scholarly journals Genome Sequences of Two Dual-Serotype-Specific Echovirus 20 Strains from Nigeria

2019 ◽  
Vol 8 (43) ◽  
Author(s):  
T. O. C. Faleye ◽  
O. M. Adewumi ◽  
D. Klapsa ◽  
M. Majumdar ◽  
J. Martin ◽  
...  
Keyword(s):  
Amino Acids ◽  
Complete Genome ◽  
Neutralization Assay ◽  
Open Reading Frames ◽  
Genome Sequences ◽  
Overlapping Open Reading Frames ◽  
Reading Frames

Here, we describe nearly complete genome sequences (7,361 nucleotides [nt] and 6,893 nt) of two echovirus 20 (E20) isolates from Nigeria that were simultaneously typed as CVB and E20 (dual serotype) by neutralization assay. Both include two overlapping open reading frames (ORFs) of 67 and 2,183 amino acids that encoded a recently described gut infection-facilitating protein and the classic enterovirus proteins, respectively.

scholarly journals Genome Sequences of Ambystoma Tigrinum Virus Recovered during a Mass Die-off of Western Tiger Salamanders in Alberta, Canada

2019 ◽  
Vol 8 (29) ◽  
Author(s):  
Oliver Lung ◽  
Michelle Nebroski ◽  
Shivani Gupta ◽  
Cameron Goater
Keyword(s):  
Amino Acids ◽  
High Mortality ◽  
Complete Genome ◽  
Open Reading Frames ◽  
Ambystoma Tigrinum ◽  
Genome Sequences ◽  
Ambystoma Tigrinum Virus ◽  
Content Type ◽  
Tiger Salamanders ◽  
Reading Frames

Complete genome sequences of six Ambystoma tigrinum viruses (ATV) were determined directly from tail clips of western tiger salamanders (Ambystoma mavortium) from 2013 (high-mortality year) and 2014 (low-mortality year) in Alberta, Canada. The genome lengths ranged from 106,258 to 106,915 bp and contained 108 open reading frames encoding predicted proteins larger than 50 amino acids.

scholarly journals Complete Genome Sequences of Pseudomonas aeruginosa Phages vB_PaeP_PcyII-10_P3P1 and vB_PaeM_PcyII-10_PII10A

2016 ◽  
Vol 4 (6) ◽  
Author(s):  
Christine Pourcel ◽  
Cédric Midoux ◽  
Libera Latino ◽  
Marie-Agnès Petit ◽  
Gilles Vergnaud
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Complete Genome ◽  
Open Reading Frames ◽  
Genome Sequences ◽  
Reading Frames

vB_PaeP_PcyII-10_P3P1 and vB_PaeM_PcyII-10_PII10A are Pseudomonas aeruginosa bacteriophages belonging, respectively, to the Lit1virus genus of the Podoviridae family and the Pbunavirus genus of the Myoviridae family. Their genomes are 72,778 bp and 65,712 bp long, containing 94 and 93 predicted open reading frames, respectively.

scholarly journals Complete Genome Sequence of a Novel Satellite Virus Associated with Cassava Plants

2017 ◽  
Vol 5 (16) ◽  
Author(s):  
Adriana N. Souza ◽  
Fábio N. Silva ◽  
Claudine M. Carvalho
Keyword(s):  
Amino Acids ◽  
Coat Protein ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Open Reading Frames ◽  
Putative Protein ◽  
Satellite Virus ◽  
Cassava Plant ◽  
Reading Frames

ABSTRACT A novel satellite virus of 1,228 bp in length was found in a single cassava plant. Bioinformatic analyses show that it has two open reading frames (ORFs) in its genome, probably encoding a coat protein of 156 and a putative protein of 90 amino acids.

scholarly journals Coding-Complete Genome Sequences of an Iteradensovirus and an Alphapermutotetra-Like Virus Identified from the Pine Processionary Moth (Thaumetopoea pityocampa) in Portugal

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Franck Dorkeld ◽  
Réjane Streiff ◽  
Carole Kerdelhué ◽  
Mylène Ogliastro
Keyword(s):  
Complete Genome ◽  
Open Reading Frames ◽  
Thaumetopoea Pityocampa ◽  
Data Sets ◽  
Genome Sequences ◽  
Virus Family ◽  
Content Type ◽  
Pine Processionary Moth ◽  
Transcriptomic Data ◽  
Reading Frames

ABSTRACT The coding-complete genome sequences of an iteradensovirus (family Parvoviridae) and an alphapermutotetra-like virus (family Permutotetraviridae) were discovered from transcriptomic data sets obtained from Thaumetopoea pityocampa larvae collected in Portugal. Each of the coding-complete genome sequences of these viruses contains three main open reading frames (ORFs).

scholarly journals Complete Genome Sequence of a Bovine Ephemeral Fever Virus Isolate from Israel

2019 ◽  
Vol 8 (41) ◽  
Author(s):  
Daniel L. W. Dorey-Robinson ◽  
Mar Fernández de Marco ◽  
Luis M. Hernández-Triana ◽  
Arran J. Folly ◽  
Lorraine M. McElhinney ◽  
...  
Keyword(s):  
Complete Genome Sequence ◽  
Complete Genome ◽  
Virus Isolate ◽  
Genomic Sequence ◽  
Fever Virus ◽  
Open Reading Frames ◽  
Genome Sequences ◽  
Bovine Ephemeral Fever Virus ◽  
Bovine Ephemeral Fever ◽  
Reading Frames

Here, we report the first complete genome of a bovine ephemeral fever virus (BEFV) isolate from an infected bovine in Israel. The genome shares 95.3% identity with a Turkish genomic sequence but contains α3 and γ open reading frames that are truncated compared to those of existing BEFV genome sequences.

scholarly journals Complete Genome Sequences of Porcine Parvovirus 2 Isolated from Swine in the Republic of Korea

2017 ◽  
Vol 5 (15) ◽  
Author(s):  
Ju-Yeon Lee ◽  
Eun-ju Kim ◽  
In-soo Cho ◽  
Kyoung-Ki Lee ◽  
Yeun-Kyung Shin
Keyword(s):  
Complete Genome ◽  
Open Reading Frames ◽  
Republic Of Korea ◽  
Porcine Parvovirus ◽  
Genome Sequences ◽  
South Korean ◽  
The Republic ◽  
Reading Frames

ABSTRACT Here, we report sequences of the porcine parvovirus 2 (PPV2) genome, isolated from pigs in the Republic of Korea in 2016. The sequences of open reading frames 1 and 2 (ORF1 and ORF2) had a 98.8 to 98.9% homology with the US135 strain and 98.8% homology with the US523 strain, respectively. This is the first study to report the PPV2 genome in South Korean pigs.

scholarly journals Genome-Wide Covariation in SARS-CoV-2

2021 ◽  
Author(s):  
Evan Cresswell-Clay ◽  
Vipul Periwal
Keyword(s):  
Complete Genome ◽  
Open Reading Frames ◽  
Whole Genome ◽  
Genome Sequences ◽  
Direct Information ◽  
Global Pandemic ◽  
Genome Wide ◽  
A Genome ◽  
Encoded Proteins ◽  
Reading Frames

AbstractThe SARS-CoV-2 virus causing the global pandemic is a coronavirus with a genome of about 30Kbase length [Song et al., 2019]. The design of vaccines and choice of therapies depends on the structure and mutational stability of encoded proteins in the open reading frames(ORFs) of this genome. In this study, we computed, using Expectation Reflection, the genome-wide covariation of the SARS-CoV-2 genome based on an alignment of ≈ 130000 SARS-CoV-2 complete genome sequences obtained from GISAID[Shu & McCauley, 2017]. We used this covariation to compute the Direct Information between pairs of positions across the whole genome, investigating potentially important relationships within the genome, both within each encoded protein and between encoded proteins. We then computed the covariation within each clade of the virus. The covariation detected recapitulates all clade determinants and each clade exhibits distinct covarying pairs.

scholarly journals Complete Genome Sequences of 10 Lactococcal Skunavirus Phages Isolated from Cheddar Cheese Whey Samples in Canada

2021 ◽  
Vol 10 (15) ◽  
Author(s):  
Laurie Doré ◽  
Gabrielle Pageau ◽  
Françoise Bourque-Leblanc ◽  
Marie-Ève Dupuis ◽  
Roxanne Lessard-Hurtubise ◽  
...  
Keyword(s):  
Complete Genome ◽  
Cheese Whey ◽  
Cheddar Cheese ◽  
Open Reading Frames ◽  
Genome Sequences ◽  
Content Type ◽  
Linear Genomes ◽  
Reading Frames ◽  
Cheese Production ◽  
Gc Contents

ABSTRACT We report the complete genome sequences of 10 virulent phages of the Skunavirus genus (Siphoviridae) that infect Lactococcus lactis strains used for cheddar cheese production in Canada. Their linear genomes range from 28,969 bp to 31,042 bp with GC contents of 34.1 to 35.1% and 55 to 60 predicted open reading frames (ORFs).

scholarly journals Hepatitis C virus complete genome sequences identified from China representing subtypes 6k and 6n and a novel, as yet unassigned subtype within genotype 6

2006 ◽  
Vol 87 (3) ◽  
pp. 629-634 ◽  
Author(s):  
Ling Lu ◽  
Tatsunori Nakano ◽  
Chunhua Li ◽  
Yongshui Fu ◽  
Steve Miller ◽  
...  
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Complete Genome ◽  
Phylogenetic Analyses ◽  
Open Reading Frames ◽  
Untranslated Regions ◽  
Genome Sequences ◽  
Entire Genome ◽  
Reading Frames ◽  
Distinct Subtype

Here, the complete genome sequences for three hepatitis C virus (HCV) variants identified from China and belonging to genotype 6 are reported: km41, km42 and gz52557. Their entire genome lengths were 9430, 9441 and 9448 nt, respectively; the 5′ untranslated regions (UTRs) contained 341, 342 and 339 nt, followed by single open reading frames of 9045, 9045 and 9057 nt, respectively; the 3′ UTRs, up to the poly(U) tracts, were 41, 51 and 52 nt, respectively. Phylogenetic analyses showed that km41 is classified into subtype 6k and km42 into subtype 6n. Although gz52557 clustered distantly with subtype 6g, it appeared to belong to a distinct subtype. Analysis with 53 and 105 partial core and NS5B region sequences, respectively, representing 17 subtypes from 6a to 6q and three unassigned isolates of genotype 6 in co-analyses demonstrated that gz52557 was equidistant from all of these isolates, indicating that it belongs to a novel subtype. However, based on a recent consensus that three or more examples are required for a new HCV subtype designation, it is suggested that gz52557 remains unassigned to any subtype.

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