Genetic analysis of genotype G57 H9N2 avian influenza virus isolate A/chicken/Tajikistan/2379/2018 recovered in Central Asia.

This paper presents genetic data on the full genome analysis of A/chicken/Tajikistan/2379/2018 H9N2 influenza virus isolated in September 2018 from chicken pathological material received from poultry farms of the Republic of Tajikistan and subtyped as H9N2 by serological and molecular methods. According to the results of hemagglutinin gene sequencing, the amino acid sequence of the cleavage site was RSSR/GLF, which is typical for low-virulent avian influenza virus. Phylogenetic analysis of the nucleotide sequence of a hemagglutinin gene fragment (nt 1-1539 of the open reading frame) showed that the A/chicken/Tajikistan/2379/2018 H9N2 isolate belongs to the Y280 genetic group of low-virulent A/H9 influenza virus, which is widespread in Southeast Asia. The complete nucleotide sequence of the viral genome was determined. Comparative analysis of all genomic segments revealed that the A/chicken/Tajikistan/2379/2018 H9N2 virus is closely related to an A/H9 influenza virus isolated in the Far East of the Russian Federation in 2018. Genetic similarity (97.1-99% identity in four out of eight viral genes) was found to isolates of an H7N9 subtype virus recovered in the Inner Mongolia and Hebei regions of China in 2017. According to the analysis of the predicted amino acid sequence of the studied isolate, the positions of some molecular markers indicate possible adaptation of the virus to mammals. Further genetic analysis showed that this virus belongs to genotype G57.

Armoured exogenous internal control for real-time PCR diagnosis of avian influenza.

An exogenous "armoured" PCR internal control (IC) short RNA was analyzed in conjunction with real-time RT-PCR method for diagnosis of avian influenza. The resistance to nucleases and increased physical stability of the IC was ensured using branched polyethyleneimine (PEI) which was in complex with IC-RNA. The option to add the IC directly to pathological material suspensions allows measurement of the nucleic acids extraction efficiency. Stability of armoured RNA-IC during storage and tissue suspension preparation was shown. The advantage of exogenous "armoured" IC was demonstrated in the experiment with AIV genome detection by qPCR in samples from different species of wild birds. The exogenous IC gave reproducible homogeneous Ct values in all tests.

Avian hepatitis E virus identified in Russian chicken flocks exhibits high genetic divergence based on the ORF2 capsid gene.

A total of 79 liver samples from clinically sick and asymptomatic chickens were tested for avian hepatitis E virus (aHEV). Samples were received from 19 farms, five of which tested positive with primers targeting the ORF2 capsid gene. The phylogenetic analysis of a 242-base-pair fragment demonstrated that the Russian aHEV isolates share between 78.2 and 96.2% over the fragment sequenced, whereas the nucleotide sequence identities between the Russian isolates and the other representatives from GeneBank varied from 76.3 to 96.2%. The homology between the studied hepatitis E viruses and swine hepatitis E virus varied between 46.9 to 48.1%. The most divergent isolate aHEV16050 showed homology of 82.6% as compared with the strains in the dendrogram. The three positive hepatitis E virus samples (aHEV16279, aHEV16050 and aHEV18196) did not cluster with the European genotype 3 as expected due to the close location of Russia to Europe, nor did they with the other two genotypes, separating to a distinct branch. The aHEV16211 grouped together with European and Chinese isolates, and the aHEV18198 with Canadian ones.