High Sequence Variability Among Little cherry virus Isolates Occurring in British Columbia

Abstract

The LC5 isolate of Little cherry virus (LChV-LC5) is one of at least two distinct viruses contributing to a severe disease of cherry (Little cherry disease [LChD]) in British Columbia. A near-complete nucleotide sequence of LChV-LC5 is available as well as polyclonal antibodies against LChV-LC5 coat protein produced in bacterial cells. A survey for LChV-LC5-infected trees in the Okanagan Valley and Kootenay region of British Columbia was carried out using enzyme-linked immunosorbent assays (ELISA) and LChV-LC5 antibodies. Reverse transcriptase polymerase chain reaction (RT-PCR) and sequence analysis of four different regions of the genomes of 31 of these isolates have been conducted. A high level of sequence variability was found: nucleotide sequence divergence between LChV-LC5 and the other sequenced isolates ranged from 0 to 19.7%, and amino acid sequence divergence ranged from 0 to 9.1%. Further examination of RT-PCR and sequence data identified six discrete groups of isolates, including a group identical to LChV-LC5. The high level of divergence in LChV-LC5 isolates occurring in British Columbia suggests that caution should be used in the selection of methods used for diagnosis during surveys for this virus.

High-Throughput Sequencing Assists Studies in Genomic Variability and Epidemiology of Little Cherry Virus 1 and 2 infecting Prunus spp. in Belgium

“…All other sampled Prunus species were confirmed to be latently infected. Their etiology varied considerably between scion and rootstock varieties and also according to season, year of sampling and sometimes co-infection as observed in earlier reports [2,3,8,21,22,27,28,29,30,31,32,33,34,35,36,41].…”

“…The LChV-1 and -2 incidence and observed variability in all surveyed regions can mainly be attributed to the contribution of different plant material sources, their co-infectious status and their mode of propagation in long-established orchards. In a context of rapid and widespread disease worldwide, aspects like multiple infections in symptomless plant reservoirs are readily known to play a key epidemiological role [8,21,27,28,29,30,31,32,33,34,35]. Severe damage has occurred on sweet and sour cherry trees on which the LChD was observed, often leading, together with possible other biotic and abiotic factors, to full tree decline in devastated old orchards, as has been reported for most sensitive sweet cherry cultivars ([8], Supplementary Material).…”

“…In Belgium, the presumably natural vector-borne spread of LChV-2 was reported in the early 1980s, suggesting selective pressure and strong virus adaptation to the local described coccoid vectors [25], probably explaining the lower variability among the Belgian LChV-2 isolates and likely supported by extensive global exchange of infected propagation material [29,30,31,32,33]. In Europe and North America, only few reports on LChV-2 vector transmission have been published, namely with Macrosteles fascifrons , Pseudococcus maritimus and Phenacoccus aceris [8,9,25,50].…”

“…The wide intra- and inter-host genetic diversity of LChV-1 and LChV-2 has been characterized only in a few countries [2,3,4,27,28,29,30,31,32,33,34,35,36]. Both viruses are confirmed to be present in Belgium, however no comprehensive phylogenetic characterization of the LChD has been published so far.…”

Yellow vein‐affected blackberries and the presence of a novel Crinivirus

“…Closteroviruses exhibit considerable variability (D’Urso et al ., 2003; IsHak et al ., 2003; Sambade et al ., 2003; Theilmann et al ., 2004) and appear to be able to maintain indel mutations as shown for Beet pseudo yellows virus (Tzanetakis & Martin, 2004b). The lack of diversity of the BYVaV sequenced regions, also observed in a few other members of the family (Offei et al ., 2004; Marco & Aranda, 2005; Turturo et al ., 2005), may be characteristic of this virus or it may be due to the relatively recent emergence of the virus in the USA.…”