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171 records – page 1 of 18.

"886-84-like" tick-borne encephalitis virus strains: Intraspecific status elucidated by comparative genomics.

https://arctichealth.org/en/permalink/ahliterature310363
Source
Ticks Tick Borne Dis. 2019 08; 10(5):1168-1172
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Date
08-2019
Author
Renat V Adelshin
Elena A Sidorova
Artem N Bondaryuk
Anna G Trukhina
Dmitry Yu Sherbakov
Richard Allen White Iii
Evgeny I Andaev
Sergey V Balakhonov
Author Affiliation
Irkutsk Anti-Plague Research Institute of Siberia and Far East, Trilisser 78, 664047, Irkutsk, Russia; Irkutsk State University, Irkutsk, Russia. Electronic address: adelshin@gmail.com.
Source
Ticks Tick Borne Dis. 2019 08; 10(5):1168-1172
Date
08-2019
Language
English
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Keywords
Animals
Arvicolinae
Encephalitis Viruses, Tick-Borne - classification - genetics
Encephalitis, Tick-Borne - epidemiology - veterinary - virology
Genome, Viral
Genomics
Genotype
Incidence
Ixodes - virology
Rodent Diseases - epidemiology - virology
Siberia - epidemiology
Abstract
Tick-borne encephalitis virus (TBEV) can cause severe meningitis, encephalitis, and meningoencephalitis. TBEV represents a pathogen of high zoonotic potential and an emerging global threat. There are three known subtypes of TBEV: Far-Eastern, Siberian and European. Since 2001 there have been suggestions that two new subtypes may be distinguished: "178-79" and "886-84". These assumptions are based on the results of the envelope gene fragment sequencing (Zlobin et al., 2001; Kovalev and Mukhacheva, 2017) and genotype-specific probes molecular hybridization (Demina et al., 2010). There is only one full-genome sequence of "178-79" strain and two identical ones of "886-84" strain can be found in GenBank. For clarification of the intraspecific position of the "886-84-like" strains group we completely sequenced six previously unknown "886-84-like" strains isolated in Eastern Siberia. As a result of applying different bioinformatics approaches, we can confirm that "886-84-like" strains group is a distinct subtype of TBEV.
PubMed ID
31253516 View in PubMed
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African Swine Fever Virus, Siberia, Russia, 2017.

https://arctichealth.org/en/permalink/ahliterature298288
Source
Emerg Infect Dis. 2018 04; 24(4):796-798
Publication Type
Historical Article
Letter
Research Support, Non-U.S. Gov't
Date
04-2018
Author
Denis Kolbasov
Ilya Titov
Sodnom Tsybanov
Andrey Gogin
Alexander Malogolovkin
Source
Emerg Infect Dis. 2018 04; 24(4):796-798
Date
04-2018
Language
English
Publication Type
Historical Article
Letter
Research Support, Non-U.S. Gov't
Keywords
African Swine Fever - epidemiology - history - virology
African Swine Fever Virus - classification - genetics
Animals
DNA, Viral
Genome, Viral
Genotype
History, 21st Century
Siberia - epidemiology
Swine
Abstract
African swine fever (ASF) is arguably the most dangerous and emerging swine disease worldwide. ASF is a serious problem for the swine industry. The first case of ASF in Russia was reported in 2007. We report an outbreak of ASF in Siberia, Russia, in 2017.
PubMed ID
29553323 View in PubMed
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[A genetic analysis of A H1N1 pandemic influenza virus in the course of the epidemic].

https://arctichealth.org/en/permalink/ahliterature123359
Source
Ter Arkh. 2012;84(3):48-54
Publication Type
Article
Date
2012
Source
Ter Arkh. 2012;84(3):48-54
Date
2012
Language
Russian
Publication Type
Article
Keywords
Amantadine - therapeutic use
Antiviral agents - therapeutic use
Drug Resistance, Viral - genetics
Genetic Testing
Genome, Viral - genetics
Humans
Influenza A Virus, H1N1 Subtype - drug effects - genetics
Influenza, Human - drug therapy - epidemiology - genetics
Oseltamivir - therapeutic use
Pandemics
Polymorphism, Genetic
Prognosis
Russia - epidemiology
Abstract
To assess genetic variability of A H1N1 pan influenza virus (IV) in the course of the epidemic and to detect a set of human nucleotide polymorphisms responsible for a severe course of the disease.
Extraction and purification of viral genomic RNA from the nasopharyngeal smears and genomic human DNA from the leukocytic fraction of venous blood was made in 230 patients from Moscow. Moscow and Sverdlovsk Regions with severe acute respirator, virus infection (ARVI). A flu virus type was established in amplification reaction with on-line detection of the products with application of primers recommended by WHO. Genetic polymorphisms of A H1N1 pan IV and human genes were determined with minisequencing reaction followed by detection of the products of MALDI-time-of-flight mass-spectrometry. Nucleotide sequences of the complete genome were revealed for 15 isolates of A H1N1 pan IV.
A H1N1 IV was identified in 77 cases (46 were pandemic, 31 seasonal). Mutations causing genetically determined resistance to adamants (amantadin, rimantadin) were detected in all 46 samples of genomic RNA of A H1N1 pan IV. Mutation leading to oseltamivir (tamiflu) resistance was found in one sample. It is shown that a severe course of A H1N1 pan IV infection is associated with genotypes predisposing to development of thromboses, bronchopulmonary diseases and hypertention. Genetic tests for prognosis of a complicated course of the flu are proposed. The revealed full-genome sequences of the segments of genomic RNA of 15 A H1N1 pan influenza viruses are deposited in GenBank.
We are the first in Russia to detect a mutant variant of A H1N1 pan IV resistant to oseltamivir We describe a set of nucleotide polymorphisms which determine a complicated course of the flu in patients with identified A H1N1 pan IV.
PubMed ID
22708423 View in PubMed
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Amplification by long RT-PCR of near full-length norovirus genomes.

https://arctichealth.org/en/permalink/ahliterature158184
Source
J Virol Methods. 2008 May;149(2):226-30
Publication Type
Article
Date
May-2008
Author
Jennifer Kostela
Melissa Ayers
John Nishikawa
Lorraine McIntyre
Martin Petric
Raymond Tellier
Author Affiliation
Metabolism Research Program, Hospital for Sick Children, Toronto, Canada.
Source
J Virol Methods. 2008 May;149(2):226-30
Date
May-2008
Language
English
Publication Type
Article
Keywords
Caliciviridae Infections - virology
Canada
Feces - virology
Genome, Viral
Humans
Molecular Epidemiology - methods
Molecular Sequence Data
Norovirus - classification - genetics - isolation & purification
Phylogeny
RNA, Viral - genetics
Reverse Transcriptase Polymerase Chain Reaction - methods
Sequence Alignment
Sequence Analysis, DNA
Abstract
A long RT-PCR method was developed to amplify the norovirus genome. Starting from RNA extracted directly from clinical samples and using broadly reactive primers, it can generate near full-length amplicons that allow for easy determination of the near complete genomic sequence. Two norovirus isolates from Toronto, Canada, in 2002 and 2005 were sequenced. This approach will facilitate molecular epidemiology studies of noroviruses.
PubMed ID
18355931 View in PubMed
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An AB recombinant and its parental HIV type 1 strains in the area of the former Soviet Union: low requirements for sequence identity in recombination. UNAIDS Virus Isolation Network.

https://arctichealth.org/en/permalink/ahliterature7511
Source
AIDS Res Hum Retroviruses. 2000 Jul 20;16(11):1047-53
Publication Type
Article
Date
Jul-20-2000
Author
K. Liitsola
K. Holm
A. Bobkov
V. Pokrovsky
T. Smolskaya
P. Leinikki
S. Osmanov
M. Salminen
Author Affiliation
Department of Infectious Disease Epidemiology, National Public Health Institute, Helsinki, Finland. kirsi.liitsola@ktl.fi
Source
AIDS Res Hum Retroviruses. 2000 Jul 20;16(11):1047-53
Date
Jul-20-2000
Language
English
Publication Type
Article
Keywords
Base Sequence
Cloning, Molecular
Genes, env
Genome, Viral
HIV Infections - epidemiology - virology
HIV-1 - classification - genetics
Humans
Male
Molecular Sequence Data
Phylogeny
Polymerase Chain Reaction
Recombination, Genetic
Research Support, Non-U.S. Gov't
Russia - epidemiology
Sequence Analysis, DNA
Substance Abuse, Intravenous - complications
Ukraine - epidemiology
Abstract
In the former Soviet Union (SU) increasing numbers of HIV-1 infections among injecting drug users (IDU) have been reported, especially in the Ukraine. The main subtype transmitted among the IDUs seems to be subtype A, but limited numbers of subtype B cases have also been reported. In Kaliningrad, Russia, an AB recombinant strain was earlier shown to be responsible for the local outbreak. Here we describe the genetic relationship of HIV-1 strains circulating among IDUs in the former SU. For subtype A and the AB recombinant strains nearly full-length genomes were sequenced, and for one subtype B strain the entire envelope gene was cloned. The relationship between the AB recombinant strain and the subtype A and subtype B strains and the mosaic structure of the recombinant was studied by phylogenetic analysis. Ukrainian A and B strains were shown to be the probable parental viruses of the Kaliningrad AB recombinant strain. In the envelope gene the recombination breakpoint could also be precisely mapped to a region of similarity of only 14 base pairs. This suggests that only short stretches of absolute sequence identity may be needed for efficient RNA recombination between HIV-1 subtypes.
PubMed ID
10933619 View in PubMed
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Analyses of restriction fragment patterns (RFPs) and pathogenicity in baby mice of equine herpesvirus 1 and 4 (EHV-1 and EHV-4) strains circulating in Danish horses.

https://arctichealth.org/en/permalink/ahliterature64540
Source
Vet Microbiol. 1995 Nov;47(1-2):199-204
Publication Type
Article
Date
Nov-1995
Author
V. Palfi
L S Christensen
Author Affiliation
National Veterinary Laboratory, Copenhagen N, Denmark.
Source
Vet Microbiol. 1995 Nov;47(1-2):199-204
Date
Nov-1995
Language
English
Publication Type
Article
Keywords
Abortion, Veterinary - virology
Animals
Animals, Suckling
Biological Assay
Brain - virology
Denmark
Female
Fetal Death - veterinary - virology
Genome, Viral
Genotype
Herpesviridae - classification - genetics - pathogenicity
Herpesviridae Infections - veterinary - virology
Herpesvirus 1, Equid - classification - genetics - pathogenicity
Horse Diseases - virology
Horses
Mice
Paralysis - veterinary - virology
Polymorphism, Restriction Fragment Length
Pregnancy
Research Support, Non-U.S. Gov't
Respiratory Tract Infections - veterinary - virology
Viscera - virology
Abstract
Twenty-five strains of equine herpesvirus 1 (EHV-1) and one strain of equine herpesvirus 4 (EHV-4) isolated from material from various clinical cases in Denmark, together with reference EHV-1 and EHV-4 strains, were compared by restriction fragment pattern (RFP) analysis and inoculation of baby mice. The RFP analyses revealed that all EHV-1 strains belonged to genome type Ip. Four fetal isolates exhibited genomic characteristics that have been suggested as specific markers of the attenuated strain Rac H, widely used as a live vaccine. As the use of five vaccines against EHV-1 and EHV-4 has never been allowed in Denmark, it is assumed that Rac H derivatives have been acquired from visiting horses and thus are now circulating in the horse population. Baby mice inoculation revealed that four biotypes could be distinguished on the basis of pathogenicity. However, no strict correlation with pathogenicity in the natural host was seen.
PubMed ID
8604552 View in PubMed
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[Analysis of changes in the gp120 V3 region as observed in some patients with HIV infected from a common infection source].

https://arctichealth.org/en/permalink/ahliterature178958
Source
Vopr Virusol. 2004 Jul-Aug;49(4):15-20
Publication Type
Article
Author
P A Romashkin
S P Saukhat
A B Shemshura
A S Pazilin
M M Garaev
Source
Vopr Virusol. 2004 Jul-Aug;49(4):15-20
Language
Russian
Publication Type
Article
Keywords
Amino Acid Sequence
Cohort Studies
Disease Outbreaks
Epitopes, B-Lymphocyte - genetics
Genetic Variation
Genome, Viral
HIV Envelope Protein gp120 - genetics
HIV Infections - epidemiology
HIV-1 - genetics - isolation & purification
Humans
Molecular Sequence Data
Peptide Fragments - genetics
Retrospective Studies
Russia - epidemiology
Sequence Alignment
Abstract
HIV-1 genome regions encoding the gp120 V3 part were sequenced in samples isolated from persons belonging to the category of those infected in the Rostov-Elista outbreak and having the common infection source. Samples were obtained from 5 patients in 1992 and in 2001. A total of 27 sequences obtained in 1992 and 35 sequences obtained in 2001, 2 to 8 sequences for each patient, were analyzed. The diversity level of V3 sequences made, in some patients, 2.2% in 1992 and went up to 4.2% in 2001 samples (p
PubMed ID
15293506 View in PubMed
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[Analysis of gag gene subtypes of HIV-1 variants isolated in Russia by comparative assessment of heteroduplex electrophoretic mobility].

https://arctichealth.org/en/permalink/ahliterature194066
Source
Vopr Virusol. 2001 May-Jun;46(3):12-6
Publication Type
Article
Author
E V Kazennova
A F Bobkov
L M Selimova
T A Khanina
V V Pokrovskii
L. Heyndrickx
G. Van der Groen
Source
Vopr Virusol. 2001 May-Jun;46(3):12-6
Language
Russian
Publication Type
Article
Keywords
Acquired Immunodeficiency Syndrome - epidemiology - virology
Electrophoresis
Genes, gag
Genetic Variation
Genome, Viral
HIV-1 - genetics - isolation & purification
Humans
Polymerase Chain Reaction
Russia - epidemiology
Abstract
Using heteroduplex mobility assay modified for gag gene analysis (HMA-gag), 37 HIV-1 samples previously genotyped by gag and env nucleotide sequencing were studied. It has been demonstrated that both sensitivity and specificity of HMA-gag were 100%. The gag gene region derived from 20 env subtype A HIV-1 isolates was analyzed by this method. AG recombinant, representing a circulating recombinant form of HIV-1 (AGlbNG) was found among five HIV-1 strains isolated from patients infected through heterosexual contacts in Russia. No novel recombinant forms were found among fifteen HIV-1 variants infected from drug users in 7 cities of Russia. The proposed HMA-gag method extends the potentialities of investigating the genetic variability of HIV-1 and in combination with the previously proposed method for env gene is a convenient approach to search for recombinant forms of this virus.
PubMed ID
11450137 View in PubMed
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[Analysis of genomes of two rubella virus strains from the 2004-2005 outbreaks in West Siberia].

https://arctichealth.org/en/permalink/ahliterature163561
Source
Vopr Virusol. 2007 Mar-Apr;52(2):16-9
Publication Type
Article
Author
L N Iashina
G I Tiunnikov
I D Petrova
S V Seregin
S S Seregin
V A Ternovoi
E M Malkova
E N Ustinova
S V Netesov
I G Drozdov
V S Petrov
Source
Vopr Virusol. 2007 Mar-Apr;52(2):16-9
Language
Russian
Publication Type
Article
Keywords
Disease Outbreaks
Genome, Viral
Humans
Molecular Epidemiology
Molecular Sequence Data
Phylogeny
Rubella - epidemiology
Rubella virus - genetics
Siberia - epidemiology
Species Specificity
Viral Envelope Proteins - genetics
Abstract
Two outbreaks of rubella infections notified in the Tomsk and Kemerovo Regions were investigated. Two rubella virus strains from one patient in each outbreak were isolated and genetically characterized. Reverse transcription polymerase chain reaction was used to reveal partial E1 gene sequence at a length of 915 nucleotides. Analysis indicated that the rubella virus strains circulating in the West-Siberian region belonged to international genetic 1g group, which had been first detected in Russia.
PubMed ID
17500233 View in PubMed
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[Analysis of the prevalence of CCR5 coreceptor antagonist resistance mutations among HIV-1 variants in Russia].

https://arctichealth.org/en/permalink/ahliterature132721
Source
Vopr Virusol. 2011 May-Jun;56(3):32-7
Publication Type
Article
Author
A V Vasil'ev
E V Kazennova
M R Bobkova
Source
Vopr Virusol. 2011 May-Jun;56(3):32-7
Language
Russian
Publication Type
Article
Keywords
Anti-HIV Agents - administration & dosage - therapeutic use
Cyclohexanes - administration & dosage - therapeutic use
Drug Resistance, Viral - drug effects
Genetic Variation
Genome, Viral - drug effects
HIV Infections - drug therapy - epidemiology - genetics
HIV-1 - drug effects - genetics
Humans
Mutation - drug effects
Phylogeny
Piperazines - administration & dosage - therapeutic use
Prevalence
Pyrimidines - administration & dosage - therapeutic use
Receptors, CCR5 - antagonists & inhibitors - genetics - metabolism
Russia
Treatment Outcome
Triazoles - administration & dosage - therapeutic use
Abstract
The authors studied the prevalence of mutations associated with resistance to the CCRS coreceptor antagonists maraviroc and vicriviroc in Russia. Most (93.6%) patients infected with HIV-1 genetic subtype A (IDU-A), predominant in the CIS countries, were found to have maraviroc resistance mutations. These mutations appear to reflect the natural genome polymorphism characteristic of the variant IDU-A. Maraviroc resistance mutations were of limited occurrence (2.8%) among the samples of virus subtype B in Russia. There were no vicriviroc resistance mutations in both the HIV-1 genetic variant IDU-A and the samples of virus subtype B. There is a need for further clinical studies evaluating the real impact of these mutations on the efficacy of maraviroc in patients infected with the HIV-1 genetic variant IDU-A.
PubMed ID
21786625 View in PubMed
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171 records – page 1 of 18.