[Evaluation of the dynamics of detection of viable SARS-CoV-2 (Coronaviridae: Betacoronavirus: Sarbecovirus) in biological samples obtained from patients with COVID-19 in a health care setting, as one of the indicators of the infectivity of the virus]

INTRODUCTION

The study of the mechanisms of transmission of the SARS-CoV-2 virus is the basis for building a strategy for anti-epidemic measures in the context of the COVID-19 pandemic. Understanding in what time frame a patient can spread SARS-CoV-2 is just as important as knowing the transmission mechanisms themselves. This information is necessary to develop effective measures to prevent infection by breaking the chains of transmission of the virus. The aim of the work is to identify the infectious SARS-CoV-2 virus in patient samples in the course of the disease and to determine the duration of virus shedding in patients with varying severity of COVID-19.

MATERIALS AND METHODS

In patients included in the study, biomaterial (nasopharyngeal swabs) was subjected to analysis by quantitative RT-PCR and virological determination of infectivity of the virus.

RESULTS

We have determined the timeframe of maintaining the infectivity of the virus in patients hospitalized with severe and moderate COVID-19. Based on the results of the study, we made an analysis of the relationship between the amount of detected SARS-CoV-2 RNA and the infectivity of the virus in vitro in patients with COVID-19. The median time of the infectious virus shedding was 8 days. In addition, a comparative analysis of different protocols for the detection of the viral RNA in relation to the identification of the infectious virus was carried out.

CONCLUSION

The obtained data make it possible to assess the dynamics of SARS-CoV-2 detection and viral load in patients with COVID-19 and indicate the significance of these parameters for the subsequent spread of the virus and the organization of preventive measures.

Phylogenetic reconstruction of the initial stages of the spread of the SARS-CoV-2 virus in the Eurasian and American continents by analyzing genomic data

Samples from complete genomes of SARS-CoV-2 isolated during the first wave (December 2019–July 2020) of the global COVID-19 pandemic from 21 countries (Asia, Europe, Middle East and America) around the world, were analyzed using the phylogenetic method with molecular clock dating. Results showed that the first cases of COVID-19 in the human population appeared in the period between July and November 2019 in China. The spread of the virus into other countries of the world began in the autumn of 2019. In mid-February 2020, the virus appeared in all the countries we analyzed. During this time, the global population of SARS-CoV-2 was characterized by low levels of the genetic polymorphism, making it difficult to accurately assess the pathways of infection. The rate of evolution of the coding region of the SARS-CoV-2 genome equal to 7.3 × 10⁻⁴ (5.95 × 10⁻⁴–8.68 × 10⁻⁴) nucleotide substitutions per site per year is comparable to those of other human RNA viruses (Measles morbillivirus, Rubella virus, Enterovirus C). SARS-CoV-2 was separated from its known close relative, the bat coronavirus RaTG13 of the genus Betacoronavirus, approximately 15–43 years ago (the end of the 20th century).

Genetic diversity and geographical distribution of the Siberian subtype of the tick-borne encephalitis virus

The tick-borne encephalitis virus (TBEV), a member of the Flaviviridae family, is currently subdivided into three main subtypes-the European (TBEV-Eu), the Far-Eastern (TBEV-FE), and the Siberian (TBEV-Sib). The TBEV-Sib is the most common subtype and found in all regions where TBEV was detected, except for Central and Western Europe. Currently, four genetic lineages have been described within TBEV-Sib. In this study, detailed analysis of TBEV-Sib genetic diversity, geographic distribution, phylogeography and divergence time of different TBEV-Sib genetic lineages based on E gene fragments, complete genome sequences, and all currently available data in the GenBank database was performed. As a result, a novel Bosnia lineage within the TBEV-Sib was identified. It was demonstrated that the Zausaev lineage is the most widely distributed among the TBEV-Sib lineages, and was detected in all studied regions except the Far East. The Vasilchenko lineage was found from Western Siberia to the Far East. The Baltic lineage is presented from Europe to Western Siberia. The Obskaya lineage was found only in Western Siberia. TBEV strains from a newly described Bosnia lineage were detected in Bosnia, the Crimean peninsula, Kyrgyzstan and Kazakhstan. The greatest divergence of the TBEV-Sib genetic variants was observed in Western Siberia. Within the TBEV-Sib, the Obskaya lineage diverged from the common ancestor the earliest, after that the Bosnia lineage was separated, then the Baltic lineage, and the Zausaev and Vasilchenko lineages diverged most recently.

DEFINITION AND COMPARATIVE ANALYSIS OF THE GENOMIC STRUCTURE OF SIBERIAN STRAINS OF TICK-BORNE ENCEPHALITIS VIRUS OF THE EUROPEAN SUBTYPE

Tick-borne encephalitis virus (TBEV) is classified into three subtypes: Far Eastern (TBEV-FE), European (TBEV-EU) and Siberian (TBEV-SIB). In Russia, these are also called genotypes 1, 2 and 3, respectively. Geographically, TBEV-EU dominates in Central and Northern Europe, but its representatives are also found to the east - along the southern part of the forest zone of extratropical Eurasia - up to Eastern Siberia and South Korea. However, the strains isolated outside Europe remain poorly investigated. In the proposed study, eight full genomes of the Siberian isolates of TBEV-EU were determined and 13 complete genomes were compared. The analysis of 152 full-genome TBEV sequences showed that the TBEV-EU has a higher degree of stability of the genome-coding region in the entire Eurasian area (3.1% of differences) compared to TBEV-FE (6.6%) and TBEV-SIB (7.8%). At the same time, the maximum differences are observed not between European and Siberian strains, as one could expect, but between the representatives from Europe - TBEV strains Mandl-2009 from Norway and Hypr from the Czech Republic. The studied strains from Siberia form the compact genetic cluster of 42 TBEV-EU strains and are divided into two subclusters - West Siberian and East Siberian variants. These variants differ in the combinations of amino acid substitutions in all proteins except NS2B. The West Siberian variant mostly circulates in the territory of Altai, and the closest relative of its representatives is Absettarov strain from the European part of Russia. The strains similar to the East Siberian variant of the European subtype were recorded in the Altai (strain 84.2, 2007) and in Belarus (N256, about 1940).

Influence of altitude on tick-borne encephalitis infection risk in the natural foci of the Altai Republic, Southern Siberia

The Altai Republic is a highly endemic area as far as tick-borne encephalitis (TBE) is concerned. The aim of the research was to study the effect of altitude on the risk of tick-borne encephalitis infection in the Altai Republic. The paper analyzes the following data: the study of ixodid ticks collected from the vegetation in 116 sites at the 200-2383m elevation above sea level in 2012-2014, TBE virus prevalence of these vectors, tick-bite incidence rate, and TBE incidence rate of the population. Species identification of 4503 specimens has shown that the most common species are Dermacentor nuttalli (45.3%), Ixodes persulcatus (33.1%), Dermacentor silvarum (9.4%), Dermacentor reticulatus (8.9%), and Haemaphysalis concinna (5.0%). A total of 2997 adult ixodid ticks were studied for the presence of the TBE virus; 2163 samples were examined by ELISA, while 834 specimens were tested by PCR. The TBE virus prevalence of Dermacentor spp. ticks in both reactions was significantly higher than of Ixodes persulcatus ticks (p<0.001). The work shows that the altitude is an important factor in the development of the epidemiological situation of tick-borne encephalitis: the higher the elevation of the area above sea level, the smaller the range of vectors. There is also a change of a leading species: in middle altitude (800-1700m above sea level) the virus is transmitted by ticks of D. nuttalli along with I. persulcatus, and in high mountains (above 1700m above sea level) D. nuttalli becomes an absolute dominant species. However, these species of ticks are less effective vectors than I. persulcatus. With the increase of altitude the tick-bite incidence rate decreases (r=-0.78, p<0.05), and TBE incidence also reduces (r=-0.67, p<0.05).

[Detection of potential sites of recombination in the Tick-borne encephalitis virus by the methods of comparative genomics]

The results of the bioinformatic search for the potential sites of the recombination in the genome-wide structures of the tick-borne encephalitis virus (TBEV) through a series of software techniques were presented in this work. The genomes of the 55 TBEV strains were assayed, 21 of them showed the presence of the recombination sites. Recombinant strains belonged to the Far Eastern (19 strains) and European (2 strains) genotypes. 22 sites of the recombination attributed were identified to five types based on position, strain, and regional characteristics. The parental strains were identified based on the genotypic and geographical parameters, which do not contradict the possibility of the formation of the recombinants. Nearly two-thirds of the sites are located in the regions of NS4a and NS4b genes, which are the "hot spots" of the recombination, most of them being concentrated in the gene NS4. It was shown that the recombination processes did not occur at the level of the genotypes (European genotype) or certain groups within the genotype (Far East) and were typical of the peripheral populations.

[Genotypes 4 and 5 of the tick-borne encephalitis virus: features of the genome structure and possible scenario for its formation]

On the basis of the comparison of complete genome structures of 32 strains and gene E fragments (160 ndt) of 643 strains and RNA isolates of tick-borne encephalitis (TBE) virus, we confirmed our previously expressed assumption (Zlobin V.I. et al, 2001) of existence, along with the three major genotypes, of genotypes 4 (strain 178-79) and 5 (strain 886-84). "Mosaic" structure of the polyprotein in the two strains was established. It manifests itself in particular in the sequences of 14 positions (C-3, E-206, NS1-54, NS-285, NS2A-100, NS2A-127, NS2A-174, NS2A-175, NS2A-225, NS3-376, NS4B-28, NS4B-96, NS5-18, NS5-671) containing the amino acids strictly conserved for each of the three major genotypes and is consistent with a uniform pattern of distribution of nucleotide substitutions that are specific for genotypes 1, 2 and 3. Possible scenario of the origin of TBE genotypes 4 and 5 was suggested.

[Detection of tick-borne encephalitis virus in Ixodes ticks collected in a natural focus of Gornyi Altai]

Enzyme immunoassay of tick-borne encephalitis virus (TBE) in the samples of Ixodes ticks collected in the outskirts of the settlement of Manzherok, Maiminsk District, Republic of Altai, revealed TBE antigen in 16.9 +/- 1.9% of the talga ticks. Real-time reverse transcription-polymerase chain reaction (RT-PCR) with specific fluorescent probes and phylogenetic analysis of the nucleotide sequences of RT-RCR products corresponding to 5'-terminal fragment of the E gene of TBE, all the virus strains isolated from the ticks collected in Gomyi Altai were referred to as the Siberian genetic type that was dominant in virus-carrying ticks in the majority of endemic areas of Russia and near abroad. Viral load assays using the real-time RT-PCR with the probes indicated the threshold cycles Ct = 25.34-28.98, which, with regard to the efficiency of RNA identification and reverse transcription, was equal to about 10(4)-10(5) viral RNA copies per tick.

[Detection of recombinations in tick-borne encephalitis virus by using computer analysis of viral genomes]

Computer programs were used to search for tick-borne encephalitis (TBE) virus recombinants among the isolates whose complete nucleotide sequences are deposited in the GenBank database. The application of RDP, Chimaera, Maximum chi2, and TOPAL programs has revealed recombinant sites in a number of sequences, which indicates that TBE virus has recombinations and that the programs are suitable for their detection.

[RT-PCR detection of deformed wing virus in the honey bee Apis mellifera L. in the Moscow Region]

Deformed wing virus (DWV) was first detected in the honey bee Apis mellifera by reverse transcriptase-polymerase chain reaction (RT-PCT) in the Moscow Region. Molecular phylogenetic analysis of the detected nucleotide sequence of the virus fragment VP2-VP1 of DWV demonstrated that the Russian virus sequence is united in the common cluster with all earlier revealed nucleotide sequences of DWV in the Genbank worldwide, which confirms the previous conclusions that this virus has recently distributed in the honey bee by Varroa destructor mite. It has been shown that the level of homology for all DWV nucleotide sequences is 98%, except for nucleoside sequence of 7D isolate from Turkey (96% homology), 96% homology with Kakugo virus and 84-86% homology with Varroa destructor virus 1; there is a preponderance of insignificant nucleotide substitutions, mainly transitions, which supports the evolutionary propinquity of 3 viruses.

[Genetic characteristics of the causative agent of tick-borne encephalitis in Mongolia]

A patient with diagnosed meningoencephalitis and a history of tick bite died in Mongolia in 2008. The purpose of this paper is to characterize the virus causing the ill person's death. The virus was identified using the phylogenetic analysis of the 520-bp fragment of the tick-borne encephalitis virus (TBEV) genome, which codes the fragment of TBEV protein E between 52-223 amino acids. TBEV RNA was detected in the samples of medulla oblongata, cerebral cortex, and pia mater of brain, but not in the cerebellar tissue. The study virus fragment was genetically closest to the representatives of the Far East subtype. Its closest relative was virus 740-84 (GenBank EU878282) isolated from large-toothed redback voles (Clethrionomys glareolus) in Buryatia and greatly differed from the Far East virus Soffin. Two amino acid substitutions (H86R and VI7A) were detected within the study protein E fragment. The paper is the first to describe the causative agent of tick-borne encephalitis on the territory of Mongolia and to discuss the evolution and pathogenicity of TBEV.

[Human bocavirus]

Human bocavirus (HBoV) is a newly identified parvovirus associated with acute respiratory infections in young children in different parts of the world. It is not inconceivable that this virus is also capable of causing acute gastroenteritis and asymptomatically persisting in infected children. HBoV is the third widespread human respiratory virus after respiratory syncytial virus and rhinovirus. Polymerase chain reaction remains the most reliable of HBoV detection in clinical samples. Phylogenetic analysis shows the presence of at least 2 circulating variants (genotypes) of HBoV.

[The genetic variability and genotyping of tick-borne encephalitis virus with deoxyoligonucleotide probes]

A panel of genotype-specific molecular probes has been designed, which is used to indicate and differentiate tickborne encephalitis (TBE) virus. It assesses the individual genetic structure of each strain since the targets for the probes are the variable sequences of all 10 virus genes, which are specific for each of three genotypes. The molecular nucleic acid hybridization by means of the panel was used to study 273 TBE virus strains. Isolated from a Eurasian area; along with the representatives of three genotypes, the virus strains, the genomic structures of which do not fit in the established concept on three genotypes, circulate in Eastern Siberia.

[The enter of viruses family Picornaviridae in residents macrophages]

Viruses enter in cells through clathrin- and dinamin-mediated uptake route-endocytosis, caveolae-mediated local destruction of cell plasma membranes, and macropinocytosis. The non-enveloped viruses to which Picornaviridae famiy is attributed are important human and animal pathogens. The aim of this study was to examine the mechanisms of penetration of viruses of this family (polio-, echo 11-, entero 71- and coxsackie B1-viruses) into resident macrophages. After attachment to the plasma membrane of macrophages the enterovirus 71 and coxsackievirus B1 penetrated into macrophages by invagination of the plasma membrane and formation of intracytoplasmic vesicules - caveoles. The poliovirus entered macrophages both by caveols formation and local destruction of plasma membranes of the host cells. Macropinocytos of polioviruses was observed after 45 min contact. The echovirus 11 entered in host macrophages by local destruction of their plasma membranes during first 15 min. Then the formation of endocytosed vesicles with included viruses was observed. The echovirus 11 went out of endocytosed vesicles by local destruction of membrane vesicles.

[Molecular epidemiology of tick-borne encephalitis]

The review presents information on the development of studies into the molecular epidemiology of tick-borne encephalitis (TBE) in Russia and foreign countries. The existence of three major virus genotypes has been established by various techniques, such as genomic fragment sequencing, molecular hybridization using genotype-specific probes, and restriction fragment length polymorphism test. Each of the genotypes prevails in different parts of a natural habitat; the Ural-Siberian genotype (a Siberian subtype) is most commonly encountered. The genetic differences between the strains belonging to different genotypes are great and comparable with differences between some mammalian flaviviruses transmitted by ticks (viruses of a TBE complex). Further studies of the molecular epidemiology of TBE are of importance in understanding the evolution of the causative agent, improving the taxonomy and the classification of flavivuruses, and designing highly effective methods for the specific diagnosis, prevention, and treatment of the disease.

[Current approaches to emergency specific prevention of tick-borne encephalitis]

Emergency specific prevention of tick-borne encephalitis (TBE) by using homologous immunoglobulin is an important element in the package of controlling measures against this viral natural and focal infection. There are annually a few hundred thousand referrals for health care facilities for tick bites. Their maximum coverage tactics via immunoglobulin prevention is medically unreal and unjustifiable. The paper presents the results of a long-term application of another approach based on preliminary rapid studies of the ticks taken from victims or the blood of patients in the period of possible development of virusemia and preventive immunoglobulin use only in the persons bitten with TBE virus-infected ticks. Examination of the material available from more than 56 thousand referrals indicated the high epidemiological (more than 99%) and economic effectiveness of the target administration of an immunological drug. By taking into account the accumulated data on a wide spread of combined foci of TBE and other tick-borne infections and the authors' own experience, it is suggested that it is necessary to organize a comprehensive differential laboratory diagnosis and emergency prevention against the whole complex of Ixodes tick-borne infections.

[Prevention of tick-borne encephalitis at the present stage: strategy and tactics]

The paper discusses the prevention of tick-borne encephalitis (TBE) under the conditions of a varying epidemiologic situation. High mortality, a change in its structure, an expansion of a nosological area, an increase in the number of anthropurgic foci in the suburbs and towns and cities, the detection of combined foci and the development of mixed forms of tick-borne infections, and clinical pathomorphism suggest that novel approaches to preventing this severe viral disease are urgent. The comprehensive nature of a prophylaxis system should envisage the use of tried-and-true specific and nonspecific measures against the entire group of tick-borne infections. Cohort vaccination should be considered as a priority measure in high TBE endemic areas. The prophylaxis system should be differentiated and adequate to the specific epidemic situation in the endemic regions.

[Complex environmental and virological monitoring in the Primorye Territory in 2003-2006]

The paper presents the results of monitoring of viruses of Western Nile (WN), Japanese encephalitis (JE), tick-borne encephalitis (TBE), Geta, Influenza A, as well as avian paramicroviruses type I (virus of Newcastle disease (ND)) and type 6 (APMV-6) in the Primorye Territory in 2003-2006. Totally throughout the period, specific antibodies to the viruses were detected by neutralization test in wild birds (7.3%, WN; 8.0%, Geta; 0.7% Batai; 2.8%, Alpine hare (Lepus timidus); by hemagglutination-inhibition test in cattle (11.4% WN; 5.9%, JE; j 3.0%, TBE; 11.6%, Geta), horses (6.1, 6.8, 0, and 25.3%, respectively), and pigs (5.4, 1.5, 0, and 5.9%, respectively) by enzyme immunoassay (IgG) in human beings (0.8, 0.5, 6.8, and 3.2%, respectively. Reverse-transcription polymerase chain reaction (RT-PCR) was used to reveal RNA of the NP segment of influenza A virus in 57.9 and 65% of the cloacal swabs from wild and domestic birds, respectively; and the HA-segment of subtype HH was not detected in 2005. HA/H5 RNA was recorded in 5.5 and 6.7% of the swabs from wild and domestic birds, respectively; 6% of the specimens from domestic birds were M-segment positive in 2006. RNA of influenza A virus NA/H7 and RNA was not detected throughout the years. In 2004, the cloacal swabs 8 isolated influenza A strains: two H3N8 and two H4N8 strains from European teals (Anas crecca), two (H3N8 and H6N2) strains from Baikal teals (A. formosa), one (H10N4) strain from shovelers (A. clypeata), and one (H4N8) from garganeys (A. querquedula). In 2004, one ND virus strain was isolated from the cloacal swabs from European teals (A. crecca). RT-PCR revealed RNA of this virus in some 8 more cloacal swabs from black ducks (A. poecilorhyncha) (3 positive specimens), pheasants (Phasianus colchicus) (n = 2), garganeys (A. querquedula) (n = 1), gadwalls (A. strepera) (n = 1), and geese (Anser anser domesticus) (n = 1). Sequencing of the 374-member fragment of the ND virus F gene, which included a proteolytic cleavage site, could assign two samples to the weakly pathogenetic variants of genotype 1, one sample to highly pathogenic variants of genotype 3a, five to highly pathogenic ones of genotype 5b. Isolation of APMV-6 (2003) from common egrets (Egretta alba) and geese (Ans. anser domesticus) is first described.

[Tick-borne encephalitis in the Russian Federation: state-of-the-art and prevention policy]

The last quarter of the 20th century in the Russian Federation was marked by an unprecedented increase in the incidence of tick-borne encephalitis (TBE) with its peaks in 1996 and 1999 when as high as 10,000 cases of the disease were notified. Its highest incidence was recorded in the Regions of the Urals and Siberia. As many as 70-80% of the persons who felt ill were urban dwellers who had been infected mainly in the anthropurgic foci occurring in abundance in the environs of cities and towns. It was found that the area of TBE had been expanded and virus-infected ticks had actively penetrated into the urban parks and small public gardens. There were as many as 70 TBE-endemic regions. As of now, it has been ascertained that TBE foci are generally combined with other infections transmitted by Ixodes ticks and caused by viruses, bacteria, rickettsia and protozoa. This result is the occurrence of mixed infections, which requires new approaches to their diagnosis, treatment, and prevention. The prevention of TBE is conventionally based on vaccination of high-risk groups comprising mainly "forest" occupations. Under the present conditions, the strategy of TBE control should be radically revised towards mass vaccination of the population living in the highly endemic areas, which will drastically reduced morbidity in the country.

Tick-borne virus diseases of human interest in Europe

Several human diseases in Europe are caused by viruses transmitted by tick bite. These viruses belong to the genus Flavivirus, and include tick-borne encephalitis virus, Omsk haemorrhagic fever virus, louping ill virus, Powassan virus, Nairovirus (Crimean-Congo haemorrhagic fever virus) and Coltivirus (Eyach virus). All of these viruses cause more or less severe neurological diseases, and some are also responsible for haemorrhagic fever. The epidemiology, clinical picture and methods for diagnosis are detailed in this review. Most of these viral pathogens are classified as Biosafety Level 3 or 4 agents, and therefore some of them have been classified in Categories A-C of potential bioterrorism agents by the Centers for Disease Control and Prevention. Their ability to cause severe disease in man means that these viruses, as well as any clinical samples suspected of containing them, must be handled with specific and stringent precautions.

[Ecology and evolution of influenza viruses in Russia (1979-2002)]

The research results on ecology and evolution of influenza A viruses, which has been conducted by the Center of Ecology and Evolution of influenza Viruses of Ivanovsky's Institute of Virology, Russian Academy of Medical Sciences, for more than 30 years, are summarized in the paper. A gene pool of influenza A viruses circulating in Russia's territory was defined. Foci of influenza A viruses were detected in natural biocenosis. Issues conditioned by the population interrelations of influenza viruses, i.e. between the populations of wild and home animals and the populations of people, are also under discussion.

[Specific determination of flaviviruses by molecular hybridization with synthetic deoxyoligonucleotide probes]

Molecular probes were designed for the purpose of specific determination of flavioviruses transmitted by the ticks of tick-borne encephalitis (TBE) and Omsk hemorrhagic fever (OHV) as well as by mosquitoes of Japanese encephalitis (JE), North Nile (NN), Murrey Valley encephalitis (MVE), Saint-Lois encephalitis (SLE), dengue 1-4 and of yellow fever (YF). The probes are synthetic deoxyoligonucleotides with the 18-20 long basis and complementary for the RNA fragments defined by computer analysis. The thus obtained probes, which specifically hybridize themselves with the sets of the TBE virus or of the OHV virus and do not hybridize themselves with other TBE viruses' sets. Group-specific probes for YE and dengue viruses as well as virus-specific probes, which are able to detect each of the above viruses without any cross effects, were suggested for indexing and identifying the flaviviruses transmitted by mosquitoes.

[Genetic typing of tick-borne encephalitis virus based on an analysis of the levels of homology of a membrane protein gene fragment]

All heretofore known genomic structures of tick-borne encephalitis (TBE) virus are analyzed. The authors prove the adequacy of using short fragment of E protein gene for characterization of philogenetic relationships between TBE strains. Three main genotypes of the virus are distinguished, one corresponding to Far Eastern variant, one to West, and the third includes strains belonging to Ural Siberian and Central Siberian and Transbaikal variants. Results of genetic typing by nucleotide sequences are confirmed by analysis of amino acid sequences of E protein fragments, specific marker amino acids in definite positions being determined for each genotype.

[Analysis of genetic variability of strains of tick-borne encephalitis virus by primary structure of a fragment of the membrane protein E gene]

Primary structures of gene fragments of E protein (160 n.b.) have been determined for 29 tick-borne encephalitis (TBE) strains isolated from different parts of a territory. Analysis of homology of nucleotide sequences of these strains and data on 6 TBE strains published by other authors showed that they can be divided into 6 groups (genotypes) by the following gene typing criteria: strain structure within the genotypes differing by no more than 9%, differences between strains of different genotypes are at least 12%. Based on these criteria, the prototype strains of the Far Eastern antigenic variant (Sofyin), Central European antigenic variant (Neudoerfle), and Vergina strain form different genotypes 1, 2, and 6, respectively. East Siberian strain Aina and Ural Siberian strain Lesopark-II belong to the same TBE virus genotype 3; two-thirds of analyzed strains belong to this genotype. Genotype 4 is represented by one strain 178-79, and genotype 5 by strain 886-84, both isolated in East Siberia.

[Vergina-like strains of tick-borne encephalitis in Russia]

The Greek strain Vergina representing an individual third serotype of tick-borne encephalitis (TBE) virus has been compared with 13 TBE strains isolated on the territory of Russia and Central Asia (in Kirghizia). A kit of deoxyoligonucleotide probes complementary to genome sites of Neudorfle strain of the TBE Central European subtype (protein C and prM genes) and of strain Sofyin of the Eastern subtype (protein E, C, M, prM, ns 1, ns 2b, ns 4b genes) was used in molecular hybridization of nucleic acids. Vergina strain was referred to the genetic variant VI prevalent in the western part of the East European plain, in Udmurtia, in the Altai mountains, and in West Siberia. By its antigenic properties Vergina strain is most close to strain Yar-90 isolated in the Yaroslavl district from Ixodes persulcatus ticks.

Antibodies against tick-borne encephalitis virus (TBEV) non-structural and structural proteins in human sera and spinal fluid

Western immunoblotting of the serum and spinal fluid of patients with tick-borne encephalitis (TBE) revealed the presence of antibodies against non-structural and internal virion proteins. Antibodies against different viral proteins have been shown to appear 8 days postinfection and to circulate for more than 2 months in case of acute TBE. Antibodies against structural glycoprotein E and non-structural glycoprotein NS1 do not prevail over antibodies against other kinds of viral proteins. The large viral non-structural proteins NS5 and NS3 and small hydrophobic proteins NS2A and NS4B can cause an effective immune response as well. There is no strong correlation between immune response spectrum and fever or meningitis forms of disease. However, sera of patients with chronic TBE contained IgM antibodies to virus-specific proteins more than 1 year later and IgG antibodies with very low titers (if any).

[Genomic changes in strains of the tick-borne encephalitis virus as a result of passages in mice]

Changes in genomes of TBE strains isolated from various sources at early stages of laboratory adaptation to white mice brain were demonstrated by molecular hybridization of nucleic acids with synthetic oligonucleotide probes, complementary RNA sites of reference TBE strains Sofyin and Neudorf. Of the 4 TBE strains passed 6 times through white mice brain in only 1 the level of RNA hybridization with 2 oligonucleotide probes was found changed, whereas in all the 3 tested strains the level of RNA hybridization with 1-2 oligonucleotide probes complementary to strain Sofyin was increased after 7-16 passages in the same system. The most noticeable changes in the genome were detected during readaptation to white mice of a TBE variant selected in passages on H. marginatum marginatum ticks.

[The genetic characteristics of the Vergina serotype of the tick-borne encephalitis virus and its pathogenetic traits]

The Greek Vergina strain of tick-borne encephalitis (TBE) virus was studied in comparison with 7 other strains by molecular hybridization of nucleic acids and by clinicomorphological markers of pathogenicity for monkeys and Syrian hamsters. By the genetical features the Vergina strain differed from the eastern and western TBE subtypes but was found to be similar to the strains of other subtypes of the Urals-Siberian, east-Siberian (Aina-1448) and Central Asian antigenic variant. This group of strains hybridized with cDNA at 65 degrees C only in the absence of 50% formamide, reacted with probe 1115 complementary to protein E gene, with 1-3 probes complementary to the conservative region of the genome but did not react with the probes corresponding to the variable regions of the genome. The Vergina strain is close to TBE genotype III. The Vergina strain was found to be virulent inducing subacute meningoencephalomyelitis which developed slowly and was accompanied by less marked morphological lesions in the cerebral cortex than those induced by the eastern subtype. The Vergina strain was demonstrated to persist in the brain, liver, spleen, and lymph node tissues.

[The electrophoretic mobility of the virus-specific proteins of tick-borne encephalitis virus strains isolated in different geographical regions of the CIS Nations]

Tick-borne encephalitis (TBE) virus strains isolated in different geographic areas were characterized by changes in electrophoretic mobility (EPM) of virus-specific proteins. Analysis of EPM of intracellular virus-specific protein E and other high molecular proteins of 42 TBE virus strains revealed similarity among the majority of them, with the exception of several strains including the Sophyin strain (Far-Eastern subtype). The most marked variability in the electrophoretic behavior of virus-specific proteins was observed with low molecular proteins prM, ns4b, ns2a.

[The geographical distribution of genetic variants of the tick-borne encephalitis virus]

Geographic distribution of 185 tick-borne encephalitis (TBE) virus strains isolated in 8 physico-geographic areas and classified into six genetic variants was analysed. The strains of genetic variant I homologous to the Sophyin prototype strain were found to occur predominantly in the Far East and also frequently found in Western and North-Western parts of the East European plain. The vast territories from lake Baikal in the East to Ukraine in the West harbor mostly the strains significantly different from the Far-Eastern Sophyin strain. Hybridization experiments with oligonucleotide probes specific for the Neudorffle strain showed that the strains genetically similar to the virus of central European encephalitis occurred also in Eastern Europe and Western Siberia. It is concluded that a relationship exists between genetic types of TBE virus and their geographic origin.

[The specific reactivity of cDNA and deoxyoligonucleotide probes, complementary to the tick-borne encephalitis virus genome, with the RNA of strains of different geographical origins]

Hybridization experiments with RNA of 143 tick-borne encephalitis (TBE) virus strains isolated in different parts of the distribution area were used to study the reactivity of kDNA- and a set of 10 synthetic deoxyoligonucleotide probes. The kDNA probe under certain conditions was shown to hybridize with RNA of all the strains under study, and under other (strict) hybridization conditions did so selectively with a small number of strains. The capacity of oligonucleotide probes for hybridization with RNA of TBE virus strains varied from 12% to 100%. The differences in the hybridization activity of kDNA- and oligonucleotide probes complementary to the genomes of the Sophyin strain (Far-Eastern subtype) and Neudorffle strain (Western subtype) with TBE virus strains were used for differentiation of the strains into six genetic variants. Comparison of the reactivity of molecular probes in experiments with RNA of TBE virus strains and viruses of the TBE complex showed that the differences of the strains belonging to different genetic variants from the prototype Sophyin strain were comparable to those of some members of the TBE complex, with the exception of Powassan virus. These data attest to the necessity of further studies dealing with specification of the taxonomy of TBE complex viruses.

[The differentiation of viruses of the tick-borne encephalitis complex by means of RNA-DNA hybridization]

Nucleic acid spot hybridization with cloned cDNA of tick-borne encephalitis (TBE) virus, strain Sofjin, was used to differentiate strains of TBE and other flaviviruses. The cDNA probe reacted with strains of TBE and flaviviruses of TBE subgroup with the exception of Powassan virus. The probe did not react with viruses of Japanese encephalitis and Gendue subgroups. The viruses of TBE subgroup and some strains of TBE virus were differentiated from TBE strain Sofjin by thermal stability of RNA-DNA hybrids. Negishi and Louping ill viruses were found to be most closely related to TBE strain Sofjin among viruses of the TBE subgroup.

[The typing of tick-borne encephalitis virus strains by the soluble antigen]

Sucrose-acetone-treated antigens (SAA) and soluble antigens (SA) prepared from them by treatment with 8 M urea for eight TBE virus strains isolated in different parts of the virus distribution area were studied in cross CFT with immune ascitic fluids (IAF) for these strains as well as for OHF and Powassan viruses. With SAA, the difference in titres with homologous and heterologous IAFs, as a rule, did not exceed twofold, whereas with SA was 32-fold. It was also noted that in the homologous system the titre of SA decreased not more than 4-fold as compared with that of the initial SAA while in the heterologous system it declined from 4- to 16-fold or more. The level of antigenic relationship of strains was expressed by the formula HAg = SA titre/SA titre X 100%. It was shown that at HAg greater than or equal to 25% the strains used for antigen and antibody generation were closely related and at HAg less than or equal to 6.25% belonged to different subtypes. The analysis of the data suggested the existence of a fourth, "Urals-Siberian" antigenic variant of TBE virus. Using the developed criteria, the 20 strains under study (with one exception) were alloted into one of the four antigenic variants or qualified as intermediate.

[The use of molecular hybridization with synthetic deoxyoligonucleotides for differentiating strains of the tick-borne encephalitis virus]

Synthetic deoxyoligonucleotides complementary to different regions of genome RNA of tick-borne encephalitis (TBE) Sofjin virus strain were used to differentiate TBE virus strains. Nine TBE strains isolated in different geographical areas from different sources and several viruses of the TBE subgroup were tested. The probes revealed genetic heterogeneity of TBE strains. The probes complementary to different regions of the genome had different specificity. The pattern of hybridization of TBE virus strains with a panel of 11 oligonucleotide probes correlated significantly with the source of the virus strain and to a smaller extent with the geographical isolation site.

Differentiation of strains of tick-borne encephalitis virus by means of RNA-DNA hybridization

Cloned cDNA and synthetic deoxyoligonucleotides, complementary to various parts of the genomic RNA of tick-borne encephalitis virus (TBEV), strain Sofjin, were used to distinguish between strains of TBEV and other flaviviruses. The cDNA probe hybridized with strains of TBEV and related flaviviruses of the TBE complex except for Powassan virus, and it did not react with flaviviruses of the Japanese encephalitis and dengue subgroups. Viruses of the TBE complex and some strains of TBEV were differentiated from TBEV strain Sofjin by the thermal stability of RNA-DNA hybrids. Negishi and louping-ill viruses were the most closely related to TBEV strain Sofjin, among viruses of the TBE complex. Eight strains of TBEV isolated in different geographical areas from different sources were tested by dot-hybridization with 11 deoxyoligonucleotide probes. The probes revealed genetic variations among strains of TBEV. The pattern of hybridization correlated with the source of virus strains: TBEV strains isolated from TBE patients reacted with more probes than strains isolated from ticks. Within a group of epidemic strains of TBEV there was a correlation between the geographical area of isolation and similarity to TBEV strain Sofjin.

[Comparison of 3 express-methods of detection of tick-borne encephalitis virus]

Comparative studies of the diagnostic value of three express methods for detection of tick-borne encephalitis virus in ticks (fluorescent antibody technique (FAT) enzyme immunoassay (EIA), and molecular hybridization of nucleic acids) and the traditional method (bioassay in white mice) showed all the three express methods to be rapid, specific, sensitive, and useful for large-scale epidemiological surveys. Notable was the high effectiveness of the method of nucleic acids hybridization which was not inferior to bioassays in suckling mice and exceeded FAT and EIA. The results of the latter seem to be affected by antigenic variations among tick-borne encephalitis virus strains.

[Use of an immunofluorescence micromethod for determining the antigens of the influenza and tick-borne encephalitis viruses]

The diagnostic possibilities of several variants of the solid-phase immunofluorescent micromethod (requiring 100-200 microliter of the reaction mixture), intended for the determination of influenza virus and tick-borne encephalitis virus antigens in material obtained from patients and ticks, have been studied. A high degree of correlation between the results obtained by the methods under investigation and the control methods has been established.

[Possibility of occurrence of mild spinal forms of poliomyelitis in subjects immunized repeatedly with live poliomyelitis vaccine]

The results of clinical, epidemiological, serological and virological examinations of patients with mild spinal forms of poliomyelitis occurring under conditions of mass immunization with oral live poliomyelitis vaccine are presented. The etiological role of poliomyelitis virus types I and III in these diseases has been established. It has been shown that multiple vaccination does not always prevent diseases but in these cases they are milder. Serological examination of patients and normal subjects suggests inadequacy of seroconversion to poliomyelitis viruses under conditions of mass vaccination of the population against poliomyelitis.