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Detection and characterization of a putative emaravirus infecting Clematis brevicaudata DC. in China

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Abstract

A novel emaravirus, tentatively named “clematis yellow mottle associated virus” (CYMaV), was identified through transcriptome sequencing and RT-PCR analysis of yellow-mottled leaf samples from Clematis brevicaudata DC. The genome of CYMaV consists of five viral RNAs: RNA1 (6591 nucleotides, nt), RNA2 (1982 nt), RNA3a (1301 nt), RNA3b (1397 nt), and RNA4 (1192 nt). The 13-nt sequences at the 5′- and 3′-termini of the CYMaV RNAs are conserved and have reverse complementary, as typically seen in emaraviruses. The proteins encoded by CYMaV shared the highest amino acid sequence similarity with those of the unclassified Karaka Okahu purepure emaravirus (KOPV), with 60.2% identity in the RNA-dependent RNA polymerase (RdRp), 44.4% in the glycoprotein precursor, and 46.9% in the nucleocapsid protein. A phylogenetic tree based on amino acid sequences of the RdRp revealed that CYMaV is most closely related to KOPV and clusters with ChMaV (chrysanthemum mosaic-associated virus, LC576445) and PCLSaV (pear chlorotic leaf spot-associated virus, MK602177) in one distinct clade. Transmission electron microscopy observation of negatively stained samples from C. brevicaudata revealed spherical virus-like particles (VLPs) approximately 100 nm in diameter. Five primers, specific for each viral RNA, were used to detect CYMaV in 11 symptomatic and two asymptomatic C. brevicaudata samples, but the results failed to show a consistent association of viral infection with symptoms. CYMaV can be considered a putative new member in the genus Emaravirus, and this marks the first report of an emaravirus found infecting C. brevicaudata plants.

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Acknowledgments

This work was supported by funds from the Natural Science Foundation of Liaoning Province (2021-MS-341) and the Program for Young and Middle-aged Scientific and Technological Innovation Talents of Shenyang City (RC210161).

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Authors and Affiliations

  1. Liaoning Key Laboratory of Urban Integrated Pest Management and Ecological Security, College of Life Science and Engineering, Shenyang University, Dadong, Shenyang, Liaoning, 110044, China

    Caixia Yang, Wenxia An & Chengyu Li

  2. National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing, 400712, China

    Mengji Cao

  3. Guangxi Citrus Breeding and Cultivation Technology Innovation Center, Guangxi Academy of Specialty Crops, Guilin, 541004, China

    Song Zhang

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  1. Caixia Yang
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  2. Wenxia An
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Correspondence to Caixia Yang.

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Yang, C., An, W., Li, C. et al. Detection and characterization of a putative emaravirus infecting Clematis brevicaudata DC. in China. Arch Virol 169, 10 (2024). https://doi.org/10.1007/s00705-023-05945-w

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