Limits...
Complete genomic sequence analysis of infectious bronchitis virus Ark DPI strain and its evolution by recombination.

Ammayappan A, Upadhyay C, Gelb J, Vakharia VN - Virol. J. (2008)

Bottom Line: The genome of Ark DPI consists of 27,620 nucleotides, excluding poly (A) tail, and comprises ten open reading frames.Possible recombination sites were found at the intergenic region of spike gene, 3'end of S1 and 3a gene.Independent recombination events may have occurred in the entire genome of Ark DPI, involving four different IBV strains, suggesting that genomic RNA recombination may occur in any part of the genome at number of sites.

View Article: PubMed Central - HTML - PubMed

Affiliation: Center of Marine Biotechnology, University of Maryland Biotechnology Institute, Baltimore, 701 East Pratt Street, Baltimore, Maryland 21202-3101, USA. ammayapp@umbi.umd.edu

ABSTRACT
An infectious bronchitis virus Arkansas DPI (Ark DPI) virulent strain was sequenced, analyzed and compared with many different IBV strains and coronaviruses. The genome of Ark DPI consists of 27,620 nucleotides, excluding poly (A) tail, and comprises ten open reading frames. Comparative sequence analysis of Ark DPI with other IBV strains shows striking similarity to the Conn, Gray, JMK, and Ark 99, which were circulating during that time period. Furthermore, comparison of the Ark genome with other coronaviruses demonstrates a close relationship to turkey coronavirus. Among non-structural genes, the 5'untranslated region (UTR), 3C-like proteinase (3CLpro) and the polymerase (RdRp) sequences are 100% identical to the Gray strain. Among structural genes, S1 has 97% identity with Ark 99; S2 has 100% identity with JMK and 96% to Conn; 3b 99%, and 3C to N is 100% identical to Conn strain. Possible recombination sites were found at the intergenic region of spike gene, 3'end of S1 and 3a gene. Independent recombination events may have occurred in the entire genome of Ark DPI, involving four different IBV strains, suggesting that genomic RNA recombination may occur in any part of the genome at number of sites. Hence, we speculate that the Ark DPI strain originated from the Conn strain, but diverged and evolved independently by point mutations and recombination between field strains.

Show MeSH

Related in: MedlinePlus

Schematic presentation of the structural region of Ark DPI genome. Entire genome of Ark DPI was analyzed for its similarity with other IBV strains. Top panel: 5'UTR & ORF1. Shadowed regions were used for comparative analysis. 5'UTR-5'-untranslated region; PL1-papain like proteinase1; Mpro-main or 3C-like proteinase; RdRp-RNA-dependent-RNA polymerase. Bottom panel: ORF2 to 3'UTR. Structural genes and their ORFs are marked by (●). Conserved sequence TGTGTTGATTATAAT in S1 gene is shown; ◆ denotes plausible recombination site in Ark DPI.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2628353&req=5

Figure 3: Schematic presentation of the structural region of Ark DPI genome. Entire genome of Ark DPI was analyzed for its similarity with other IBV strains. Top panel: 5'UTR & ORF1. Shadowed regions were used for comparative analysis. 5'UTR-5'-untranslated region; PL1-papain like proteinase1; Mpro-main or 3C-like proteinase; RdRp-RNA-dependent-RNA polymerase. Bottom panel: ORF2 to 3'UTR. Structural genes and their ORFs are marked by (●). Conserved sequence TGTGTTGATTATAAT in S1 gene is shown; ◆ denotes plausible recombination site in Ark DPI.

Mentions: Analysis of the structural region of Ark DPI clearly demonstrates that it is a chimera of three strains. The S1 gene of Ark DPI is probably derived from Ark 99 (97% identical) and because of genetic mutations in the S1 region, Ark DPI may have evolved independently. There is an A-T rich sequence TGTGTTGATTATAAT (Fig. 3) at the 3'terminus of S1 gene (~300 nts upstream from the end of S1 gene) which is conserved among most of the IBV strains. The S1 gene of Ark 99 maintains its identity with Ark DPI up to this conserved region, but from this point onwards to the end of S2, the nucleotide sequence is 100% identical to JMK strain. The recombination between JMK and Ark 99 had taken place presumably between above mentioned conserved region and intergenic (IG) region of S gene, which is located 49 nts upstream of start codon of S gene. It is speculated that IG sequences serve as "hot spots" for recombination because of its consensus nature [23]. Gray and JMK strains share 99% homology both in the S1 and S2 genes of Ark DPI, but JMK shows greater identity than Gray strain, as shown in Table 2. It is interesting that very few residues in the S1 gene make the Gray strain nephrotropic, whereas JMK is pneumotropic [24].


Complete genomic sequence analysis of infectious bronchitis virus Ark DPI strain and its evolution by recombination.

Ammayappan A, Upadhyay C, Gelb J, Vakharia VN - Virol. J. (2008)

Schematic presentation of the structural region of Ark DPI genome. Entire genome of Ark DPI was analyzed for its similarity with other IBV strains. Top panel: 5'UTR & ORF1. Shadowed regions were used for comparative analysis. 5'UTR-5'-untranslated region; PL1-papain like proteinase1; Mpro-main or 3C-like proteinase; RdRp-RNA-dependent-RNA polymerase. Bottom panel: ORF2 to 3'UTR. Structural genes and their ORFs are marked by (●). Conserved sequence TGTGTTGATTATAAT in S1 gene is shown; ◆ denotes plausible recombination site in Ark DPI.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2628353&req=5

Figure 3: Schematic presentation of the structural region of Ark DPI genome. Entire genome of Ark DPI was analyzed for its similarity with other IBV strains. Top panel: 5'UTR & ORF1. Shadowed regions were used for comparative analysis. 5'UTR-5'-untranslated region; PL1-papain like proteinase1; Mpro-main or 3C-like proteinase; RdRp-RNA-dependent-RNA polymerase. Bottom panel: ORF2 to 3'UTR. Structural genes and their ORFs are marked by (●). Conserved sequence TGTGTTGATTATAAT in S1 gene is shown; ◆ denotes plausible recombination site in Ark DPI.
Mentions: Analysis of the structural region of Ark DPI clearly demonstrates that it is a chimera of three strains. The S1 gene of Ark DPI is probably derived from Ark 99 (97% identical) and because of genetic mutations in the S1 region, Ark DPI may have evolved independently. There is an A-T rich sequence TGTGTTGATTATAAT (Fig. 3) at the 3'terminus of S1 gene (~300 nts upstream from the end of S1 gene) which is conserved among most of the IBV strains. The S1 gene of Ark 99 maintains its identity with Ark DPI up to this conserved region, but from this point onwards to the end of S2, the nucleotide sequence is 100% identical to JMK strain. The recombination between JMK and Ark 99 had taken place presumably between above mentioned conserved region and intergenic (IG) region of S gene, which is located 49 nts upstream of start codon of S gene. It is speculated that IG sequences serve as "hot spots" for recombination because of its consensus nature [23]. Gray and JMK strains share 99% homology both in the S1 and S2 genes of Ark DPI, but JMK shows greater identity than Gray strain, as shown in Table 2. It is interesting that very few residues in the S1 gene make the Gray strain nephrotropic, whereas JMK is pneumotropic [24].

Bottom Line: The genome of Ark DPI consists of 27,620 nucleotides, excluding poly (A) tail, and comprises ten open reading frames.Possible recombination sites were found at the intergenic region of spike gene, 3'end of S1 and 3a gene.Independent recombination events may have occurred in the entire genome of Ark DPI, involving four different IBV strains, suggesting that genomic RNA recombination may occur in any part of the genome at number of sites.

View Article: PubMed Central - HTML - PubMed

Affiliation: Center of Marine Biotechnology, University of Maryland Biotechnology Institute, Baltimore, 701 East Pratt Street, Baltimore, Maryland 21202-3101, USA. ammayapp@umbi.umd.edu

ABSTRACT
An infectious bronchitis virus Arkansas DPI (Ark DPI) virulent strain was sequenced, analyzed and compared with many different IBV strains and coronaviruses. The genome of Ark DPI consists of 27,620 nucleotides, excluding poly (A) tail, and comprises ten open reading frames. Comparative sequence analysis of Ark DPI with other IBV strains shows striking similarity to the Conn, Gray, JMK, and Ark 99, which were circulating during that time period. Furthermore, comparison of the Ark genome with other coronaviruses demonstrates a close relationship to turkey coronavirus. Among non-structural genes, the 5'untranslated region (UTR), 3C-like proteinase (3CLpro) and the polymerase (RdRp) sequences are 100% identical to the Gray strain. Among structural genes, S1 has 97% identity with Ark 99; S2 has 100% identity with JMK and 96% to Conn; 3b 99%, and 3C to N is 100% identical to Conn strain. Possible recombination sites were found at the intergenic region of spike gene, 3'end of S1 and 3a gene. Independent recombination events may have occurred in the entire genome of Ark DPI, involving four different IBV strains, suggesting that genomic RNA recombination may occur in any part of the genome at number of sites. Hence, we speculate that the Ark DPI strain originated from the Conn strain, but diverged and evolved independently by point mutations and recombination between field strains.

Show MeSH
Related in: MedlinePlus