Complete nucleotide sequences of M and L RNAs from a new pepper-infecting tospovirus , Pepper chlorotic spot virus

Pepper chlorotic spot virus (PCSV), newly found in Taiwan, was identified as a new tospovirus based on the molecular characterization of its S RNA. In this study, the complete M and L RNA sequences of PCSV were determined. The M RNA has 4795 nucleotides (nts), encoding the NSm protein of 311 aa (34.5 kDa) in the viral (v) strand and the glycoprotein precursor (Gn/Gc) of 1122 aa (127.6 kDa) in the viral complementary (vc) strand. The L RNA has 8859 nts, encoding the RNA-dependent RNA polymerase (RdRp) of 2873 aa (330.8 kDa) in the vc strand. Analyses of the NSm, Gn/Gc and RdRp of PCSV revealed that PCSV is phylogenetically clustered within the watermelon silver mottle virus-related clade. Based on the whole genome sequence, PCSV is closely related to Tomato necrotic ringspot virus and should be classified as a new tospovirus species. Viruses classified within the plant-infecting genus Tospovirus of the family Bunyaviridae are characterized by quasi-spherical enveloped particles of 80-120 nm in diameter. They possess a tripartite genome of three singlestranded RNA segments named L, M and S according to their size [1]. The L RNA is of negative sense and contains a large open reading frame (ORF) encoding an RNA-dependent RNA polymerase (RdRp) in the viral complementary (vc) strand [2]. Both M RNA and S RNA are ambisense, consisting of two ORFs flanked by an A-U rich intergenic region (IGR) that forms a hairpin structure and serves as the transcriptional terminator [3]. The M RNA encodes a movement protein NSm in the viral (v) strand and the glycoproteins Gn and Gc in the vc strand [4, 5]. The v strand of S RNA encodes the gene silencing suppressor NSs [6, 7], and its vc strand encodes the structural nucleocapsid protein (NP) [8]. The classification of tospoviruses is based on their vector specificity, plant host range, serological relationship and the amino acid (aa) identity of the NP, set at a threshold cut-off of lower than 90% [1]. In 2009, a disease causing mottling and deformation on leaves and fruits of sweet pepper was observed in Sinyi Township, Nantou County of central Taiwan. The crude sap of symptomatic sweet pepper samples reacted with antisera against two tospoviruses, capsicum chlorosis virus (CaCV) and watermelon silver mottle virus (WSMoV). A virus isolate, denoted TwPep3, was obtained from the diseased pepper sample and identified as a new tospovirus species belonging to the WSMoV serogroup, provisionally K. -S. Huang and C. -H. Tai contributed equally to this study. Electronic supplementary material The online version of this article (doi:10.1007/s00705-017-3260-1) contains supplementary material, which is available to authorized users. & Tsung-Chi Chen kikichenwolf@hotmail.com & Fuh-Jyh Jan fjjan@nchu.edu. tw 1 Department of Plant Pathology, National Chung Hsing University, Taichung 40227, Taiwan 2 Bureau of Animal and Plant Health Inspection and Quarantine, Council of Agriculture, Executive Yuan, Zhongzheng Dist. , Taipei 10070, Taiwan 3 Plant Pathology Division, Taiwan Agricultural Research Institute, Wufeng, Taichung 41362, Taiwan 4 Department of Biotechnology, Asia University, Wufeng, Taichung 41354, Taiwan 5 Department of Medical Research, China Medical University Hospital, China Medical University, Taichung 40402, Taiwan