Nucleotide sequence of porcine circovirus associated with postweaning multisystemic wasting syndrome in pigs

Abstract

This article describes the nucleotide sequence of a porcine circovirus (PCV) which possesses a high degree of association with postweaning multisystemic wasting syndrome (PMWS), a newly described disease of young pigs. The DNA sequence of this PMWS-associated PCV (pmws PCV) has 68% homology with that of a previously published nonpathogenic strain of PCV. The strains appear to be closely related yet distinct from one another.

FIG. 1

Map depicting the eight overlapping fragments of pmws PCV genomic DNA that were PCR amplified and sequenced in this study. The scale at the top represents nucleotide position numbers derived from a published np PCV sequence (17). This is a circular genome; therefore, nucleotide position 1759 abuts nucleotide position 1. Arrows denote location and orientation of primers that were used for PCR and sequencing. The eight overlapping horizontal lines below the graduated scale represent the eight portions of pmws PCV genomic DNA that were PCR amplified and sequenced. The dashed line in the 8F/15R PCR product indicates where legible sequence ended because it was too far from either primer. The nucleotide sequences from all eight PCR products result in an accumulated total of 6,480 nt. After all of the sequences were aligned, we observed that approximately 1,450 nt were sequenced at least three times and that 320 nt were sequenced twice.

FIG. 2

Nucleotide sequence of pmws PCV (GenBank accession no. AF027217 [this study]) aligned with np PCV (GenBank accession no. U49186 [17]). Numbering used here is based upon numbering that was used for np PCV, where nt position 1 is the first A residue immediately downstream of the putative nick site in the nonanucleotide motif. Total genome sizes are 1,768 nt for pmws PCV and 1,759 nt for np PCV. Homologous nucleotides are indicated by asterisks. Potential polyadenylation sites are overlined in the putative viral strand and underlined in the complementary strand.

FIG. 3

Alignments of predicted amino acid sequences of several ORFs in pmws PCV and np PCV. Potential glycosylation signal sequences (asparagine sequons NXS or NXT, where X = any amino acid [6]) are overlined in pmws PCV and underlined in np PCV. The proteins encoded by ORF1 would be 314 aa long and have a molecular mass of 35.8 kDa in pmws PCV, be 312 aa long and have a molecular mass of 35.7 kDa in np PCV, and have 86% homology. The proteins encoded by ORF2 would be 233 aa long and 27.8 kDa in pmws PCV, 233 aa long and 27.8 kDa in np PCV, and have 66% homology. The proteins encoded by ORF3 would be 104 aa and 11.9 kDa in pmws PCV and 206 aa and 23.2 kDa in np PCV and have 62% homology. The proteins encoded by ORF4 would be 59 aa and 6.5 kDa in pmws PCV and 115 aa and 13.3 kDa in np PCV and have 83% homology. The proteins encoded by ORF7 would be 19 aa and 1.9 kDa in pmws PCV and 56 aa and 6.0 kDa in np PCV and have 79% homology. The proteins encoded by ORF8 would be 21 aa and 2.3 kDa in pmws PCV and 37 aa and 4.3 kDa in np PCV and have 67% homology. All amino acid sequence alignments shown involve the full-length proteins in pmws PCV and the homologous portions of appropriate lengths for their counterparts in np PCV. Thus, the arrows shown at the ends of protein sequences encoded by ORFs 3, 4, 7, and 8 in np PCV indicate that these proteins continue further, and their remaining sequences are not shown.

FIG. 4

(a) Alignment of the putative DNA replication sequences in pmws PCV and np PCV. Homology is indicated by an asterisk. (b) Comparison of the stem-loop structures predicted from the sequences in panel a. In both panels the nonanucleotide sequence motifs are in bold-faced type, and arrows mark the putative nick sites. The A residues immediately downstream of these nick sites are used as the starting point for numbering these genomes. All sequences are given in the 5′-to-3′ direction.