Molecular characterization of infectious bronchitis viruses (IBVs) isolated between 1998 and 2002 from chickens in Russia was performed. More than 250 field samples were tested by reverse transcriptase-polymerase chain reaction using two sets of primers corresponding to the most conserved 3'-untranslated region and the most variable S1 gene region of the viral genome. Ninety-one IBV isolates were characterized by phylogenetic analysis of the S1 gene hypervariable region comprising 136 to 558 nucleotides. The major group of isolates (38 viruses) showed very close sequence relationship with strains of the Massachusetts genotype circulating in Russia since the early 1970s. The analysed region of the other 22 Russian IBVs was similar (from 89 to 98% identity) to that from the strains of European genotypes including D274 (nine isolates), 793/B (10 isolates), and B1648, 624/I and Italy-02 (one isolate in each group). Two isolates from very distant geographic locations in Russia (Far East and the European part) clustered together with Chinese strains of QXIBV genotype. None of the remaining 27 Russian isolates showed a close sequence relationship with known IBV strains available in sequence databases. The majority of these variant viruses clustered into the six novel Russian genotypes, often correlating with their geographic location. The remaining five of them were placed outside these unique groups, also representing new genotypes. These data for the first time demonstrated the high genetic diversity of IBV isolates circulating in Russia.

Infectious bronchitis virus (IBV) isolates recovered in Russia, Ukraine, and Kazakhstan between 2007 and 2010 were subjected to molecular characterization and compared with those isolated a decade ago. The IBV genome was detected in 202 out of 605 field samples from chickens with various clinical signs. Partial sequencing of the S1 gene revealed 153 vaccine strains and 49 field isolates of several genetic groups. Massachusetts, 793/B and D274 remained the predominant IBV genotypes along with QX, whereas B1648, Italy-02, Arkansas and variants accounted for about 12% of the total number. Three IBVs contained recombinant S1 gene sequences comprising genome fragments of QX-type field isolates and vaccine strains H120 (UKR/02/2009) or 4/91 (RF/03/2010), and vaccine strains H120 and D274 (RF/01/2010). The results of the present study showed a significant decline in prevalence of variant IBVs and a further spread of QXtype isolates in commercial chicken flocks in Russia as compared with the 1998 to 2002 data.

Two approaches for simultaneous identification of both Foot-and-mouth disease virus (FMDV) and Swine vesicular disease virus (SVDV) are described: (1) a single-step reverse transcription-PCR with three primers and (2) a PCR-ELISA assay with two universal primers for genome amplification and two virus-specific probes for identification. These methods are based on the use of 3D gene universal PCR primers, the structure of which was optimized and refined due to the close relationship between the two viruses belonging to different genera of the Picornaviridae family. In procedure (1), a three-primer PCR containing one universal antisense primer and two virus-specific primers was shown to differentiate between FMDV and SVDV in one reaction, due to the different length of the amplified DNA fragments (600 and 340 base pairs, respectively). In procedure (2), the two viruses were identified by PCR-ELISA, i.e. PCR for the 3D gene followed by two parallel hybridizations with FMDV and SVDV-specific probes in microplate wells and ELISA detection. The application of universal primers could halve the number of PCR experiments in both cases, as compared to the usual virus-specific PCR procedures. Also, we investigated the 3D gene structure of several SVDV strains isolated at different times. No essential changes were detected in the regions coding for conserved motifs of the RNA-dependent RNA polymerase recognized by our universal primers. The multi-primer PCR was successfully tested on 38 FMDV and 15 SVDV strains, and the PCR-ELISA on 32 FMDV and 16 SVDV strains including clinical material from disease cases.

No abstract

Avian infectious bronchitis is one of the most common viral infections causing enormous economic losses in the global poultry industry. Due to the lack of mechanisms to correct errors during genome replication, the virus can quickly mutate and generate new strains. This is facilitated by widespread use of live vaccines, simultaneous circulation of field viruses belonging to different serotypes in one flock and rapid spread of the virus. Previous studies of avian infectious bronchitis virus strains and isolates identified in the Russian Federation poultry farms showed that 50% of samples tested positive for the 4-91, D274, H-120, Ma5 vaccine strains, and the other half of samples tested positive for the field viruses belonging to eight GI genetic lineages, while the G1-19 (QX) lineage was dominant. The paper presents identification and genotyping results of the avian infectious bronchitis virus in one of the poultry farms in the Saratov Oblast (the Russian Federation) in 2018–2019. The samples of internal organs and blood, as well as oropharyngeal and cloacal swabs were taken from chicks and layers of different ages in the parent and replacement flocks. The vaccine strain, GI-19 field isolates and variant isolates that do not belong to any of the known genetic lineages were detected. Analysis of test results within a two-year period showed that it is important to study samples taken from birds of different ages. The virus undergoes modification and adaptation inducing new genetic forms by infecting several poultry generations, due to which the heterogeneity of the virus population is ob­served not only in the poultry farm as a whole or in a separate department, but also within one organism. The identified isolates showed tropism for the tissues of intestine, reproductive organs, and, in rare cases, trachea and lungs. The data obtained indicate that, despite the vaccination used, a genetically diverse population of the infectious bronchitis virus circulates in the poultry farm, while the infection may not manifest itself at an early age, but may affect the flock productivity in the future due to pathological changes in the reproductive organs of laying chickens.