Pathogens in Ixodes persulcatus and Ixodes ricinus ticks (Acari, Ixodidae) in Karelia (Russia).

Ixodid ticks (Acarina, Ixodidae) are vectors of dangerous human infections. The main tick species that determine the epidemiological situation for tick-borne diseases in northern Europe are Ixodes ricinus and Ixodes persulcatus. In recent years, significant changes in the number and distribution of these species have been observed, accompanied by an expansion of the sympatric range. This work summarizes the data of long-term studies carried out in Karelia since 2007 on the infection of I. persulcatus and I. ricinus ticks with various pathogens, including new viruses with unclear pathogenic potential. As a result, tick-borne encephalitis virus (TBEV, Siberian genotype), Alongshan virus, several representatives of the family Phenuiviridae, Borrelia afzelii, Borrelia garinii, Ehrlichia muris, Candidatus Rickettsia tarasevichiae and Candidatus Lariskella arthropodarum were identified. Data were obtained on the geographical and temporal variability of tick infection rates with these main pathogens. The average infection rates of I. persulcatus with TBEV and Borrelia burgdorferi sensu lato were 4.4% and 23.4% and those of I. ricinus were 1.1% and 11.9%, respectively. We did not find a correlation between the infection rate of ticks with TBEV, B. burgdorferi s.l. and Ehrlichia muris/chaffeensis with the sex of the vector. In general, the peculiarities of the epidemiological situation in Karelia are determined by the wide distribution and high abundance of I. persulcatus ticks and by their relatively high infection rate with TBEV and B. burgdorferi s.l. in most of the territory, including the periphery of the range.

[VACCINE-ASSOCIATED PARALYTIC POLIOMYELITIS IN RUSSIAN FEDERATION DURING THE PERIOD OF CHANGES IN VACCINATION SCHEDULE (2006-2013 yy.)].

The results of virologic testing of clinical materials and epidemiological analysis of vaccine-associated paralytic poliomyelitis (VAPP) cases obtained in 2006-2013 during AFP surveillance are presented. Among the 2976 cases of AFP 30 cases were VAPP. 15 cases were observed in OPV recipients, whereas 15 cases were observed in non-vaccinated contacts. The age of the patients varied from 4 months to 5.5 years (13.6 ± 12.4 months old). Children younger than 1 year constituted 63.3% of the group; boys were dominant (73.3%); 53.3% of children were vaccinated with OPV; the time period between receipt of OPV and onset of palsy was from 2 to 32 days (18.7 ± 8.2). Lower paraparesis was documented in 48.3% of patients; lower monoparesis in 37.9%; upper monoparesis, in 6.9%; tetraparesis with bulbar syndrome, in 6%. The majority of the patients (85.7%) had an unfavorable premorbid status. The violations of the humoral immunity were found in 73.9% cases: CVID (52.9%), hypogammaglobulinemia (41.2%); selective lgA deflciency (5.9%). In 70.6% cases damage to humoral immunity was combined with poor premorbid status. The most frequently observed (76%, p < 0.05) represented the single type of poliovirus--type 2 (44%) and type 3 (32%). All strains were of the vaccine origin, the divergence from the homotypic Sabin strains fell within the region of the gene encoding VPI protein, which did not exceed 0.5% of nucleotide substitutions except vaccine derived poliovirus type 2--multiple recombinant (type 2/type 3/ type 2/type 1) with the degree of the divergence of 1.44% isolated from 6-month old unvaccinated child (RUS08063034001). The frequency of the VAPP cases was a total of 1 case per 3.4 million doses of distributed OPV in 2006-2013; 2.2 cases per 1 million of newborns were observed. This frequency decreased after the introduction of the sequential scheme of vaccination (IPV, OPV) in 2008-2013 as compared with the period of exclusive use of OPV in 2006-2007: 1 case per 4.9 million doses, 1.4 cases per million newborns and 1 case per 1.9 million doses, 4.9 cases per 1 million newborns, respectively. The study has been financed from Russian Federation budget within the framework of the Program for eradication of poliomyelitis in the Russian Federation, WHO Polio eradication initiative, WHO's European Regional Bureau, Russian Foundation for Basic Research (project No. 15-15-00147).

Prevalence of Kemerovo virus in ixodid ticks from the Russian Federation.

The prevalence of Kemerovo virus in ixodid ticks collected in 2008-2012 from 11 regions of the Russian Federation was investigated by real-time reverse-transcription PCR (RT-PCR). The presence of Kemerovo virus in Ixodes persulcatus, Ixodes ricinus, and Dermacentor reticulatus was confirmed. Virus prevalence depended on the region and varied from zero to 10.1%.

The 2010 outbreak of poliomyelitis in Tajikistan: epidemiology and lessons learnt.

A large outbreak of poliomyelitis, with 463 laboratory-confirmed and 47 polio-compatible cases, took place in 2010 in Tajikistan. Phylogenetic analysis of the viral VP1 gene suggested a single importation of wild poliovirus type 1 from India in late 2009, its further circulation in Tajikistan and expansion into neighbouring countries, namely Kazakhstan, Russia, Turkmenistan and Uzbekistan. Whole-genome sequencing of 14 isolates revealed recombination events with enterovirus C with cross-overs within the P2 region. Viruses with one class of recombinant genomes co-circulated with the parental virus, and representatives of both caused paralytic poliomyelitis. Serological analysis of 327 sera from acute flaccid paralysis cases as well as from patients with other diagnoses and from healthy people demonstrated inadequate immunity against polio in the years preceding the outbreak. Evidence was obtained suggesting that vaccination against poliomyelitis, in rare cases, may not prevent the disease. Factors contributing to the peculiarities of this outbreak are discussed. The outbreak emphasises the necessity of continued vaccination against polio and the need, at least in risk areas, of quality control of this vaccination through well planned serological surveillance.

GAG-binding variants of tick-borne encephalitis virus.

Previously different authors described various flavivirus mutants with high affinity to cell glycosaminoglycans and low neuroinvasiveness in mice that were obtained consequently passages in cell cultures or in ticks. In present study the analysis of TBEV isolates has shown existence of GAG-binding variants in natural virus population. Affinity to GAG has been evaluated by sorption on heparin-Sepharose. GAG-binding phenotype corresponds to such virus properties, like small plaque phenotype in PEK cells, absence of hemagglutination at pH 6.4, and low neuroinvasiveness in mice. Mutations increasing charge of E protein were necessary but not sufficient for acquisition of GAG-binding phenotype. Molecular modeling and molecular dynamics simulation have shown that the flexibility of E protein molecule could bear influence on the phenotypic manifestation of substitutions increasing charge of the virions.

[On the taxonomic rank of ciscaucasicus and its relationships with the pygmy wood mouse Sylvaemus uralensis inferred from the mtDNA cytochrome b gene sequence].

To specify the taxonomic rank of form ciscaucasoides (independent species Sylvaemus ciscaucasoides, or intraspecific form of pygmy wood mouse, S. uralensis), a 402-bp the mtDNA cytochrome b gene fragment (402 bp) was examined in S. ciscaucasoides individuals from six geographic localities of the Caucasus and Ciscaucasus, (Krasnodar krai and Adygeya Republic) and 17 S. uralensis individuals from seven localities of the Russian Plai (Saratov oblast, Smolensk oblast, Voronezh oblast, Tula oblast, Moscow oblast, and Tver' oblast). For comparison, the cytochrome b gene was partly sequenced in the samples of yellow necked, S. flavicollis (n = 2, Samara oblast), and Caucasian, S. ponticus (n = 6, Krasnodar krai), wood mice. One Mus musculus specimen from Western Europe, whose nucleotide sequences were deposed in the GenBank, was used as intergeneric outgroup. Phylogenetic trees for the forms examined were constructed based on the mtDNA sequence variation and using the neighbor joining and maximum parsimony methods. The network of the cytochrome b haplotypes was also constructed. The level of genetic divergence was evaluated using Kimura's two-parameter algorithm. Based on the data on the sequence variation in a 402-bp mtDNA cytochrome b gene fragment, the hypothesis on the species status of the ciscaucasicus form was. The mean intergroup distances (d) between the geographic groups of S. uralensis varied from 0.0036 to 0.0152. At the same time, the distances between the pygmy wood mice and the group of S.flavicollis-S. ponticus varies in the range from 0.0860 to 0.0935, and the level of intergeneric genetic differentiation (Sylvaemus-Mus) is higher than the latter index (d = 0.142). Ciscaucasoides should be considered as geographic substitution form of S. uralensis. Furthermore, the Caucasian populations of S. uralensis (= ciscaucasoides) were characterized by a threefold lower value of intergroup genetic divergence (d = 0.0062) than the East European populations (d= 0.0179). This finding pointed to some isolation of Caucasian populations of pygmy wood mouse and depletion of their gene pool. However other molecular genetic data (similarity of nucleotide composition and consistence of the levels of intra- and intergroup distances) suggest the absence of geographic subdivision between Caucasian and East European populations ofS. uralensis relative to the molecular marker examined.

[Variable mechanisms of RNA-recombination].

Recombination is widespread among RNA viruses but underlying mechanisms remain poorly understood. Until recently, replicative template switching was considered the only possible mechanism of RNA recombination but new evidence suggests that other variants of replicative mechanisms may also exist. In addition, nonreplicative recombination (i.e., joining of preexisting molecules) of genomes of RNA viruses is possible. Recombination is an efficient tool contributing to both variability and stability of the viral RNA genomes. Nonreplicative joining of RNA pieces in the form of trans-splicing is an important physiological mechanism in at least certain organisms. It is conceivable that RNA-recombination has contributed, and perhaps is still contributing, to the evolution of DNA genomes.

Diverse Mechanisms of RNA Recombination.

Recombination is widespread among RNA viruses, but many molecular mechanisms of this phenomenon are still poorly understood. It was believed until recently that the only possible mechanism of RNA recombination is replicative template switching, with synthesis of a complementary strand starting on one viral RNA molecule and being completed on another. The newly synthesized RNA is a primary recombinant molecule in this case. Recent studies have revealed other mechanisms of replicative RNA recombination. In addition, recombination between the genomes of RNA viruses can be nonreplicative, resulting from a joining of preexisting parental molecules. Recombination is a potent tool providing for both the variation and conservation of the genome in RNA viruses. Replicative and nonreplicative mechanisms may contribute differently to each of these evolutionary processes. In the form of trans splicing, nonreplicative recombination of cell RNAs plays an important role in at least some organisms. It is conceivable that RNA recombination continues to contribute to the evolution of DNA genomes.

Nonreplicative RNA recombination in poliovirus.

Current models of recombination between viral RNAs are based on replicative template-switch mechanisms. The existence of nonreplicative RNA recombination in poliovirus is demonstrated in the present study by the rescue of viable viruses after cotransfections with different pairs of genomic RNA fragments with suppressed translatable and replicating capacities. Approximately 100 distinct recombinant genomes have been identified. The majority of crossovers occurred between nonhomologous segments of the partners and might have resulted from transesterification reactions, not necessarily involving an enzymatic activity. Some of the crossover loci are clustered. The origin of some of these "hot spots" could be explained by invoking structures similar to known ribozymes. A significant proportion of recombinant RNAs contained the entire 5' partner, if its 3' end was oxidized or phosphorylated prior to being mixed with the 3' partner. All of these observations are consistent with a mechanism that involves intermediary formation of the 2',3'-cyclic phosphate and 5'-hydroxyl termini. It is proposed that nonreplicative RNA recombination may contribute to evolutionarily significant RNA rearrangements.

Poliovirus neurovirulence correlates with the presence of a cryptic AUG upstream of the initiator codon.

Poliovirus mutants with extended (> 150-nt) deletions in the 5'-untranslated region between the internal ribosome entry site and the initiator codon have been selected previously (Pilipenko et al., Cell 68, 119-131, 1992; Gmyl et al., J. Virol. 67, 6309-6316, 1993). These deletions were transferred into the genome of a mouse-pathogenic poliovirus strain and found to be strongly attenuating. The deletions can be considered as covering three structural elements, a stem-loop (domain E) with a conserved cryptic AUG and two spacers, upstream and downstream of it. In an attempt to identify putative essential determinants of neurovirulence in these individual structural elements, appropriate mutants were engineered. The results demonstrated that neither of the above elements is essential for neurovirulence. The results strongly suggested that the presence of a cryptic AUG in the oligopyrimidine/AUG tandem followed, at a sufficient distance, by the initiator codon was necessary to ensure the neurovirulent phenotype of our constructs. On the other hand, the attenuated phenotype appeared to correlate with the occurrence of the initiator AUG as a moiety of the oligopyrimidine/AUG tandem. Possible mechanisms underlying these effects are discussed. Identification of the cryptic AUG as an essential determinant for neurovirulence provides a rational basis for the design of genetically stable attenuated poliovirus variants.

A model for rearrangements in RNA genomes.

Engineered mutants of Theiler's murine encephalomyelitis virus (TMEV) and poliovirus having altered spacing between the oligopyrimidine and AUG moieties of a translational control element are known to generate pseudorevertants with deletions or insertions that tend to restore the wild-type structure of this element. The primary structure of the rearranged region of these pseudorevertants suggests that short direct repeats are strongly preferred as parting and anchoring sites during the jumps of the nascent strand 3' end. When the parting and anchoring sites are separated by a long RNA segment, they can be brought in close proximity by an appropriate folding of the template strand. On the basis of evidence derived from the analysis of the pseudorevertant genomes, it is proposed that a class of RNA rearrangements (some recombinations, deletions, insertions) proceed through the following steps: (i) pausing of the nascent strand caused by misincorporations (or other reasons); (ii) dissociation of the RNA polymerase together with the 3' end of the nascent strand (a kind proof-reading); and (iii) re-annealing of the nascent and template strands (precise or imprecise, but with the 3' base paired) and resumption of the synthesis.

[The critical significance of a conserved single-stranded interdomain linker in the 5'-untranslated region of poliovirus RNA]. / Kriticheskoe znachenie konservativnogo odnotsepochechnogo mezhdomennogo linkera v 5'-netransliruemoi oblasti poliovirusnoi RNK.

Translation of polioviral RNA is initiated by interaction of a small ribosomal subunit with internal segments of the 5'-untranslated region (5'UTR). Several mutations were constructed within 5'UTR segment 425-449. All of them (including a single C444-->U replacement) inhibited in vitro translation, which decreased about 10-fold. Two mutant constructs, pPV12-05 (C444-->U) and pPV12K (containing also an AAUU insert between positions 441 and 442) produced plaques on monolayers of susceptible cells. All the viruses isolated from these plaques exhibited a reversion at position 444; the template activities of the revertant RNAs were restored completely or significantly. The results show the importance of the relevant 5'UTR segment for the initiation of polioviral RNA translation.

Attenuation of Theiler's murine encephalomyelitis virus by modifications of the oligopyrimidine/AUG tandem, a host-dependent translational cis element.

A set of Theiler's murine encephalomyelitis virus mutants with engineered alterations in the conserved oligopyrimidine/AUG tandem (E. V. Pilipenko, A. P. Gmyl, S. V. Maslova, G. A. Belov, A. N. Sinyakov, M. Huang, T. D. K. Brown, and V. I. Agol, J. Mol. Biol. 241:398-414, 1994) were assayed for their growth potential in BHK-21 cells (as reflected in plaque size) and for neurovirulence upon intracerebral inoculation of mice. Tandem-destroying mutations, which included substitutions in the oligopyrimidine moiety and extended insertions into the oligopyrimidine/AUG spacer, exerted relatively little effect on the plaque size but ensured a high level of attenuation. The attenuated mutants exhibited remarkable genetic stability upon growth in BHK-21 cells. However, the brains of rare animals that developed symptoms after the inoculation with high doses of these mutants invariably contained pseudorevertants with the oligopyrimidine/AUG tandem restored by diverse deletions or an AUG-generating point mutation. The AUG moiety of the tandem in the revertant genomes was represented by either a cryptic codon or initiator codon. The results demonstrate that the tandem, while dispensable for the Theiler's murine encephalomyelitis virus growth in BHK-21 cells, is essential for neurovirulence in mice. Thus, the oligopyrimidine/AUG tandem is a host-dependent cis-acting control element that may be essential for virus replication under certain conditions. The functional activity of the tandem was retained when its oligopyrimidine or AUG moieties were made double stranded. A possible role of the tandem in the cap-independent internal initiation of translation on the picornavirus RNA templates is discussed.

Starting window, a distinct element in the cap-independent internal initiation of translation on picornaviral RNA.

Initiation of translation on picornaviral RNA templates occurs via cap-independent ribosome binding to a cis-acting element, internal ribosome entry site (IRES). Mapping of the starting point of translation relative to the IRES was attempted using Theiler's murine encephalomyelitis virus (TMEV) RNA as a model. The possibility that the starting point is determined by the conserved oligopyrimidine upstream of the initiator codon was studied. In contrast to poliovirus, neither the conserved oligopyrimidine nor an AUG at a fixed distance downstream of this oligopyrimidine are required for efficient translation of the TMEV RNA in Krebs-2 extracts or reticulocyte lysates or for viral infectivity; mutants lacking the oligopyrimidine/AUG tandem were stable upon passage in BHK-21 cells. A short template segment, the starting window, was defined, wherefrom ribosomes begin translation or downstream scanning depending, respectively, on the presence or absence of a good-context AUG within this window. Using a collection of the engineered TMEV mutant RNAs, the starting window was mapped to 16-17 nt downstream of the IRES and was found to be approximately a dozen nt long. The efficiency of translation initiation from an AUG linearly increased upon the 5'-->3' displacement of the initiator codon within the window. The competence of the starting window did not appear to depend markedly on its primary structure; however, it was completely inactivated ("closed") with concomitant dramatic inhibition of total protein synthesis upon conversion of the corresponding RNA segment into a double-stranded form.

Genetic studies on the poliovirus 2C protein, an NTPase. A plausible mechanism of guanidine effect on the 2C function and evidence for the importance of 2C oligomerization.

Poliovirus RNA replication is known to be inhibited by millimolar concentrations of guanidine. A variety of guanidine-resistant (gr) and guanidine-dependent (gd) poliovirus strains were selected, and mutations responsible for the phenotypic alterations were mapped to distinct loci of the viral NTP-binding pattern containing protein 2C. Together with already published results, our data have demonstrated that the overwhelming majority of guanidine mutants of poliovirus 2C can be assigned to one of the two classes, N (with a change in Asn179) or M (with a change in Met187). As inferred from the structure/function relations in other NTP-binding proteins, both these "main" mutations should reside in a loop adjoining the so-called B motif known to interact with the Mg2+ involved in the NTP splitting. In classes M (always) and N (not infrequently), these B motif mutations were combined with mutations in, or close to, motif A (involved in binding of the NTP phosphate moieties) and/or motif C (another conserved element of a subset of NTP-binding proteins). These data strongly support the notion that the region of polypeptide 2C involved in the NTP utilization is affected by the guanidine mutations and by the presence of the drug itself. The mutations, however, never altered highly conserved amino acid residues assumed to be essential for the NTP binding or splitting. These facts and some other considerations led us to propose that guanidine affects coupling between the NTP binding and/or splitting, on the one hand, and the 2C function (related to conformational changes), on the other. Both N and M classes of mutants contain gr and gd variants, and the gr/gd interconversion as well as modulations of the guanidine phenotype can be caused by additional mutations within each class; sometimes, these additional substitutions are located far away from the "main" mutations. It is suggested that the target for guanidine action involves long-range tertiary interactions. Under conditions restrictive for the individual growth of each parent, efficient reciprocal intra-allelic complementation between guanidine-sensitive (gs) and gd strains (of M or N classes) was observed. The complementation occurred at the level of viral RNA synthesis. These data allowed us to propose that oligomerization of polypeptide 2C is an essential step in the replication of viral genome.

Functional and genetic plasticities of the poliovirus genome: quasi-infectious RNAs modified in the 5'-untranslated region yield a variety of pseudorevertants.

Poliovirus RNA species with nucleotides 564 to 571 deleted or with a secondary structure domain (positions 564 to 629) replaced by a shorter irregular oligonucleotide have been engineered previously; these RNAs have been considered quasi-infectious (yielding a single late revertant plaque) and dead, respectively (E. Pilipenko, A. Gmyl, Y. Svitkin, S. Maslova, A. Sinyakov, and V. Agol, Cell 68:119-131, 1992). By using large amounts of these RNAs for transfections, revertant clones with a great variety of genetic changes (point mutations, insertions of foreign sequences, short or extended deletions) were isolated. The pattern of these changes supported the notion that an appropriately spaced oligopyrimidine-AUG tandem is important for efficient poliovirus RNA translation. Structural features within and around this tandem modulated the initiation efficiency. The functional and genetic plasticities of the poliovirus genome are briefly discussed.

Prokaryotic-like cis elements in the cap-independent internal initiation of translation on picornavirus RNA.

Initiation of translation on picornavirus RNAs is accomplished through internal binding of ribosomes to a complex cis-acting element. Here we show that efficient function of this element involves two appropriately spaced smaller elements: UUUCC and an AUG. This conclusion emerged from analysis of the genome structures of spontaneous revertants of mutant polioviruses with extended insertions between the UUUCC and AUG motifs. It was confirmed by the results obtained with specially designed constructs. A similarity to the prokaryotic translation initiation mechanism, which involves the Shine-Dalgarno sequence, is emphasized, but in the picornavirus system the position of the UUUCC must be strictly fixed relative to upstream cis-acting elements, and the AUG may not necessarily serve as an initiation codon.