Complete Nucleotide Analysis of the Structural Genome of the Infectious Bronchitis Virus Strain Md27 Reveals its Mosaic Nature

Ammayappan, Arun; Vakharia, Vikram N.

doi:10.3390/v1031166

Cited by 7 publications

(10 citation statements)

References 30 publications

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“…The insertions of aspartic acid, glycine and serine in the sequences of the isolates may affect antigenicity of the virus, and this will be a question for further studies on serotyping of the isolates. Our results are consistent to those were obtained by previous studies (Ammayappan and Vakharia, 2009;Liu et al, 2009).…”

Section: Discussionsupporting

confidence: 94%

“…Previously it has been reported that Ark-like strains have a deletion of three nucleotides in the S1 gene at nucleotides positions 69-71 (Ammayappan and Vakharia, 2009) but in this context, we have observed insertion rather than deletion in S1 unit of the sequences of D388/ QX-like strains. These insertions and deletions possibly have some significance in the properties related to S1 functions.…”

Section: Discussioncontrasting

confidence: 67%

“…It is unclear how the QX viruses spread to Europe. There were more cases of QX-like virus infection with presentation of nephritis rather than proventriculitis, and false layers in mature hens reported from Belgium, China, France, Germany, The Netherlands, Russia, Taiwan and UK (Ammayappan and Vakharia, 2009;Beato et al, 2005;Bochkov et al, 2006;Worthington et al, 2008;Zhou et al, 2004). Similar type of IBV isolates has been reported in Israel and Korea (Meir et al, 2004;Park et al, 2005).…”

Section: Discussionmentioning

confidence: 53%

“…The appearance of two new economically important field strains of IBV QX-like and Italy-02 in commercial poultry flocks in Western Europe (Beato et al, 2005;Worthington et al, 2008) has further raised the need for a better understanding of the epidemiology of IB all over the world. Clinically, the D388/QX-like and ITA-02 genotypes are characterized by nephritis, production of severe disease symptoms and mortality (Ammayappan and Vakharia, 2009). Such symptoms have not been observed in Sweden, where signs of infection are limited to poor growth in broilers.…”

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Emergence of novel strains of avian infectious bronchitis virus in Sweden

Abro

Renström

Ullman

et al. 2012

Veterinary Microbiology

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Infectious bronchitis virus (IBV) causes avian infectious bronchitis, an important disease that produces severe economic losses in the poultry industry worldwide. Recent IBV infections in Sweden have been associated with poor growth in broilers, drop in egg production and thin egg shells in layers. The complete spike gene of selected isolates from IBV cases was amplified and sequenced using conventional RT-PCR. Nucleotide and amino acid sequence comparisons have shown that the recent isolates bear 98.97% genetic similarity with strains of the QX-like genotype. The phylogenetic analysis revealed that strains predominant in the nineties, which were of the Massachusetts type, have been replaced by D388/QX-like strains, however the evolutionary link could not be established. The homology between the two genotypes was 79 and 81%. Remarkably, a strong positive selection pressure was determined, mostly involving the S1 subunit of the S gene. This strong selective pressure resulted in recombination events, insertions and deletions in the S gene. Two new isolates generated from recombination were found with nucleotide sequence diverging 1.7-2.4% from the D388/QX-like branch, indicating the emergence of a new lineage. The study demonstrates a constant evolution of IBV that might be in relation to increased poultry farming, trade and vaccine pressure. The findings underscore the importance of continuous monitoring to control spread of infections, as well as to timely adjust diagnostic methods, molecular epidemiological studies, development and use of vaccines that are adapted to the changing disease scenario.

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Section: Discussionsupporting

confidence: 94%

Section: Discussioncontrasting

confidence: 67%

Section: Discussionmentioning

confidence: 53%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Emergence of novel strains of avian infectious bronchitis virus in Sweden

Abro

Renström

Ullman

et al. 2012

Veterinary Microbiology

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show abstract

“…The assembly of contiguous sequences of ck/CH/LGX/130530, tl/CH/LDT3/03 and LDT3-A was performed with GeneDoc software (Ammayappan and Vakharia, 2009). Both the S1 gene and complete genomic sequences of IBV isolate ck/CH/LGX/130530 were used for BLAST searching of the National Center for Biotechnology Information (NCBI) database.…”

Section: Sequence Analysismentioning

confidence: 99%

Altered pathogenicity of a tl/CH/LDT3/03 genotype infectious bronchitis coronavirus due to natural recombination in the 5′- 17 kb region of the genome

Han

Zhang

et al. 2016

Virus Research

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An infectious bronchitis coronavirus, designated as ck/CH/LGX/130530, was isolated from an IBV strain H120-vaccinated chicken in this study. Analysis of the S1 gene showed that isolate ck/CH/LGX/130530 was a tl/CH/LDT3/03-like virus, with a nucleotide sequence similarity of 99%. However, a complete genomic sequence analysis showed that ck/CH/LGX/130530 was more closely related to a Massachusetts type strain (95% similarity to strain H120) than to the tl/CH/LDT3/03 strain (86%), suggesting that recombination might have occurred during the origin of the virus. A SimPlot analysis of the complete genomic sequence confirmed this hypothesis, and it showed that isolate ck/CH/LGX/130530 emerged from a recombination event between parental IBV H120 strain and pathogenic tl/CH/LDT3/03-like virus. The results obtained from the pairwise comparison and nucleotide similarity showed that the recombination breakpoint was located in the nsp14 gene at nucleotides 17055-17083. In line with the high S1 gene sequence similarity, the ck/CH/LGX/130530 isolate was serotypically close to that of the tl/CH/LDT3/03 strain (73% antigenic relatedness). Furthermore, vaccination with the LDT3-A vaccine, which was derived from the tl/CH/LDT3/03 strain by serial passaging in chicken eggs, provided good protection against challenge with the tl/CH/LDT3/03 strain, in contrast to the poor protection offered with the H120 vaccine. Interestingly, isolate ck/CH/LGX/130530 exhibited low pathogenicity toward specific-pathogen-free chickens compared with the nephropathogenic tl/CH/LDT3/03 strain, which was likely due to natural recombination in the 5' 17-kb region of the genome. Our results also indicate that the replicase gene of IBV isolate ck/CH/LGX/130530 is associated with viral pathogenicity.

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Sequence analysis of infectious bronchitis virus isolates from the 1960s in the United States

2012

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To better understand the molecular epidemiology of infectious bronchitis virus (IBV) in the United States following the introduction of commercial IBV vaccines, we sequenced the S1 and N structural protein genes of thirteen IBV field isolates collected in the 1960s. Analysis of the S1 sequence showed that seven isolates were of the Massachusetts (Mass) genotype, five were SE17, and one was of the Connecticut (Conn) genotype, suggesting that these three IBVs were circulating in commercial poultry raised in different regions in the United States during the 1960s. The S1 genes of Mass-type isolates had high levels of sequence variation, representing 81.3-81.9 % nucleotide (nt) and 77.3-78.7 % amino acid (aa) identity when compared to those of the SE17-type isolates. In contrast, the N genes from the same isolates were less variable (>92 % nt and >93 % aa identity) when compared to those of the SE17-type isolates. Phylogenetic analysis based on the S1 gene indicated that one isolate (L748) was more closely related to the Mass type. In contrast, phylogenetic analysis based on the N gene showed that L748 was more closely related to the SE17 type, indicating that there had been exchange of S1 genetic materials between Mass- and SE17-like viruses. In addition, the Mass-type isolates had high levels of sequence identity in the S1 gene compared with widely used modified live vaccines (Mass41, Ma5 and H120) and modern field strains from the USA and other countries, suggesting a common ancestor.

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Complete Nucleotide Analysis of the Structural Genome of the Infectious Bronchitis Virus Strain Md27 Reveals its Mosaic Nature

Cited by 7 publications

References 30 publications

Emergence of novel strains of avian infectious bronchitis virus in Sweden

Emergence of novel strains of avian infectious bronchitis virus in Sweden

Altered pathogenicity of a tl/CH/LDT3/03 genotype infectious bronchitis coronavirus due to natural recombination in the 5′- 17 kb region of the genome

Sequence analysis of infectious bronchitis virus isolates from the 1960s in the United States

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