Advanced technologies in diagnostics of viral diseases of unknown etiology

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Abstract

Unveiling origin of infectious diseases with unknown etiology is one of the major issues in contemporary medicine, since a laboratory-confirmed diagnosis may, unfortunately, be obtained solely in very few cases. Because the majority of the most common mid-latitude infections display a typical overt clinical picture, this problem has not been paid a proper attention until recently. Recent rise in incidence rate of infectious diseases lacking typical clinical signs observed lately makes it extremely important to consider the problem more closely. It is believed that such trend is due to a whole body of reasons, including impaired sanitary control, increased both internal and external migration flows, refusal of vaccination in case of long-lasting epidemic wellbeing, emergence of atypical bacterial strains of bacteria resulting from irrational antibiotic therapy etc. Viruses constitute the largest group of organisms on our planet accounting for them as the most common causative agent of infectious diseases of unknown etiology. Some estimates obtained by mathematical modeling propose that at least 320,000 types of viruses capable of infecting mammals may exist, most of which have not been described yet. Hence, monitoring circulation of the known viral pathogens, tracing down their spreading and changes in genome nucleotide sequence as well as revealing new types of viruses become important aspects of epidemiological surveillance necessary for timely response to emerging threats, prediction and early detection of outbreaks both in humans and animals. This review summarizes traditional molecular genetics methods for detection of viral pathogens, such as PCR, real-time PCR, Sanger sequencing with pre-cloning, and methods based on the second and third generation sequencing. Therefore, a more detailed overview was provided to diverse methods based on using such technologies because viral infectious agents investigated with high-throughput sequencing (or NGS — Next Generation Sequencing) has been increasingly appreciated as feasible for diagnostics, disease control, molecular epidemiology and infection control. Finally, a special attention was also paid to the approaches used to enrich the viral genetic material in samples containing low amount of pathogen nucleic acids.

About the authors

K. F. Khafizov

Central Research Institute of Epidemiology; Center of Strategical Planning of the Ministry of Health

Author for correspondence.
Email: kkhafizov@gmail.com
ORCID iD: 0000-0001-5524-0296

Kamil F. Khafizov - PhD (Biology), Scientific Group Leader, CRIE; Head of the Laboratory for the Development of New Genomics Methods, CSP.

111123, Moscow, Novogireevskaya str. 3a,Phone: +7 917 597-20-85 (mobile)


Russian Federation

A. S. Speranskaya

Central Research Institute of Epidemiology; Lomonosov Moscow State University

Email: hanna.s.939@gmail.com
ORCID iD: 0000-0001-6326-1249

Speranskaya A.S., PhD, Researcher, Department of Molecular Diagnostics and Epidemiology, CRIE; Researcher, Department of Higher Plants, Lomonosov MSU

Moscow

Russian Federation

A. D. Matsvay

Central Research Institute of Epidemiology; Moscow Institute of Physics and Technology

Email: arity767@gmail.com
ORCID iD: 0000-0002-6301-9169

Matsvay A.D., Junior Researcher, Department of Molecular Diagnostics, Group for the Development of New Diagnostic Methods Based on Next-Generation Sequencing, CRIE; Laboratory Assistant, Laboratory of Historical Genetics, Radiocarbon Analysis and Applied Physics, MIPT.

Dolgoprudny, Moscow Region Russian Federation

G. A. Shipulin

Center of Strategical Planning of the Ministry of Health

Email: shipgerman@gmail.com
ORCID iD: 0000-0002-3668-6601

Shipulin G.A., PhD (Medicine), Deputy Director on Science and Production, CSP.

Moscow

Russian Federation

V. G. Dedkov

St. Petersburg Pasteur Institute; Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases

Email: vgdedkov@yandex.ru
ORCID iD: 0000-0002-5500-0169

Dedkov V.G., PhD (Medicine), Deputy Director on Science, St.PPI; Leading Researcher, Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases.

St. Petersburg, Moscow Russian Federation

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