Novel picornavirus (family Picornaviridae) from freshwater fishes (Perca fluviatilis, Sander lucioperca, and Ameiurus melas) in Hungary

AbstractIn this study, a novel picornavirus (perchPV/M9/2015/HUN, GenBank accession no. MW590713) was detected in eight (12.9%) out of 62 faecal samples collected from three (Perca fluviatilis, Sander lucioperca, and Ameiurus melas) out of 13 freshwater fish species tested and genetically characterized using viral metagenomics and RT-PCR methods. The complete genome of perchPV/M9/2015/HUN is 7,741 nt long, excluding the poly(A) tail, and has the genome organization 5’UTRIRES-?/P1(VP0-VP3-VP1)/P2(2A1NPG↓P-2A2H-box/NC-2B-2C)/P3(3A-3BVPg-3CPro-3DPol)/3’UTR-poly(A). The P1, 2C, and 3CD proteins had 41.4%, 38.1%, and 47.3% amino acid sequence identity to the corresponding proteins of Wenling lepidotrigla picornavirus (MG600079), eel picornavirus (NC_022332), and Wenling pleuronectiformes picornavirus (MG600098), respectively, as the closest relatives in the genus Potamipivirus. PerchPV/M9/2015/HUN represents a potential novel fish-origin species in an unassigned genus in the family Picornaviridae.

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Multiple Types of Novel Enteric Bopiviruses (Picornaviridae) with the Possibility of Interspecies Transmission Identified from Cloven-Hoofed Domestic Livestock (Ovine, Caprine and Bovine) in Hungary

Viruses ◽

10.3390/v13010066 ◽

2021 ◽

Vol 13 (1) ◽

pp. 66

Author(s):

Zoltán László ◽

Péter Pankovics ◽

Gábor Reuter ◽

Attila Cságola ◽

Ádám Bálint ◽

...

Keyword(s):

Novel Species ◽

Phylogenetic Analyses ◽

Interspecies Transmission ◽

Background Information ◽

Type Ii ◽

Rt Pcr ◽

Faecal Samples ◽

The Family ◽

Domestic Livestock

Most picornaviruses of the family Picornaviridae are relatively well known, but there are certain “neglected” genera like Bopivirus, containing a single uncharacterised sequence (bopivirus A1, KM589358) with very limited background information. In this study, three novel picornaviruses provisionally called ovipi-, gopi- and bopivirus/Hun (MW298057-MW298059) from enteric samples of asymptomatic ovine, caprine and bovine respectively, were determined using RT-PCR and dye-terminator sequencing techniques. These monophyletic viruses share the same type II-like IRES, NPGP-type 2A, similar genome layout (4-3-4) and cre-localisations. Culture attempts of the study viruses, using six different cell lines, yielded no evidence of viral growth in vitro. Genomic and phylogenetic analyses show that bopivirus/Hun of bovine belongs to the species Bopivirus A, while the closely related ovine-origin ovipi- and caprine-origin gopivirus could belong to a novel species “Bopivirus B” in the genus Bopivirus. Epidemiological investigation of N = 269 faecal samples of livestock (ovine, caprine, bovine, swine and rabbit) from different farms in Hungary showed that bopiviruses were most prevalent among <12-month-old ovine, caprine and bovine, but undetectable in swine and rabbit. VP1 capsid-based phylogenetic analyses revealed the presence of multiple lineages/genotypes, including closely related ovine/caprine strains, suggesting the possibility of ovine–caprine interspecies transmission of certain bopiviruses.

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First report of cucurbit chlorotic yellows virus (CCYV) infecting pumpkin in India

Plant Disease ◽

10.1094/pdis-07-21-1473-pdn ◽

2021 ◽

Author(s):

Ashwini Kumar ◽

Bichhinna Maitri Rout ◽

Shakshi Choudhary ◽

Amish K. Sureja ◽

V. K. Baranwal ◽

...

Keyword(s):

Amino Acid ◽

Amino Acid Sequence ◽

Amino Acid Sequence Identity ◽

Rt Pcr ◽

Specific Primers ◽

First Report ◽

Virus Particles ◽

Sequence Identity ◽

Cp Gene ◽

Cucurbit Chlorotic Yellows Virus

Pumpkin (Cucurbita moschata), a member of the family Cucurbitaceae, is widely cultivated throughout the world including India. During August 2020 to January 2021, stunted pumpkin plants (cv. Pusa Vishwas), showing chlorotic patches, mosaic, and vein banding on leaves (e-Xtra Fig.1), were observed in the experimental fields of the Indian Agricultural Research Institute (IARI), New Delhi, India. Leaf-dip electron microscopy (EM) of the symptomatic plants (12 out of 37 samples) revealed the association of long flexuous virus particles measuring 650-950nm×10-12nm, suggestive of the presence of either crinivirus or potyvirus or both. Subsequently, a reverse transcription-polymerase chain reaction (RT-PCR) was performed on RNA extracted from the samples that had long flexuous virus particles using generic primers for criniviruses i.e. CriniPol-F: GCY CCS AGR GTK AAT GA and CriniPol-R: ACC TTG RGA YTT RTC AAA targeting partial RNA-dependent RNA polymerase coding region (Martin et al. 2003) and specific primers for papaya ringspot virus (PRSV) targeting a part of 3’ NIb and full coat protein (CP) gene (Basavaraj et al., 2019) separately. All tested samples were positive for both crinivirus and PRSV as expected size amplicons were obtained, accounting for about 32% prevalence. As PRSV is a well-studied virus infecting cucurbits, further work was not carried on this virus and only the RT-PCR amplicon indicative of crinivirus (~515 bp) was cloned into the pGEM-T easy cloning vector (Promega, Madison, WI) and sequenced for further confirmation of the virus presence. The obtained sequence (GenBank accession No MZ318672) shared up to 90% nucleotide and 100% amino acid sequence identity with the corresponding genomic region of a cucurbit chlorotic yellows virus (CCYV) isolate from Greece (LT841297). To confirm the identity of the crinivirus species present in the same pumpkin sample, the CP gene (753bp) was amplified and sequenced using CCYV CP gene-specific primers CP-F (5’-ATG GAG AAG ACY GAC AAT AAA CAA AAT GAT GA-3’) and CP-R (5’-TTA TTT ACT ACA ACC TCC CGG TGC CAA C-3’) (modified from Kheireddine et al. 2020). Sequence analysis using the BioEdit tool (version 2.0) revealed that the crinivirus present in pumpkin (KC577202) shared 95 to 100% nucleotide (and 98 to 100% amino acid) sequence identity with the corresponding gene sequences of CCYV isolates originating from cucurbitaceous hosts from diverse locations. The presence of CCYV was further validated by a whitefly transmission-based bioassay followed by RT-PCR confirmation. The bioassay was performed by the whitefly species Bemisia tabaci (biotype Asia II7) using the acquisition access period and inoculation access period of 24 hours each. Six whitefly individuals per plant were used for inoculating ten pumpkin plants (cv. Pusa Vishwas) at the first true leaf stage grown in pots containing soilrite as the medium in insect-proof cages. All ten plants inoculated using whiteflies exhibited chlorosis and stunting symptoms 12-15 days post-inoculation (e-Xtra Fig.2) and were found positive for CCYV in RT-PCR assay performed using CCYV CP gene-specific primers. Though CCYV had been reported worldwide (Tzanetakis et al. 2013), its occurrence had not been reported from India. Results of the present study confirm the infection of pumpkin plants by CCYV and constitute the first report of its presence in India. Further, there is a need to investigate the extent of its spread and impact of this virus on the production of cucurbitaceous crops in the country.

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Two Novel Negative-Sense RNA Viruses Infecting Grapevine Are Members of a Newly Proposed Genus within the Family Phenuiviridae

Viruses ◽

10.3390/v11080685 ◽

2019 ◽

Vol 11 (8) ◽

pp. 685 ◽

Cited By ~ 7

Author(s):

Alfredo Diaz-Lara ◽

Beatriz Navarro ◽

Francesco Di Serio ◽

Kristian Stevens ◽

Min Sook Hwang ◽

...

Keyword(s):

Nucleocapsid Protein ◽

High Throughput Sequencing ◽

Movement Protein ◽

Rna Viruses ◽

Rt Pcr ◽

Rna Dependent Rna Polymerase ◽

Sequence Identity ◽

The Family ◽

Putative Movement Protein ◽

Negative Sense

Two novel negative-stranded (ns)RNA viruses were identified by high throughput sequencing in grapevine. The genomes of both viruses, named grapevine Muscat rose virus (GMRV) and grapevine Garan dmak virus (GGDV), comprise three segments with each containing a unique gene. Based on sequence identity and presence of typical domains/motifs, the proteins encoded by the two viruses were predicted to be: RNA-dependent RNA polymerase (RdRp), nucleocapsid protein (NP), and putative movement protein (MP). These proteins showed the highest identities with orthologs in the recently discovered apple rubbery wood viruses 1 and 2, members of a tentative genus (Rubodvirus) within the family Phenuiviridae. The three segments of GMRV and GGDV share almost identical sequences at their 5′ and 3′ termini, which are also complementary to each other and may form a panhandle structure. Phylogenetics based on RdRp, NP and MP placed GMRV and GGDV in the same cluster with rubodviruses. Grapevine collections were screened for the presence of both novel viruses via RT-PCR, identifying infected plants. GMRV and GGDV were successfully graft-transmitted, thus, they are the first nsRNA viruses identified and transmitted in grapevine. Lastly, different evolutionary scenarios of nsRNA viruses are discussed.

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Genogroup I avian picobirnavirus detected in Brazilian broiler chickens: a molecular epidemiology study

Journal of General Virology ◽

10.1099/vir.0.054783-0 ◽

2014 ◽

Vol 95 (1) ◽

pp. 117-122 ◽

Cited By ~ 21

Author(s):

René Ribeiro Silva ◽

Delana Andreza Melo Bezerra ◽

Jane Haruko Lima Kaiano ◽

Darleise de Souza Oliveira ◽

Rodrigo Vellasco Duarte Silvestre ◽

...

Keyword(s):

Molecular Epidemiology ◽

Broiler Chickens ◽

Gene Sequencing ◽

Positive Sample ◽

Epidemiology Study ◽

Rt Pcr ◽

Nucleotide Level ◽

Faecal Samples ◽

The Family ◽

Dsrna Genome

Picobirnavirus (PBV) belongs to the family Picobirnaviridae. Picobirnaviruses contain a bisegmented dsRNA genome that is non-enveloped. A total of 85 pooled faecal samples were collected from the poultry of 37 farms from the Metropolitan Mesoregion of Belém (MMB), Pará state, Brazil. The viral RNA from each sample was analysed by PAGE and reverse transcriptase PCR (RT-PCR). For each county affected, at least one positive sample was selected, cloned and sequenced. The samples showed a positivity of 15.3 % (13/85) by PAGE and 49.4 % (42/85) by RT-PCR. Sequencing of these strains demonstrated a considerable RdRp gene heterogeneity that ranged from 56.1 to 100 % at the nucleotide level compared with prototypes of different species and water sewage, and from 50.3 to 100 % among themselves. Avian picobirnavirus (AvPBV) was detected in MMB broiler farms and showed a heterogeneous relationship with the prototypes used. This report includes what is believed to be the first gene sequencing of AvPBV in Brazilian broiler chickens.

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Types A and B of Beet necrotic yellow vein virus Occur in Poland

Plant Disease ◽

10.1094/pd-90-1261b ◽

2006 ◽

Vol 90 (9) ◽

pp. 1261-1261 ◽

Cited By ~ 1

Author(s):

N. Borodynko

Keyword(s):

Amino Acid ◽

Amino Acid Sequence ◽

Sugar Beet ◽

Amino Acid Sequence Identity ◽

Type A ◽

Yellow Vein ◽

Enzyme Linked Immunosorbent Assay ◽

Type B ◽

Rt Pcr ◽

Sequence Identity

Beet necrotic yellow vein virus (BNYVV) is the type member of the genus Benyvirus and the causal agent of rhizomania disease of sugar beet. Since 1999, BNYVV is becoming one of the most important viruses of sugar beet in Poland. BNYVV is represented by three types, frequently A and B and rarely P, however, in Poland, type A only was recorded (2). In 2005, a survey was conducted to determine the incidence of types A and B of BNYVV in Poland. Thirty samples of sugar beet plants with rhizomania-like symptoms were collected from six fields in the western, southern, and northern areas of Poland. All samples were analyzed by double antibody sandwich-enzyme linked immunosorbent assay (DAS-ELISA) with commercial antiserum (Bio-Rad, Hercules, CA). Infection of BNYVV was found in 26 samples. The presence of the virus in these samples was confirmed by reverse transcription-polymerase chain reaction (RT-PCR). The total RNA extracted from sugar beet was tested with specific primers designed to amplify a fragment of the RNA2 for BNYVV (1). Multiplex (m) RT-PCR with two sets of primers, rhizo AF/rhizo AR and rhizo BF/rhizo BR (2), was used to distinguish A and B types of BNYVV. Two obtained mRT-PCR products were sequenced and compared with other sequences available in GenBank. A 121-nt amplicon sequence (GenBank Accession No. DQ 228872) had 100% nucleotide and amino acid sequence identity with all BNYVV type B sequences (e.g., Stourton-GenBank Accession No. AY682695) (2). A 171-nt amplicon sequence (GenBank Accession No. DQ228871) had 100% nucleotide and amino acid sequence identity with all BNYVV type A sequences (e.g., Ravenna-GenBank Accession No. AY 654282) (2). Type A was detected in 23 BNYVV-infected sugar beet plants from five fields located in western and southern Poland while type B was found in three samples from one field in northern Poland. To my knowledge, this is the first report of the natural occurrence of BNYVV type B in Poland. References: (1) A. Maunier et al. Appl. Environ. Microbiol. 69:2356, 2003. (2) C. Ratti et al. J. Virol. Methods 124:41, 2005.

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Dragonfly cyclovirus, a novel single-stranded DNA virus discovered in dragonflies (Odonata: Anisoptera)

Journal of General Virology ◽

10.1099/vir.0.030338-0 ◽

2011 ◽

Vol 92 (6) ◽

pp. 1302-1308 ◽

Cited By ~ 80

Author(s):

Karyna Rosario ◽

Milen Marinov ◽

Daisy Stainton ◽

Simona Kraberger ◽

Elizabeth J. Wiltshire ◽

...

Keyword(s):

Viral Metagenomics ◽

Nucleotide Identity ◽

Ssdna Virus ◽

Single Strain ◽

Genome Wide ◽

Faecal Samples ◽

The Family ◽

Circular Ssdna ◽

A New Species ◽

Dragonfly Species

Dragonfly cyclovirus (DfCyV), a new species of ssDNA virus discovered using viral metagenomics in dragonflies (family Libellulidae) from the Kingdom of Tonga. Metagenomic sequences of DfCyV were similar to viruses of the recently proposed genus Cyclovirus within the family Circoviridae. Specific PCRs resulted in the recovery of 21 DfCyV genomes from three dragonfly species (Pantala flavescens, Tholymis tillarga and Diplacodes bipunctata). The 1741 nt DfCyV genomes share >95 % nucleotide identity and are classified into 11 subtypes representing a single strain. The DfCyV genomes share 48–63 % genome-wide nucleotide identity with cycloviruses identified in human faecal samples. Recombination analysis revealed three recombinant DfCyV genomes, suggesting that recombination plays an important role in cyclovirus evolution. To our knowledge, this is the first report of a circular ssDNA virus identified in insects, and the data may help elucidate evolutionary links among novel Circoviridae recently identified in animals and environmental samples.

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The First Complete Genome Sequence of a Novel Tetrastichus brontispae RNA Virus-1 (TbRV-1)

Viruses ◽

10.3390/v11030257 ◽

2019 ◽

Vol 11 (3) ◽

pp. 257

Author(s):

E Meng ◽

Baozhen Tang ◽

Francisco Sanchez-Garcia ◽

Ting Qiao ◽

Lang Fu ◽

...

Keyword(s):

Genome Sequence ◽

Complete Genome Sequence ◽

Complete Genome ◽

Amino Acid Sequence Identity ◽

Rna Virus ◽

Complete Sequence ◽

Matrix Proteins ◽

Sequence Identity ◽

The Family ◽

Family Rhabdoviridae

The complete sequence of a novel RNA virus isolated from Tetrastichus brontispae (TbRV-1) was determined to be 12,239 nucleotides in length with five non-overlapping, linearly arranged coding sequences (CDS), potentially encoding nucleoproteins, hypothetical proteins, matrix proteins, glycoproteins, and RNA-dependent RNA polymerases. Sequence analysis indicated that the RNA-dependent RNA polymerase of TbRV-1 shares a 65% nucleotide and 67% amino acid sequence identity with Hubei dimarhabdovirus 2, suggesting that TbRV-1 is a member of the dimarhabdovirus supergroup. This corresponded to the result of the phylogenetic analysis. The affiliation of TbRV-1 with members of the family Rhabdoviridae was further validated by similar transcription termination motifs (GGAACUUUUUUU) to the Drosophila sigmavirus. The prevalence of TbRV-1 in all tissues suggested that the virus was constitutive of, and not specific to, any wasp tissue. To our knowledge, this is the first report on the complete genome sequence of a dimarhabdovirus in parasitoids.

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First Report of broad bean wilt virus-2 in marigold (Tagetes erecta L.) in China

Plant Disease ◽

10.1094/pdis-01-21-0078-pdn ◽

2021 ◽

Author(s):

Li Yongqiang ◽

Zheng Dong ◽

Annihaer Abuduwaili ◽

Xulong Wang ◽

Hang Yin ◽

...

Keyword(s):

Sequence Analysis ◽

Broad Bean ◽

Tagetes Erecta ◽

Rt Pcr ◽

Specific Primer ◽

Genome Coverage ◽

Sequence Identity ◽

The Family ◽

Wilt Virus ◽

Broad Bean Wilt Virus

Broad bean wilt virus 2 (BBWV-2), a member of the genus Fabavirus in the family Secoviridae mainly transmitted by aphids, has been recognized as a severe pathogen affecting the production of horticultural and ornamental plants worldwide (Xia et al. 2020). The virus was reported to infect many plant species mostly belonging to the family Fabaceae in China (Wang et al. 2017). In August 2018, marigold plants with the symptom of mosaic were observed in the field of Huairou, Beijing (Figure S1). Total RNA was extracted from symptomatic leaf samples from a single plant with TRIzol reagent (Invitrogen, Carlsbad, CA) with a standard procedure following the manufacturer′s instructions, and small RNAs were isolated for deep sequencing library construction with Illumina TruSeq Small RNA Sample Prep Kit (Illumina, San Diego, CA, USA). The high-throughput sequencing was carried out on an Illumina HiSeq2500 platform. After raw data process, 8,911,917 clean reads were gained and further de novo assembled into contigs with CLC Genomics Workbench software. BLASTN and BLASTX analysis against the GenBank database showed that 81 of the 9,495 assembled contigs shared high nucleotide (nt) sequence identity with the bipartite genome of BBWV-2 isolate Gyp (KX686589-KX686590 for RNA1 and RNA2, 89% of the genome coverage and 90% nt identity) and 34 with high nt sequence identity of cucumber mosaic virus(CMV) from Tagetes erecta (EU665000-EU665002 for RNA1-RNA3,89% of the genome coverage and 96% nt sequence identity) with sequence coverage ranging from 24-fold to 8,078-fold at different genome positions. To further confirm the presence of BBWV-2, a RNA2 specific primer pair targeting the coat protein region (F1423-1448,5-CTGACAGAGGAATACTATTTCCAAAG-3;R2692-2719,5-CCTGTAAAATTGATATCTCCGGACAAAC-3) was designed from the obtained HTS sequence and reverse transcription-polymerase chain reaction (RT-PCR) was conducted. The 1.3 kb amplicon was ligated to pMD19-T vector (TaKaRa, Dalian, China) and sequenced. Sequence analysis showed it (BBWV-2-marigold, MW322809) shared 99% nt sequence identity with the Gyp isolate infecting Gynura procumbens from South Korea (LC497425.1). Phylogenetic analysis constructed with MEGA6 with the CP nt sequence of other reported BBWV-2 isolates showed BBWV-2-marigold clustered closely with the isolates from South Korea infecting Gynura procumbens (Figure S2), in accordance with the sequence identity analysis. Further RT-PCR with primer pair targeting the RNA1 (F3025-3050 5-GACAGAGTGATATTCCTAATCGAGAT-3; R4035-4062CACTCAATGC AATAAAGGTCTGGCACCT) was conducted and specific bands with the expected size of 1.0 kb were obtained in the agarose gel (data not shown), which further confirmed the existence of BBWV-2.A total of 16 marigold leaf samples(7 from Huairou and 9 from Yanqing) with mosaic symptom were collected and tested by RT-PCR with the abovementioned primer pair, and 4 from Huairou were BBWV-2 positive. Sequence analysis showed that these 4 isolates shared 100% nt sequence identity with the former sequenced isolateBBWV-2-marigold. Furthermore, CMV specific primer pair targeting the CP (F: 5-ATGGACAAATCTGGATCTCCCAAT-3/R: 5-CTAAGTCGGG AGCATCCGTGAGAT-3) were designed to detect the existence of CMV in these samples and results showed that all these 16 samples were positive for CMV. To the best of our knowledge, this is the first report of BBWV-2 in marigold in China.These findings will assist investigations on the epidemiology of diseases caused by BBWV2 in China.

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Discovery of a Novel Glucagon-like Peptide (GCGL) and Its Receptor (GCGLR) in Chickens: Evidence for the Existence of GCGL and GCGLR Genes in Nonmammalian Vertebrates

Endocrinology ◽

10.1210/en.2012-1586 ◽

2012 ◽

Vol 153 (11) ◽

pp. 5247-5260 ◽

Cited By ~ 23

Author(s):

Yajun Wang ◽

Fengyan Meng ◽

Yu Zhong ◽

Guian Huang ◽

Juan Li

Keyword(s):

Amino Acids ◽

Spinal Cord ◽

Amino Acid ◽

Amino Acid Sequence Identity ◽

Brain Regions ◽

Rt Pcr ◽

Adult Chicken ◽

Sequence Identity ◽

High Amino Acid ◽

Glucagon Like Peptide

Abstract Glucagon (GCG), glucagon-related peptides, and their receptors have been reported to play important roles including the regulation of glucose homeostasis, gastrointestinal activity, and food intake in vertebrates. In this study, we identified genes encoding a novel glucagon-like peptide (named GCGL) and its receptor (GCGLR) from adult chicken brain using RACE and/or RT-PCR. GCGL was predicted to encode a peptide of 29 amino acids (cGCGL1–29), which shares high amino acid sequence identity with mammalian and chicken GCG (62–66%). GCGLR is a receptor of 430 amino acids and shares relatively high amino acid sequence identity (53–55%) with the vertebrate GCG receptor (GCGR). Using a pGL3-CRE-luciferase reporter system, we demonstrated that synthetic cGCGL1–29, but not its structurally related peptides, i.e. exendin-4 and GCG, could potently activate GCGLR (EC50: 0.10 nm) expressed in Chinese hamster ovary cells, indicating that GCGLR can function as a GCGL-specific receptor. RT-PCR assay revealed that GCGL expression is mainly restricted to several tissues including various brain regions, spinal cord, and testes, whereas GCGLR mRNA is widely expressed in adult chicken tissues with abundant expression noted in the pituitary, spinal cord, and various brain regions. Using synteny analysis, GCGL and GCGLR genes were also identified in the genomes of fugu, tetraodon, tilapia, medaka, coelacanth, and Xenopus tropicalis. As a whole, the discovery of GCGL and GCGLR genes in chickens and other nonmammalian vertebrates clearly indicates a previously unidentified role of GCGL-GCGLR in nonmammalian vertebrates and provides important clues to the evolutionary history of GCG and GCGL genes in vertebrates.

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Complete Genome Sequence of Papaya Ringspot Virus Isolated from Genetically Modified Papaya in Hainan Island, China

Genome Announcements ◽

10.1128/genomea.01056-15 ◽

2015 ◽

Vol 3 (5) ◽

Cited By ~ 2

Author(s):

Guangyuan Zhao ◽

Pu Yan ◽

Wentao Shen ◽

Decai Tuo ◽

Xiaoying Li ◽

...

Keyword(s):

Genome Sequence ◽

Complete Genome Sequence ◽

Complete Genome ◽

Virus Isolate ◽

Genetically Modified ◽

Hainan Island ◽

Ringspot Virus ◽

Papaya Ringspot Virus ◽

Rt Pcr ◽

Sequence Identity

The complete genome sequence (10,326 nucleotides) of a papaya ringspot virus isolate infecting genetically modified papaya in Hainan Island of China was determined through reverse transcription (RT)-PCR. The virus shares 92% nucleotide sequence identity with the isolate that is unable to infect PRSV-resistant transgenic papaya.

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