scholarly journals Chicken Astrovirus (CAstV) Molecular Studies Reveal Evidence of Multiple Past Recombination Events in Sequences Originated from Clinical Samples of White Chick Syndrome (WCS) in Western Canada

Viruses ◽  
2020 ◽  
Vol 12 (10) ◽  
pp. 1096
Author(s):  
Victor Palomino-Tapia ◽  
Darko Mitevski ◽  
Tom Inglis ◽  
Frank van der Meer ◽  
Emily Martin ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Point Mutations ◽  
Open Reading Frame ◽  
Clinical Samples ◽  
Western Canada ◽  
The Novel ◽  
Genome Sequences ◽  
Sequence Comparisons ◽  
Reading Frame ◽  
Detection Software

In this study, we aimed to molecularly characterize 14 whole genome sequences of chicken astrovirus (CAstV) isolated from samples obtained from white chick syndrome (WCS) outbreaks in Western Canada during the period of 2014–2019. Genome sequence comparisons showed all these sequences correspond to the novel Biv group from which no confirmed representatives were published in GenBank. Molecular recombination analyses using recombination detection software (i.e., RDP5 and SimPlot) and phylogenetic analyses suggest multiple past recombination events in open reading frame (ORF)1a, ORF1b, and ORF2. Our findings suggest that recombination events and the accumulation of point mutations may have contributed to the substantial genetic variation observed in CAstV and evidenced by the current seven antigenic sub-clusters hitherto described. This is the first paper that describes recombination events in CAstV following analysis of complete CAstV sequences originated in Canada.

scholarly journals Mutation Profile of SARS-CoV-2 Genome Sequences Originating from Eight Israeli Patient Isolates

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Galia Zaide ◽  
Inbar Cohen-Gihon ◽  
Ofir Israeli ◽  
Dana Stein ◽  
Ohad Shifman ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Nonsynonymous Substitution ◽  
Genetic Variations ◽  
Open Reading Frame ◽  
Care Homes ◽  
Clinical Samples ◽  
Genome Sequences ◽  
Reading Frame ◽  
Mutation Profile ◽  
Asymptomatic Individuals

ABSTRACT We report the genome sequences and the identification of genetic variations in eight clinical samples of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Samples were collected from nasopharyngeal swabs of symptomatic and asymptomatic individuals from five care homes for elderly and infirm persons in Israel. The sequences obtained are valuable, as they carry a newly reported nonsynonymous substitution located within the nucleoprotein open reading frame.

scholarly journals Expression and strain variation of the novel “small open reading frame” (smorf) multigene family in Babesia bovis

2012 ◽  
Vol 42 (2) ◽  
pp. 131-138 ◽  
Author(s):  
Lucas M. Ferreri ◽  
Kelly A. Brayton ◽  
Kerry S. Sondgeroth ◽  
Audrey O.T. Lau ◽  
Carlos E. Suarez ◽  
...  
Keyword(s):  
Multigene Family ◽  
Open Reading Frame ◽  
Babesia Bovis ◽  
The Novel ◽  
Strain Variation ◽  
Reading Frame ◽  
Small Open Reading Frame

scholarly journals Expression of the Novel Hepatitis C Virus Core+1/ARF Protein in the Context of JFH1-Based Replicons

2015 ◽  
Vol 89 (9) ◽  
pp. 5164-5170 ◽  
Author(s):  
Ioly Kotta-Loizou ◽  
Ioannis Karakasiliotis ◽  
Niki Vassilaki ◽  
Panagiotis Sakellariou ◽  
Ralf Bartenschlager ◽  
...  
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Core Gene ◽  
Open Reading Frame ◽  
The Novel ◽  
Reading Frame ◽  
The Core ◽  
Virus Core ◽  
First Time ◽  
Arf Protein

Hepatitis C virus contains a second open reading frame within the core gene, designated core+1/ARF. Here we demonstrate for the first time expression of core+1/ARF protein in the context of a bicistronic JFH1-based replicon and report the production of two isoforms, core+1/L (long) and core+1/S (short), with different kinetics.

scholarly journals Complete sequence of a duck astrovirus associated with fatal hepatitis in ducklings

2009 ◽  
Vol 90 (5) ◽  
pp. 1104-1108 ◽  
Author(s):  
Yu Fu ◽  
Meng Pan ◽  
Xiaoyan Wang ◽  
Yongliang Xu ◽  
Xiaoyu Xie ◽  
...  
Keyword(s):  
Molecular Biology ◽  
Viral Hepatitis ◽  
Phylogenetic Analyses ◽  
Complete Sequence ◽  
Sequence Analyses ◽  
Sequence Comparisons ◽  
Reading Frame ◽  
Recent Outbreak

Duck astroviruses (DAstVs) are known to cause duck viral hepatitis; however, little is known regarding their molecular biology. Here, we report the complete sequence of a DAstV associated with a recent outbreak of fatal hepatitis in ducklings in China. Sequence analyses indicated that the genome of DAstV possessed a typical astrovirus organization and also exhibited two unique features. The polyadenylated genome comprised 7722 nt, which is the largest among astroviruses sequenced to date. The ORF2 of DAstV was not in the same reading frame as either ORF1a or ORF1b, which was distinct from all other astroviruses. Sequence comparisons and phylogenetic analyses revealed that DAstV was more closely related to turkey astrovirus (TAstV) type 2, TAstV-3 and TAstV/MN/01 (a possible new TAstV serotype) than to TAstV-1 or other astroviruses. These findings suggest that astroviruses may transmit across ducks and turkeys.

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 Molecular Characterization and Functional Analysis of an AGAMOUS-like Gene CiAG from Pecan

HortScience ◽  
2016 ◽  
Vol 51 (6) ◽  
pp. 664-668 ◽  
Author(s):  
Jiyu Zhang ◽  
Min Wang ◽  
Zhenghai Mo ◽  
Gang Wang ◽  
Zhongren Guo
Keyword(s):  
Flower Development ◽  
Carya Illinoinensis ◽  
Open Reading Frame ◽  
Base Pairs ◽  
Sequence Comparisons ◽  
Multiple Sequence ◽  
Reading Frame ◽  
Vegetative Tissues ◽  
Current Growth

The floral homeotic C-function gene AGAMOUS (AG) has been shown to be critical in the determination of stamen and carpel identity in Arabidopsis. In the present study, a new homologue of AGAMOUS gene from pecan [Carya illinoinensis (Wangenh.) K. Koch], denoted by CiAG, was isolated and its function was characterized. The complementary DNA (cDNA) of CiAG contains an open reading frame of 687 base pairs (bp) encoding 227 amino acids. Multiple sequence comparisons revealed that CiAG had the typical MIKC structure. Phylogenetic analysis indicated that CiAG is closely related to C-lineage AG. The expression of CiAG was highly accumulated in the reproductive tissues (staminate flowers, pistillate flowers, and fruitlets) than in vegetative tissues (leaves and current-growth branches). Arabidopsis overexpressing CiAG exhibited earlier flowering. The homeotic transformations of petals into stamen organs were observed in 35S::CiAG transgenic plants. All these results indicated that CiAG plays a key role in the process of flower development of pecan.

scholarly journals Complete Genome Sequences of Three Novel Saimiri sciureus Papillomavirus Types Isolated from the Cervicovaginal Region of Squirrel Monkeys

2018 ◽  
Vol 6 (1) ◽  
Author(s):  
Zigui Chen ◽  
Charles E. Wood ◽  
Christian R. Abee ◽  
Robert D. Burk
Keyword(s):  
Nucleotide Sequence ◽  
Complete Genome ◽  
Squirrel Monkeys ◽  
Open Reading Frame ◽  
Saimiri Sciureus ◽  
Genome Sequences ◽  
Reading Frame ◽  
Sequence Identities

ABSTRACT The complete genome sequences of three novel Saimiri sciureus papillomavirus (SscPV) types (SscPV1 to SscPV3) isolated from the cervicovaginal region of squirrel monkeys were characterized. These three PV types share 78.1 to 83.3% nucleotide sequence identities with each other across the complete L1 open reading frame and cluster in the genus Dyoomikronpapillomavirus.

scholarly journals Robiginitomaculum antarcticum gen. nov., sp. nov., a member of the family Hyphomonadaceae, from Antarctic seawater

2007 ◽  
Vol 57 (11) ◽  
pp. 2595-2599 ◽  
Author(s):  
Kiyoung Lee ◽  
Hong Kum Lee ◽  
Tae-Hwan Choi ◽  
Jang-Cheon Cho
Keyword(s):  
New Genus ◽  
Phylogenetic Analyses ◽  
Fatty Acid Content ◽  
Salinity Range ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
The Novel ◽  
Sequence Comparisons ◽  
The Family ◽  
The Antarctic

A seawater bacterium, designated IMCC3195T, was isolated from the Antarctic coast. Cells of the novel strain were Gram-negative, rusty-coloured, strictly aerobic, chemoheterotrophic, non-budding and non-motile rods or vibrioids that possessed a thin prostheca. Based on 16S rRNA gene sequence comparisons, the novel strain was most closely related to the genera Hyphomonas (89.4–90.9 %), Maricaulis (90.1–90.4 %), Hirschia (89.0 %) and Oceanicaulis (87.9 %) of the family Hyphomonadaceae. Phylogenetic analyses also showed the Antarctic isolate to be only distantly related to the genera of stalked bacteria of marine origin in the family Hyphomonadaceae. The DNA G+C content of the novel strain was 60.3 mol% and the predominant cellular fatty acids were C18 : 1 ω7c (41.9 %), C17 : 1 ω8c (21.4 %) and C17 : 0 (14.3 %). The major quinone was Q-10. Several phenotypic and chemotaxonomic characteristics, including optimum temperature and salinity range for growth, cell morphology, pigmentation and fatty acid content, differentiated the novel strain from other related genera in the family Hyphomonadaceae. From the taxonomic evidence collected in this study, it is suggested that strain IMCC3195T (=KCCM 42687T=NBRC 103098T) represents a new genus and novel species in the family Hyphomonadaceae, for which the name Robiginitomaculum antarcticum gen. nov., sp. nov. is proposed.

scholarly journals Phylogenetic relationships among sandfly fever group viruses (Phlebovirus: Bunyaviridae) based on the small genome segment

2007 ◽  
Vol 88 (8) ◽  
pp. 2312-2319 ◽  
Author(s):  
Fangling Xu ◽  
Hongli Chen ◽  
Amelia P. A. Travassos da Rosa ◽  
Robert B. Tesh ◽  
Shu-Yuan Xiao
Keyword(s):  
Genetic Divergence ◽  
Phylogenetic Relationships ◽  
Phylogenetic Analyses ◽  
Genome Segment ◽  
Open Reading Frame ◽  
Reading Frame ◽  
Small Genome ◽  
Sequence Identity ◽  
Nucleoprotein N ◽  
Antigenic Relationships

The phleboviruses are more diverse in terms of arthropod vectors and antigenic relationships than most other genera of arthropod-borne viruses. In this study, 30 sandfly fever group viruses from the Naples, Sicilian, Punta Toro, Icoaraci and Frijoles serocomplexes were sequenced. Phylogenetic analyses were performed based on the sequence of the open reading frame for the nucleoprotein (N) and non-structural (NSs) protein genes of the small (S) segment. The five resultant genotypic lineages correlated with the serological grouping and were similar to analysis of M segment sequences. The sequence identity for N and NSs genes within the Sicilian, Naples, Punta Toro, Icoaraci and Frijoles serocomplexes was determined. The results indicated that genetic divergence for the S segment is lower than that for the M segment, suggesting that the S segment is more stable during evolution.

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