Identification of sequence changes responsible for the attenuation of avian infectious bronchitis virus strain Arkansas DPI

Abstract

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.

Fig. 1

Organization of the infectious bronchitis virus genome. The genome of Ark DPI is 27,620 nt long, excluding the poly (A) tract. Middle ten genes and their ORFs. The scale indicates the approximate positions and sizes of genes in the Ark DPI genome. Bottom putative domains of ORF1a/1b polyprotein: nsp non-structural protein; Ac acidic domain; X unknown domain X; PL1 papain-like proteinase1; PL2 papain-like proteinase 2; Y unknown domain Y; HD hydrophobic domain; 3CL 3C-like proteinase; G growth-factor-like protein (GFL); RdRp RNA-dependent RNA polymerase; Hel helicase; ExoN exoribonuclease; Ne nidoviral uridylate-specific endoribonuclease; MT 2′-O-ribose methyltransferase. Top details of spike protein. SP signal peptide; RRSRR/S spike protein cleavage site between 544 and 545aa; TM transmembrane domain of spike protein. Nucleotide nt and amino acid AA differences between ArkDPI 11 and 101 and their approximate positions are depicted