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

      Ammayappan, A.; Upadhyay, C.; Vakharia, V.N. (2008)
      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. Copyright 2008 Ammayappan et al
    • Identification of sequence changes responsible for the attenuation of avian infectious bronchitis virus strain Arkansas DPI

      Ammayappan, A.; Upadhyay, C.; Vakharia, V.N. (2009)
      Infectious bronchitis virus (IBV) is the causal agent of infectious bronchitis, which still remains one of the most important poultry diseases worldwide because of numerous serotypes and variants. A virulent strain of IBV, isolated from Arkansas (Ark), was propagated in embryonated eggs (Ark DPI 11). Following 101 serial passages in embryonated eggs, an attenuated strain of IBV was established (Ark DPI 101) that does not induce histopathological lesions in the tracheae of infected chicks. To identify sequence changes responsible for the attenuation of IBV, complete genome sequences of both virulent and attenuated Ark DPI viruses were obtained. Comparison of the genome sequences of the virulent and attenuated Ark DPI viruses reveals that these viruses are similar and differ only by 21 nucleotides, resulting in 17 amino acids changes. Most of those substitutions are located in the replicase 1a and spike genes. No differences were observed in gene 3, M or 5a, and only one nucleotide substitution each was present in 5b, N and 3?UTR. By comparing the deduced amino acid sequences of virulent and attenuated viruses, we identified sequence changes responsible for the adaptation and attenuation of the IBV-Ark DPI strain.