Novel degenerate primer sets for the detection and identification of emaraviruses reveal new chrysanthemum species.

This study used sequence data for emaraviruses to design new degenerate primer sets that identify an extensive range of known and unknown emaraviruses. Sequence alignment of the amino acid and nucleotide sequences of RNA-dependent RNA polymerases for 11 accessions among nine emaraviruses confirmed the presence of seven conserved motifs (Pre-A, F, A, B, C, D, and E). Subsequently, new degenerate primers were designed based on motifs F, A, and B, which were the most conserved among the seven motifs. Reverse transcription-polymerase chain reaction using these primers detected known emaraviruses more efficiently than previously known primers. These new primers enabled the identification of a partial nucleotide sequence of a putative novel emaravirus from chrysanthemum leaves showing mosaic or yellowish ringspot symptoms known to be associated with eriophyid mites, Paraphytoptus kikus. These sequences were specifically detected from the symptomatic leaves of a chrysanthemum, and the putative emaravirus was tentatively named chrysanthemum mosaic-associated virus.
PMID: 33045282 [PubMed - as supplied by publisher]

Source: Journal of Virological Methods - October 9, 2020 Category: Virology Authors: Kubota K, Chiaki Y, Yanagisawa H, Yamasaki J, Horikawa H, Tsunekawa K, Morita Y Tags: J Virol Methods Source Type: research