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Open Access Short report

Detection of novel viruses in porcine fecal samples from China

Jie-mei Yu, Jin-song Li, Yuan-yun Ao and Zhao-jun Duan*

Author Affiliations

National Institute for Viral Disease Control and Prevention, China CDC, 100052, Beijing, China

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Virology Journal 2013, 10:39  doi:10.1186/1743-422X-10-39

Published: 30 January 2013

Abstract

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.

Findings

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.

Keywords:
454 Pyrosequencing; Astroviruses; Bocavirus; Parechovirus