B5:H1_A_1
Genomic viral RNA was isolated using the QIAamp Viral RNA mini kit (Qiagen). cDNA was generated by reverse-transcription with Superscript II (Life Technologies) using random hexamer primers. The majority of the genome sequence was amplified via PCR using eight primer pairs, generating overlapping PCR fragments 1-2.5 kb in length. Amplified genome fragments were purified using the QIAquick PCR Purification Kit (Qiagen), and the eight fragments from each virus population were combined to create an equimolar mixture. Libraries were prepared from the pooled viral amplicons using the Nextera XT Kit (Illumina Inc.) and the Nextera Index Kit (Illumina Inc.). Samples were sequenced via paired-end, 75-bp read Illumina HiSeq 2000 (Illumina Inc.) at the Yale Center for Genome Analysis.