| In recent years, there are many emerging pathogens in swine herds, especially small DNA viruses, which directly or indirectly cause enormous economic losses for swine industries at home and broad. Porcine circovirus type 2 (PCV2) (a number of the family Circovirdae,genus Circovirus), porcine torque teno virus (PTTV) (a number of the floating genus Anellovirus) and porcine bocavirus (PBoV) (a number of the family Parvoviridae, subfamily Parvovirinae, genus Bocavirus) are all small DNA viruses, the length of their genome varies from 1.7 kb to 5.2 kb. In this study, we mainly described their molecular epidemiology as follows.For molecular epidemiology of PCV2, conventional PCR results showed that PCV2 had significantly higher prevalence (61.3%, 117/191) in 2009 than that (19.4%, 61/315) in 2008 in submitted clinical samples (P<0.05). Previous differential PCR was optimazed and used to distinguish different PCV2 strains in random selected 118 PCV2 positive DNA, the results showed that positive rates of PCV2a/2e, PCV2c/2d and co-infection were 30.5%, 37.3% and 32.2%, respectively. Co-infection was not detected in 41 healthy samples, but PCV2 single infection (10/41) occurred. We obtained complete genome of four PCV2 strains from two co-infected samples (GX0841 and BJ0901), the phylogenetic analysis indicated that they belonged to four different genotypes (PCV2a, PCV2d, PCV2e and PCV2f). Moreover, complete genome of another sixteen PCV2 strains were amplified by PCR and rolling-circle amplification (RCA), the phylogenetic analysis indicated that they belonged to five different genotypes. Interestingly, PCV2c was not detected in China. Porcine reproductive and respiratory syndrome virus (PRRSV) and classical swine fever virus (CSFV) had significantly higher prevalence (55.6% and 30.8%, respectively) in PCV2 positive samples than that (36.5% and 17.6%, respectively) in PCV2 negative samples (P<0.05).For molecular epidemiology of PTTV, PCR results showed that there was no significant difference in infection rates of PTTV (83.3%, 50/60 vs 77%, 147/191) in submitted diseased samples from 2008 to 2009 (P>0.05), however, which was higher than that (48.8%, 20/41) in healthy samples. We found that multiple different PTTV strains infected the same sample when PCR products were cloned. Sequence alignment results showed PTTV2 had more variation than PTTV1 in non-encoding region, which mainly presented 11 or 12+21 nucleotide insertion. The phylogenetic analysis also indicated that their evolution relationship was very far among different PTTV2 strains. There was no significant difference on PRRSV prevalence in PTTV1 positive samples (42.7%, 56/131) and PTTV1 negative samples (45%, 27/60) (P>0.05), while the significant differences on PRRSV prevalence occurred in PTTV2 positive samples (52.4%, 54/103)and PTTV2 negative samples (33%, 29/88) (P<0.01). CSFV had significantly higher prevalence (32.8% and 37.9%, respectively) in PTTV1 and PTTV2 positive samples than that (15% and 14.8%, respectively) in PTTV1 and PTTV2 negative samples (P<0.01).For molecular epidemiology of PBoV, we first developed a PCR method for the detection of PBoV, which had good specificity, sensitivity and reproducibility. 191 clinical diseased samples and 41 healthy samples were detected, and the results showed that PBoV was widespread in swine herds, which had significantly higher prevalence (39.3%, 75/191) in diseased samples, especially in weaning piglets (69.7%, 69/99) than that (7.3%, 3/41) in healthy samples. Sequence alignment results showed partial VP1/VP2 genes of PBoV were quite conserved (99%~100% homology). The significantly higher differences on PRRSV prevalence (66.7%, 50/75) occurred in PBoV positive samples than that (28.4%, 33/116) in PBoV negative samples (P<0.05). However, there was no significant difference on CSFV prevalence, although CSFV had higher incidence rates (33.3%, 25/75) in PBoV positive samples than that (23.3%, 27/116) in PBoV negative samples (P>0.05).
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