scholarly journals Biological and Molecular Characterization of a New Cucurbit-Infecting Tobamovirus

2001 ◽  
Vol 91 (6) ◽  
pp. 565-571 ◽  
Author(s):  
Y. Antignus ◽  
Y. Wang ◽  
M. Pearlsman ◽  
O. Lachman ◽  
N. Lavi ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Mosaic Virus ◽  
Genome Organization ◽  
Economic Losses ◽  
Its Sequence ◽  
Subgroup Ii ◽  
Cucumber Fruit ◽  
The Family ◽  
Serological Data

An uncharacterized virus was isolated from greenhouse-grown cucumber plants. Biological and serological data described in the present study indicated that the virus belonged in the genus Tobamovirus. The host range of the virus included several plant species within the family Cucurbitaceae. The virus designated Cucumber fruit mottle mosaic virus (CFMMV) causes severe mottling or mosaic on cucumber fruits, and its fast spread within greenhouses could lead to significant economic losses in cucumber crops. The genome of CFMMV has been completely sequenced and its genome organization was typical of a Tobamovirus. However, its sequence was distinct from other described viruses within the group of cucurbit-infecting Tobamoviruses. Comparisons of sequences and phylogenetic analysis suggested that the cucurbit-infecting Tobamoviruses be separated into two subgroups: subgroup I comprising the strains and isolates referred to in the literature as Cucumber green mottle mosaic virus (CGMMV) (CV3, CV4, CGMMV-W, CGMMV-SH, and CGMMV-Is) and subgroup II comprising CFMMV, Kyuri green mottle mosaic virus (KGMMV), and the Yodo strain of CGMMV, which is closely related to KGMMV and may be considered a strain of it.

scholarly journals Molecular characterization of two recombinant isolates of telosma mosaic virus infecting Passiflora edulis from Fujian Province in China

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8576
Author(s):  
Lixue Xie ◽  
Fangluan Gao ◽  
Jianguo Shen ◽  
Xiaoyan Zhang ◽  
Shan Zheng ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Mosaic Virus ◽  
Plant Virus ◽  
Economic Losses ◽  
Monophyletic Clade ◽  
Passiflora Edulis ◽  
Potyvirus Species ◽  
Sequence Identities ◽  
Recombination Breakpoints

Telosma mosaic virus (TeMV) is an important plant virus causing considerable economic losses to passion fruit (Passiflora edulis) production worldwide, including China. In this study, the complete genome sequence (excluding the poly (A) tail) of two TeMV isolates, Fuzhou and Wuyishan, were determined to be 10,050 and 10,057 nucleotides, respectively. Sequence analysis indicated that Fuzhou and Wuyishan isolates share 78–98% nucleotide and 83–99% amino acid sequence identities with two TeMV isolates of Hanoi and GX, and a proposed new potyvirus, tentatively named PasFru. Phylogenetic analysis indicated that these TeMV isolates and PasFru were clustered into a monophyletic clade with high confidences. This indicated that PasFru and the four TeMV isolates should be considered as one potyvirus species. Two recombination breakpoints were identified within the CI and NIb genes of the Fuzhou isolate, and also within the P1 gene of the Wuyishan isolate. To the best of our knowledge, this is the first report of TeMV recombinants worldwide.

scholarly journals Phylogenomic Characterization of Lopma Virus and Praja Virus, Two Novel Rodent-Borne Arteriviruses

Viruses ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 1842
Author(s):  
Bert Vanmechelen ◽  
Zafeiro Zisi ◽  
Sophie Gryseels ◽  
Joëlle Goüy de Bellocq ◽  
Bram Vrancken ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Genome Organization ◽  
Complete Genome ◽  
Evolutionary History ◽  
Rna Viruses ◽  
Novel Species ◽  
Genome Sequences ◽  
Animal Pathogens ◽  
The Family

Recent years have witnessed the discovery of several new viruses belonging to the family Arteriviridae, expanding the known diversity and host range of this group of complex RNA viruses. Although the pathological relevance of these new viruses is not always clear, several well-studied members of the family Arteriviridae are known to be important animal pathogens. Here, we report the complete genome sequences of four new arterivirus variants, belonging to two putative novel species. These new arteriviruses were discovered in African rodents and were given the names Lopma virus and Praja virus. Their genomes follow the characteristic genome organization of all known arteriviruses, even though they are only distantly related to currently known rodent-borne arteriviruses. Phylogenetic analysis shows that Lopma virus clusters in the subfamily Variarterivirinae, while Praja virus clusters near members of the subfamily Heroarterivirinae: the yet undescribed forest pouched giant rat arterivirus and hedgehog arterivirus 1. A co-divergence analysis of rodent-borne arteriviruses confirms that they share similar phylogenetic patterns with their hosts, with only very few cases of host shifting events throughout their evolutionary history. Overall, the genomes described here and their unique clustering with other arteriviruses further illustrate the existence of multiple rodent-borne arterivirus lineages, expanding our knowledge of the evolutionary origin of these viruses.

scholarly journals Metagenomic Analysis of Marigold: Mixed Infection Including Two New Viruses

Viruses ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1254
Author(s):  
Hang Yin ◽  
Zheng Dong ◽  
Xulong Wang ◽  
Shuhao Lu ◽  
Fei Xia ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Mosaic Virus ◽  
Complete Genome ◽  
Plum Pox Virus ◽  
Cryptic Virus ◽  
Sequence Identity ◽  
Complete Genome Sequence Analysis ◽  
Wilt Virus ◽  
Broad Bean Wilt Virus

Marigold plants with symptoms of mosaic, crinkle, leaf curl and necrosis were observed and small RNA and ribo-depleted total RNA deep sequencing were conducted to identify the associated viruses. Broad bean wilt virus 2, cucumber mosaic virus, turnip mosaic virus, a new potyvirus tentatively named marigold mosaic virus (MMV) and a new partitivirus named as marigold cryptic virus (MCV) were finally identified. Complete genome sequence analysis showed MMV was 9811 nt in length, encoding a large polyprotein with highest aa sequence identity (57%) with the putative potyvirus polygonatumkingianum virus 1. Phylogenetic analysis with the definite potyviruses based on the polyprotein sequence showed MMV clustered closest to plum pox virus. The complete genome of MCV comprised of dsRNA1 (1583 bp) and dsRNA2 (1459 bp), encoding the RNA-dependent RNA polymerase (RdRp), and coat protein (CP), respectively. MCV RdRp shared the highest (75.7%) aa sequence identity with the unclassified partitivirus ambrosia cryptic virus 2, and 59.0%, 57.1%, 56.1%, 54.5% and 33.7% with the corresponding region of the definite delta-partitiviruses, pepper cryptic virus 2, beet cryptic virus 3, beet cryptic virus 2, pepper cryptic virus 1 and fig cryptic virus, respectively. Phylogenetic analysis based on the RdRp aa sequence showed MCV clustered into the delta-partitivirus group. These findings enriched our knowledge of viruses infecting marigold, but the association of the observed symptom and the identified viruses and the biological characterization of the new viruses should be further investigated.

scholarly journals Molecular characterization of porcine epidemic diarrhoea virus (PEDV) in Poland reveals the presence of swine enteric coronavirus (SeCoV) sequence in S gene

PLoS ONE ◽  
2021 ◽  
Vol 16 (10) ◽  
pp. e0258318
Author(s):  
Marta Antas ◽  
Monika Olech ◽  
Anna Szczotka-Bochniarz
Keyword(s):  
Phylogenetic Analysis ◽  
Molecular Characterization ◽  
Rna Virus ◽  
Economic Losses ◽  
High Morbidity ◽  
Antigenic Analysis ◽  
S Gene ◽  
Porcine Epidemic Diarrhoea Virus ◽  
Diarrhoea Virus

Porcine epidemic diarrhoea (PED) is a highly contagious enteric viral disease of pigs with a high morbidity and mortality rate, which ultimately results in huge economic losses in the pig production sector. The etiological agent of this disease is the porcine epidemic diarrhoea virus (PEDV) which is an enveloped, positive single-stranded RNA virus. The aim of this study was to perform molecular characterization of PEDV to identify the strains circulating in Poland. In this study, 662 faecal samples from 2015 to 2021 were tested with reverse transcription quantitative real-time PCR (RT-qPCR) and the results showed that 3.8% of the tested samples revealed a positive result for PEDV. A phylogenetic analysis of the complete genome and complete S gene sequences showed that Polish PEDV strains belonged to the G1b (S-INDEL) subgroup and were closely related to the European PEDV strains isolated from 2014 to 2019. Furthermore, RDP4 analysis revealed that the Polish PEDV strains harboured a recombinant fragment of ~400 nt in the 5’ end of S gene with PEDV and swine enteric coronavirus (SeCoV) being the major and minor parents, respectively. Antigenic analysis showed that the aa sequences of neutralizing epitopes were conserved among the Polish PEDV strains. Only one strain, #0100/5P, had a unique substitution in the COE epitope. However, Polish PEDV strains showed several substitutions, especially in the COE antigen, as compared to the classical strain CV777. To the best of our knowledge, this is the first report concerning the molecular characterization of porcine epidemic diarrhoea virus strains, as well as the first phylogenetic analysis for PEDV in Poland.

FURTHER CHARACTERIZATION OF TULIP SEVERE MOSAIC VIRUS SUPPORTS CLASSIFICATION AS A MEMBER OF GENUS AMPELLOVIRUS IN THE FAMILY CLOSTEROVIRIDAE

2011 ◽  
pp. 239-245 ◽  
Author(s):  
K.T.K. Pham ◽  
G.J. Blom-Barnhoorn ◽  
V.P. Bijman ◽  
M.E.C. Lemmers ◽  
A.F.L.M. Derks
Keyword(s):  
Mosaic Virus ◽  
The Family

scholarly journals Co-Isolation and Characterization of Two Pandoraviruses and a Mimivirus from a Riverbank in Japan

Viruses ◽  
2019 ◽  
Vol 11 (12) ◽  
pp. 1123 ◽  
Author(s):  
Motohiro Akashi ◽  
Masaharu Takemura
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Analysis ◽  
Virus Isolation ◽  
Random Amplified Polymorphic Dna ◽  
Isolation And Characterization ◽  
The Family ◽  
Complete Sequences ◽  
Infected Amoeba ◽  
Giant Viruses

Giant viruses, like pandoraviruses and mimiviruses, have been discovered from diverse environments, and their broad global distribution has been established. Here, we report two new isolates of Pandoravirus spp. and one Mimivirus sp., named Pandoravirus hades, Pandoravirus persephone, and Mimivirus sp. isolate styx, co-isolated from riverbank soil in Japan. We obtained nearly complete sequences of the family B DNA polymerase gene (polB) of P. hades and P. persephone; the former carried two known intein regions, while the latter had only one. Phylogenetic analysis revealed that the two new pandoravirus isolates are closely related to Pandoravirus dulcis. Furthermore, random amplified polymorphic DNA analysis revealed that P. hades and P. persephone might harbor different genome structures. Based on phylogenetic analysis of the partial polB sequence, Mimivirus sp. isolate styx belongs to mimivirus lineage A. DNA staining suggested that the Pandoravirus spp. asynchronously replicates in amoeba cells while Mimivirus sp. replicates synchronously. We also observed that P. persephone- or Mimivirus sp. isolate styx-infected amoeba cytoplasm is extruded by the cells. To the best of our knowledge, we are the first to report the isolation of pandoraviruses in Asia. In addition, our results emphasize the importance of virus isolation from soil to reveal the ecology of giant viruses.

scholarly journals Complete nucleotide sequence and genome organization of Grapevine leafroll-associated virus 3, type member of the genus Ampelovirus

2004 ◽  
Vol 85 (7) ◽  
pp. 2099-2102 ◽  
Author(s):  
Kai-Shu Ling ◽  
Hai-Ying Zhu ◽  
Dennis Gonsalves
Keyword(s):  
Phylogenetic Analysis ◽  
Nucleotide Sequence ◽  
Fusion Protein ◽  
Complete Genome Sequence ◽  
Genome Organization ◽  
Complete Nucleotide Sequence ◽  
Open Reading Frames ◽  
The Family ◽  
Mealy Bug ◽  
Reading Frames

This study reports on the complete genome sequence of Grapevine leafroll-associated virus 3, the type member of the genus Ampelovirus. The genome is 17 919 nt in size and contains 13 open reading frames (ORFs). Previously, the sequence of 13 154 nt of the 3′-terminal of the genome was reported. The newly sequenced portion contains a 158 nt 5′ UTR, a single papain-like protease and a methyltransferase-like (MT) domain. ORF1a encodes a large polypeptide with a molecular mass of 245 kDa. With a predicted +1 frameshift, the large fusion protein generated from ORF1a/1b would produce a 306 kDa polypeptide. Phylogenetic analysis using MT domains further supports the creation of the genus Ampelovirus for mealy-bug-transmitted viruses in the family Closteroviridae.

Molecular characterization of Cucumber mosaic virus subgroup II isolate associated with cucumber in Bangladesh

2021 ◽  
Author(s):  
Tridib Kumar Paul ◽  
Mohammad Mahmood Hasan ◽  
Tasnin Khan Eusufzai ◽  
Md. Moniruzzaman Hasan ◽  
Saiful Islam ◽  
...  
Keyword(s):  
Cucumber Mosaic Virus ◽  
Mosaic Virus ◽  
Molecular Characterization ◽  
Subgroup Ii

scholarly journals Characterization of Winter Dysentery Bovine Coronavirus Isolated from Cattle in Israel

Viruses ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 1070
Author(s):  
Dan David ◽  
Nick Storm ◽  
Waksman Ilan ◽  
Asaf Sol
Keyword(s):  
Phylogenetic Analysis ◽  
Genetic Variants ◽  
Dairy Farms ◽  
Molecular Data ◽  
Economic Losses ◽  
Bovine Coronavirus ◽  
Local Strains ◽  
Esterase Gene ◽  
Winter Dysentery

Bovine coronavirus (BCoV) is the causative agent of winter dysentery (WD). In adult dairy cattle, WD is characterized by hemorrhagic diarrhea and a reduction in milk production. Therefore, WD leads to significant economic losses in dairy farms. In this study, we aimed to isolate and characterize local BCoV strains. BCoV positive samples, collected during 2017–2021, were used to amplify and sequence the S1 domain of S glycoprotein and the full hemagglutinin esterase gene. Based on our molecular analysis, local strains belong to different genetic variants circulating in dairy farms in Israel. Phylogenetic analysis revealed that all local strains clustered together and in proximity to other BCoV circulating in the area. Additionally, we found that local strains are genetically distant from the reference enteric strain Mebus. To our knowledge, this is the first report providing molecular data on BCoV circulating in Israel.

scholarly journals Characterization of a novel virus infected watermelon in Indonesia based on viral particle using electron microscope

2017 ◽  
Author(s):  
Budi Setiadi Daryono ◽  
Fauziatul Fitriyah ◽  
alin liana ◽  
Utari Saraswati ◽  
Keiko T. Natsuaki
Keyword(s):  
Electron Microscope ◽  
Mosaic Virus ◽  
Viral Particle ◽  
Plant Viruses ◽  
Electron Microscope Investigation ◽  
Viral Particles ◽  
Cucumber Fruit ◽  
Novel Virus ◽  
New Form

Most of the cucurbits diseases in Indonesia are caused by plant viruses. Tobamovirus is one of the viral genera recently infected cucurbits. The members of cucurbits-infecting Tobamovirus are Cucumber green mottle mosaic virus (CGMMV), Kyuri green mottle mosaic virus (KGMMV), Cucumber fruit mottle mosaic virus (CFMMV), Zucchini green mottle mosaic virus (ZGMMV), and Cucumber mottle virus (CuMoV). A research on the occurrence of cucurbits-infecting Tobamovirus in Indonesia was carried out in 2011. Based on the result, a new characteristic of viral particle were found in watermelon. The viral particle was previously identified as CGMMV based on electron microscope investigation revealed presence of rod-shaped and not enveloped virions. The virions were straight about 300 nm long and 28–30 nm in diameter. However, in some electron micrograph shows rare characteristic of the viral particle. The viral particles could joint each other to bend a new form. Two viral particles were able to joint and formed an angle. Moreover, some of viral particles could joint and form a longer viral particle (800-1100 nm), two to four times longer than CGMMV particle, but the both diameter of the virus are similar. These characteristics indicate that the viral particle is a novel virus, different from CGMMV or other Tobamovirus members.

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