[Characteristic of the new Khatanga virus genotype].

Complete nucleotide sequence of the S-segment and partial sequences of M- and L-segments (981 and 1005 nucleotide respectively) have been determined in 20 strains of California encephalitis serocomplex, isolated in Yakitiya, Sakhalin, and Kamchatka. The phylogenetic analysis ofgenomic S-, M-, and L-segments showed that all 20 strains are related to Khatanga virus (La Cross subtype of California encephalitis serotype). Eight strains belong to group 2 of Khatanga virus while the remaining 12 make up a new (third) genetic group of this virus having original S- and M-segments and L-segment similar to that of the second group.

[A possible association of fatal pneumonia with mutations of pandemic influenza A/H1N1 sw1 virus in the receptor-binding site of the HA1 subunit].

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.

[Detection of amino acid substitutions of asparaginic acid for glycine and asparagine at the receptor-binding site of hemagglutinin in the variants of pandemic influenza A/H1N1 virus from patients with fatal outcome and moderate form of the disease].

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 first break-through of the genotype 2.3.2 of high-virulence influenza A virus A/HSN1, which is new for Russia, in the Far East].

The epizootic etiologically associated with highly pathogenic avian influenza H5N1 genotype 2.3.2 that is new for Russia among wild and domestic birds in the south of the Primorye Territory during spring migration in April 2008 has been decoded. About 25% of the wild birds of a water complex, which include European teals (Anas crecca), mallard ducks (Anas platyrhynchos), great-crested grebes (Podiceps cristatus), are involved in viral circulation in the area of the Suifun-Khankai plain. Chicken embryos and the cell lines MDCK, SPEV, BHK-21, SW-13 were used to isolate 3 strains from recently deceased hens (A/chicken/Primorje/1/08, A/chicken/Primorje/11/08, and A/chicken/Primorje/12/08) and one strain from a European teal (A/Anas crecca/Primorje/8/08). The strains were deposited in the State Collection of Viruses of the Russian Federation, D. I. Ivanovsky Research Institute of Virology, Russian Academy of Medical Sciences. The nucleotide sequences of the full-sized genomes of A/chicken/Primorje/1/08 and A/Anas crecca/Primorje/8/08 were sent to the International databank GenBank. The strains from domestic and wild birds were shown to be identical. The isolated strains are most close to the strains Alchicken/Viet Nam/10/05, A/chicken/Guangdong/178/04, and A/duck/Viet Nam/12/05. Molecular genetic analysis has indicated that the strains isolated are susceptible to rimantadine and ozeltamivir and less adapted to mammalian cells (particularly, they contain E627 in RV2, which agrees with the biological properties of these strains in vitro). Penetration of the newly isolated virus into the Far East ecosystem provides in the foreseeable future a way for infecting the birds wintering in America and Australia in the nesting places, with further carriage of viral populations there in the period of autumn migrations.

[Interpretation of the epizootic outbreak among wild and domestic birds in the south of the European part of Russia in December 2007].

The paper presents the results of interpreting the epizootic outbreak etiologically associated with high-virulent influenza virus A/H5N1 among domestic and wild birds in the Zernogradsky and Tselinsky districts of the Rostov Region. Epizooty was characterized by a high infection rate in the synanthropic birds of a ground-based complex. RT-PCT revealed influenza virus A/H5 in 60% of pigeons and crows and in around 20% of starlings, and in 10% of tree sparrows. Fifteen viral strains from chickens (Gallus gallus domesticus), Indian ducks (Cairina moschata), rooks (Corvus frugilegus), rock pigeons (Columba livia), tree sparrows (Passer montanus), common starlings (Sturnus vulgaris), and great white herons (Egretta alba) were isolated and deposited in the State Collection of Viruses of the Russian Federation. Full-sized genomes of 5 strains were sequenced and deposited in the international database GenBank. The isolated strains belong to the Quinhai-Siberian (2.2) genotype, an Iranian-Northern Caucasian subgroup, they are phylogenetically closest to the strain A/chicken/Moscow/2/2007 (inducing epizooty among poultry in the near-Moscow Region in February 2007) and have 13 unique amino acid replacements as the consensus of the Quinhai-Siberian genotypes in the proteins PB2, PA, HA, NP, NA, and M2, by preserving thereby 4 unique replacements first describes for the strain A/chicken/Moscow/2/2007. The findings are indicative of a different mechanism that is responsible for bringing the virus into the northeastern part of the Azov Sea area in September 2007 (during the fall migration of wild birds) and in December 2007 in the south-western Rostov Region where a human factor cannot be excluded. Mass infection of synanthropic birds endangers the further spread of epizooty, including that in the central regions of the Russian Federation in spring after near migrants return after wintering.

[Epizooty caused by high-virulent influenza virus A/H5N1 of genotype 2.2 (Qinghai-Siberian) among wild and domestic birds on the paths of fall migrations to the north-western part of the Azov Sea basin (Krasnodar Territory)].

Isolation, followed by the sequencing the full-size genome of strains of A/chicken/Krasnodarl300/07 and A/Cygnus cygnus/Krasnodar/329/07, has shown that they belong to genotype 2.2 (Qinghai-Siberian). The strains were deposited at the State Virus Collection of the Russian Federation and nucleotide consequences were at the International databank GenBank. The strains contained 10 unique amino acid replacements in reference to the consensus of the Qinghai-Siberian genotype in the PB2, PA, HA, NA, and NS1, which suggests that regional variants may form in different parts of an area.

[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.

[Rimantadine and arbidol sensitivity of influenza viruses that caused epidemic morbidity rise in Russia in the 2004-2005 season].

The study of the activity of arbidol against epidemic influenza A and B virus strains (2002-2005) in the cultured MDCK cells showed the higher sensitivity of enzyme immunoassay than that of hemagglutination test. The influenza A virus strains tested, including those resistant to rimantadine (5 microg/ml), were sensitive to arbidol (10 microg/ml). The population of influenza B virus strains was heterogeneous in this indicator, 43% of the strains being less sensitive to arbidol. There was an increase in the number of rimantadine-resistant influenza A(H3N2) virus strains (10-18%) in our country during 3 epidemic seasons. The sequencing analysis of protein M2-endoding gene revealed the amino acid replacement of serine by asparagine in position 31, which is characteristic of rimantadine-resistant strains. Arbidol in combination with rimantadine potentiated the effect of viral reproduction in the cultured cells, as compared with the effect produced by the same concentrations of the drugs used alone.

[Highly pathogenic influenza A/H5N1 virus-caused epizooty among mute swans (Cygnus olor) in the lower estuary of the Volga River (November 2005)].

Molecular virological studies of the field material collected in the epicenter of epizooty with high mortality among mute swans (Cygnus olor) in the area of the lower estuary of the Volga River (November 2005) could establish the etiological role of highly pathogenic influenza A (HPAI) virus of the subtype H5N1. Ten HPAI/H5N1 strains deposited at the State Collection of Viruses of the Russian Federation with the priority dated December 1, 2005 were isolated from the cloacal/tracheal swabs and viscera of sick and freshly died mute swans. Complete nucleotide sequences of all fragments of the genome of 6 strains have been deposited in the Gene Bank. The paper discusses the molecular genetic characteristics of isolated strains.

[The use of the polymerase chain reaction for the identification of Clostridium botulinum type A strains]. / Ispol'zovanie polimeraznoi tsepnoi reaktsii dlia identifikatsii shtammov Clostridium botulinum tipa A.

Polymerase chain reaction (PCR) for the identification of C.botulinum of type A was developed. As primers, oligonucleotides corresponding to sequences 913 -- 932 and 1852 -- 1871 of the gene of type A botulinic neurotoxin were used. The study revealed that under optimum conditions the positive result of the reaction was registered only when the DNA of C.botulinum strains of type A (11 strains) was used, but not that of C.botulinum strains of other types (11 strains of type B, 5 strains of type C, 2 strains of type D, 6 strains of type E and 1 strain of type G). High sensitivity, specificity and rapidity of PCR open good prospects for its practical use.