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

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.

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Creation of a new genus in the family Secoviridae substantiated by sequence variation of newly identified strawberry latent ringspot virus isolates

Archives of Virology ◽

10.1007/s00705-019-04437-0 ◽

2019 ◽

Vol 165 (1) ◽

pp. 21-31 ◽

Cited By ~ 1

Author(s):

A. M. Dullemans ◽

M. Botermans ◽

M. J. D. de Kock ◽

C. E. de Krom ◽

T. A. J. van der Lee ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Amino Acid ◽

Complete Genome ◽

New Genus ◽

Sequence Data ◽

Amino Acid Sequences ◽

Ringspot Virus ◽

Genome Sequences ◽

The Family ◽

Virus Isolates

Abstract To obtain insight into the sequence diversity of strawberry latent ringspot virus (SLRSV), isolates from collections and diagnostic samples were sequenced by high-throughput sequencing. For five SLRSV isolates, the complete genome sequences were determined, and for 18 other isolates nearly complete genome sequences were determined. The sequence data were analysed in relation to sequences of SLRSV and related virus isolates available in the NCBI GenBank database. The genome sequences were annotated, and sequences of the protease-polymerase (Pro-Pol) region and coat proteins (CPs) (large and small CP together) were used for phylogenetic analysis. The amino acid sequences of the Pro-Pol region were very similar, whereas the nucleotide sequences of this region were more variable. The amino acid sequences of the CPs were less similar, which was corroborated by the results of a serological comparison performed using antisera raised against different isolates of SLRSV. Based on these results, we propose that SLRSV and related unassigned viruses be assigned to a new genus within the family Secoviridae, named “Stralarivirus”. Based on the phylogenetic analysis, this genus should include at least three viruses, i.e., SLRSV-A, SLRSV-B and lychnis mottle virus. The newly generated sequence data provide a basis for designing molecular tests to screen for SLRSV.

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Characterization of the first Pseudomonas grimontii bacteriophage, PMBT3

Archives of Virology ◽

10.1007/s00705-021-05173-0 ◽

2021 ◽

Author(s):

Sabrina Sprotte ◽

Erik Brinks ◽

Natalia Wagner ◽

Andrew M. Kropinski ◽

Horst Neve ◽

...

Keyword(s):

Electron Microscopy ◽

Complete Genome Sequence ◽

Complete Genome ◽

Phage Genome ◽

Genome Sequences ◽

Significant Similarity ◽

Protein Encoding ◽

The Family ◽

Encoding Genes

AbstractThe complete genome sequence of the virulent bacteriophage PMBT3, isolated on the proteolytic Pseudomonas grimontii strain MBTL2-21, showed no significant similarity to other known phage genome sequences, making this phage the first reported to infect a strain of P. grimontii. Electron microscopy revealed PMBT3 to be a member of the family Siphoviridae, with notably long and flexible whiskers. The linear, double-stranded genome of 87,196 bp has a mol% G+C content of 60.4 and contains 116 predicted protein-encoding genes. A putative tellurite resistance (terB) gene, originally reported to occur in the genome of a bacterium, was detected in the genome of phage PMBT3.

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Biological and Molecular Characterization of a New Cucurbit-Infecting Tobamovirus

Phytopathology ◽

10.1094/phyto.2001.91.6.565 ◽

2001 ◽

Vol 91 (6) ◽

pp. 565-571 ◽

Cited By ~ 46

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.

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Complete Genome Sequences of Enterococcus rotai LMG 26678 T and Enterococcus silesiacus LMG 23085 T

Genome Announcements ◽

10.1128/genomea.01387-16 ◽

2016 ◽

Vol 4 (6) ◽

Cited By ~ 1

Author(s):

Ana C. Lauer ◽

Ben W. Humrighouse ◽

Vladimir Loparev ◽

Patricia L. Shewmaker ◽

Anne M. Whitney ◽

...

Keyword(s):

Complete Genome ◽

Optical Mapping ◽

Novel Species ◽

Molecular Methods ◽

The Novel ◽

Genome Sequences ◽

Illumina Technology

The inclusion of molecular methods in the characterization of the novel species Enterococcus horridus necessitated the sequencing and assembly of the genomes of the closely related Enterococcus rotai and Enterococcus silesiacus . Sequencing using Illumina technology in combination with optical mapping led to the generation of closed genomes for both isolates.

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A Family of Genes Clustered at the Triplo-lethal Locus of Drosophila melanogaster Has an Unusual Evolutionary History and Significant Synteny With Anopheles gambiae

Genetics ◽

10.1093/genetics/165.2.613 ◽

2003 ◽

Vol 165 (2) ◽

pp. 613-621 ◽

Cited By ~ 2

Author(s):

Douglas R Dorer ◽

Jamie A Rudnick ◽

Etsuko N Moriyama ◽

Alan C Christensen

Keyword(s):

Phylogenetic Analysis ◽

Drosophila Melanogaster ◽

Anopheles Gambiae ◽

Evolutionary History ◽

Codon Bias ◽

Good Target ◽

The Family ◽

Genes Encoding ◽

And Function ◽

Gambiae Genome

Abstract Within the unique Triplo-lethal region (Tpl) of the Drosophila melanogaster genome we have found a cluster of 20 genes encoding a novel family of proteins. This family is also present in the Anopheles gambiae genome and displays remarkable synteny and sequence conservation with the Drosophila cluster. The family is also present in the sequenced genome of D. pseudoobscura, and homologs have been found in Aedes aegypti mosquitoes and in four other insect orders, but it is not present in the sequenced genome of any noninsect species. Phylogenetic analysis suggests that the cluster evolved prior to the divergence of Drosophila and Anopheles (250 MYA) and has been highly conserved since. The ratio of synonymous to nonsynonymous substitutions and the high codon bias suggest that there has been selection on this family both for expression level and function. We hypothesize that this gene family is Tpl, name it the Osiris family, and consider possible functions. We also predict that this family of proteins, due to the unique dosage sensitivity and the lack of homologs in noninsect species, would be a good target for genetic engineering or novel insecticides.

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Metagenomic Analysis of Marigold: Mixed Infection Including Two New Viruses

Viruses ◽

10.3390/v13071254 ◽

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.

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Complete Genome Sequences of Six Measles Virus Strains

Genome Announcements ◽

10.1128/genomea.00184-18 ◽

2018 ◽

Vol 6 (13) ◽

Cited By ~ 1

Author(s):

My V. T. Phan ◽

Claudia M. E. Schapendonk ◽

Bas B. Oude Munnink ◽

Marion P. G. Koopmans ◽

Rik L. de Swart ◽

...

Keyword(s):

Next Generation Sequencing ◽

Complete Genome ◽

Measles Virus ◽

Genetic Characterization ◽

Critical Component ◽

Wild Type ◽

Genome Sequences ◽

Virus Strains ◽

Generation Sequencing

ABSTRACT Genetic characterization of wild-type measles virus (MV) strains is a critical component of measles surveillance and molecular epidemiology. We have obtained complete genome sequences of six MV strains belonging to different genotypes, using random-primed next generation sequencing.

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Complete Genome Sequences of Two Subgenotype 1b Newcastle Disease Viruses Isolated from Sansui Sheldrake Ducks in Guizhou, China

Genome Announcements ◽

10.1128/genomea.01347-16 ◽

2016 ◽

Vol 4 (6) ◽

Author(s):

Yan Hu ◽

Zhiqiang Duan ◽

Xinqin Ji ◽

Jiafu Zhao ◽

Houqiang Xu ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Newcastle Disease ◽

Complete Genome ◽

Class I ◽

Guizhou Province ◽

Genome Sequences

Here, we report the complete genome sequences of two Newcastle disease viruses, Sheldrake duck/China/Guizhou/01/2016 and Sheldrake duck/China/Guizhou/02/2016, isolated from Sansui Sheldrake ducks in Guizhou Province, China. The genome of the isolates is 15,198 nucleotides in length. Phylogenetic analysis revealed that the isolates are clustered into subgenotype 1b in class I.

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