Initially, 200 µ of nasal-throat swabs collected at disease episodes and a negative control containing viral transport medium were first treated with 20 U of turbo DNase (Ambion, Life Technology, Carlsbad, CA, USA) and 50 U of RNase I (Ambion) at 37 °C for 30 min [17 (link)]. Viral RNA was then isolated from nuclease-treated materials using a QIAamp 96 Virus QIAcube HT Kit (QIAGEN GmbH, Hilden, Germany), following the manufacturer’s instructions for nucleic acid extraction. The nucleic acid output was then recovered in 50 μL of elution buffer (provided with the QIAamp kit).
Double-stranded DNA synthesis, random amplification, and library preparation were carried out as previously described [6 (link)]. The prepared library was sequenced using the MiSeq reagent kit V3 in an Illumina MiSeq platform (Illumina, San Diego, CA, USA. The double indexes of Nextera XT Index Kit (Illumina) was used to multiplex and differentiate the samples in each run.
Double-stranded DNA synthesis, random amplification, and library preparation were carried out as previously described [6 (link)]. The prepared library was sequenced using the MiSeq reagent kit V3 in an Illumina MiSeq platform (Illumina, San Diego, CA, USA. The double indexes of Nextera XT Index Kit (Illumina) was used to multiplex and differentiate the samples in each run.
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