Illumina deep sequencing corresponding to human serum sample from a child infected with MXPyV polyomavirus
Anonymized samples were collected from 96 children with acute diarrheal disease from 3 different states in Mexico between 2008 – 2009.  Diarrhea was defined as three or more loose or liquid stools per day, and samples were taken from children prior to treatment with rehydration and antibiotics (if indicated).  Viral particles were purified from stool samples by generating a suspension consisting of 1 mL phosphate-buffered saline, 0.1 g of glass beads, 100 ?L of chloroform, and 0.2 g of feces, shaking x 5 min using a mechanical shaker, spinning x 20 min at 1,000g in a centrifuge, and recovering the supernatant.  500 µL of supernatant were then passed through a 0.45 µm filter and treated with a cocktail of nucleases (Turbo DNAse, Ambion and RNAseA, Invitrogen) prior to nucleic acid extraction using the PureLink 96 Viral RNA/DNA Kit (Invitrogen).  Sample cDNA libraries were prepared from extracted nucleic acid using a random PCR amplification method, separately barcoded, and sequenced on an Illumina HiSeq 2000 as previously described (10, 28).  Raw Illumina sequences consisting of 75 base pair (bp) paired-end reads were filtered to exclude low-complexity, homopolymeric, and low-quality sequences, and then processed through an automated pipeline for pathogen identification as previously described (28).  Sequences corresponding to MXPyV were identified on the basis of viral BlastX homology at a threshold E-score cutoff of 10E-5. After whole-genome sequencing of the MXPyV polyomavirus, all deep sequencing reads corresponding to the viral genome were identified by BlastN homology at a threshold E-score cutoff of 10E-8 and deposited in this dataset.