Detection of novel viruses in porcine fecal samples from China.
BACKGROUND
Pigs are well known source of human infectious disease. To better understand the spectrum of viruses present in pigs, we utilized the 454 Life Sciences GS-FLX high-throughput sequencing platform to sequence stool samples from healthy pigs.


RESULTS
Total nucleic acid was extracted from stool samples of healthy piglets and randomly amplified. The amplified materials were pooled and processed using a high-throughput pyrosequencing technique. The raw sequences were deconvoluted on the basis of the barcode and then processed through a standardized bioinformatics pipeline. The unique reads (348, 70 and 13) had limited similarity to known astroviruses, bocaviruses and parechoviruses. Specific primers were synthesized to assess the prevalence of the viruses in healthy piglets. Our results indicate extremely high rates of positivity.


CONCLUSIONS
Several novel astroviruses, bocaviruses and Ljungan-like viruses were identified in stool samples from healthy pigs. The rates of isolation for the new viruses were high. The high detection rate, diverse sequences and categories indicate that pigs are well-established reservoirs for and likely sources of different enteric viruses.
National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China.
Jie-mei
JM
Yu
Jin-song
JS
Li
Yuan-yun
YY
Ao
Zhao-jun
ZJ
Duan
D000818:Animals; D044822:Biodiversity; D002681:China; D016000:Cluster Analysis; D005243:Feces / Q000821:virology*; D059014:High-Throughput Nucleotide Sequencing; D008969:Molecular Sequence Data; D010802:Phylogeny; D013552:Swine; D014780:Viruses / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*