Discovery and Survey of a New Mandarivirus Associated with Leaf Yellow Mottle Disease of Citrus in Pakistan

Abstract

During biological indexing for viruses in citrus trees, in a collection of Symons sweet orange (SSO) (Citrus sinensis L. Osbeck) graft inoculated with bark tissues of citrus trees from the Punjab Province in Pakistan, several SSO trees exhibited leaf symptoms of vein yellowing and mottle. High-throughput sequencing by Illumina of RNA preparation depleted of ribosomal RNAs from one symptomatic tree, followed by BLAST analyses, allowed identification of a novel virus, tentatively named citrus yellow mottle-associated virus (CiYMaV). Genome features of CiYMaV are typical of members of the genus Mandarivirus (family Alphaflexiviridae). Virus particles with elongated flexuous shape and size resembling those of mandariviruses were observed by transmission electron microscopy. The proteins encoded by CiYMaV share high sequence identity, conserved motifs, and phylogenetic relationships with the corresponding proteins encoded by Indian citrus ringspot virus (ICRSV) and citrus yellow vein clearing virus (CYVCV), the two current members of the genus Mandarivirus. Although CYVCV is the virus most closely related to CiYMaV, the two viruses can be serologically and biologically discriminated from each other. A reverse-transcription PCR method designed to specifically detect CiYMaV revealed high prevalence (62%) of this virus in 120 citrus trees from the Punjab Province, Pakistan, where the novel virus was found mainly in mixed infection with CYVCV and citrus tristeza virus. However, a preliminary survey on samples from 200 citrus trees from the Yunnan Province, China failed to detect CiYMaV in this region, suggesting that the molecular, serological, and biological data provided here are timely and can help to prevent the spread of this virus in citrus-producing countries.

Is There a “Biological Desert” With the Discovery of New Plant Viruses? A Retrospective Analysis for New Fruit Tree Viruses

“…A detection method was designed specifically for CiYMaV and revealed high prevalence (62%) in 120 citrus trees from the Punjab Province in Pakistan, where the novel virus was found mainly in mixed infections with citrus yellow vein clearing virus (CYVCV; 45%) or CTV (9.2%). However, a preliminary survey on samples from 200 citrus trees from the Yunnan province in China failed to detect CiYMaV in this region (Wu et al, 2020).…”

“…For apricot vein clearing-associated virus (AVCaV), PCR amplicons of 330 bp from the replicase gene were obtained from two samples (Elbeaino et al, 2014). In contrast, the nucleotide sequence of the entire CP from 58 different CiYMaV isolates was determined and aligned (Wu et al, 2020). The population diversity of blackberry vein bandingassociated virus (BVBaV) was studied on 25 isolates for three genes (Thekke-Veetil et al, 2013).…”

“…For BLSV, six cultivars were successfully infected through graft transmissions; meanwhile, mechanical inoculation with purified BLSV particle into forty seedlings of highbush blueberry failed (Isogai et al, 2012). Three publications (CCDaV, CiYMaV, and PLPaV) confirmed the presence of co-infecting viruses on grafted plants (Loconsole et al, 2012b;He et al, 2017;Wu et al, 2020). Eight publications did not mention weather another virus along with the studied one (NSPaV, CCDaV, CYVCV, CiLV-C2, CVEV, IrCRSaV, CiLV-N, and RLBV).…”

Identification, full-length genome sequencing, and field survey of citrus vein enation virus in Italy

“…High-throughput sequencing (HTS) is the most effective technology for detection of viruses in plants (Maliogka et al, 2018). This has allowed identification of several novel viruses in citrus hosts (Loconsole et al, 2012a;Loconsole et al, 2012b;Roy et al, 2013;Vives et al, 2013;Harakava et al, 2017;Ramos-González et al, 2017;Chabi-Jesus et al, 2018;Navarro et al, 2018a;Navarro et al, 2018b;Chabi-Jesus et al, 2020;Wu et al, 2020;Xuan et al, 2020). The present study, based on HTS data, reports the first identification of CVEV in Italy.…”

Exotic and Emergent Citrus Viruses Relevant to the Mediterranean Region

“…Recently, HTS sequencing allowed the identification of a novel virus with elongated flexuous virions resembling those of Mandarivirus, tentatively named citrus yellow mottleassociated virus (CiYMaV). The use of the antibody MAB 26A1 in serological testing allows the new virus to be distinguished from CYVCV [147].…”