scholarly journals Genomic characterization of the unclassified bovine enteric virus Newbury agent-1 (Newbury1) endorses a new genus in the family Caliciviridae

Virology ◽  
2006 ◽  
Vol 350 (1) ◽  
pp. 240-250 ◽  
Author(s):  
S.L. Oliver ◽  
E. Asobayire ◽  
A.M. Dastjerdi ◽  
J.C. Bridger
Keyword(s):  
New Genus ◽  
Enteric Virus ◽  
The Family ◽  
Genomic Characterization

scholarly journals Genomic characterization of three novel Pseudomonas phages within the subfamily of Autographivirinae isolated from organic waste

2020 ◽  
Author(s):  
Jacob B Jørgensen ◽  
Amaru M Djuurhus ◽  
Alexander B. Carstens ◽  
Witold Kot ◽  
Cindy E. Morris ◽  
...  
Keyword(s):  
Pseudomonas Syringae ◽  
Organic Waste ◽  
New Genus ◽  
Open Reading Frames ◽  
Genomic Comparison ◽  
Double Stranded Dna ◽  
The Family ◽  
Genomic Characterization ◽  
Reading Frames

AbstractThree phages targeting Pseudomonas syringae GAW0113 have been isolated from organic waste samples: Pseudomonas phage Bertil, Misse and Strit. The phages have double-stranded DNA genomes ranging from 41342 to 41374 bp in size comprising 50 to 51 open reading frames. The three phages genomes are highly similar and genomic comparison analyses shows that they all belong to the Autographivirinae subfamily of the family Podoviridae. The phages are however only distantly related to other members of this family, and have limited gene synteny with type-phages of other genera within Autographivirinae, suggesting that the newly isolated phages could represent a new genus.

scholarly journals Characterization of a new picornavirus isolated from the freshwater fish Lepomis macrochirus

2014 ◽  
Vol 95 (3) ◽  
pp. 601-613 ◽  
Author(s):  
Marisa Barbknecht ◽  
Sol Sepsenwol ◽  
Eric Leis ◽  
Maren Tuttle-Lau ◽  
Mark Gaikowski ◽  
...  
Keyword(s):  
Freshwater Fish ◽  
New Genus ◽  
Lepomis Macrochirus ◽  
Leader Peptide ◽  
Fish Kill ◽  
Sequence Identity ◽  
Phylogenetic Cluster ◽  
The Family ◽  
Sport Fish

The freshwater fish Lepomis macrochirus (bluegill) is common to North American waters, and important both ecologically and as a sport fish. In 2001 an unknown virus was isolated from bluegills following a bluegill fish kill. This virus was identified as a picornavirus [termed bluegill picornavirus (BGPV)] and a diagnostic reverse transcriptase PCR was developed. A survey of bluegills in Wisconsin waters showed the presence of BGPV in 5 of 17 waters sampled, suggesting the virus is widespread in bluegill populations. Experimental infections of bluegills confirmed that BGPV can cause morbidity and mortality in bluegills. Molecular characterization of BGPV revealed several distinct genome characteristics, the most unusual of which is the presence of a short poly(C) tract in the 3′ UTR. Additionally, the genome encodes a polyprotein lacking a leader peptide and a VP0 maturation cleavage site, and is predicted to encode two distinct 2A proteins. Sequence comparison showed that the virus is most closely related to a phylogenetic cluster of picornaviruses that includes the genera Aquamavirus, Avihepatovirus and Parechovirus. However, it is distinct enough, for example sharing only about 38 % sequence identity to the parechoviruses in the 3D region, that it may represent a new genus in the family Picornaviridae.

scholarly journals Rediscovery and genomic characterization of bovine astroviruses

2011 ◽  
Vol 92 (8) ◽  
pp. 1888-1898 ◽  
Author(s):  
Herman Tse ◽  
Wan-Mui Chan ◽  
Hoi-Wah Tsoi ◽  
Rachel Y. Y. Fan ◽  
Candy C. Y. Lau ◽  
...  
Keyword(s):  
Roe Deer ◽  
Mammalian Species ◽  
Capreolus Capreolus ◽  
Genetic Distances ◽  
Genome Sequences ◽  
Sea Lions ◽  
The Family ◽  
Genomic Characterization ◽  
Similar Organization

The genus Mamastrovirus belongs to the family Astroviridae and consists of at least six members infecting different mammalian hosts, including humans, cattle and pigs. In recent years, novel astroviruses have been identified in other mammalian species like roe deer, bats and sea lions. While the bovine astrovirus was one of the earliest astroviruses to have been studied, no further research has been performed recently and its genome sequence remains uncharacterized. In this report, we describe the detection and genomic characterization of astroviruses in bovine faecal specimens obtained in Hong Kong. Five of 209 specimens were found to be positive for astrovirus by RT-PCR. Two of the positive specimens were found to contain sequences from two different astrovirus strains. Complete genome sequences of approximately 6.3 kb in length were obtained for four strains, which showed similar organization of the genome compared to other astroviruses. Phylogenetic analysis confirmed their identities as members of the genus Mamastrovirus, and showed them to be most closely related to the Capreolus capreolus astrovirus. Based on the pairwise genetic distances among their full-length ORF2 sequences, these bovine astroviruses may be assigned into at least three different genotype species. Sequence analysis revealed evidence of potential recombination in ORF2. In summary, we report the first genome sequences of bovine astroviruses and clearly establish the species status of the virus. Additionally, our study is among the first to report co-infection by different astrovirus genotypes in the same host, which is an essential step for recombination to occur.

Genomic characterization of Ralstonia solanacearum phage ϕRS138 of the family Siphoviridae

2015 ◽  
Vol 161 (2) ◽  
pp. 483-486 ◽  
Author(s):  
Bich Van Truong Thi ◽  
Nguyen Huan Pham Khanh ◽  
Ryuta Namikawa ◽  
Kaito Miki ◽  
Akihiro Kondo ◽  
...  
Keyword(s):  
Ralstonia Solanacearum ◽  
The Family ◽  
Genomic Characterization

scholarly journals Characterization of a novel circo-like virus in Aedes vexans mosquitoes from Germany: evidence for a new genus within the family Circoviridae

2015 ◽  
Vol 96 (4) ◽  
pp. 915-920 ◽  
Author(s):  
Mutien-Marie Garigliany ◽  
Jessica Börstler ◽  
Hanna Jöst ◽  
Marlis Badusche ◽  
Daniel Desmecht ◽  
...  
Keyword(s):  
New Genus ◽  
Aedes Vexans ◽  
The Family

scholarly journals Characterization of a novel member of the family Caulimoviridae infecting Dioscorea nummularia in the Pacific, which may represent a new genus of dsDNA plant viruses

PLoS ONE ◽  
2018 ◽  
Vol 13 (9) ◽  
pp. e0203038 ◽  
Author(s):  
Amit C. Sukal ◽  
Dawit B. Kidanemariam ◽  
James L. Dale ◽  
Robert M. Harding ◽  
Anthony P. James
Keyword(s):  
New Genus ◽  
Plant Viruses ◽  
The Pacific ◽  
The Family

scholarly journals Co-cultivation of microbial sub-communities in microfluidic droplets facilitates high-resolution genomic dissection of microbial ‘dark matter’

2020 ◽  
Vol 12 (11) ◽  
pp. 263-274
Author(s):  
James Y Tan ◽  
Sida Wang ◽  
Gregory J Dick ◽  
Vincent B Young ◽  
David H Sherman ◽  
...  
Keyword(s):  
Dark Matter ◽  
Microbial Communities ◽  
Ecological Interactions ◽  
Healthy Human ◽  
Encapsulated Cells ◽  
Microfluidic Droplets ◽  
The Family ◽  
Culture Independent ◽  
Genomic Characterization

Abstract While the ‘unculturable’ majority of the bacterial world is accessible with culture-independent tools, the inability to study these bacteria using culture-dependent approaches has severely limited our understanding of their ecological roles and interactions. To circumvent cultivation barriers, we utilize microfluidic droplets as localized, nanoliter-size bioreactors to co-cultivate subsets of microbial communities. This co-localization can support ecological interactions between a reduced number of encapsulated cells. We demonstrated the utility of this approach in the encapsulation and co-cultivation of droplet sub-communities from a fecal sample collected from a healthy human subject. With the whole genome amplification and metagenomic shotgun sequencing of co-cultivated sub-communities from 22 droplets, we observed that this approach provides accessibility to uncharacterized gut commensals for study. The recovery of metagenome-assembled genomes from one droplet sub-community demonstrated the capability to dissect the sub-communities with high-genomic resolution. In particular, genomic characterization of one novel member of the family Neisseriaceae revealed implications regarding its participation in fatty acid degradation and production of atherogenic intermediates in the human gut. The demonstrated genomic resolution and accessibility to the microbial ‘dark matter’ with this methodology can be applied to study the interactions of rare or previously uncultivated members of microbial communities.

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