Co-infection of HK1772+HJ
Viral RNA was extracted from 140 L supernatant using QIAamp viral RNA mini kit (Qiagen) and eluted with 40 L buffer AVE. 8 L RNA was transcribed into cDNA with SuperScriptTM III Reverse Transcriptase (Invitrogen) in a 20 L reaction with primer 454-Tag1-U12 (GCC GGA GCT CTG CAG ATA TCA GCR AAA GCA GG). Eight gene segments were amplified by Q5 High Fidelity DNA polymerase (NEB) using a pair of primers (454-Tag1-U12: GCC GGA GCT CTG CAG ATA TCA GCR AAA GCA GG; 454-Tag1-U13: GCC GGA GCT CTG CAG ATA TCA GTA GAA ACA AGG) from 10 L cDNA template in a 100 L reaction according to the recommended protocol. PCR products were purified using MinElute Reaction Cleanup Kit (Qiagen). Nextera XT DNA Sample Prep Kit (Illumina) was used for library preparation and Illumina MiSeq was used for Pair-End sequencing at Centre for PanorOmic Sciences, the University of Hong Kong. All data were analysed on CLC Genomic workbench (version 20) (Qiagen) with the minimal variant frequency set up at 1%.