CURRENT POSSIBILITIES AND POTENTIAL DEVELOPMENT OF MOLECULAR ENTEROVIRUS SURVEILLANCE. EXPERIENCE OF RUSSIAN FEDERATION

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  • Authors: Lukashev A.N.1, Golitsina L.N.2, Vakulenko Y.A.1, Akhmadishina L.V.1, Romanenkova N.I.3, Sapega E.Y.4, Morozova N.S.5, Novikova N.A.2, Trotsenko O.E.4, Ivanova O.E.6,7
  • Affiliations:
    1. Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, Sechenov First Moscow State Medical University, Moscow
    2. Nizhny Novgorod Science Research institute of Epidemiology and Microbiology n.a. academician I.N. Blokhina, Nizhny Novgorod
    3. St. Petersburg Pasteur Institute, St. Petersburg
    4. Khabarovsk Research Institute of Epidemiology and Microbiology, Khabarovsk
    5. Federal Center of Hygiene and Epidemiology of the Inspectorate for Customers Protection of Rospotrebnadzor, Moscow
    6. Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Moscow
    7. Institute of Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Moscow
  • Issue: Vol 8, No 4 (2018)
  • Pages: 452-464
  • Section: MOLECULAR BASES OF EPIDEMIOLOGY, DIAGNOSTICS, PREVENTION AND TREATMENT OF INFECTIOUS DISEASES
  • URL: https://iimmun.ru/iimm/article/view/828
  • DOI: https://doi.org/10.15789/2220-7619-2018-4-452-464

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Abstract

Abstract. Enteroviruses are small RNA viruses, which are ubiquitous and commonly cause outbreaks with various clinical manifestations. In 2006, the Program on enterovirus surveillance was approved in the Russian Federation. Over the last years, molecular-biological and bioinformatics methods for enterovirus epidemiology studies have been developed both in Russia and worldwide. Currently, identification of enteroviruses is carried out by analyzing nucleotide sequence of the full-length VP1 genome region (ca. 900 nt). Routinely, it is sufficient to obtain a partial VP1 genome region sequence (ca. 300 bp) for enteroviruse verification in most cases; however, a more stringent type criterion of 80% sequence identity should be used compared to the 75% sequence identity cut-off for the complete VP1 genome region. Further sequence analysis may be performed by using Bayesian phylogenetic methods, which allow using molecular clock to trace outbreak emergence. Enteroviruses accumulate about 0.5–1% nucleotide substitutions per year. Therefore, a short genome fragment may be used to analyze virus phylodynamics at the level of international transfers and circulating virus variants. On a shorter timescale, a full-length VP1 genome region or a complete genome sequence are preferred for investigating molecular epidemiology, because a short sequence allows to reliably distinguish not more than 1–2 transmission events per year. Thus, determining enterovirus sequences for full-length VP1 genome region or full-genome sequence is preferred for examining viral outbreaks. It is increasingly apparent that analyzing available enterovirus nucleotide sequences reveals limitations related to uneven surveillance efficacy in various countries and short length of genome fragment measured in routine control. As a result, a proper global-scale analysis of enterovirus molecular epidemiology remains problematic. Over the last 20 years, the number of available enterovirus nucleotide sequences increased by hundred times, but understanding emergence of enterovirus infection outbreaks remains limited. Further development of enterovirus surveillance would require new methods for sewage monitoring, affordable high-throughput sequencing and harmonization of global surveillance systems.

About the authors

A. N. Lukashev

Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, Sechenov First Moscow State Medical University, Moscow

Author for correspondence.
Email: alexander_lukashev@hotmail.com

PhD, MD (Medicine), Professor, Director

119435, Malaya Pirogovskaya str., 20/1,
Phone: +7 (499) 246-80-49

Russian Federation

L. N. Golitsina

Nizhny Novgorod Science Research institute of Epidemiology and Microbiology n.a. academician I.N. Blokhina, Nizhny Novgorod

Email: fake@neicon.ru
PhD (Biology), Leading Researcher, Laboratory of Molecular Epidemiology of Viral Infections Russian Federation

Y. A. Vakulenko

Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, Sechenov First Moscow State Medical University, Moscow

Email: fake@neicon.ru
Junior Researcher, Research Department Russian Federation

L. V. Akhmadishina

Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, Sechenov First Moscow State Medical University, Moscow

Email: fake@neicon.ru
PhD (Medicine), Head of the Clinical Diagnostic Laboratory Russian Federation

N. I. Romanenkova

St. Petersburg Pasteur Institute, St. Petersburg

Email: fake@neicon.ru
PhD (Medicine), Leading Researcher, Laboratory of Etiology and Control of Viral Infections Russian Federation

E. Yu. Sapega

Khabarovsk Research Institute of Epidemiology and Microbiology, Khabarovsk

Email: fake@neicon.ru
PhD (Medicine), Head of Enterovirus Surveillance Center Russian Federation

N. S. Morozova

Federal Center of Hygiene and Epidemiology of the Inspectorate for Customers Protection of Rospotrebnadzor, Moscow

Email: fake@neicon.ru
Head of Epidemiological Surveillance Department Russian Federation

N. A. Novikova

Nizhny Novgorod Science Research institute of Epidemiology and Microbiology n.a. academician I.N. Blokhina, Nizhny Novgorod

Email: fake@neicon.ru
PhD (Biology), Professor Russian Federation

O. E. Trotsenko

Khabarovsk Research Institute of Epidemiology and Microbiology, Khabarovsk

Email: fake@neicon.ru
PhD, MD (Medicine), Professor, Director Russian Federation

O. E. Ivanova

Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Moscow; Institute of Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Moscow

Email: fake@neicon.ru
PhD, MD (Medicine), Professor, Head of Poliomyelitis and Other Enterovirus Infections Russian Federation

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Copyright (c) 2018 Lukashev A.N., Golitsina L.N., Vakulenko Y.A., Akhmadishina L.V., Romanenkova N.I., Sapega E.Y., Morozova N.S., Novikova N.A., Trotsenko O.E., Ivanova O.E.

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