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.

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 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 Full-length sequences of 11 hepatitis C virus genotype 2 isolates representing five subtypes and six unclassified lineages with unique geographical distributions and genetic variation patterns

2012 ◽  
Vol 93 (6) ◽  
pp. 1173-1184 ◽  
Author(s):  
Chunhua Li ◽  
Hong Cao ◽  
Ling Lu ◽  
Donald Murphy
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Complete Genome ◽  
Pcr Amplification ◽  
Full Length ◽  
African Origin ◽  
Genome Sequences ◽  
Virus Genotype ◽  
Variation Patterns ◽  
Genotype 2

In this study, we characterized full-length hepatitis C virus (HCV) genome sequences for 11 genotype 2 isolates. They were isolated from the sera of 11 patients residing in Canada, of whom four had an African origin. Full-length genomes, each with 18–25 overlapping fragments, were obtained by PCR amplification. Five isolates represent the first complete genomes of subtypes 2d, 2e, 2j, 2m and 2r, while the other six correspond to variants that do not group within any assigned subtypes. These sequences had lengths of 9508–9825 nt and each contained a single ORF encoding 3012–3106 aa. Predicted amino acids were carefully inspected and unique variation patterns were recognized, especially for a 2e isolate, QC64. Phylogenetic analysis of complete genome sequences provides evidence that there are a total of 16 subtypes, of which 11 have been described here. Co-analysis with 68 partial NS5B sequences also differentiated 18 assigned subtypes, 2a–2r, and eight additional lineages within genotype 2, which is consistent with the analysis of complete genome sequences. The data from this study will now allow 10 assigned subtypes and six additional lineages of HCV genotype 2 to have their full-length genomes defined. Further analysis with 2021 genotype 2 sequences available in the HCV database indicated that the geographical distribution of these subtypes is consistent with an African origin, with particular subtypes having spread to Asia and the Americas.

scholarly journals Complete genomes for hepatitis C virus subtypes 6f, 6i, 6j and 6m: viral genetic diversity among Thai blood donors and infected spouses

2007 ◽  
Vol 88 (5) ◽  
pp. 1505-1518 ◽  
Author(s):  
Ling Lu ◽  
Chunhua Li ◽  
Yongshui Fu ◽  
Lakkana Thaikruea ◽  
Satawat Thongswat ◽  
...  
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Complete Genome ◽  
Blood Donors ◽  
Pairwise Comparison ◽  
Genome Sequences ◽  
New Information ◽  
Hcv Transmission ◽  
Similar Range ◽  
Genomic Regions

In this study, the first complete genome sequences for hepatitis C virus (HCV) subtypes 6f, 6i, 6j and 6m, obtained from infected blood donors in Chiang Mai, Thailand, are reported. Pairwise genome-wide nucleotide similarities between some of these isolates were higher than the 75–80 % value used previously to define different HCV subtypes. To investigate further, the entire genomes of four prototype isolates, Th602 (6i), Th553 (6j), B4/92 (6m) and D86/93 (6n), were sequenced. Pairwise comparison of these sequences gave a similar range of nucleotide similarities, thereby providing new information for HCV subtype classification. In order to study the hypothesis of interspousal HCV transmission, four additional complete HCV genome sequences were obtained from two infected Thai blood donors and their spouses, C-0044 and C-0046 (6f), and C-0192 and C-0185 (6m). Pairwise comparison of the sequences revealed that C-0044 and C-0046 share a nucleotide similarity of 98.1 %, whilst C-0185 and C-0192 have a similarity of 97.8 %. Several other studies of partial HCV sequences of different genomic regions from HCV-infected couples have shown nucleotide similarities ranging from 96.3 to 100 %. The similarities of the complete genome sequences from the two couples in the current study are consistent with HCV transmission between spouses.

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 The Previously Unidentified, Divergent Badnavirus Species Cacao red vein-banding virus is Associated with Cacao Swollen Shoot Disease in Nigeria

Plant Disease ◽  
2019 ◽  
Vol 103 (6) ◽  
pp. 1302-1308 ◽  
Author(s):  
Nomatter Chingandu ◽  
Lelia Dongo ◽  
Osman A. Gutierrez ◽  
Judith K. Brown
Keyword(s):  
Phylogenetic Analyses ◽  
Pcr Amplification ◽  
West African ◽  
Open Reading Frames ◽  
Nucleotide Identity ◽  
Genome Sequences ◽  
Foliar Symptoms ◽  
Field Samples ◽  
Polymerase Chain ◽  
Reading Frames

Cacao swollen shoot disease (CSSD) of Theobroma cacao was reported in Nigeria in 1944; however, no badnaviral genome sequences have been found associated with the symptomatic trees. In 2017, leaf samples (n = 18) were collected from cacao trees from Osun and Oyo, Nigeria showing foliar symptoms that included red vein-banding and shoot swelling, and variable secondary mosaic, mottling, and fern-like pattern symptoms. Abutting primers designed around previously determined 500-bp intergenic region sequences were used for polymerase chain reaction (PCR) amplification. Of the 18 samples, 9 yielded an approximately 7,000-bp, apparently genome-size product. The nine genomes were sequenced and found to encode four open reading frames, and to share 86 to 99% nucleotide identity. Pairwise analysis of the Nigerian genomes with 21 previously reported CSSD badnaviruses, at the complete genome and reverse-transcription ribonuclease H (1,230 bp) sequence levels, indicated 71 to 75 and 72 to 76% nucleotide identity, respectively. Phylogenetic analysis of the nine complete genomes indicated that the closest relatives of the divergent Nigerian isolates were previously described West African CSSD badnaviruses. Based on pairwise comparisons and phylogenetic analyses, the Nigerian CSSD isolates constitute a previously unrecognized Badnavirus sp., herein named Cacao red vein-banding virus (CRVBV). Primers designed based on the CRVBV genome sequences amplified a 1,068-bp fragment from 16 of 18 field samples tested by PCR, suggesting the possible existence of additional CRVBV variants.

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 Genome Sequences of Two GH Clade SARS-CoV-2 Strains Isolated from Patients with COVID-19 in South Korea

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Minwoo Kim ◽  
Youn-Jung Lee ◽  
Jae Sun Yoon ◽  
Jin Young Ahn ◽  
Jung Ho Kim ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
South Korea ◽  
Open Reading Frames ◽  
Untranslated Regions ◽  
Genome Sequences ◽  
Nonsynonymous Substitutions ◽  
Sequence Identity ◽  
Reading Frames

ABSTRACT We report the genome sequences of two GH clade severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains isolated from nasopharyngeal swabs from patients with coronavirus disease 2019 (COVID-19) in South Korea. These strains had two mutations in the untranslated regions and seven nonsynonymous substitutions in open reading frames, compared with Wuhan/Hu-1/2019, showing 99.96% sequence identity.

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 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.

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