Analysis of the complete genome sequence of black queen cell virus JL1 from infected honeybees in China

2016 ◽  
Vol 106 (5) ◽  
pp. 561-568 ◽  
Author(s):  
Q. Yang ◽  
Z.-Y. Song ◽  
X. Feng ◽  
J. Zhang ◽  
Y. Zheng ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Genetic Relationships ◽  
Black Queen Cell Virus ◽  
Chain Reaction ◽  
Reading Frame ◽  
Queen Cell ◽  
Polymerase Chain ◽  
Complete Genomic

AbstractThere are six strains of the complete genomic sequences of black queen cell virus (BQCV) published in the GenBank, including South Africa (AF183905), South Korea (JX149531), Hungary 10 (EF517515), Poland 4 (EF517519), Poland 5 (EF517520) and Poland 6 (EF517521). Based on the six BQCV strains published in the GenBank, ten pairs of primers were designed in the present study using reverse transcription polymerase chain reaction to obtain the first complete genome sequence of a BQCV strain in China, called the BQCV China-JL1 strain (KP119603). A phylogenetic tree was then built to analyse their genetic relationships. The BQCV China-JL1 strain showed 86–93% similarity with the six strains published in the GenBank. The BQCV China-JL1 strain consisted of 8358 nucleotides (nt). The 5′-proximal open reading frame (ORF1) initiated at nt position 546 and terminated at nt position 4676, ORF3 initiated at nt position 4891 and terminated at nt position 5433, and the 3′-proximal ORF (ORF2) was located between nt positions 5750 and 8203.

scholarly journals Coding-Complete Genome Sequence of a Black Queen Cell Virus Isolate from Honey Bees (Apis mellifera) in Italy

2020 ◽  
Vol 9 (28) ◽  
Author(s):  
Raied Abou Kubaa ◽  
Annalisa Giampetruzzi ◽  
Rocco Addante ◽  
Maria Saponari
Keyword(s):  
Apis Mellifera ◽  
Genome Sequence ◽  
Honey Bees ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Virus Isolate ◽  
High Similarity ◽  
Black Queen Cell Virus ◽  
Queen Cell ◽  
Genome Phylogeny

ABSTRACT In this study, we documented the complete coding genome sequence of a Black queen cell virus (BQCV) isolate from honey bees in Italy. This genome sequence illustrates a high similarity with other BQCV isolates reported worldwide and could provide insights into BQCV genome phylogeny and divergence.

scholarly journals Complete Genome Sequence of Potato Virus T from Bolivia, Obtained from a 33-Year-Old Sample

2018 ◽  
Vol 7 (18) ◽  
Author(s):  
Ian P. Adams ◽  
Jorge Abad ◽  
Cesar E. Fribourg ◽  
Neil Boonham ◽  
Roger A. C. Jones
Keyword(s):  
Genome Sequence ◽  
Potato Virus ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Genomic Sequence ◽  
Complete Genomic Sequence ◽  
Potato Sample ◽  
Type Isolate ◽  
Andean Potato ◽  
Complete Genomic

We present the complete genomic sequence of a Potato virus T (PVT) isolate originally obtained from a Bolivian potato sample collected in 1976, and we compare it with the genome of the PVT type isolate from Peru. There is an 81% nucleotide identity between the two genomes of this Andean potato virus.

scholarly journals Complete Genome Sequence of a Novel Human Gammapapillomavirus Isolated from Skin

2017 ◽  
Vol 5 (34) ◽  
Author(s):  
Rosario N. Brancaccio ◽  
Alexis Robitaille ◽  
Sankhadeep Dutta ◽  
Dana E. Rollison ◽  
Nicole Fischer ◽  
...  
Keyword(s):  
Human Papillomavirus ◽  
Next Generation Sequencing ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Open Reading Frame ◽  
Next Generation ◽  
Degenerate Pcr ◽  
Reading Frame ◽  
Generation Sequencing

ABSTRACT A novel human papillomavirus (HPV ICB1) was fully characterized from a skin swab by using a sensitive degenerate PCR protocol combined with next-generation sequencing. The L1 open reading frame of HPV ICB1 shares 70.54% nucleotide homology with its closest relative, HPV164, and thus constitutes a novel human gammapapillomavirus.

scholarly journals Complete Genome Sequence of Human Coronavirus NL63 CN0601/14, First Isolated in South Korea

2018 ◽  
Vol 6 (12) ◽  
Author(s):  
Jeong-Min Kim ◽  
Seung-Tae Kim ◽  
Jeong-Sun Yang ◽  
Sung Soon Kim ◽  
Hyang-Min Cheong
Keyword(s):  
South Korea ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Open Reading Frame ◽  
Genome Sequences ◽  
Human Coronavirus ◽  
Reading Frame

ABSTRACT We report here the complete genome sequence of the human coronavirus NL63 CN0601/14 strain, first isolated from South Korea. It contains 18-nucleotide discontinuous deletions of the open reading frame 1a (ORF1a) and spike regions. This study will aid in our understanding of the complete genome sequences of isolated coronaviruses in South Korea.

scholarly journals Complete Genome Sequence of a Novel Human Betapapillomavirus Isolated from a Skin Sample

2017 ◽  
Vol 5 (13) ◽  
Author(s):  
Sankhadeep Dutta ◽  
Alexis Robitaille ◽  
Dana E. Rollison ◽  
Massimo Tommasino ◽  
Tarik Gheit
Keyword(s):  
Human Papillomavirus ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Genetic Characterization ◽  
Open Reading Frame ◽  
Skin Sample ◽  
Reading Frame ◽  
Beta 2

ABSTRACT We report the genetic characterization of a new papillomavirus (HPV_MTS1) isolated and fully cloned from a skin swab. The L1 open reading frame of HPV_MTS1 was 85% identical to its closest human papillomavirus (HPV) type 80, which belongs to the species beta-2 of the genus Betapapillomavirus, hence qualifying it as a new HPV type.

scholarly journals First Complete Genome Sequence of Suakwa aphid-borne yellows virus from East Timor

2016 ◽  
Vol 4 (4) ◽  
Author(s):  
Solomon Maina ◽  
Owain R. Edwards ◽  
Luis de Almeida ◽  
Abel Ximenes ◽  
Roger A. C. Jones
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
East Timor ◽  
Nucleotide Identity ◽  
Genomic Rna ◽  
Rna Sequence ◽  
Complete Genomic

We present here the first complete genomic RNA sequence of the polerovirus Suakwa aphid-borne yellows virus (SABYV), from East Timor. The isolate sequenced came from a virus-infected pumpkin plant. The East Timorese genome had a nucleotide identity of 86.5% with the only other SABYV genome available, which is from Taiwan.

scholarly journals Complete Genomic Sequence of Dengue Virus Serotype 4 Isolated from Plasma Collected from a Haitian Child in 2014

2017 ◽  
Vol 5 (40) ◽  
Author(s):  
Maha A. Elbadry ◽  
Sarah K. White ◽  
Julia C. Loeb ◽  
Massimiliano S. Tagliamonte ◽  
Marco Salemi ◽  
...  
Keyword(s):  
South America ◽  
Dengue Virus ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Genomic Sequence ◽  
Complete Genomic Sequence ◽  
Virus Serotype ◽  
Genotype Ii ◽  
Complete Genomic

ABSTRACT While data are limited, there is increasing evidence that infections by dengue viruses are endemic in Haiti. In 2014, an outbreak caused by dengue virus 4 (DENV-4) followed a chikungunya fever outbreak. We present here the complete genome sequence of one isolate grouped within the genotype II South America and Caribbean DENV-4 clades.

scholarly journals Complete Genome Sequence of Heat-Resistant Newcastle Disease Virus Strain HR09

2017 ◽  
Vol 5 (44) ◽  
Author(s):  
Yongzhong Cao ◽  
Qian Liu ◽  
Xiaorong Zhang ◽  
Hai Hu ◽  
Yantao Wu
Keyword(s):  
Newcastle Disease Virus ◽  
Disease Virus ◽  
Genome Sequence ◽  
Virus Strain ◽  
Newcastle Disease ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Genomic Information ◽  
Heat Resistant ◽  
Complete Genomic

ABSTRACT In this study, the complete genome sequence of the heat-resistant Newcastle disease virus (NDV) strain HR09, which was isolated in China in the 1990s, was determined and characterized phylogenetically. This is the first report regarding the complete genomic information of a thermostable NDV strain from China.

scholarly journals Complete genome sequence analysis of a novel bunyavirus isolated from Paris polyphylla var. yunnanensis

2021 ◽  
Author(s):  
Zeli Chen ◽  
Rex Frimpong Anane ◽  
Zhe Wang ◽  
Like Gao ◽  
Lu Chen ◽  
...  
Keyword(s):  
Amino Acid ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Rna Virus ◽  
Amino Acid Sequences ◽  
Reading Frame ◽  
Leaf Chlorosis ◽  
Paris Polyphylla ◽  
Complete Genome Sequence Analysis

Abstract A novel negative-stranded (ns) RNA virus tentatively named “Yunnan manyleaf paris rhizome negative-stranded virus 1” (YMPrNSV1), was isolated from a Paris polyphylla var. yunnanensis plant exhibiting leaf chlorosis and mosaic symptoms in Yunnan. Its complete genome sequence was determined using Illumina and Sanger sequencing. The genomes composed of three RNA segments (L, M and S) with each one containing a single open reading frame. Based on sequence identity and the presence of typical bunya-like domains/motifs, the proteins encoded by YMPrNSV1 were predicted to be: RNA-dependent RNA polymerase (RdRp), putative movement protein (MP), and nucleocapsid protein (NP). Sequence comparison analyses showed that the RdRp, MP and NP of YMPrNSV1 are highly similar to those of watermelon crinkle leaf-associated virus 2 (WCLaV-2), with 69.1%, 50.4% and 60.9% amino acid sequence identities respectively. Phylogenetic analysis based on deduced amino acid sequences of RdRp and NP suggested that YMPrNSV1 clustered with coguviruses in a clade, and that WCLaV-2 is the known closely related species to YMPrNSV1. Base on the above results, YMPrNSV1 should be regarded as a new member of genera Coguvirus, within the family Phenuiviridae.

scholarly journals Complete genome sequence of a novel mitovirus isolated from Paris polyphylla var. yunnanensis

2021 ◽  
Author(s):  
Zeli Chen ◽  
Lu Chen ◽  
Rex Frimpong Anane ◽  
Zhe Wang ◽  
Like Gao ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Rna Virus ◽  
Genome Structure ◽  
Complementary Sequence ◽  
Reading Frame ◽  
A Genome ◽  
Paris Polyphylla ◽  
The Family

Abstract Paris mitovirus 1 (ParMV1) is a positive-sense RNA virus isolated from diseased Paris polyphylla var. yunnanensis plants in Wenshan, Yunnan. The complete genome sequence of ParMV1 consists of 2,751 nucleotides with a genome structure typical of the mitoviruses. ParMV1 genome has a single open reading frame (ORF: 358-2,637 nt) that encodes RNA-dependent RNA polymerase (RdRp) with a molecular mass of 86.42 kDa. ParMV1 contains six conserved motifs (Ι-VΙ) that are unique to mitoviruses. In addition, the 5′and 3′ terminals of the genome have a stable secondary structure, and the reverse complementary sequence forms a panhandle structure. Comparative genome analysis revealed that ParMV1 shares 23.1–40.6% amino acid (aa) and 32.3–45.7% nucleotide (nt) sequence identities with the RdRp of other mitoviruses. The phylogenetic tree inferred from RdRp aa sequence showed that ParMV1 clusters with mitoviruses, and hence should be considered as a new member of the genus Mitovirus in the family Motiviridae. This is the first report of a novel mitovirus infecting Paris polyphylla var. yunnanensis.

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