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Kemerovo virus (KEMV) is a member of the Great Island virus genetic group, belonging to the tick-borne arboviruses of the genus Orbivirus within the family Reoviridae. Nine strains of KEMV, which were isolated from various locations in Russia, were sequenced by high-throughput sequencing to study their intraspecific diversity and the interspecific relationships of viruses within the Great Island genetic group. For the first time, multiple reassortment within KEMV was reliably demonstrated. Different types of independently emerged alternative reading frames in segment 9 and heterogeneity of the viral population in one of the KEMV strains were found. The hypothesis of the role of an alternative open reading frame (ORF) in segment 9 in KEMV cellular tropism was not confirmed in this study., Competing Interests: Declaration of Competing Interest The authors declare that they have no competing interests., (Copyright © 2019 Elsevier GmbH. All rights reserved.)

Paramushir virus belongs to Sakhalin virus genogroup within Orthonairovirus genus and is one of the poorly studied viruses with unknown pathogenicity. At the moment, only one nearly complete sequence of Paramushir virus genome, isolated in 1972, is available. Two new strains of PARV were isolated in 2015 from a sample collected at the Tyuleniy Island in the Okhotsk Sea and sequenced using a combination of high throughput sequencing and specific multiplex PCR. Both strains are closely related to the early sequenced PARV strain LEIV-1149 K. The signs of intersegment reassortment and probable recombination were revealed, which point to a high variability potential of Paramushir virus and may lead to the formation of strains with novel properties, different from those of the predecessors. The new data regarding Paramushir virus can promote a better understanding of the diversity and relations within Orthonairovirus genus and help define intragenic demarcation criteria, which have not yet been established., (Copyright © 2018 Elsevier GmbH. All rights reserved.)

The accuracy and sensitivity of deep sequencing were assessed using viral standards (pNL4-3 and pLAI.2) of both DNA and RNA. The sequencing accuracy did not depend on the type of nucleic acid, but critically depended on the number of reads and threshold of sensitivity to minor viral populations. With coverage of more than 236 reads, the accuracy of viral RNA sequencing was equal to or exceeded 99.9%, with a sensitivity threshold to minor nucleotides of 20%. When the sensitivity threshold was below 1%, reduced accuracy dynamics were clearly visible even when the coverage was massive (more than 9.000 reads). It was found that the floating sensitivity threshold allowed the sequencing accuracy to be maintained at an acceptable level in cases of low coverage (less than 1.500-2.000) of reads. These results indicate the quality that can be expected with a specific number of reads and sensitivity threshold. Deep sequencing is a very powerful tool that can significantly improve the value of study results, but despite its superior performance, it should be used with caution regarding its sensitivity to minor populations below 1%., (Copyright © 2018 Elsevier B.V. All rights reserved.)

Advances in the next generation sequencing (NGS) technologies have significantly increased our ability to detect new viral pathogens and systematically determine the spectrum of viruses prevalent in various biological samples. In addition, this approach has also helped in establishing the associations of viromes with many diseases. However, unlike the metagenomic studies using 16S rRNA for the detection of bacteria, it is impossible to create universal oligonucleotides to target all known and novel viruses, owing to their genomic diversity and variability. On the other hand, sequencing the entire genome is still expensive and has relatively low sensitivity for such applications. The existing approaches for the design of oligonucleotides for targeted enrichment are usually involved in the development of primers for the PCR-based detection of particular viral species or genera, but not for families or higher taxonomic orders. In this study, we have developed a computational pipeline for designing the oligonucleotides capable of covering a significant number of known viruses within various taxonomic orders, as well as their novel variants. We have subsequently designed a genus-specific oligonucleotide panel for targeted enrichment of viral nucleic acids in biological material and demonstrated the possibility of its application for virus detection in bird samples. We have tested our panel using a number of collected samples and have observed superior efficiency in the detection and identification of viral pathogens. Since a reliable, bioinformatics-based analytical method for the rapid identification of the sequences was crucial, an NGS-based data analysis module was developed in this study, and its functionality in the detection of novel viruses and analysis of virome diversity was demonstrated.

Human adenovirus 7 (hAdv7) 19BOVLB/Volgograd/Rus/2014 was isolated from the autopsy material from an adult with fatal pneumonia in Volgograd, Russia, in March 2014. Whole-genome sequencing of the virus isolate was performed., (Copyright © 2016 Yatsyshina et al.)

Aim: Establish genetic characteristics, carry out phylogenetic analysis and determination of molecular markers of resistance to etiotropic preparations against influenza A/H3N2 and B viruses that had circulated in Russia in 2013 - 2015., Materials and Methods: 80 biological samples containing influenza A/H3N2 virus RNA and 31 samples containing influenza B virus RNA were studied. Sequencing of PCR fragments was carried out inABI-3 100 PRIZMTM GeneticAnalyzer (AppliedBiosystems, USA) and using MiSeq (Illumina, USA). Data treatment and analysis was carried out using CLC v.3.6.5., DNASTAR and BioNumerics v.6.5. programs., Results: In 2013 -2014 A/Texas/50/2012-like-clade 3C.3 influenza A/H3N2 viruses dominated, 10% belonged to subclade 3C.2a and 10% - to 3C.3b. Most of the viruses (8 1%) of 2014 - 2015 were of 3C.2a clade, the portion of viruses belonging to 3C.3b and 3C.3a was 9 and 10%. Yamagata-like viruses predominated among the studied influenza B viruses, only 1 virus of 2014 - 2015 belonged to Victoria lineage, 1 reassortant of Yamagata and Victoria lineages was detected. Rimantadine- resistance mutationS3 lN(M2 protein) was detected in all the influenza A/H3N2 viruses. Mutations determining resistance to oseltamivir (NA gene) were not detected in influenza A/H3N2 and B viruses., Conclusion: Increase of influenza morbidity in 2014 - 2015 was determined by the emergence of influenza A/H3N2 and B viruses, antigenically distinct from those that had circulated previously and those included into the vaccine, thus resulting in the WHO decision to change A/ H3N2 and B components of the 2015 - 2016 vaccine: Simultaneous circulation of 2 lineages of influenza B virus and emergence of their reassortants gives evidence on the necessity of use of quadrivalent vaccines, containing both lineages.