Viral tagging reveals discrete populations in Synechococcus viral genome sequence space

Nature ◽  
2014 ◽  
Vol 513 (7517) ◽  
pp. 242-245 ◽  
Author(s):  
Li Deng ◽  
J. Cesar Ignacio-Espinoza ◽  
Ann C. Gregory ◽  
Bonnie T. Poulos ◽  
Joshua S. Weitz ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Sequence Space ◽  
Viral Genome ◽  
Viral Genome Sequence ◽  
Discrete Populations

scholarly journals Rapid selection of P323L in the SARS-CoV-2 polymerase (NSP12) in humans and non-human primate models and confers a large plaque phenotype

2021 ◽  
Author(s):  
Xiaofeng Dong ◽  
Hannah Goldswain ◽  
Rebekah Penrice-Randal ◽  
Ghada Shawli ◽  
Tessa Prince ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Viral Genome ◽  
Recombinant Virus ◽  
Primate Model ◽  
Large Plaque ◽  
Viral Genome Sequence ◽  
New Variant ◽  
Minor Variant ◽  
Rapid Emergence ◽  
Human Primate

The mutational landscape of SARS-CoV-2 varies at both the dominant viral genome sequence and minor genomic variant population. An early change associated with transmissibility was the D614G substitution in the spike protein. This appeared to be accompanied by a P323L substitution in the viral polymerase (NSP12), but this latter change was not under strong selective pressure. Investigation of P323L/D614G changes in the human population showed rapid emergence during the containment phase and early surge phase of wave 1 in the UK. This rapid substitution was from minor genomic variants to become part of the dominant viral genome sequence. A rapid emergence of 323L but not 614G was observed in a non-human primate model of COVID-19 using a starting virus with P323 and D614 in the dominant genome sequence and 323L and 614G in the minor variant population. In cell culture, a recombinant virus with 323L in NSP12 had a larger plaque size than the same recombinant virus with P323. These data suggest that it may be possible to predict the emergence of a new variant based on tracking the distribution and frequency of minor variant genomes at a population level, rather than just focusing on providing information on the dominant viral genome sequence e.g., consensus level reporting. The ability to predict an emerging variant of SARS-CoV-2 in the global landscape may aid in the evaluation of medical countermeasures and non-pharmaceutical interventions.

scholarly journals Complete viral genome sequence and discovery of novel viruses by deep sequencing of small RNAs: A generic method for diagnosis, discovery and sequencing of viruses

Virology ◽  
2009 ◽  
Vol 388 (1) ◽  
pp. 1-7 ◽  
Author(s):  
Jan F. Kreuze ◽  
Ana Perez ◽  
Milton Untiveros ◽  
Dora Quispe ◽  
Segundo Fuentes ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Deep Sequencing ◽  
Small Rnas ◽  
Viral Genome ◽  
Viral Genome Sequence ◽  
Complete Viral Genome

scholarly journals Two Complete Genome Sequences of Phasey Bean Mild Yellows Virus, a Novel Member of the Luteoviridae from Australia

2016 ◽  
Vol 4 (1) ◽  
Author(s):  
Murray Sharman ◽  
Monica Kehoe ◽  
Brenda Coutts ◽  
Joop van Leur ◽  
Fiona Filardo ◽  
...  
Keyword(s):  
Cicer Arietinum ◽  
Genome Sequence ◽  
Viral Genome ◽  
Complete Genome ◽  
Subterranean Clover ◽  
Trifolium Subterraneum ◽  
Genome Sequences ◽  
Viral Genome Sequence ◽  
Macroptilium Lathyroides

We present here the complete genome sequences of a novel polerovirus from Trifolium subterraneum (subterranean clover) and Cicer arietinum (chickpea) and compare these to a partial viral genome sequence obtained from Macroptilium lathyroides (phasey bean). We propose the name phasey bean mild yellows virus for this novel polerovirus.

scholarly journals Transmission dynamics of SARS-CoV-2 on the Diamond Princess uncovered using viral genome sequence analysis

Gene ◽  
2021 ◽  
Vol 779 ◽  
pp. 145496
Author(s):  
Kunikazu Hoshino ◽  
Tatsuji Maeshiro ◽  
Nao Nishida ◽  
Masaya Sugiyama ◽  
Jiro Fujita ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Genome Sequence ◽  
Viral Genome ◽  
Transmission Dynamics ◽  
Genome Sequence Analysis ◽  
Viral Genome Sequence

Evolution of hepatitis B viral load and viral genome sequence during adefovir dipivoxil therapy

2004 ◽  
Vol 11 (1) ◽  
pp. 74-83 ◽  
Author(s):  
B. Werle ◽  
K. Cinquin ◽  
P. Marcellin ◽  
S. Pol ◽  
M. Maynard ◽  
...  
Keyword(s):  
Viral Load ◽  
Hepatitis B ◽  
Genome Sequence ◽  
Viral Genome ◽  
Adefovir Dipivoxil ◽  
Viral Genome Sequence

scholarly journals Complete Genome Sequence of Bovine Adenovirus Type 7 Strain Fukuroi, Isolated from a Cow with Respiratory Disease

2021 ◽  
Vol 10 (10) ◽  
Author(s):  
Asuka Kumagai ◽  
Sayo Kajikawa ◽  
Ayako Miyazaki ◽  
Shinichi Hatama
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Viral Genome ◽  
Complete Genome ◽  
Adenovirus Type ◽  
Prototype Strain ◽  
Sequencing Technology ◽  
Bovine Adenovirus ◽  
Next Generation Sequencing Technology ◽  
Generation Sequencing

ABSTRACT We determined the complete genome sequence of the bovine adenovirus type 7 prototype strain Fukuroi using next-generation sequencing technology. We found that the viral genome is 30,034 bp long and has the shortest inverted terminal repeats among known adenoviruses.

scholarly journals Near-Complete Genome Sequence of a Fish Nervous Necrosis Virus Isolated from a Clinical Disease Outbreak in Farm-Reared Bream Sparus aurata in Spain

2018 ◽  
Vol 6 (1) ◽  
Author(s):  
Panagiota Stathopoulou ◽  
Nausika Rafailidou ◽  
Kostas Tzokas ◽  
Costas Batargias ◽  
George Tsiamis
Keyword(s):  
Phylogenetic Tree ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Viral Genome ◽  
Complete Genome ◽  
Sparus Aurata ◽  
Disease Outbreak ◽  
Nervous Necrosis Virus ◽  
Necrosis Virus ◽  
Viral Nervous Necrosis

ABSTRACT Sparus aurata larvae infected by viral nervous necrosis were collected from an aquaculture fish farm. The isolated viral genome, composed of two segments (RNA1 and RNA2), was sequenced and analyzed comparatively. Phylogenetic tree analyses revealed that the isolated strain is a reassortant, exhibiting a red-spotted grouper nervous necrosis virus (RGNNV)-type RNA1 and a striped jack nervous necrosis virus (SJNNV)-type RNA2.

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