Sequencing libraries were prepared following the SureSelect version 1.7 target enrichment system (Agilent, Santa Clara, CA, USA) [33 (link)]. Briefly, 50 μL of DNA was sheared acoustically using an LE220 sonicator (Covaris, Brighton, UK). Fragmented DNA was end-repaired, A-tailed, and adaptor-ligated using the KAPA LTP library preparation kit (KAPA Biosystems, Wilmington, DE, USA). The resultant HCMV-enriched libraries were then indexed and sequenced on a MiSeq (Illumina, San Diego, CA, USA) with v3 chemistry to yield 300 × 300 nt paired-end reads datasets.
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