Occurrence of Two Little Cherry Viruses in Sweet Cherry in Washington State

Abstract

Little cherry disease, one of the major viral diseases of sweet cherry (Prunus avium) worldwide, is associated with either of two closteroviruses, Little cherry virus 1 (LChV-1) and Little cherry virus 2 (LChV-2). Two sets of primers corresponding to a portion of the replicase gene of LChV-1 and LChV-2 were used in one-tube reverse-transcription polymerase chain reactions to detect these viruses in total RNA extracts of field-collected sweet cherry tissues. LChV-1 and LChV-2 were detected both alone and in combination in five sweet cherry orchards in Washington State. Sequence analysis of a 240-nucleotide (nt) fragment of the replicase open reading frame (ORF)1b and a 232-nt fragment from a portion of ORF8 and the 3′ untranslated region (UTR) of LChV-1 indicated that North American (NA) isolates shared 90 to 99% nucleotide identity in both genome segments analyzed. In contrast, comparisons of NA isolates to two Eurasian isolates of LChV-1 indicated shared nucleotide identities of 79 to 82% in the replicase fragment and 89 to 90% in the ORF8/3′UTR fragment. Sequence variation in the replicase region did not affect detection of LChV-1 in 12 isolates using the replicase-specific primers reported here. This article represents the first report of LChV-1 and LChV-2 in sweet cherry in Washington.

High-Throughput Sequencing Reveals Further Diversity of Little Cherry Virus 1 with Implications for Diagnostics

“…To determine the most suitable primer pair for the accurate detection of all isolates of LChV1, detection primer pairs reported in the literature were retrieved and compared with all available full-length genomic sequences ( Figure 5 ). In most cases, these detection primers showed either multiple mismatches with some isolates (up to 10–12 mismatches for the 6 for primer of Matic et al [ 2 ]) or mismatches affecting the two 3′-most nucleotides of the primer (in particular the LCUW7090 primer of Bajet et al [ 22 ]). Such mismatches are highly likely to either preclude amplification of some isolates or severely affect the sensitivity of detection.…”

“…Although growing evidence suggests that LChV1 isolates could be largely latent in many of their hosts it is still included in many certification and quarantine schemes and several LChV1 isolates have been tentatively associated with specific syndromes in sweet cherry and in other Prunus species [ 2 , 3 , 22 ]. Regarding the isolates analyzed in the present study, no clear conclusions can be drawn concerning their pathogenicity because as is very frequently the case the trees hosting them were co-infected with several viruses including in some cases different LChV1 genotypes.…”

“…The sequences of all primers reported to date for the detection of the virus were compared in silico with LChV1 complete genome sequences in order to determine the primer pair exhibiting the broadest detection range (Figure 4) [ 2 , 3 , 7 , 8 , 21 , 22 , 23 , 24 , 25 ].…”

Insights into the genetic diversity and evolution of Little cherry virus 1

“…So far the molecular variability of LChV-1 has been barely studied, with most of the past efforts focusing on short fragments of the RdRp, the CPm and the 3 0 end of ORF8 (Bajet et al, 2008;Matic et al, 2009;Candresse et al, 2013). Phylogenetic relationships between LChV-1 isolates obtained from remote geographical regions and/ or originating from different Prunus trees have shown that classification according to geographic origin or host is probably not feasible (Matic et al, 2009;Candresse et al, 2013).…”

Small RNA NGS Revealed the Presence of Cherry Virus A and Little Cherry Virus 1 on Apricots in Hungary

“…Since that time, the presence of its distinct variants has been connected with other disorders such as Kwanzan stunting [ 35 ] and Shirofugen stunt disease [ 36 ]. Infection of cherry by LChV-1 has been reported all over the world [ 37 , 38 , 39 , 40 ], usually as a coinfection with CVA. Moreover, its presence was also reported from different hosts (almond, peach and plum) [ 35 , 41 ] and recently from apricot [ 17 ].…”