“…The library preparation, next-generation sequencing (NGS) procedure, and de novo assembly were conducted using the Neb next ultra RNA first-strand synthesis module (New England BioLabs, Ipswich, MA), MiniSeq (Illumina, San Diego, CA) and CLC Genomics Workbench version 11 (QIAGEN, Venlo, Limburg, Netherlands), respectively, as previously described. 9 To confirm the JEV pool source, viral RNA was extracted from the final supernatant of the virus isolation process using the rapid viral RNA screening method described in Faizah et al 10 Detergent mixture was used for extraction and reverse transcription-polymerase chain reaction (RT-PCR) using a PrimeScript One-Step RT-PCR Kit version 2 (Takara Bio, Shiga, Japan) was used for sequence amplification. A primer set targeting the JEV envelope gene (JEV955f: 5 9 -TGYTGGTCGCTCCGGCTTA-3 9 ; JEV1606R: 3'-GACY-TYGAMCCACGGTCAT-5 9 ) was used.…”