About the project
Relevance
Introduction of NGS into laboratory practice for the identification of viral infections has an enormous potential for obtaining fundamental information on the viral composition of a human in various conditions, including viral respiratory infections, as well as developing the system of epidemiological monitoring of the spread of infections. The combination of sequence-independent amplification with NGS may potentially detect viral and non-viral pathogens in a clinical sample without specific targeting, as well as get additional genetic information about the viruses - including the immune status of the individual and medical genomic data. This method has been successfully used for identification and genomic characterization of influenza A and hepatitis C viruses.
As a result of the project implementation, it is expected to obtain maps of the virome of the human upper respiratory tract in viral respiratory infections with the description of the viruses, their properties, the danger for a human, infectious potential and more. The nucleic acid sequences will be analyzed to identify viruses, the assembly and phylogenetic analysis. NGS method will be evaluated in comparison with the multiplex PCR variant for the diagnosis of viral infections.
Project objective
The aim of the project is the study of the viral diversity of the human respiratory tract by NGS sequencing, identification of pathogens, including rare, zoonotic, asymptomatic and previously uncommon viruses, and evaluation of bioinformatics data for practical use in the fight against infectious diseases in humans.
Expected and achieved results
Based on the PCR results, adenovirus, coronavirus, rhinovirus, and parainfluenza virus 4 were identified in the nasopharyngeal samples.
NGS sequencing results showed human viruses (15 genera), eukaryotic host (non-human) viruses (11 genera), and 28 bacteriophages.
Among the viruses associated with ARVI, enterovirus (human rhinovirus, HRV-A), roseolovirus (human betaherpesvirus 7, HBV-7) and lymphocryptovirus (Epstein-Barr virus, EBV), as well as Torque teno virus 16, 12 were found. Among the phage hosts associated with ARVI, Streptococcus spp, Pseudomonas aeruginosa, and Burkholderia spp. were identified.
Based on the sequencing data, the complete genome of the rhinovirus RvA1B/KZ/2021/87 was assembled and placed in GenBank under the number OP886969.
Based on the research results, scientific articles have been published in peer-reviewed international journals Microorganisms (2022, Q2), PeerJ (2023, Q2), Microbiology Resource Announcements (Q4), and one article is under review (manuscript PONE-D-23-26190) in the journal PlusOne (Q2).
List of publications and patents
1. Sandybayev, N., Beloussov, V., Strochkov, V., Solomadin, M., Granica, J., Yegorov, S. Next Generation Sequencing Approaches to Characterize the Respiratory Tract Virome. Microorganisms. 2022, 10, 2327. https://doi.org/10.3390/microorganisms10122327 (WoS, Q2).
2. Sandybayev N, Beloussov V, Strochkov V, Solomadin M, Granica J, Yegorov S. Characterization of viral pathogens associated with symptomatic upper respiratory tract infection in adults during a low COVID-19 transmission period. PeerJ. 2023, 11:e15008. https://doi.org/10.7717/peerj.15008 (WoS, Q2).
3. Strochkov V., Beloussov V., Solomadin M., Granica J., Yegorov S., Orkara S., Sandybayev N. Full genome sequence of a human rhinovirus A1B, obtained in Kazakhstan. Microbiology Resource Announcements. 2023. https://doi.org/10.1128/MRA.00749-23 (WoS, Q4).
Information for potential users
The results of NGS sequencing of the human upper respiratory tract virome during ARVI, obtained as part of the project, showed a real picture of the diversity of respiratory and non-respiratory viral and bacterial infections in humans, which can be used to improve anti-epidemiological and preventive measures of health services.
Members of the research group
Strochkov Vitaliy
Scopus Author ID: 37000312900
ORCID: 0000-0003-3399-2942
Beloussov Vyacheslav
Candidate of Biological Sciences
ORCID: 0000-0003-1922-156X
Solomadin Maxim
ORCID: 0000-0003-4219-1055
