Complete genome sequence and pathogenicity of two swine parainfluenzavirus 3 isolates from pigs in the United States

Abstract

Two novel paramyxoviruses, 81-19252 (Texas81) and 92-7783 (ISU92), isolated from the brains of pigs in the United States in the 1980s and 1990s, were characterized. The complete genome of Texas81 virus was 15,456 nucleotides (nt) in length, that of ISU92 was 15,480 nt, and both genomes consisted of six nonoverlapping genes, predicted to encode nine proteins, with conserved and complementary 3' leader and 5' trailer regions and conserved gene starts, gene stops, and trinucleotide intergenic sequences similar to those in paramyxoviruses. The corresponding genes from these two viruses were similar in length, except for the F genes, of which the ISU92 form had an additional 24-nt U-rich 3' untranslated region. The P genes of swine viruses were predicted to produce V and D mRNAs by RNA editing (one to four G insertions in Texas81 and one to nine G insertions in ISU92) or C mRNA by alternative translation initiation. Sequence-specific features related to virus replication and host-specific amino acid signatures indicated that these viruses originated from bovine parainfluenzavirus 3 (bPIV3). Phylogenetic analysis of individual genes suggested that these viruses are novel members of the genus Respirovirus of the Paramyxovirinae subfamily and may be grouped into two subgenotypes of genotype A of bPIV3. Our comprehensive studies revealed that these swine PIV3 are variants of bPIV3 and were possibly transferred from cattle to pigs but failed to establish an active enzootic state. These two viruses were mildly pathogenic to conventionally reared pigs, and results from a limited enzyme-linked immunosorbent assay-based serosurvey of swine farms in Minnesota and Iowa in 2007 and 2008 were negative.

FIG. 1.

Phylogenetic analysis was performed using parsimony (PAUP 4.01) with 1,000 bootstrap replicates, based on the M gene. (A) Analysis of deduced sPIV3 M protein amino acid sequences compared with sequences from other members of the Paramyxoviridae. (B) Phylogenetic analysis of PIV3 genotypes based on deduced M protein amino acid sequences. The numbers over the branches indicate the percentage of 1,000 bootstrap replicates that supports each phylogenetic branch. Strain information and GenBank accession numbers are presented in Materials and Methods. HeV, Hendra virus; BeV, Beilong virus; NiV, Nipah virus; J-V, J-virus; PPRV, peste-des-petits-ruminants virus; MoV, Mossman virus; DMV, dolphin morbillivirus; CDV, canine distemper virus; MeV, measles virus; RPV, rinderpest virus; TPMV, Tupaia paramyxovirus; NDV, Newcastle disease virus; aPMV6, avian paramyxovirus 6; aPMV2, avian paramyxovirus 2; aMPV, avian metapneumovirus; hMPV, human metapneumovirus; SV5, simian virus 5; MenV, Menangle virus; TioV, Tioman virus; LPMV, La Piedad Michoacán paramyxovirus; MuV, mumps virus; FDLV, Fer-de-Lance virus; and ASPV, Atlantic salmon paramyxovirus.

FIG. 2.

ELISA results for experimentally inoculated pigs. The optical density (OD) values of serum samples from experimentally inoculated pigs as determined by indirect ELISA were plotted. The cutoff value was set at two times the mean of the negative-serum OD value +1 standard deviation based on checkerboard titration of known positive and negative serum samples against ISU92 virus antigen. Pre, preinoculation.