Occurrence and genetic diversity of Blackcurrant reversion virus found on various cultivated and wild Ribes in Latvia

Abstract

A large-scale survey was carried out to assess the occurrence, natural host range and genetic diversity of Blackcurrant reversion virus (BRV) in cultivated and wild Ribes in Latvia using RT-PCR and sequence analyses of 3 0 NTR of BRV RNA2. The virus was detected in all surveyed habitats in most of the studied Ribes, except gooseberries, Ribes sanguineum, Ribes laxiflorum and crossbreeds between blackcurrants and gooseberries. The overall occurrence of BRV was 27%, although it varied significantly among the surveyed Ribes habitats, exceeding 40% in home gardens and germplasm collections. Among cultivated Ribes, blackcurrants were the most infected and BRV was detected in all commonly grown cultivars. The virus was detected for the first time in Ribes aureum, Ribes fragrans, Ribes nigrum var. pauciflorum and Ribes fasciculatum var. chinense. The sequence identities of the studied fragments of RNA2 3 0 NTR varied from 92.8% to 99.7% among 26 BRV isolates from various cultivated, ornamental and wild hosts from Latvia and from 91.1% to 97.1% when they were compared with 27 corresponding sequences from GenBank. Phylogenetic analyses revealed that the major clustering of isolates was not related to host, origin or symptoms. Grouping of BRV isolates based on host or location was identified within the phylogenetic subclusters. Several well-supported clades were formed within the subclusters, including a group of BRV isolates from redcurrants that had unique nucleotide substitutions. Five putative recombinants were identified for the first time among BRV isolates from Latvia, Finland, Scotland and the Czech Republic.

Cecidophyopsis mites and blackcurrant reversion virus on Ribes hosts: Current scientific progress and knowledge gaps

“…Most of the studies have focused on cultivar resistance, and plants often were immediately eradicated (Dolan, MacFarlane, McGavin, Brennan, & McNicol, 2011; Špak, Kubelkova, Pribylova, & Špakova, 2009); therefore, the data on BRV distribution in several countries are limited. A recent study (Zuļģe, Gospodaryk, & Moročko‐Bičevska, 2018) showed that BRV is common on various Ribes in orchards, home gardens, greeneries and also in wild habitats in Latvia. The situation could be similar in other regions where Ribes are common.…”

“…Infected redcurrants have faint flowers and leaves (Bremer & Heikinheimo, 1979). BRD was also found on R. bracteosum (subgenus Ribes , section Botrycarpum ), R. spicatum (subgenus Ribes , section Ribes ), R. alpinum (Bremer & Heikinheimo, 1979; Thresh, 1970), R. aureum , R. fragrans (subgenus Ribes , section Botrycarpum ) and R. fasciculatum (subgenus Berisia , section Hemibotrya ) that are common as ornamentals and can be reservoirs for BRV spread (Zuļģe et al, 2018). Other Ribes species and hybrids were demonstrated as susceptible to BRV by graft inoculation (Adams & Thresh, 1987) but natural infections have not been reported.…”

“…RT‐PCR based methods allowed to study BRV distribution in various hosts and regions (Dolan et al, 2011; Jones & McGavin, 2002; Latvala, Lemmetty, et al, 1997; Latvala, Susi, et al, 1997; Lehto et al, 1997; Lemmetty et al, 2001; Lemmetty, Susi, Latvala, & Lehto, 1998; Pluta et al, 2000; Tapio et al, 1997; Zuļģe et al, 2018; Zurn et al, 2019). RT‐PCR confirmed that full blossom disease on redcurrants in the Czech Republic was caused by BRV (Přibylová, Spak, Kubelkova, & Lemmetty, 2004; Špak, Kubelkova, Pribylova, Špakova, & Petrzik, 2009).…”

“…RT‐PCR confirmed that full blossom disease on redcurrants in the Czech Republic was caused by BRV (Přibylová, Spak, Kubelkova, & Lemmetty, 2004; Špak, Kubelkova, Pribylova, Špakova, & Petrzik, 2009). Any direct relation of symptoms, hosts or sample origin with the phylogeny of BRV was not demonstrated except some well‐supported groups within subclusters were found related to the host and location (Lemmetty & Lehto, 1999; Přibylová et al, 2008; Zuļģe et al, 2018). The reason for mixed clustering of BRV from various hosts and geographic origins could be because of the virus spread by mites, international exchange of planting material, and possible recombination events in the genome (Zuļģe et al, 2018).…”

“…The 5′ non‐translated regions (NTRs) of gRNA‐1 (66 nt) and gRNA‐2 (161 nt) are short, while 3′NTRs are long (1,360 and 1,363 nt, respectively), perhaps because of the peculiarities of RNA translation mechanisms (Latvala‐Kilby & Lehto, 1999; Pacot‐Hiriart et al, 2001). The 3′NTRs of type and 10 field isolates were found to be highly conserved (Lehto, Lemmetty, & Keranen, 2004) therefore used for PCR primer design, detection and genetic characterisation (Lehto et al, 2004; Lemmetty et al, 2001; Přibylová et al, 2008; Zuļģe et al, 2018). Excluding the first 24 nt of the 3′NTR of gRNA‐1, it is 95% identical with the 3′NTR of gRNA‐2 (Pacot‐Hiriart et al, 2001).…”