Molecular characterization and phylogenetic analysis of the complete genome of a porcine sapovirus from Chinese swine

Abstract

Background: Porcine sapovirus was first identified in the United States in 1980, hitherto, several Asian countries have detected this virus. In 2008, the first outbreak of gastroenteritis in piglets caused by porcine sapovirus in China was reported. The complete genome of the identified SaV strain Ch-sw-sav1 was sequenced and analyzed to provide gene profile for this outbreak.

Methods: The whole genome of Ch-sw-sav1 was amplified by RT-PCR and was sequenced. Sequence alignment of the complete genome or RNA dependent RNA polymerase (RdRp) gene was done. 3' end of ORF2 with 21-nt nucleotide insertion was further analyzed using software.

Results: Sequence analysis indicated that the genome of Ch-sw-sav1 was 7541 nucleotide long with two ORFs, excluding the 17 nucleotides ploy (A) at the 3' end. Phylogenetic analysis based on part of RdRp gene of this strain showed that it was classified into subgroup GIII. Sequence alignment indicated that there was an inserted 21-nt long nucleotide sequence at the 3' end of ORF2. The insertion showed high antigenicity index comparing to other regions in ORF2.

Conclusion: Ch-sw-sav1 shared similar genetic profile with an American PEC strain except the 21-nt nucleotide at the 3' end of ORF2. The insert sequence shared high identity with part gene of Sus scrofa clone RP44-484M10.

Figure 1

Genomic characteristic of Ch-sw-sav1. A. Schematic of the genomic organization of Ch-sw-sav1 showing the two predicted ORFs: ORF1, encoding a polyprotein fused to and contiguous with the capsid protein (VP1), forming a large polyprotein; and ORF2 encoding a small basic protein (VP2) of unknown function. B. Schematic of the conserved nucleotide sequence motifs at the 5' termini of the genomic and predicted subgenomic RNAs. The Kozak context, favorable for translation initiation, is underlined. C. Aligned nucleotide and predicted amino acid sequences at the junction between ORF1 and ORF2. ORF2 overlaps the 3' end of ORF1 by 4nt (underlined).

Figure 2

Phylogenetic tree generated for the sequences in the complete genome. Phylogenetic tree constructed on the basis of the complete genome sequence. All sequences were collected from GenBank. The virus detected in this study was marked with black triangle. Trees were prepared using the Treeview programs and all branches supported based on 100 bootstrapped data sets.

Figure 3

Unrooted phylogenetic tree of calicivirus RdRp gene sequences constructed by the neighbor-joining method. Phylogenetic tree constructed on the basis of concentrated RdRp gene sequence. Trees were prepared using the Treeview programs and are based on 100 bootstrapped data sets. All sequence used in this analysis were collected from GenBank. The virus detected in this study was marked with black triangle and it was composed of a cluster with PEC/swine-Id3/2005/HUN and Sapovirus swine/NC- QW270/03/US, they also belong to porcine SaV genotype GIII.

Figure 4

Nucleotide acid alignment of 3' end sequences of VP2 among six porcine SaV strains. The numbers above the alignment show the nucleotide location in the ORF2. The nucleotide with the white background is differential. The inserted sequence of Ch-sw-sav1 is from 27-nt to 46-nt

Figure 5

Antigen index analysis of 3' end sequences of VP2 among six porcine SaV strains. Antigen index is analysed by protean using DNAstar software. The regions marked by scale are the site of inserted sequence.