TaqMan-LAMP primer design

Six PPMV-1-specific LAMP primers and a probe targeting the F gene were designed based on the genomic sequence of PPMV-1 (GenBank number {"type":"entrez-nucleotide","attrs":{"text":"HM063425.1","term_id":"295003978","term_text":"HM063425.1"}}HM063425.1) using Primer Explorer version 5 (primerexplorer.jp/lampv5e/index.html). The primers included two outer primers (F3 and B3), two inner primers (FIP and BIP), and two loop primers (LoopF and LoopB), as well as a TaqMan probe (Fig. ​(Fig.11 and Table ​Table1).1). Primers were synthesized by GENEWIZ (GENEWIZ, Suzhou, China), dissolved in RT-PCR-grade water (Invitrogen) to a final concentration of 100 µM, and stored at -20°C. The sequences of the primer binding sites were compared to the corresponding sites in other related viruses to identify sequence variations, insertions or deletions.

Primer information. Location and partial sequences of the primer sets targeting the PPMV-1 F gene. F3 and B3 are outer primers, FIP (F1c-F2) and BIP (B1c-B2) are inner primers, LoopF and LoopB are loop primers. The probe contained the fluorophore FAM (6-carboxy-fluorescein) and BHQ (Black Hole Quencher). The F1c and F2 sequences form the FIP primer, and B1c and B2 form the BIP primer. The primers are depicted in different colors, with yellow used for outer primers, indigo for loop primers, magenta for FIP, green for BIP, and red for the probe.

Sequences of the primers and probe used in this study