Capsid protein sequence diversity of avian nephritis virus

Abstract

The capsid gene sequences of 25 avian nephritis viruses (ANVs), collected in the UK, Germany and Belgium from the 1980s to 2008, were determined and compared with those of serotype 1 (ANV-1) and serotype 2 (ANV-2) ANV isolates. Amino acid identities as low as 51% were determined. Pairwise comparisons supported by phylogenetic analysis identified six ANVs, including ANV-1 and ANV-2, which shared<80% amino acid identities with one another, and which were selected to be representative of six groups. The ANVs were not distributed according to geographical location or year of sampling, and the detection of ANVs from five different groups in 11 samples sourced from six flocks belonging to the same UK organization within a 4-month period indicated that sequence-diverse ANVs were co-circulating. Amino acid alignments demonstrated the existence of variable regions throughout the capsid protein, nine of which were selected for detailed comparisons. With most ANVs, the variable region sequences were similar to those of one of the six representative ANVs, but some ANV capsids displayed novel variable region profiles, in which variable regions that were characteristic of more than one representative ANV were present. Phylogenetic analysis based on C-terminal sequences of approximately 260 amino acids and SimPlot analysis provided evidence that RNA recombination events located in the 1250 to 1350 nucleotide region resulted in new combinations of the N-terminal and C-terminal capsid regions. The high level of capsid sequence diversity observed in the present study has important implications for both the control and diagnosis of ANV infections.

High-resolution melt curve analysis to confirm the presence of co-circulating isolates of avian nephritis virus in commercial chicken flocks

“…The 3′ UTR phylogenetic tree had two major branches, with isolates from capsid groups 1, 2 and 3 clustering on one branch and isolates Table 2. Percentage identity for the capsid protein amino acid (bold) and nucleotide (italic) sequence from ANV strains identified in this study and those reported in Todd et al (2011).…”

“…Nucleotide identities of 86-99% were found between the polymerase gene of ANV isolates in the United States (Pantin-Jackwood, 2006). The capsid gene on the other hand is the most variable with the capsid gene of European and Asian isolates having nucleotide identities of 56-100% (Todd et al, 2011). The non-structural protein gene in Hungarian ANV isolates had nucleotide identities between 76% and 86% (Mandoki et al, 2006).…”

“…Confidence intervals were generated from 1000 bootstrap replicates. Capsid gene sequence from six reference strains (Todd et al, 2011; GenBank accession nos: NC003790, AB046864, HQ330481, HQ330482, HQ330483, HQ330504 -see Supplementary Table 2) were aligned with the ANV capsid sequences obtained in this study.…”

“…The current study aims to investigate the genetic diversity of the Australian isolates of ANV, to determine which groups of ANVs are circulating based on the amino acid sequence typing described by Todd et al (2011), and to develop a sensitive polymerase chain reaction (PCR) test able to detect all known ANVs based on the nucleotide sequence data obtained.…”

“…Although these studies examined viruses from different countries, the findings suggest that the rate of mutation varies between different genes/genomic regions of ANV, with the largest variation found in the capsid gene. Todd et al (2011) established a grouping system for ANV based on the protein sequence variation of the capsid gene of European and Asian ANV isolates. In this typing system, six groups were identified with isolates having 80% or higher capsid amino acid similarity placed in the same group.…”