scholarly journals Short regions of sequence identity between the genomes of human and rodent parvoviruses and their respective hosts occur within host genes for the cytoskeleton, cell adhesion and Wnt signalling

2006 ◽  
Vol 87 (12) ◽  
pp. 3567-3575 ◽  
Author(s):  
Jonathan R. Kerr ◽  
Nicola Boschetti
Keyword(s):  
Cell Adhesion ◽  
Parvovirus B19 ◽  
Prototype Strain ◽  
Wnt Signalling ◽  
Host Genome ◽  
Virus Species ◽  
Genome Sequences ◽  
Sequence Identity ◽  
Intergenic Regions ◽  
Host Genes

Our understanding of the mechanism(s) of pathogenesis and persistence of vertebrate parvoviruses remains incomplete. With the recent availability of the complete genome sequences of human, rat and mouse, and the ability to search these sequences and to locate matches to exact genomic regions, further insight into the interaction of parvoviruses with their human and rodent hosts is possible. To determine the extent and nature of sequence identity between candidate parvoviruses and their respective hosts, blast searches of the genome sequences of adeno-associated virus, parvovirus B19, mouse parvovirus, the prototype strain and immunosuppressant variant of minute virus of mouse, Kilham rat virus and rat parvovirus were performed against the genome(s) of their respective hosts (human, rat and mouse) using the resources of the NCBI and the Celera Discovery System. Regions of identity and similarity were mapped to their precise location in their particular host genome. For each virus, between one and 12 identical regions were found. Each identical region was 17–26 nt and was generally found at multiple sites within the particular host genome. These identical regions were predominantly located in non-coding regions of particular host genes and in intergenic regions. The ontology of host genes in which identical regions were found for each of the nine virus–host interactions highlighted several pathways/processes, including the cytoskeleton, cell adhesion and Wnt signalling. Within each virus species, these homologous regions were highly conserved (100 % identity in 16 out of 23 alignments where more than one sequence was available). All of these aspects suggest a particular advantage to the viruses of the presence of these sequences.

scholarly journals Sequences of Seven Complete Genomes of Human Parvovirus B19

2018 ◽  
Vol 7 (11) ◽  
Author(s):  
Yuhuan Qiu ◽  
Zehui Zhao ◽  
Jianming Qiu
Keyword(s):  
United States ◽  
Human Plasma ◽  
Parvovirus B19 ◽  
The United States ◽  
Human Parvovirus B19 ◽  
Genome Sequences ◽  
Complete Genomes ◽  
Inverted Terminal Repeats ◽  
Terminal Repeats

We are reporting the sequences of seven complete genomes of parvovirus B19, which were extracted from human plasma specimens collected in the United States. The seven B19 genome sequences, which are 5,596 nucleotides long and include the inverted terminal repeats (ITRs), share an identity of 96.73%.

scholarly journals Four Novel Mycoviruses from the Hypovirulent Botrytis cinerea SZ-2-3y Isolate from Paris polyphylla: Molecular Characterisation and Mitoviral Sequence Transboundary Entry into Plants

Viruses ◽  
2022 ◽  
Vol 14 (1) ◽  
pp. 151
Author(s):  
Qiong Wang ◽  
Qi Zou ◽  
Zhaoji Dai ◽  
Ni Hong ◽  
Guoping Wang ◽  
...  
Keyword(s):  
Botrytis Cinerea ◽  
Amino Acid Sequence Identity ◽  
Horizontal Transmission ◽  
Plant Mitochondria ◽  
Full Length ◽  
Genome Sequences ◽  
Rna Dependent Rna Polymerase ◽  
New Members ◽  
Sequence Identity ◽  
Paris Polyphylla

A hypovirulent SZ-2-3y strain isolated from diseased Paris polyphylla was identified as Botrytis cinerea. Interestingly, SZ-2-3y was coinfected with a mitovirus, two botouliviruses, and a 3074 nt fusarivirus, designated Botrytis cinerea fusarivirus 8 (BcFV8); it shares an 87.2% sequence identity with the previously identified Botrytis cinerea fusarivirus 6 (BcFV6). The full-length 2945 nt genome sequence of the mitovirus, termed Botrytis cinerea mitovirus 10 (BcMV10), shares a 54% sequence identity with Fusarium boothii mitovirus 1 (FbMV1), and clusters with fungus mitoviruses, plant mitoviruses and plant mitochondria; hence BcMV10 is a new Mitoviridae member. The full-length 2759 nt and 2812 nt genome sequences of the other two botouliviruses, named Botrytis cinerea botoulivirus 18 and 19 (BcBoV18 and 19), share a 40% amino acid sequence identity with RNA-dependent RNA polymerase protein (RdRp), and these are new members of the Botoulivirus genus of Botourmiaviridae. Horizontal transmission analysis showed that BcBoV18, BcBoV19 and BcFV8 are not related to hypovirulence, suggesting that BcMV10 may induce hypovirulence. Intriguingly, a partial BcMV10 sequence was detected in cucumber plants inoculated with SZ-2-3y mycelium or pXT1/BcMV10 agrobacterium. In conclusion, we identified a hypovirulent SZ-2-3y fungal strain from P. polyphylla, coinfected with four novel mycoviruses that could serve as potential biocontrol agents. Our findings provide evidence of cross-kingdom mycoviral sequence transmission.

scholarly journals Three of a Kind: Genetically Similar Tsukamurella Phages TIN2, TIN3, and TIN4

2015 ◽  
Vol 81 (19) ◽  
pp. 6767-6772 ◽  
Author(s):  
Zoe A. Dyson ◽  
Joseph Tucci ◽  
Robert J. Seviour ◽  
Steve Petrovski
Keyword(s):  
Genome Sequencing ◽  
Nucleotide Sequence Identity ◽  
Genome Architecture ◽  
Genome Sequences ◽  
Sludge Treatment ◽  
Content Type ◽  
Sequence Identity ◽  
Enrichment Techniques ◽  
Replication Module ◽  
Highly Virulent

ABSTRACTThreeTsukamurellaphages, TIN2, TIN3, and TIN4, were isolated from activated sludge treatment plants located in Victoria, Australia, using conventional enrichment techniques. Illumina and 454 whole-genome sequencing of theseSiphoviridaeviruses revealed that they had similar genome sequences, ranging in size between 76,268 bp and 76,964 bp. All three phages shared 74% nucleotide sequence identity to the previously describedGordoniaphage GTE7. Genome sequencing suggested that phage TIN3 had suffered a mutation in one of its lysis genes compared to the sequence of phage TIN4, to which it is genetically very similar. Mass spectroscopy data showed the unusual presence of a virion structural gene in the DNA replication module of phage TIN4, disrupting the characteristic modular genome architecture ofSiphoviridaephages. All three phages appeared highly virulent on strains ofTsukamurella inchonensisandTsukamurella paurometabola.

scholarly journals Complete Genome Sequence of Brucella canis Strain 118, a Strain Isolated from Canine

2012 ◽  
Vol 194 (23) ◽  
pp. 6680-6680 ◽  
Author(s):  
Guangjun Gao ◽  
Jing Li ◽  
Tiefeng Li ◽  
Zhengfang Zhang ◽  
Liping Wang ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Host Adaptation ◽  
Host Genome ◽  
Genome Sequences ◽  
Content Type ◽  
Brucella Canis

ABSTRACTBrucella canisinfects several species of animals, and canine is the preferred host. Genome sequences of strains from different hosts are valuable for comparative analysis of host adaptation and microevolution. Here, we report the genome sequence ofBrucella canisstrain 118, a strain isolated from canine.

scholarly journals Complete Genome Sequence of Human Coronavirus OC43 Isolated from Mexico

2016 ◽  
Vol 4 (6) ◽  
Author(s):  
B. T. Taboada ◽  
P. Isa ◽  
M. A. Espinoza ◽  
F. E. Aponte ◽  
M. A. Arias-Ortiz ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Genome Sequences ◽  
Human Coronavirus ◽  
Sequence Identity ◽  
New Generation Sequencing ◽  
New Generation ◽  
Metagenomic Approach ◽  
Generation Sequencing

We report the complete genome sequence of the first Mexican human coronavirus (HCoV) OC43, obtained by new-generation sequencing and a metagenomic approach, isolated from a child hospitalized with pneumonia. The genome is closely related to the other OC43 genome sequences available, ranging from 99.8% to 98.2% nucleotide sequence identity.

scholarly journals A nucleotide sequence comparison of coxsackievirus B4 isolates from aquatic samples and clinical specimens

1993 ◽  
Vol 110 (2) ◽  
pp. 389-398 ◽  
Author(s):  
M. S. Hughes ◽  
E. M. Hoey ◽  
P. V. Coyle
Keyword(s):  
Nucleotide Sequence ◽  
Clinical Specimen ◽  
Prototype Strain ◽  
Epidemiological Studies ◽  
Genomic Region ◽  
Amino Acid Sequences ◽  
Nucleotide Level ◽  
Clinical Specimens ◽  
Coxsackievirus B4 ◽  
Sequence Identity

SUMMARYTen coxsackievirus B4 (CVB4) strains isolated from clinical and environmental sources in Northern Ireland in 1985–7, were compared at the nucleotide sequence level. Dideoxynucleotide sequencing of a polymerase chain reaction (PCR) amplified fragment, spanning the VP1/P2A genomic region, classified the isolates into two distinct groups or genotypes as defined by Rico-Hesse and colleagues for poliovirus type 1. Isolates within each group shared approximately 99% sequence identity at the nucleotide level whereas ≤86% sequence identity was shared between groups. One isolate derived from a clinical specimen in 1987 was grouped with six CVB4 isolates recovered from the aquatic environment in 1986–7. The second group comprised CVB4 isolates from clinical specimens in 1985–6. Both groups were different at the nucleotide level from the prototype strain isolated in 1950. It was concluded that the method could be used to sub-type CVB4 isolates and would be of value in epidemiological studies of CVB4. Predicted amino acid sequences revealed non-conservation of the tyrosine residue at the VP1/P2A cleavage site but were of little value in distinguishing CVB4 variants.

scholarly journals Comparative Genomics ofCryptosporidium

2013 ◽  
Vol 2013 ◽  
pp. 1-8 ◽  
Author(s):  
Aurélien J. Mazurie ◽  
João M. Alves ◽  
Luiz S. Ozaki ◽  
Shiguo Zhou ◽  
David C. Schwartz ◽  
...  
Keyword(s):  
Genome Organization ◽  
Distinct Species ◽  
Genome Sequences ◽  
Cryptosporidium Hominis ◽  
Gene Deletions ◽  
Structural Alterations ◽  
Phenotypic Differences ◽  
Apicomplexan Parasites ◽  
Sequence Identity ◽  
Local Sequence

Until recently, the apicomplexan parasites,Cryptosporidium hominisandC. parvum, were considered the same species. However, the two parasites, now considered distinct species, exhibit significant differences in host range, infectivity, and pathogenicity, and their sequenced genomes exhibit only 95–97% identity. The availability of the complete genome sequences of these organisms provides the potential to identify the genetic variations that are responsible for the phenotypic differences between the two parasites. We compared the genome organization and structure, gene composition, the metabolic and other pathways, and the local sequence identity between the genes of these twoCryptosporidiumspecies. Our observations show that the phenotypic differences betweenC. hominisandC. parvumare not due to gross genome rearrangements, structural alterations, gene deletions or insertions, metabolic capabilities, or other obvious genomic alterations. Rather, the results indicate that these genomes exhibit a remarkable structural and compositional conservation and suggest that the phenotypic differences observed are due to subtle variations in the sequences of proteins that act at the interface between the parasite and its host.

scholarly journals Genome Sequences of Three Turkey Orthoreovirus Strains Isolated in Hungary

2015 ◽  
Vol 3 (6) ◽  
Author(s):  
Eszter Dandár ◽  
Enikő Fehér ◽  
Ádám Bálint ◽  
Péter Kisfali ◽  
Béla Melegh ◽  
...  
Keyword(s):  
United States ◽  
The United States ◽  
Genome Sequences ◽  
Sequence Identity ◽  
Close Relationship ◽  
Turkey Reovirus

We have investigated the genomic properties of three turkey reovirus strains—19831M09, D1246, and D1104—isolated in Hungary in 2009. Sequence identity values and phylogenetic calculations indicated genetic conservativeness among the studied Hungarian strains and a close relationship with strains isolated in the United States.

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