Viral RNA (0.05–1.7 mg) was fragmented by incubation at 94°C for 8 minutes in 19.5 μl of fragmentation buffer (Illumina, San Diego, CA). First and second strand synthesis, adapter ligation, and amplification of the library were performed using the Illumina TruSeq RNA Samplec Preparation kit as per the manufacturer’s protocol. Cluster formation of the library DNA templates was performed using the TruSeq PE Cluster Kit v3 (Illumina) and the Illumina cBot workstation as per the manufacturer’s protocol. Paired-end 50 base sequencing by synthesis was performed using TruSeq SBS kit v3 (Illumina) on an Illumina HiSeq 1500 as per the manufacturer’s protocol.
All reads were assembled using a pipeline previously described [7 (link)] and were assembled using the Venezuelan equine encephalitis virus strain 68U201 (GenBank accession #: U34999.1; [35 (link)]) as a reference sequence. Diversity was calculated using Shannon entropy [36 ] and a cut off of 1% was used for the analysis.
All reads were assembled using a pipeline previously described [7 (link)] and were assembled using the Venezuelan equine encephalitis virus strain 68U201 (GenBank accession #: U34999.1; [35 (link)]) as a reference sequence. Diversity was calculated using Shannon entropy [36 ] and a cut off of 1% was used for the analysis.
Free full text: Click here
