Infectious bursal disease virus: identification of the novel genetic group and reassortant viruses

The results of the phylogenic analysis of the nucleotide sequence of the IBDV A and B genome segments have been presented. Traditionally the IBDV isolates are classified based on the phylogenic analysis of the hypervariable region of the VP2 gene. The analysis of the VP2 gene segments of the isolates detected in the Russian Federation demonstrated that most of them belong to the genetic group comprising highly virulent IBDV isolates. However, not all isolates belonging to one genetic group have the same phenotypic characteristics. This is related to the fact that the virulence is determined not only based on the characteristics of the VP2 gene (A segment) but on the characteristics of the VP1 gene (B segment) as well. The IBDV genome segmentation allows formation of reassortant viruses which can be identified as a result of the genome segment analysis. The phylogenic analysis of the nucleotide sequences of VP2 and VP1 genes of 28 IBDV isolates detected at RF, Ukrainian and Kazakh poultry establishments in 2007 and 2019 showed that 15 of them are reassortant viruses. Different combinations of the genome segments have been identified among these reassortant viruses. Detection of different combinations of IBDV genome segments is indicative of the fact that the heterogeneous virus population circulates on the poultry farms. Pathogenicity studies of the three IBDV isolates showed that the most virulent was an isolate having two genome segments characteristic of the highly virulent virus. Two reassortant viruses having only one genome segment A or B, characteristic of the infectious bursal disease, demonstrated less pronounced virulent properties

Genetic analysis of nucleotide sequences of neuraminidase gene of highly pathogenic avian influenza A/H5N8 virus isolates recovered in the Russian Federation in 2020

Avian influenza is a highly dangerous viral disease that causes huge economic damage to poultry farming. Currently, highly virulent influenza virus with N8 neur- aminidase subtype is quite often detected in populations of domestic and wild birds in various countries of the world. The article provides data on complete nucleotide sequences of the neuraminidase gene of highly pathogenic avian influenza virus isolates recovered in the second half of 2020 from pathological material received from four regions of the Russian Federation. The conducted research showed that the subtype of the isolated virus was N8. According to the phylogenetic analysis, isolates of N8 virus belong to group 8C.4. During the phylogenetic analysis of the neuraminidase, we also took into account data on hemagglutinin classification, according to which H5N8 virus isolates belong to a widespread clade 2.3.4.4. Viruses of the clade were first registered in 2010 in China and they have been circulating up to now. The paper also provides data of a comparative analysis of nucleotide sequences of the studied isolates and the isolates from the international GenBank and GISAID databases, recovered in other countries from 2007 to 2020. During the analysis of the amino acid sequence of the studied isolates, no substitutions were found in the positions that affect resistance to neuraminidase inhibitors. The complete nucleotide sequences of the neuraminidase gene of the avian influenza virus subtype N8 (isolates A/domestic goose/OMSK/1521-1/2020, A/duck/Chelyabinsk/1207-1/2020, A/duck/Saratov/1578-2/2020, A/goose/Tatarstan/1730-2/2020) are published in the international GenBank and GISAID databases. Based on the analysis of the nucleotide sequences of the studied isolates, the article shows gradual evolution of the N8 subtype virus

Epidemiological monitoring of avian influenza in the Republic of Crimea in 2019–2020

The paper presents results of avian influenza epidemiological monitoring in the Republic of Crimea in 2019–2020. The attention was focused on the study of water basins of the Azov and Black Seas, the Sivash Lagoon and freshwater lakes in the Feodosia Urban Okrug, Leninsky, Sovetsky, Nizhnegorsky, Chernomorsky and Saksky Raions to detect the avian influenza virus circulation. Examination of the above mentioned areas showed that some freshwater reservoirs became shallow and dry, and aquatic vegetation degraded. The natural biotope analysis conducted in 2019 and 2020 showed a decreased number of semiaquatic wild birds. The pathological material was sampled from semiaquatic and migratory wild birds, as well as from poultry kept in poultry farms and backyards. The collected samples were tested using real-time RT-PCR. In 2019, the AIV type A (H9) genome was detected in one fecal sample taken from wild birds near Kuchuk-Adzhigol Lake in Feodosia Urban Okrug. The AIV type A (H5) genome was detected in 2020 during laboratory testing of pathological material taken from the remains of a mute swan within the shoreline of a freshwater lake near the Ermakovo settlement of the Dzhankoysky Raion. The genetic analysis was performed in the FGBI “ARRIAH” (Vladimir), and the N8 subtype neuraminidase of the influenza virus isolate was determined. The comparative genetic analysis of 258 bp nucleic acid sequences of the AIV H gene fragment showed that the identified isolate belongs to the Asian genetic lineage of highly pathogenic AIV subtype H5 (clade 2.3.4.4) associated with the epidemic spread in Asia, Europe, the Middle East and Africa in 2016–2020

Rabies re-emergence after long-term disease freedom (Amur Oblast, Russia)

Retrospective descriptive epizootological study was conducted in the Amur Oblast (Russian Far East), where a rabies outbreak was reported in 2018. The aim of the study was to analyze probable routes of rabies introduction and features of its spatial and temporal spread in the territory that remained free from this infection from 1972 to 2018. In 2018–2021, altogether 1,416 animals were examined for the infection with the rabies virus. Forty-seven animal rabies cases were confirmed; the proportion of wild animals (Vulpes vulpes, Nyctereutes procyonoides, Canis lupus) amounted to 66%. The first cases were detected within 30 km from the state border with China. Nucleotide sequences of the nucleoprotein gene of three rabies virus isolates were determined and their belonging to the Arctic-like-2 genetic lineage was established. Genetically closest rabies virus isolates have been found in Heilongjiang Province (China, 2011, 2018) and Jewish Autonomous Oblast (Russia, 1980). GIS and open Earth remote sensing data were used to map the rabies cases. After 2018, the epizootic spread within the forest-steppe landscapes of the Zeya-Bureya Plain, where human and animal rabies cases had been earlier reported (until 1972). The front of the epizootic spread in a north-eastern direction at an average speed of 59 (16–302) km during one epizootic cycle. The introduction of the rabies virus was most likely along the Amur River valley from downstream regions of Russia and China that are rabies infected

CLONING OF GENES ENCODING TRANSMEMBRANE PROTEINS AND PROTEINS RESPONSIBLE FOR AFRICAN SWINE FEVER VIRUS VIRULENCE

Results of cloning X69R, A179L, E248R, I215L and DP96R genes of ASF virus Krasnodar 07/17 isolate and analysis of their nucleotide sequences are presented. Obtained clones were added to the previously constructed clone library comprising clones of 8 genes of Krasnodar 06/12 isolate. Clones containing X69R, A179L, E248R, I215L and DP96R genes of ASF virus Krasnodar 07/17 isolate will be used for recombinant protein obtaining and testing for their effect on in vitro virus reproduction and their role in the virus infectivity, level of clinical manifestations and virulence. Prokaryotic vector, pJET1.2/ blunt, was used. Thus, the clone library available at the FGBI “ARRIAH” Reference Laboratory for African swine fever was supplemented by pJET1.2-X69R, pJET1.2-A179L, pJET1.2-E248R, pJET1.2-I215L and pJET1.2-DP96R plasmid constructions containing 5 genes of ASF virus Krasnodar 07/17 isolate. Proportion of cloned virus genes was 3.01% of Krasnodar 07/17 isolate genome, hence, total amount of the clone library has reached 7.82%

CLONING OF GENES ENCODING TRANSMEMBRANE PROTEINS AND PROTEINS RESPONSIBLE FOR AFRICAN SWINE FEVER VIRUS VIRULENCE

Results of cloning X69R, A179L, E248R, I215L and DP96R genes of ASF virus Krasnodar 07/17 isolate and analysis of their nucleotide sequences are presented. Obtained clones were added to the previously constructed clone library comprising clones of 8 genes of Krasnodar 06/12 isolate. Clones containing X69R, A179L, E248R, I215L and DP96R genes of ASF virus Krasnodar 07/17 isolate will be used for recombinant protein obtaining and testing for their effect on in vitro virus reproduction and their role in the virus infectivity, level of clinical manifestations and virulence. Prokaryotic vector, pJET1.2/ blunt, was used. Thus, the clone library available at the FGBI “ARRIAH” Reference Laboratory for African swine fever was supplemented by pJET1.2-X69R, pJET1.2-A179L, pJET1.2-E248R, pJET1.2-I215L and pJET1.2-DP96R plasmid constructions containing 5 genes of ASF virus Krasnodar 07/17 isolate. Proportion of cloned virus genes was 3.01% of Krasnodar 07/17 isolate genome, hence, total amount of the clone library has reached 7.82%

Analysis of whole genome sequence of strain "0" of avian infectious laryngotracheitis virus

Data on identification and analysis of whole genome nucleotide sequence of strain «O» of avian infectious laryngotracheitis virus are demonstrated. In the process of the whole genome sequence mapping a number of unique and significant nucleotide properties has been identified in genes that code surface proteins responsible for interacting with cell receptors. Strain «O» has been demonstrated to belong to phylogenetic group 1 subgroup 1 (1.1). Genetic relatedness of domestic strain «0» to other vaccine strains widely used in global poultry industry such as Serva, Cover, Hudson and Fowl laryngo has been determined. The mapped nucleotide sequence has been deposited in the international GenBank database under the accession number KU128407. It is the first complete genetic characterization of the domestic vaccine strain

PHYLOGENETIC ANALYSIS OF FMDV ISOLATES RECOVERED IN POST-SOVIET STATES AND MONGOLIA IN 2016

Federal Centre for Animal Health (FGBI “ARRIAH", Vladimir, Russia) is an OIE Regional Reference Laboratory for Foot-and-Mouth Disease for Eastern Europe, Central Asia and Transcaucasia and FAO Reference Centre for Foot-and-Mouth Disease for Central Asia and Western Eurasia. The FGBI “ARRIAH's" objectives as a Regional Reference Laboratory/ Centre include continuous FMDV monitoring in post-Soviet states, detection of new genetic virus variants and matching their antigenic properties with antigenic properties of available vaccine virus strains. The paper demonstrates results of phylogenetic analysis of foot-and-mouth disease virus (FMDV) that caused the disease in Armenia, Zabaikalsky Krai (Russia), Middle Asia and Mongolia in 2016. The test results are indicative of the fact that FMD outbreaks in Armenia were caused by the virus belonging to A/G-VII genetic lineage that was widely spread in the Near East in 2015 and had been never reported in post-Soviet states before. The FMD outbreaks in the Zabaikalsky Krai in November -December 2016 were caused by the exotic for Russia FMD virus of O/Ind-2001d genetic lineage. In Middle Asia FMD was caused by O/ME-SA/PanAsia-2 virus belonging to the O/ME-SA/PanAsia-2 genetic lineage and endemic for the region. In Mongolia the FMD outbreak was caused by the virus belonging to A/Sea-97 genetic lineage that had been previously reported in this country in 2013. Results of the virus genotyping are of particular importance for adjustment of the disease control measures

GENOMIC ABERRATIONS IN DNA OF AFRICAN SWINE FEVER VIRUS CIRCULATING IN THE TERRITORY OF THE RUSSIAN FEDERATION

The paper is devoted to analysis of genome variability of African swine fever (ASF) virus isolates recovered in the Russian Federation territory. Complete nucleotide sequences of the following ASF virus isolate genomes were obtained by pyrosequencing: Kashino 04/13, Odintsovo 02/14 and Karamzino 02/13. Multiple single insertions and deletions as well as distinctly localized two tandem repeats were found by comparative analysis of genomes of the said isolates and Georgia 2007/1 isolate. Notably that 17-nucleotide tandem repeat was detected in 9R/10R intergenic region of MGF505 multigene family in genomes of Shikhobalovo 10/13 and Karamzino 02/13 isolates for the first time

RESULTS OF GENE DIAGNOSIS OF LUMPY SKIN DISEASE IN THE DAGESTAN AND CHECHEN REPUBLICS-THE FIRST OFFICIAL CONFIRMATION OF THE DISEASE OCCURRENCE IN THE RUSSIAN FEDERATION TERRITORY

In September 2015 a disease with clinical signs characteristic of lumpy skin disease (bovine contagious nodular dermatitis) was registered in cattle in the Republic of Dagestan and Republic of Chechnya. Laboratory diagnosis was carried out in the Reference Laboratory for highly dangerous animal diseases of the FGBI «ARRIAH». Lumpy skin disease virus was detected by polymerase chain reaction (PCR) in samples from the diseased animals. Sequencing of the PCR products confirmed the detected virus identification results. The above-mentioned tests were the first official confirmation of lumpy skin disease occurrence in the territory of the Russian Federation