WGS of SLCMV-Chanthaburi
Sample was quantified and qualified by NanoDrop (Thermo Fisher Scientific Inc.), Qubit2.0 Fluorometer(Invitrogen, Carlsbad, CA, USA), and 1% agrose gel.Next generation sequencing library preparations were constructed following the manufacturersprotocol (NEBNext Ultra DNA Library Prep Kit for Illumina). For each sample, 1 g was randomlyfragmented to <500 bp by sonication (Covaris S220). The fragments were treated with End Prep EnzymeMix for end repairing, 5 Phosphorylation and dA-tailing in one reaction, followed by a T-A ligation to addadaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using AxyPrep MagPCR Clean-up (Axygen), and fragments of ~410 bp (with the approximate insert size of 350 bp) wererecovered. Each sample was then amplified by PCR for 8 cycles using P5 and P7 primers, with bothprimers carrying sequences which can anneal with flowcell to perform bridge PCR and P7 primer carryinga six-base index allowing for multiplexing. The PCR products were cleaned up using AxyPrep Mag PCRClean-up (Axygen), validated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA),and quantified by Qubit2.0 Fluorometer (Invitrogen, Carlsbad, CA, USA).Then libraries with different indexes were multiplexed and loaded on an Illumina HiSeq instrumentaccording to manufacturers instructions (Illumina, San Diego, CA, USA). Sequencing was carried outusing a 2x150 paired-end (PE) configuration; image analysis and base calling were conducted by theHiSeq Control Software (HCS) + RTA 2.7 (Illumina) on the HiSeq instrument