Genotyping of Cucumber mosaic virus isolates in western New York State during epidemic years

Abstract

In the early 2000s an epidemic of cucumber mosaic virus (CMV) spread within the Midwestern and Eastern US affecting snap and dry bean (Phaseolus vulgaris L.) cultivation. Fifty one CMV isolates from this period were partially characterized from varied hosts by sequencing a section from each of the three genomic RNAs. Aside from one subgroup II strain from pepper, all isolates, including those from snap bean, fell within the IA subgroup. The nucleotide sequence diversity of virus populations sampled at multiple sites and at different years was significantly higher than that of a population from single site in a single year, although in general the number of polymorphisms was low (<11%). Complementary DNA (cDNA) clones of Bn57, a representative isolate from snap bean, were engineered for the production of infectious in vitro RNA transcripts initiated from a T7 promoter. Infections from these cDNAs resulted in symptoms consistent with those of the original field isolate, indicating that a satellite RNA is not involved in symptom expression in snap bean. These infectious clones were used to assess symptom determinants and the effects of virus infection on plant growth. Inoculations with pseudorecombinants derived from Bn57 and the non-bean infecting strain Fny confirmed RNA2 as a specific determinant for snap bean infection. Bn57, along with almost all isolates identified in this study contained the Y631 locus in the 2a protein, a determinant for systemic infection in bean. The presence of this locus extended to all non-bean hosts except two pepper infecting isolates. Infection by Bn57 in snap bean had a significant effect on pod number and mass with a 55 and 41 percent reduction in greenhouse assays, respectively. To our knowledge Bn57 is the first CMV strain isolated from P. vulgaris to be fully sequenced and cloned, providing a useful tool for analyses of CMV-host interactions.

Metagenomic Analysis of Plant Virus Occurrence in Common Bean (Phaseolus vulgaris) in Central Kenya

“…Those for the three genomic RNAs in S11 were MH567347, MH567348, and MH567349, and those for S12 were MH567350, MH567351, and MH567354. These sizes are consistent with those reported elsewhere (Thompson et al, 2015).…”

“…CMV can be subdivided into two main phylogenetic Subgroups I and II, sharing 70–75% nucleotide sequence identity making them taxonomically separate species. Subgroup I can be further subdivided into IA and IB, with IB being predominantly Asian in distribution (Palukaitis and García-Arenal, 2003; Jacquemond, 2012; Kim et al, 2014; Thompson et al, 2015). BLAST search and neighbor-joining phylogenetic analysis showed that the genomic sequences of RNAs 1, 2 of the CMV isolated in central Kenya most closely associate with corresponding CMV RNA segments of South Korean origin, sharing up to 94 and 92% nucleotide sequence identity respectively, that belong to CMV Subgroup IA.…”

“…Additionally, these approaches cannot detect other viruses present. For example, the cucumovirus, cucumber mosaic virus is (like BCMV and BCMNV) vectored non-persistently by aphids (horizontal transmission) and transmitted vertically through seed (Morales, 2006), and can cause serious disease epidemics in common bean (Gildow et al, 2008; Thompson et al, 2015). Perhaps more importantly, such focused methods will not reveal the presence of unsuspected or novel viruses infecting the crop or the presence of co-infecting viruses in the same plant (Syller, 2012).…”

Probing of RNA structures in a positive sense RNA virus reveals selection pressures for structural elements

“…In this study, we use selective 2′-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq) v2.1 ( 40 ) and covariation analysis to analyze the complete sequence of RNA3 from CMV strain Bn57 ( 41 ). Using SHAPE-Seq, we directly compare nucleotide flexibility across RNA3 in infected cell lysates and in vitro refolded purified viral RNA and present predicted secondary structure maps of RNA3 using SHAPE-Seq data to restrain secondary structure predictions.…”

Identification and Safety Assessment of Cucumber Mosaic Virus Coat Protein in Genetically Modified Pepper (Capsicum annuum)

“…CMV, the most frequently occurring virus in peppers, belongs to the genus Cucumovirus in the plant virus family Bromoviridae, and it infects over 1000 plant species in 85 families (El-Borollosy and Oraby, 2012). Since it was discovered as the causal disease agent of cucurbit hosts in 1916 (Doolittle, 1916;Jagger, 1916), CMV has been reported to infect cucumber, melon, zucchini, soybean, and tobacco (Baskaran et al, 2016;Mochizuki et al, 2014;Roossinck et al, 1990;Thompson et al, 2015). In Korea, the virus is associated with over 33% of chili pepper infections, and causes losses valued at approximately $200 million dollars each year.…”