Analysis of Avian Orthoavulavirus 1 Detected in the Russian Federation between 2017 and 2021.

Newcastle disease virus (NDV, Avian orthoavulavirus type 1, AOAV-1) is a contagious high-impact poultry pathogen with infections detected worldwide. In the present study, 19,500 clinical samples from wild bird species and poultry collected from 28 regions of Russia between 2017 and 2021 were screened for the presence of the AOAV-1 genome. NDV RNA was detected in 15 samples from wild birds and 63 samples from poultry. All isolates were screened for a partial sequence of the fusion (F) gene that included the cleavage site. Phylogenetic analysis demonstrated that lentogenic AOAV-1 I.1.1, I.1.2.1, and II genotypes were dominant among vaccine-like viruses in the territory of the Russian Federation. A vaccine-like virus with a mutated cleavage site (112-RKQGR^L-117) was detected in turkeys. Among the virulent AOAV-1 strains, viruses of the XXI.1.1, VII.1.1, and VII.2 genotypes were identified. The cleavage site of viruses of the XXI.1.1 genotype had a 112-KRQKR^F-117 amino acid sequence. The cleavage site of viruses with VII.1.1 and VII.2 genotypes had a 112-RRQKR^F-117 amino acid sequence. The data collected by the present study demonstrate the distribution and dominance of the virulent VII.1.1 genotype in the Russian Federation between 2017 and 2021.

H5N1 avian influenza outbreak in the Far East of Russia in 2008: new introduction.

In April 2008 an avian influenza outbreak was diagnosed in Primorsky Krai, Russia, during the spring migration of wild birds, and A/Chicken/Primorsky/85/08 H5N1 isolate was recovered. The virus had more than 99% genetic identity with A/Whooper Swan/Hokkaido/1/08 H5N1 and A/Whooper Swan/Hokkaido/2/08 H5N1 viruses that were isolated in April 2008 in Japan. The amino acid sequence of the hemagglutinin cleavage site (PQRERRRKRGLF) and intravenous pathotyping index value (IVPI 2.80) were determined; on this basis the virus was characterized as highly pathogenic. The hemagglutinin gene of the virus was shown to belong to clade 2.3.2 while other genes (PB1, PB2, PA, NP, NA, M, NS) were characteristic of Fujian-like sublineage, recovered in the territory of Russia for the first time.

Updated unified phylogenetic classification system and revised nomenclature for Newcastle disease virus.

Several Avian paramyxoviruses 1 (synonymous with Newcastle disease virus or NDV, used hereafter) classification systems have been proposed for strain identification and differentiation. These systems pioneered classification efforts; however, they were based on different approaches and lacked objective criteria for the differentiation of isolates. These differences have created discrepancies among systems, rendering discussions and comparisons across studies difficult. Although a system that used objective classification criteria was proposed by Diel and co-workers in 2012, the ample worldwide circulation and constant evolution of NDV, and utilization of only some of the criteria, led to identical naming and/or incorrect assigning of new sub/genotypes. To address these issues, an international consortium of experts was convened to undertake in-depth analyses of NDV genetic diversity. This consortium generated curated, up-to-date, complete fusion gene class I and class II datasets of all known NDV for public use, performed comprehensive phylogenetic neighbor-Joining, maximum-likelihood, Bayesian and nucleotide distance analyses, and compared these inference methods. An updated NDV classification and nomenclature system that incorporates phylogenetic topology, genetic distances, branch support, and epidemiological independence was developed. This new consensus system maintains two NDV classes and existing genotypes, identifies three new class II genotypes, and reduces the number of sub-genotypes. In order to track the ancestry of viruses, a dichotomous naming system for designating sub-genotypes was introduced. In addition, a pilot dataset and sub-trees rooting guidelines for rapid preliminary genotype identification of new isolates are provided. Guidelines for sequence dataset curation and phylogenetic inference, and a detailed comparison between the updated and previous systems are included. To increase the speed of phylogenetic inference and ensure consistency between laboratories, detailed guidelines for the use of a supercomputer are also provided. The proposed unified classification system will facilitate future studies of NDV evolution and epidemiology, and comparison of results obtained across the world.

Darwin's approach to X-ray diffraction on lateral crystalline structures.

Darwin's dynamical theory of X-ray diffraction is extended to the case of lateral (i.e., having a finite length in the lateral direction) crystalline structures. This approach allows one to calculate rocking curves as well as reciprocal-space maps for lateral crystalline structures having a rectangular cross section. Numerical modelling is performed for these structures with different lateral sizes. It is shown that the kinematical approximation is valid for thick crystalline structures having a small length in the lateral direction.