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Инфекция и иммунитет. 2018; 8: 452-464

СОВРЕМЕННЫЕ ВОЗМОЖНОСТИ И НАПРАВЛЕНИЯ РАЗВИТИЯ МОЛЕКУЛЯРНОЭПИДЕМИОЛОГИЧЕСКОГО МОНИТОРИНГА В НАДЗОРЕ ЗА ЭНТЕРОВИРУСНЫМИ ИНФЕКЦИЯМИ. ОПЫТ РОССИЙСКОЙ ФЕДЕРАЦИИ

Лукашев А. Н., Голицына Л. Н., Вакуленко Ю. А., Ахмадишина Л. В., Романенкова Н. И., Сапега Е. Ю., Морозова Н. С., Новикова Н. А., Троценко О. Е., Иванова О. Е.

https://doi.org/10.15789/2220-7619-2018-4-452-464

Аннотация

Резюме. Энтеровирусы — мелкие РНК-содержащие вирусы, которые распространены повсеместно и регулярно становятся причиной вспышек заболеваемости с различной симптоматикой. В Российской Федерации с 2006 г. действует надзор за энтеровирусами. За эти годы в России и в мире были отработаны молекулярно-биологические и биоинформатические инструменты для изучения эпидемиологии энтеровирусов. В настоящее время идентификация энтеровирусов в мире осуществляется практически исключительно на основании анализа нуклеотидной последовательности области генома VP1 (около 900 нуклеотидов). При этом в рутинной работе определяется только фрагмент этой области генома (около 300 нуклеотидов). В большинстве случаев этого достаточно, чтобы достоверно типировать вирус, однако точность анализа короткого участка генома ниже, и достоверным критерием типа для короткого фрагмента следует считать 80% сходства нуклеотидной последовательности, а не 75%, как в случае полной области генома VP1. Для даль нейшего анализа полученных нуклеотидных последовательностей в настоящее время широко применяются Байесовы филогенетические методики, которые позволяют использовать метод молекулярных часов в расследовании вспышек заболеваемости. Энтеровирусы накапливают порядка 0,5–1% нуклеотидных замен в год, поэтому даже короткий фрагмент генома позволяет анализировать филодинамику вирусов на уровне передачи между странами или смены циркулирующего варианта вируса. На более короткой временной шкале короткий фрагмент ограниченно пригоден для изучения молекулярной эпидемиологии, поскольку позволяет достоверно различать не более 1–2 случаев передачи вируса в год. Таким образом, для расследования вспышек желательно определение нуклеотидной последовательности полной области генома VP1 или полногеномной последовательности. В результате анализа имеющихся в базах данных нуклеотидных последовательностей энтеровирусов все более очевидными становятся ограничения, связанные с неравномерной эффективностью надзора в разных странах мира и короткой длиной фрагмента генома, определяемой при рутинном надзоре. Как следствие, полноценный анализ молекулярной эпидемиологии энтеровирусов в глобальном масштабе остается проблематичным. Количество известных нуклеотидных последовательностей энтеровирусов за последние 20 лет выросло в сотни раз, однако понимание закономерностей возникновения вспышек энтеровирусной инфекции практически отсутствует. Эффективное развитие надзора за энтеровирусами потребует внедрения новых методов исследования сточных вод, экономически эффективного высокопроизводительного секвенирования, гармонизации систем надзора в разных странах мира.

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Russian Journal of Infection and Immunity. 2018; 8: 452-464

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

Lukashev A. N., Golitsina L. N., Vakulenko Y. A., Akhmadishina L. V., Romanenkova N. I., Sapega E. Yu., Morozova N. S., Novikova N. A., Trotsenko O. E., Ivanova O. E.

https://doi.org/10.15789/2220-7619-2018-4-452-464

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.

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