Extensive Genome-wide Variability of Human Cytomegalovirus in Congenitally Infected Infants
The DNA in pooled amplicons was sheared by sonication on a Sonic Dismembrator 550 (Fisher) until the median size was ~350bp.  The DNA library was prepared as stated previously [65].  Briefly, DNA was end-repaired using the End-Repair Enzyme Mix (NEB), and A-tailed using the ATP and Klenow (exo-) (NEB).  Adapters with appropriate barcodes were ligated onto the modified DNA ends.  The library was then size selected on a 2% agarose gel, to produce a library with a median size of 350bp   /- 50bp.  The library was amplified with Illumina primers (P/N 1003454) (www.illumina.com).  Once prepared, the libraries were combined in appropriate ratios and submitted for paired-end sequencing on the Illumina GAII