Poorly conserved p15 proteins of cileviruses retain elements of common ancestry and putative functionality: a theoretical assessment on the evolution of cilevirus genomes.

The genus Cilevirus groups enveloped single-stranded (+) RNA virus members of the family Kitaviridae, order Martellivirales. Proteins P15, scarcely conserved polypeptides encoded by cileviruses, have no apparent homologs in public databases. Accordingly, the open reading frames (ORFs) p15, located at the 5?-end of the viral RNA2 molecules, are considered orphan genes (ORFans). In this study, we have delved into ORFs p15 and the relatively poorly understood biochemical properties of the proteins P15 to posit their importance for viruses across the genus and theorize on their origin. We detected that the ORFs p15 are under purifying selection and that, in some viral strains, the use of synonymous codons is biased, which might be a sign of adaptation to their plant hosts. Despite the high amino acid sequence divergence, proteins P15 show the conserved motif [FY]-L-x(3)-[FL]-H-x-x-[LIV]-S-C-x-C-x(2)-C-x-G-x-C, which occurs exclusively in members of this protein family. Proteins P15 also show a common predicted 3D structure that resembles the helical scaffold of the protein ORF49 encoded by radinoviruses and the phosphoprotein C-terminal domain of mononegavirids. Based on the 3D structural similarities of P15, we suggest elements of common ancestry, conserved functionality, and relevant amino acid residues. We conclude by postulating a plausible evolutionary trajectory of ORFans p15 and the 5?-end of the RNA2 of cileviruses considering both protein fold superpositions and comparative genomic analyses with the closest kitaviruses, negeviruses, nege/kita-like viruses, and unrelated viruses that share the ecological niches of cileviruses

Detecção de vírus transmitidos por Ácaros Brevipalpus em espécies fruteiras e ornamentais.

RESUMO ? A agricultura representa mais de 20% do PIB brasileiro e o mercado de plantas fruteiras e ornamentais tem crescido nos últimos anos. No entanto, muitas destas plantas são suscetíveis a patógenos, como os vírus transmitidos por ácaros Brevipalpus (VTB). Os VTBs possuem duas moléculas de RNA de fita simples como genoma e são taxonomicamente classificados nos gêneros Cilevirus e Dichorhavirus. O objetivo deste estudo foi realizar um levantamento dos VTBs presentes em diversas hospedeiras vegetais que apresentavam sintomas de manchas cloróticas e necróticas em folhas ou frutos, frequentemente associadas à presença de ácaros Brevipalpus. Amostras foram coletadas e maceradas com nitrogênio líquido em almofariz e pistilo. O RNA total foi extraído com TRIzol e, após a síntese de cDNA, foi realizada a PCR com primers específicos para os principais VTBs encontrados no Brasil. A deteção de amplicons de tamanhos esperados nos géis de agarose 1% revelou a presença de três cilevirus em diferentes hospedeiras vegetais. Em amostras de laranjeira oriundas do cinturão citrícola de São Paulo e Minas Gerais, a estirpe SJP do citrus leprosis virus C foi prevalente, enquanto a estirpe CRD foi detectada em amostras coletadas fora desta região. O solanum violifolium ringspot virus foi identificado em amostra de Solanum violifolium de São Paulo e passion fruit green spot virus (PfGSV) em amostras de Schefflera sp. de Piracicaba e de orquídeas, hibisco e Barleria sp. de São Paulo. A detecção de PfGSV em Barleira sp. representa o primeiro relato de um cilevirus nesta hospedeira.N. 21822

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

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

Levantamento de vírus de plantas no Estado do Acre.

São escassas as informações sobre vírus presentes naturalmente infetando plantas cultivadas ou não, no Estado do Acre. A fim de complementar estas parcas informações, foi realizada uma viagem de levantamento de viroses nos municípios de Cruzeiro do Sul, Mâncio Lima, Guajará e arredores (Pè da Terra, AC, Badejo do Meio, AM), Rio Branco e Xapurí, como parte do Programa Biota da Fapesp, em Outubro, 2018

Molecular epidemiology of Citrus Leprosis Virus C: a new viral lineage and phylodynamic of the main viral subpopulations in the Americas.

Despite the importance of viral strains/variants as agents of emerging diseases, genetic and evolutionary processes affecting their ecology are not fully understood. To get insight into this topic, we assessed the population and spatial dynamic parameters of citrus leprosis virus C (CiLV-C, genus Cilevirus, family Kitaviridae). CiLV-C is the etiological agent of citrus leprosis disease, a non-systemic infection considered the main viral disorder affecting citrus orchards in Brazil. Overall, we obtained 18 complete or near-complete viral genomes, 123 complete nucleotide sequences of the open reading frame (ORF) encoding the putative coat protein, and 204 partial nucleotide sequences of the ORF encoding the movement protein, from 430 infected Citrus spp. samples collected between 1932 and 2020. A thorough examination of the collected dataset suggested that the CiLV-C population consists of the major lineages CRD and SJP, unevenly distributed, plus a third one called ASU identified in this work, which is represented by a single isolate found in an herbarium sample collected in Asuncion, Paraguay, in 1937. Viruses from the three lineages share about 85% nucleotide sequence identity and show signs of inter-clade recombination events. Members of the lineage CRD were identified both in commercial and non-commercial citrus orchards. However, those of the lineages SJP were exclusively detected in samples collected in the citrus belt of São Paulo and Minas Gerais, the leading Brazilian citrus production region, after 2015. The most recent common ancestor of viruses of the three lineages dates back to, at least, ?1500 years ago. Since citrus plants were introduced in the Americas by the Portuguese around the 1520s, the Bayesian phylodynamic analysis suggested that the ancestors of the main CiLV-C lineages likely originated in contact with native vegetation of South America. The intensive expansion of CRD and SJP lineages in Brazil started probably linked to the beginning of the local citrus industry. The high prevalence of CiLV-C in the citrus belt of Brazil likely ensues from the intensive connectivity between orchards, which represents a potential risk toward pathogen saturation across the region