Genomic Sequence of the First Porcine Rotavirus Group H Strain in the United States

The genomic sequence of a rotavirus group H was identified in the intestine of a diarrheal pig in the United States, designated RVH/Pig-wt/USA/MN9.65/2008/GxP[x].

Here, we report the first genomic sequence for all 11 segments of a porcine RVH strain from the United States. On 16 April 2008, the University of Minnesota Veterinary Diagnostic Laboratory received three intestinal samples from 4-week-old pigs with clinical signs of diarrhea, coughing, and failure to thrive. These samples from Minnesota were homogenized together, as previously described (12), and determined to be positive for RVA, RVB, RVC, and RVH by reverse transcription-PCR (RT-PCR) (13,14).
We used a previously described viral metagenomics approach to enrich and sequence viral nucleic acids, followed by MiSeq and de novo assembly of the resulting reads (15). Briefly, viral RNA was reversely transcribed and amplified using a random primer. A next-generation sequencing (NGS) library was prepared, using the Nextera XT kit; sequencing followed using Illumina's MiSeq platform. A total of 766,560 reads were generated, de novo assembled, and analyzed in the bioinformatics pipeline, as described previously (16).
Nucleotide sequence accession numbers. The sequences for RHV/MN9.65/2008 have been deposited in GenBank under accession numbers KU254582 to KU254592.

ACKNOWLEDGMENTS
The findings and conclusions in this report are those of the author(s) and do not necessarily represent the official position of the Centers for Disease Control and Prevention. Names of specific vendors, manufacturers, or products are included for public health and informational purposes; inclusion does not imply endorsement of the vendors, manufacturers, or products by the Centers for Disease Control and Prevention or the U.S. Department of Health and Human Services.

FUNDING INFORMATION
This work was funded by federal appropriations to the Centers for Disease Control and Prevention through the Advanced Molecular Detection Initiative line item.