Search

The prototype strain LEIV-K306 of the Batken virus (BKNV) was isolated from the Ixodidae ticks Hyalomma marginatum Koch, 1844 collected from sheep near town Batken (Kirgizstan) in the April 1970. Later, the BKNV was isolated in Kirgizstan from the mixed pool of the Aedes caspius Pallas, 1771 and Culex hortensis Ficalbi, 1889 mosquitoes. From the very beginning, the BKNV was discussed to be very close to the Dhori virus (DHOV) (Orthomyxoviridae, Thogotovirus) isolated from the Ixodidae ticks Hyalomma dromedarii Koch, 1844 in India. In this work, virtually complete genome sequence (MiSeq, Illumina) of the BKNV was determined (ID GenBank KJ396672-4). Structural and non-structural proteins of the BKNV have a high level of homology with DHOV - 98% (PB1) and 96% (PB2, PA, NP, M). Homology of HA protein between the BKNV and DHOV is 90%, which accounts for antigenic difference between these close relative viruses. Since the differences in the other structural and non-structural proteins are about 96-98%, the BKNV could be suggested as the topotypic DHOV strain for Central Asia, Transcaucasia, and Northern Caspian region. The evolution divergence of the BKNV and DHOV for HA could be explained by local ecologic peculiarities of the BKNV areal.

Unidentified Khurdun virus (KHURV) was isolated in 2001 from coot (Fulica atra, Linnaeus, 1758) in the Volga River delta (Astrakhan Region, Russian Federation). Here we report that the KHUV genome was de novo sequenced (on Illumina platform) and the KHURV was classified as a novel prototypic bunyavirus. The KHURV genome comprises three negative-sense RNA segments (L, M, and S); its terminal nucleotide sequences are canonical for the Orthobunyavirus genus. Based on the results of the molecular-genetic and phylogenetic analysis we suggest that the KHURV belongs to the genus Orthobunyavirus (Bunyaviridae).

The receptor specificity (RS) of pandemic influenza A(H1N1) pdm09 virus strains deposited into the State Collection of Viruses of the Russian Federation, D. I. Ivanovsky Research Institute of Virology, Ministry of Health and Social Development of Russia, in the 2009-2010 and 2010-2011 epidemic seasons to a panel of 9 sialoglycopolymers (SGP). The strains were divided into 3 groups according to the W(3/6) index proposed by the authors, which was equal to the amount of reactivities to unbranched alpha2-3-SGP to that of reactivities to unbranched alphal-6-SGP: W(3/6) < or = 1.0; 1.0 < W(3/6) < or = 1.5. The W(3/6) < or = 1.5 group showed a predominance of a2-3-RS, attended by the high incidence of fatal primary viral pneumonias (FPVP) (60.0%) and amino acid replacements in the HA1 receptor-binding site (RBS) (80.0%): D222{G, N} and Q223R. The 1.0 < W(3/6) < or = 1.5 group was characterized by mixed alpha2-3/alpha2-6-RS with the incidence of FPVP (29.7%) and amino acid replacements in the HA1 RBS (40.5%) (D222{G, N, V} and Q223), respectively. In the W(3/6) < or = 1.0 group, alpha2-6-RS was prevalent, FPVPs were absent and amino acid replacements in HA1 RBS (D222{G, E}) were seen only in 6.0% of cases. The number of strains with increased specificity to alpha2-3-sialosides increased in the 2010-2011 epidemic season as compared to the previous season. With their further spread among the population, there may be a rise in cases of severe primary viral pneumonias with possible fatal outcomes, which can be, however, accompanied by a decrease in the capacity of mutants to air-dropwise transmission.

Analysis of taxonomic structure of Orthomyxoviridae was undertaken in view of its anticipated evolution. Four concepts of circulation of influenza A viruses in the biosphere are discussed, viz. anthrponose, zooanthroponose, metastrongilose, and protozoan. All of them may be considered in the framework of the general zooantroponose concept. Influenza B and C viruses can not be regarded as strictly anthroponose. Comparative molecular-genetic analysis of the genus Thogotovirus provides a basis for the designation of Thogoto and Batken-Dhori as independent geni. It is speculated that t he proof of transmission of Isaviruses by copepods Caligus elongates and Lepeophtheirus salmonis (Crustacea: Copepoda) may open up a new line of developments in arborvirology since crustacean vectors of viruses have never been described before.

The paper gives the results of sequence analysis of 150 positive samples in real-time RT-PCR, including 47 autopsy materials from patients (including 10 pregnant women), who died from fatal pneumonia mainly in November-December 2009, in whom the lifetime etiological diagnosis had not been made and hence no early etiotropic therapy performed. 70% of the primary materials from the deceased patients were found to have pandemic influenza A(H1N1) v mutants in the lung tissue with D222G (15%), D222N (15%), D222E (2%) substitutions, as well as a mixture of mutants (38%). Nasopharyngeal lavages from 3 Chukotka deceased patients exhibited only consensus (nonmutant) D222 virus variants; there was a mixture of consensus and mutant virus variants in the trachea and a mixture of mutant ones in the lung. Preliminary data from the study of the interaction of the hemagglutinin of two strains having D222G and D222N mutations with 9 oligosaccharides imitating the variants of cell receptors for influenza A virus suggest that there is a double receptor specificity for alpha2'-3' and alpha2'-6'-sialosides with a preponderance of alpha2'-3'-specificity. Further spread of the mutants that have acquired a high virulence and preserved their capacity for the respiratory route of human infection may lead to the situation similar to that seen in the 1918-1919 pandemic. Another scenario for evolution of the virus is to preserve its receptor specificity for alpha2'-3'-sialosides and high virulence with losses of alpha2'-6' specificity and capacity for aerosol transmission, by damping the pandemic.

The paper analyzes the amino acid sequence of the receptor-binding site of hemagglutinin (HA) in the variants of pandemic influenza A/H1N1 swl from 18 patients with moderate (n=1) and fatal (n=17) forms of the disease in 2009. Nine samples contained asparaginic acid at position 222 of HA1 (D). This site exhibited mutations in 9 samples: D222G (n=3), D222N (n=3), and D222G/D222N (n=3). In one patient with the moderate form of the disease, D222G mutation was revealed after the second passage in the developing chick embryos; this mutation was not found in the primary sample from the patient. The findings suggest the mutant variants of the virus start to circulate among the population, which requires, firstly, continuation of molecular virological monitoring of the pandemic situation and, secondly, further study of the impact of amino acid substitutions at the receptor-binding site of HA1 on the increased virulence of influenza A virus.

The paper describes the trend in the spread of pandemic influenza A(H1N1) swl virus in the Far East, which started in this region 2-3 months later than that in the European part of Russia. By mid-October seasonal epidemic influenza was practically displaced by pandemic one.

The review describes the phenotypic properties, structure, and expression pattern of West Nile virus genome (Flaviviridae, Flavivirus, Japanese encephalitis antigenic complex), as well as the clinical picture and pathogenesis of its etiologically related disease West Nile fever. It also analyzes the available data on the impact of genetic mutations in the genome on the biological properties of the virus.

The population interactions of West Nile virus in the middle and lower regions of the Volga delta in 2001-2006 were studied. The authors established major species of the mosquitoes Anopheles messeae, An. hyrcanus, Culex piplens, Cx modestus, Coquilletidia richiardii in anthropogenic biocenoses and An. hyrcanus, Coq. richiardii in the natural ones; vertebrates - crows (Corvidae) and domestic animals in the anthropogenic biocenoses and cormorants in the natural ones. The ticks Hyalomma marginatum were found to play an active role in the circulation of the virus and in the stability of infection foci. The epicenter of an endemic area is situated in the anthropogenic biocenoses of the middle belt where high infection rates were found in humans (20-40% immune stratum), mosquitoes, and birds. A complete sequence of 14 strains was detected in 44% from 1 to 5 nucleotide replacements to a genome, most frequently at E154 positions Asn --> Ser and Ser --> Pro, which prevents glycosylation and reduces neuroinvasion. Analysis of 100 RT-PCR-positive samples revealed the absolute predominance of genotypes 1 with single findings of genotype 2 and 4.

Solid-phase enzyme immunoassay, neutralization test, and the hemagglutination-inhibition test were used to study the sera from human beings (152 samples), agricultural animals (n = 77), hares (n = 3), and wild birds (n = 69), collected in 2006-2007 in the Kuban River estuary (Temryuk District, Krasnodar Territory). There were specific antibodies against viruses of West Nile (WH), tick-borne encephalitis (TBE) (Flaviviridae, Flavivirus), Sindbis (Togaviridae, Alphavirus), the antigenic complex of California, Batai (Bunyaviridae, Orthobunyavirus), Dhori (Orthomyxoviridae, Thogotovirus). The findings suggest the presence of arboviruses from 6 transmitting mosquitoes and ticks in the study area and human infection by the viruses of the antigenic complex of California (20-47%), Batai (3-15%), West Nile (3-12%), Dhori (2%). The index agricultural animals (horses, cattle) were observed to have specific antibodies to the viruses of WN (8-15%), TBE (0-2%), Sindbis (2-9%), the antigenic complex of California (27-54%). Out of the representatives of the wild fauna, virus-neutralizing antibodies to Sindbis virus were found in European hares (Lepus europaeus), California complex virus in gulls (Larus argentatus) and terns (Sterna hirundo), WN and Sindbis viruses in herons (Ardea purpurea), and WN and California complex viruses in bald-coots (Fulica atra).

The paper analyzes the results of isolation of Newcastle disease virus (NDV) strains from 336 swaps of 31 wild bird species collected in the 2001 summer in the Volga estuary (Astrakhan Region). Twenty-seven NDV strains were isolated from little terns (Sterna albifrons) (n=11; infection rate, 24.4%), great cormorants (Phalacrocorax carbo) (n=6; 11.1%), coots (Fulica atra) (n=8; 6.5%), sandwich terns (Sterna sandvicensis) (n=1; 100%), and common redshanks (Tringa totanus) (n=1; 50.0%). Four strains were sequenced by the 374 n. a. residue fragment from the beginning of the F gene, one of them was by the full F gene, and another (Stemal/Astrakhan/2755/2001) was by the full genome. Nucleotide sequences have allowed the authors to classify corresponding NDV strains as 5b genotype and the analysis of the amino acid sequence of the F-protein cleavage site has shown them to belong to a non-pathogenic group.

The genome of the NDV strain Sterna/Astrakhan/2755/2001 isolated from a wild bird of the Volga River delta in 2001 was completely sequenced. The phylogenetic analysis of the strain investigated and other NDV strains clearly demonstrated that Sterna/Astrakhan/2755/ 2001 belonged to the lineage 5b. Comparative analysis of molecular genetic markers of pathogenicity of strain Sterna/Astrakhan/2755/ 2001 allows its velogenic character to be suggested.

Sera sampled from 2,884 farming animals in the Astrakhan region in 2001 to 2004 were investigated by the hemagglutination inhibition test (HIT) in order to indicate specific antibodies to West Nile virus (WNV). HIT-positive samples were investigated by the neutralization test (NT). WNV antibodies were detected in all the examined species of animals: horses (the proportion of positive tests throughout the observation averaged 9.8%; the agreement with NT results was 94.1%), cattle (6,4 and 72.%), camels (5.2 and 41.7%), pigs (3.1 and 75%), and sheep (2.2 and 57.1). Relationships between the environmental features of WNV in different natural zones, the infection rate, and the conditions of keeping farming animals in the Astrakhan region are analyzed.

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.

Comprehensive virological, serological as well as genetic studies of the ecology of West Nile Virus (WNV) as well as of some other arboviruses were undertaken in different ecosystems in the territories of the Astrakhan Region and of the Kalmyk Republic. The main carriers (mosquitoes, ticks, birds and mammals) were defined as involved in the circulation of viruses within the natural and anthropogenic biocenosis. Phylogenetic examinations of isolated strains and samples, which were positive in RT-PCR, showed an absolute predominance of genotype I virus that was most closely related to American and Israeli strains. At the same time, epidemic strains had up to 6% of nucleotide differences versus the historic strains isolated in the same region 20-30 years ago. Besides, the circulation of genotype IV was discovered; it was characterized by a lower pathogenicity, which, possibly, ensures the shaping of a pronounced immune interlayer bearing no epidemic consequences. An analysis of the study results on the WNV ecology denotes the epicenter of the endemic territory located in the middle part of the Volga delta.

Thirty-three persons infected with West Nile fever were detected in 2002 in the Astrakhan Region; the diagnosis was confirmed serologically and the maximal number of the infected was registered in August, same year. The indices of the specific humoral immunity varied from 3.3% to 27.1%. A monitoring determined the highest infection risk among the residents of the Volga middle delta.

Infection of birds, residing in the Volga lower and middle delta, with West Nile Virus (WNV) genome was detected by the RT-PCR method. A total of 315 samples of bird organs, collected in the Astrakhan region in August 2001, were examined. Positive results, with various severity degrees, were found in coots (15.1%) and in cormorants (14.3%) in the lower delta. As for the middle delta, the infection rate among coots, herons, sea-gulls and terms was found to be identical and amounted to 8-13%, it was essentially higher in cormorants--42%. The infection rate of land-based birds did not exceed 5% in synanthropic biocenosis. According to a partial sequencing of the 5'-end region of WNV genome, all positive tests can be described as belonging to the 1st WNV genotype. The obtained results are indicative of a high activity of circulation of WNV among the birds of the water and near-water complexes in the mentioned region.

Four strains identified as West Nile fever virus by inhibited hemagglutination and neutralization tests, enzyme immunoassay, and reverse transcription polymerase chain reaction were isolated during a virological examination of birds and their collected ticks in the natural and synanthropic biocenoses of the Volga delta. The strains were isolated from the great cormorant (Phalacrocorax carbo), the crow (Corvus corone) and its collected Hyalomma marginatum nymphs. The types of interpopulational relations in the ecological system wild-birds-virus-mosquitoes-synanthroic birds-ticks are discussed.

In August, 2001, in the middle zone of the delta of the Volga River, the Astrakhan region, during investigation of the natural foci of West Nile fever and Crimean--Congo hemorrhagic fever (CCHF), the material from the hare (Lepus europaeus, Pallas, 1778 (Lagomorpha, Leporidae) and collected from it the ticks Hyalomna marginatum Koch 1844, was obtained. 4 strains of Dhori virus (Orthomyxoviridae, Thogotovirus) and 2 strains of CCHF virus (Bunyaviridae, Nairovirus) were isolated. This is the first isolation of Thogotovirus genus virus from the wild vertebrates. Considering the overlap of the Dhori virus and CCHF virus areas, similar ecology and the isolation both viruses from the same pool of the ticks, the necessity for the use of the test-system for indication of the viruses, differential diagnosis and accumulation of the data concerning the role of Dhori virus in the human and farm animals pathology is discussed.

Reviews modern data on laboratory diagnosis (virological, immunobiochemical, molecular biological methods) and differential diagnosis of herpesvirus infection induced by various Herpesviridae.