First Report of Cherry Virus T Infection in Common Fig ( Ficus carica L.)

The common fig (Ficus carica L.) is economically important worldwide for fruit production and ornamental use (Kislev et al. 2006). Due to widespread grafting and use of self-rooted cuttings, numerous viruses have been identified in fig trees (Preising et al. 2021; Mijit et al. 2017). During a disease survey in Spring 2026, a fig plant showing virus-like dwarf symptoms was collected from a commercial greenhouse in Heshuo County, Xinjiang, China (Fig. S1A). To identify the potential viral pathogen, leaves were pooled and subjected to high-throughput sequencing. RNA-Seq on an Illumina HiSeq4000 platform generated 41,993,906 clean paired-end reads (150 bp) after quality control and was de novo assembled using Trinity (v2.8.5). BLASTN and sequence demarcation tool (SDT v1.3) analysis revealed the largest contig (6,846 nt) matching a Japanese Ficus tepovirus A (FiVA) isolate (100% coverage, 98.39% identity, MH898491.1), and cherry virus T (ChVT) (100% coverage, 86.63% identity to isolate 2/15a, NC_076873.1), classified by ICTV in the species Tepovirus tafavii, family Betaflexiviridae (Marias et al. 2020). Low-abundance reads of fig badnavirus 1 and fig virus A were also detected. We therefore performed small RNA-seq on the same sample and found a predominance of 21- and 22-nt siRNAs mapping to the assembled tepovirus genome (Fig. S1B), suggesting active replication of this tepovirus in fig. Its presence was further confirmed by RT-PCR using two independent primer pairs designed from the assembled contig (Table S1; Fig. S1C). The complete genome was determined by RT-PCR, rapid amplification of cDNA ends (RACE) (Table S1; Fig. S1D), and Sanger sequencing (Ykang, Hangzhou, China), assembled using DNAMAN 8.0, yielding a 6,846-nt genome (GenBank accession no. PZ351581), consistent with the RNA-seq data. The genome exhibits typical tepovirus organization with three overlapping ORFs encoding a replication-associated protein (REP), movement protein (MP), and capsid protein (CP) (Fig. S1E). SDT analysis showed aa identities of 91.58% (REP), 92.38% (MP) and 96.36% (CP) with ChVT. Since different species in the family Betaflexiviridae are expected to have less than 80% aa identity in REP and CP, FiVA and our isolate should both be regarded with ChVT as members of the same species. We therefore designated our isolate ChVT-Fig-XJ. Phylogenetic analysis of REP and CP aa sequences showed that ChVT-Fig-XJ clusters with FiVA and ChVT within the genus Tepovirus (Fig. S2A and B). After mechanical inoculation of crude virion extracts onto healthy fig and Nicotiana benthamiana plants, RT-PCR detected the virus (5/7 fig at 30 dpi; 2/5 N. benthamiana at 12 dpi) but there were no visible symptoms (Fig. S3A and B), while the two other viruses identified in RNA-seq data were not detected. It remains uncertain whether the dwarf symptom in the original fig plant was caused by virus infection. Field surveys in the same fig orchard confirmed natural infection, with an incidence rate of approximately 30% (2/7) (Fig. S3C). This is the first report of ChVT in fig, extending its natural host range. The discovery adds to fig virome complexity in China and highlights the need to investigate the role of ChVT with co-infecting viruses in fig disease development.