Sweet cherry is a major fruit crop of increasing economic importance. CVA is among the most common viruses infecting sweet cherry [
24,
25]. In some regions of China, the CVA detectable rate in sweet cherry leaf samples is high, up to ~ 60% [
25]. Molecular evolution studies on CVA can help us to understand the important features of RNA viruses, such as the population structure and the underlying evolutionary mechanisms. Several such studies have recently been published. Gao et al
. (2017) reported the genetic diversity of CVA isolates from China by analyzing three genomic regions that corresponded to the coat protein, RNA-dependent RNA polymerase, and the core region, which resulted in at least seven major clusters [
19]. Moreover, 75 full-length CVA sequences were assembled from next-generation sequencing data by Kesanakurti et al
. (2017), Phylogenetic analysis resulted in six major groupings [
26]. In our study, the genetic diversity and evolution of 75 sequences were further analyzed using PCA and phylogenetic tree construction, and five clades were classified—types 1–4 and Admix (Fig.
1). Nucleotide diversity analysis in different groups showed that the UTR sequence is conserved, indicating that it may have regulation and control functions.
Conserved stem-loop structures that function as translational enhancers have been previously identified in viruses [
27‐
29]. To date, several types of translational enhancers have been reported in different RNA viruses possessing different structural characteristics [
10,
11,
30,
31]. IRESs are unique RNA elements, which use stable and dynamic RNA structures to recruit ribosomes and drive protein synthesis. However, some IRESes did not present a remarkable secondary structure. This IRES activity requires a Watson–Crick base-pairing interaction between the IRES and 18S rRNA of 40S ribosomal subunits, which has been found in RNA2 of the blackcurrant conversion virus (BRV). In this study, the RNA structure of CVA 5′-UTR was first identified by combining phylogenetic and predictive strategies, and CVA 5′-UTR was found to regulate translation. According to the structural evolution analysis, the RNA structure of CVA 5′-UTR was conserved, the loop of which is particularly rich in pyrimidine. And it suggests that the polypyrimidine sequences could interact with a region of 18S rRNA to enhance translation activity [
21‐
23]. In addition, a similar model has been found in eukaryotic cells. Indeed, UTRs and most noncoding RNAs produced in eukaryotes are either not conserved or so highly conserved that they have many biological functions [
7]. Although several conserved secondary structure motifs in viral genomes have been identified by alignment-based structure prediction, the underlying structural evolutionary mechanism remains unclear.