Detection and partial genome sequence of a new umbra-like virus of papaya discovered in Ecuador

Quito-Avila, Diego F.; Álvarez, Robert; Ibarra, M. A.; Martín, Robert R.

doi:10.1007/s10658-015-0675-y

Cited by 33 publications

(22 citation statements)

References 13 publications

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“…In 2016, a papaya sentinel plant (cv. Sunrise), previously used as part of a study on the epidemiology of papaya virus Q (PpVQ) and its relationship with papaya ringspot virus (PRSV) [19,20], was maintained under greenhouse conditions for further investigation. The study was conducted in Los Ríos, the largest papaya producing province of Ecuador, where sentinel plants were scattered in a 2-year old field and monitored for four months.…”

Section: Methodsmentioning

confidence: 99%

“…The study was conducted in Los Ríos, the largest papaya producing province of Ecuador, where sentinel plants were scattered in a 2-year old field and monitored for four months. The selected plant was subjected to virus testing using the reverse-transcription (RT)-PCR assay described by Quito-Avila et al[20]. The plant tested positive for PRSV but not for PpVQ.…”

Section: Methodsmentioning

confidence: 99%

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Sequencing, genome analysis and prevalence of a cytorhabdovirus discovered in Carica papaya

Medina-Salguero

Cornejo-Franco

Grinstead³

et al. 2019

PLoS ONE

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The complete genome of a new rhabdovirus infecting papaya ( Carica papaya L.) in Ecuador, named papaya virus E, was sequenced and characterized. The negative-sense single-stranded RNA genome consists of 13,469 nucleotides with six canonical open reading frames (ORFs) and two accessory short ORFs predicted between ORFs corresponding to P3 (movement protein) and M (matrix protein). Phylogenetic analyses using amino acid sequences from the nucleocapsid, glycoprotein and polymerase, grouped the virus with members of the genus Cytorhabdovirus , with rice stripe mosaic virus, yerba mate chlorosis-associated virus and Colocasia bobone disease-associated virus as closest relatives. The 3’ leader and 5’ trailer sequences were 144 and 167 nt long, respectively, containing partially complementary motifs. The motif 3’-AUUCUUUUUG-5’, conserved across rhabdoviruses, was identified in all but one intergenic regions; whereas the motif 3’-ACAAAAACACA-5’ was found in three intergenic junctions. This is the first complete genome sequence of a cytorhabdovirus infecting papaya. The virus was prevalent in commercial plantings of Los Ríos, the most important papaya producing province of Ecuador. Recently, the genome sequence of bean-associated cytorhabdovirus was reported. The genome is 97% identical to that of papaya virus E, indicating that both should be considered strains of the same virus.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Sequencing, genome analysis and prevalence of a cytorhabdovirus discovered in Carica papaya

Medina-Salguero

Cornejo-Franco

Grinstead³

et al. 2019

PLoS ONE

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“…The sequence obtained from the smaller, 4.5 kb RNA, corresponds to a virus related to species in the genus Umbravirus , here named PMeV2-ES. PMeV2-ES has high similarity to PMeV-Mx and to PpVQ, a new umbra-like virus recently described in Ecuador [ 34 ]. PMeV-Mx was detected in papaya plants showing typical symptoms of sticky disease in Mexico [ 12 ].…”

Section: Discussionmentioning

confidence: 99%

The dsRNA Virus Papaya Meleira Virus and an ssRNA Virus Are Associated with Papaya Sticky Disease

et al. 2016

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Papaya sticky disease, or “meleira”, is one of the major diseases of papaya in Brazil and Mexico, capable of causing complete crop loss. The causal agent of sticky disease was identified as an isometric virus with a double stranded RNA (dsRNA) genome, named papaya meleira virus (PMeV). In the present study, PMeV dsRNA and a second RNA band of approximately 4.5 kb, both isolated from latex of papaya plants with severe symptoms of sticky disease, were deep-sequenced. The nearly complete sequence obtained for PMeV dsRNA is 8,814 nucleotides long and contains two putative ORFs; the predicted ORF1 and ORF2 display similarity to capsid proteins and RdRp's, respectively, from mycoviruses tentatively classified in the family Totiviridae. The sequence obtained for the second RNA is 4,515 nucleotides long and contains two putative ORFs. The predicted ORFs 1 and 2 display 48% and 73% sequence identity, respectively, with the corresponding proteins of papaya virus Q, an umbravirus recently described infecting papaya in Ecuador. Viral purification in a sucrose gradient allowed separation of particles containing each RNA. Mass spectrometry analysis indicated that both PMeV and the second RNA virus (named papaya meleira virus 2, PMeV2) were encapsidated in particles formed by the protein encoded by PMeV ORF1. The presence of both PMeV and PMeV2 was confirmed in field plants showing typical symptoms of sticky disease. Interestingly, PMeV was detected alone in asymptomatic plants. Together, our results indicate that sticky disease is associated with double infection by PMeV and PMeV2.

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“…Primers were designed to amplify a fragment of the viral nucleocapsid gene and used in a virus survey of commercial papaya plantings in five provinces (Los Ríos, Guayas, Manabí, Santa Elena and Sucumbíos) of Ecuador. Total RNA extraction and RT-PCR was done as described [20]. Up to five positive samples from each location were also used to amplify a fragment of the virus polymerase.…”

Section: Methodsmentioning

confidence: 99%

Characterization of a new cytorhabdovirus discovered in papaya (Carica papaya) plantings of Ecuador and its relationship with a bean-infecting strain from Brazil

Quito-Avila

Medina-Salguero

Cornejo-Franco

et al. 2019

Preprint

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DQA) 23 24 ¶ These authors contributed equally to this work. 25 26 Abstract 27 The complete genome of a new rhabdovirus infecting papaya (Carica papaya L.) 28 was sequenced and characterized. The genome consists of 13,469 nucleotides with29 six canonical open reading frames (ORFs) predicted from the antigenomic strand. In 30 addition, two overlapping short ORFs were predicted between ORFs 3 and 4. 31 Phylogenetic analyses using amino acid sequences from the nucleocapsid, 32 glycoprotein and polymerase, grouped the virus with members of the genus 33 Cytorhabdovirus, with rice stripe mosaic virus, yerba mate chlorosis-associated 34 virus and Colocasia bobone disease-associated virus as closest relatives. The 3' 35 leader and 5' trailer sequences were 144 and 167 nt long, respectively. Each end 36 contains complementary sequences prone to form panhandle structures. The motif 37 3'-AUUCUUUUUG-5', conserved across rhabdoviruses, was identified in all but one 38 intergenic regions; whereas the motif 3'-ACAAAAACACA-5' was found in three 39 intergenic junctions. This is the first complete genome of a cytorhabdovirus 40 infecting papaya. The virus was prevalent in commercial plantings of Los Ríos, the 41 most important papaya producing province of Ecuador. During the final stage of this 42 manuscript preparation, the genome of a bean-associated cytorhabdovirus became 43 available. Nucleotide identity (97%) between both genomes indicated that the two 44 viruses are strains of the same species, for which we propose the name papaya 45 cytorhabdovirus E. 46 47 Introduction 48 The Rhabdoviridae, a negative-sense RNA virus family, contains viruses that infect a 49 wide range of hosts including vertebrates, invertebrates and plants [1]. Virions have a 50 helical, bullet-shape morphology, surrounded by a host-derived membrane [2]. 51 Rhabdovirus genomes range from 11 to 16 kilobases (kbp) with only non-segmented 52 ones classically assigned to the taxa. However, virus species with bipartite genomes 53 have recently been included in the family [3,4]. Based on host type, genomic 54 organization and other biological features, rhabdoviruses currently are organized in 13 55 genera: Cytorhabdovirus, Dichorhavirus, Ephemerovirus, Lyssavirus, 56 Novirhabdovirus, Nucleorhabdovirus, Perhabdovirus, Sigmavirus, Sprivivirus, 57 Tibrovirus, Tupoavirus, Varicosavirus and Vesiculovirus 58 (http:ictvonline.org/virusTaxonomy.asp). Next generation sequencing (NGS) 59 techniques have led to the discovery of several novel rhabdovirus species for which 60 new genera have been proposed [5,6,7].61 The genome organization of rhabdoviruses has a canonical arrangement of five genes: 62 3'-N-P-M-G-L-5' that encode the nucleocapsid protein, phosphoprotein, matrix 63 protein, glycoprotein and the large polymerase, respectively. Terminal regions have 64 non-coding regulatory sequences denoted, respectively, as 3'-leader (l) and 5' trailer 65 (t) [8-9]. Additional "accessory" genes have been observed in arrangements that differ 66 among rhabdoviruses [10]. 67 6...

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Detection and partial genome sequence of a new umbra-like virus of papaya discovered in Ecuador

Cited by 33 publications

References 13 publications

Sequencing, genome analysis and prevalence of a cytorhabdovirus discovered in Carica papaya

Sequencing, genome analysis and prevalence of a cytorhabdovirus discovered in Carica papaya

The dsRNA Virus Papaya Meleira Virus and an ssRNA Virus Are Associated with Papaya Sticky Disease

Characterization of a new cytorhabdovirus discovered in papaya (Carica papaya) plantings of Ecuador and its relationship with a bean-infecting strain from Brazil

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