter, it was soon reported in such diverse localities as Russia, Africa and the Middle East (Amin et al, 2012;Bochkov et al, 2006;Toffan et al, 2011).…”

“…Thus, all strains falling in the GI-19 lineage have been previously assigned to the QX clade, also called LX4 Li et al, 2013;Liu et al, 2009) and A2 (Ji et al, 2011;Li et al, 2010). Confusingly, the same genetic group has also been referred to as Korean-II (K-II) (Lee et al, 2008) and Japanese-III (JP-III) clusters (Ariyoshi et al, 2010;Mase et al, 2004). Of note, a recently submitted sequence (KC577395) shows that the lineage had arisen in China by 1993.…”

Decreased neutralizing antigenicity in IBV S1 protein expressed from mammalian cells

“…The present work employed the TM86 IBV strain, an isolate of genotype JP-II that originally was recovered from a field chicken; this strain subsequently has been used as a vaccine strain (Ariyoshi et al, 2010;Mase et al, 2004). TM86 was propagated in specific-pathogen-free (SPF) chicken embryonated eggs.…”

Change of pathotype and phylogenetic analysis of infectious bronchitis virus detected in Kagoshima prefecture, Japan

“…Because of easier and faster identification, the S1 genotyping of 53 IBV became to be utilized as a tool for vaccine selection, as the relationship between serotype 54 and S1 genotype of IBV became clear [1, 13, 22]. 5 6 R unni n g H ea d: PA TH O TY P E A N D PH Y LO GE N E T IC A N A LYS I S O F IBV 7 8 J ir o Iw am ot o 1 ) , D ai su ke Ok ada 1 ) , S you ei Ki t a h ar a 1 ) , Ke ni chi C hi t ose 1 ) 9 1) K a gosh i m a P r ef ect ur al K a goshi m a C e nt r al Li ve st o ck H ygi e ne Se r vi c e C ent er , 1 67 8 10 Y uda, Hi ga shi i c hi ki -ch o, H iok i, K a go shi m a, 8 9 9-22 0 1, Jap an.…”

“…Because of easier and faster identification, the S1 genotyping of 53 IBV became to be utilized as a tool for vaccine selection, as the relationship between serotype 54 and S1 genotype of IBV became clear [1, 13, 22]. More than twenty vaccines for IB were commercialized in Japan now.…”