Illumina sequencing

DNA libraries were prepared using TruSeq Nano DNA low-throughput sample preparation kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. DNA templates were mechanically sheared by an M220 focused ultrasonicator (Covaris, Woburn, MA, USA). The fragmented amplicons were size-selected, A-tailed, ligated with indexes and adapters, and enriched by PCR. The quality and concentration of libraries were evaluated using the DNA 1000 chip kit (Agilent Technologies, Santa Clara, CA, USA) on a bioanalyzer (Agilent Technologies). The libraries were quantified by qPCR using Library Quantification Kit (KAPA Biosystems, Wilmington, MA, USA) on a Quantstudio 5 Flex Real-Time PCR System (Applied Biosystems). The pooled libraries were sequenced on a MiSeq benchtop sequencer (Illumina) with 2 × 150 bp using a MiSeq reagent kit v2 (Illumina). Adapter and index sequences were trimmed from the raw data and filtered reads were mapped to the reference genomic sequences of SFTSV SPL114A by CLC Genomics Workbench (v7.5.2; Qiagen). The consensus sequences were extracted from analyzed viral reads.