A Novel Lineage of Cile-Like Viruses Discloses the Phylogenetic Continuum Across the Family Kitaviridae

Abstract

An increasing number of plant species have been recognized or considered likely reservoirs of viruses transmitted by Brevipalpus mites. A tiny fraction of these viruses, primarily those causing severe economic burden to prominent crops, have been fully characterized. In this study, based on high-throughput sequencing, transmission electron microscopy analyses of virions in plant-infected tissues, viral transmission experiments, and the morphoanatomical identification of the involved Brevipalpus mites, we describe molecular and biological features of viruses representing three new tentative species of the family Kitaviridae. The genomes of Solanum violifolium ringspot virus (SvRSV, previously partially characterized), Ligustrum chlorotic spot virus (LigCSV), and Ligustrum leprosis virus (LigLV) have five open reading frames (ORFs) > 500 nts, two distributed in RNA1 and three in RNA2. RNA1 of these three viruses display the same genomic organization found in RNA1 of typical cileviruses, while their RNA2 are shorter, possessing only orthologs of genes p61, p32, and p24. LigCSV and LigLV are more closely related to each other than to SvRSV, but the identities between their genomic RNAs were lower than 70%. In gene-by-gene comparisons, ORFs from LigCSV and LigLV had the highest sequence identity values (nt sequences: 70–76% and deduced amino acid sequences: 74–83%). The next higher identity values were with ORFs from typical cileviruses, with values below 66%. Virions of LigLV (≈ 40 nm × 55 nm) and LigCSV (≈ 54 nm × 66 nm) appear almost spherical, contrasting with the bacilliform shape of SvRSV virions (≈ 47 nm × 101 nm). Mites collected from the virus-infected plants were identified as Brevipalpus papayensis, B. tucuman, and B. obovatus. Viruliferous B. papayensis mites successfully transmitted LigCSV to Arabidopsis thaliana. SvRSV, LigCSV, and LigLV seem to represent novel sub-lineages of kitaviruses that descent on parallel evolutionary branches from a common ancestor shared with the tentative cile-like virus hibiscus yellow blotch virus and typical cileviruses. Biological and molecular data, notably, the phylogenetic reconstruction based on the RdRp proteins in which strong support for monophyly of the family Kitaviridae is observed, mark an advance in the understanding of kitavirids.

Arboviruses and symbiotic viruses cooperatively hijack insect sperm-specific proteins for paternal transmission

“…1a). Phylogenetic analysis based on amino acid sequences of RdRp showed that RdFV clustered with plant-infecting furoviruses in Virgaviridae family, which contained plant virgavirus lineages and unclassified insect-infecting virga-like virus group, such as Hubei virga-like viruses [38][39][40] (Fig. S1).…”

“…Phylogenetic analysis showed that the insect-specific RdFV, gramineous plants-infecting furovirues, and insect-specific Hubei virgalike viruses belong to Virgaviridae family [38][39][40] . The close phylogenetic relationship between insect-infecting virgaviruses and their plantinfecting counterparts suggests that they might share the common virus origin(s) 39,45 .…”

High-throughput sequencing application in the detection and discovery of viruses associated with the regulated citrus leprosis disease complex

“…Interestingly, both CiLV-C2 and CiLV-C2H encodes a 7-kDa transmembrane protein (p7) ( Roy et al., 2013b ; Melzer et al., 2013 ) but the ORF p7 is absent in the CiLV-C2H2 genome as the similar genome structure was observed in the RNA2 genome segment of CiLV-C ( Locali-Fabris et al., 2006 ). The RNA2 genome sequences between ORF1 (p15) and ORF2 (p61) [with or without p7 ORF] are the most variable region among cileviruses ( Ramos-González et al., 2022 ). Current demarcation criteria for species of the genus Cilevirus are based on <85% aa sequence identity for the proteome but there is no cut off value was determined for cilevirus strain identification.…”

Citrus Bright Spot Virus: A New Dichorhavirus, Transmitted by Brevipalpus azores, Causing Citrus Leprosis Disease in Brazil

“…Transmission assays also proved that B. papayensis , B. obovatus, and B. yothersi are, at least under our experimental conditions, unable to transmit CiBSV isolates. It should be noted that these experiments were carried out in conditions equivalent to those commonly described for the transmission of other Brevipalpus -transmitted viruses [ 7 , 29 ]. Further studies could be performed using citrus seedlings as test plants to assess the transmission efficiency of CiBSV by B. azores .…”