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


CONCLUSIONS
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.
Yang
Shixing
S
School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai 200240, PR China. yangshixing@sjtu.edu.cn
Zhang
Wen
W
Shen
Quan
Q
Huang
Fen
F
Wang
Yan
Y
Zhu
Jianguo
J
Cui
Li
L
Yang
Zhibiao
Z
Hua
Xiuguo
X
D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D017250:Caliciviridae Infections / Q000662:veterinary* / Q000821:virology; D017124:Conserved Sequence; D005243:Feces / Q000821:virology; D016679:Genome, Viral; D008969:Molecular Sequence Data; D010802:Phylogeny; D029341:Sapovirus / Q000737:chemistry / Q000235:genetics*; D016415:Sequence Alignment; D013552:Swine; D013553:Swine Diseases / Q000821:virology*