Determination and analysis of the full-length chicken parvovirus genome

Abstract

Viral enteric disease in poultry is an ongoing problem in many parts of the world. Many enteric viruses have been identified in turkeys and chickens, including avian astroviruses, rotaviruses, reoviruses, and coronaviruses. Through the application of a molecular screening method targeting particle-associated nucleic acid (PAN), we recently described the detection and partial characterization of a novel enteric parvovirus in chickens. Subsequent surveys of intestinal homogenates from turkeys and chickens in the United States revealed widespread occurrence of parvovirus in poultry. Here we report the first full genome sequence of a novel chicken parvovirus, ChPV ABU-P1. ChPV ABU-P1 genome organization, predicted amino acid sequence, and phylogenetic relationships with other described parvoviruses are discussed.

Fig. 1

A graphical representation of the genome organization of (A) ChPV ABU-P1, (B) the TuPV 1078, and (C) bovine bocavirus, a parvovirus with an overall genome organization similar to ChPV ABU-P1. The full genome length in nucleotides and the number of amino acids in each encoded protein are indicated. ITR = inverted terminal repeat.

Fig. 2

Full-length nucleotide sequence of the ChPV genome. The terminal repeat sequences are shaded gray, and the palindromic (hairpin-forming) regions are overlined with an arrow. TATA boxes, Inr's, and CAAT boxes are underlined and indicated with a label. Start and stop codons for each of the major and minor ORFs are boxed; a putative alternative start codon for the VP2 ORF is boxed and shaded. The P-loop motif and downstream residues involved in NTP binding are shaded and in bold type. Putative polyadenylation signals are underlined.

Fig. 2

Full-length nucleotide sequence of the ChPV genome. The terminal repeat sequences are shaded gray, and the palindromic (hairpin-forming) regions are overlined with an arrow. TATA boxes, Inr's, and CAAT boxes are underlined and indicated with a label. Start and stop codons for each of the major and minor ORFs are boxed; a putative alternative start codon for the VP2 ORF is boxed and shaded. The P-loop motif and downstream residues involved in NTP binding are shaded and in bold type. Putative polyadenylation signals are underlined.

Fig. 3

A phylogenetic tree prepared using the full coding sequence of the indicated parvoviruses. Representative genera within the Parvovirinae are indicated. The evolutionary relationships were inferred using the Neighbor-Joining method. Phylogenetic analyses were conducted using MEGA4. GenBank Accession numbers for ChPV, GU214704; TuPV 1078, GU214705; and TuPV 260, GU214706.