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.
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.
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.
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.
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.
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.
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
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.
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.
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.