vavilovВавиловский журнал генетики и селекцииVavilov Journal of Genetics and Breeding2500-3259Institute of Cytology and Genetics of Siberian Branch of the RAS10.18699/vjgb-26-12vavilov-4987Research ArticleГЕНЕТИКА МИКРООРГАНИЗМОВMICROBIAL GENETICSОднонуклеотидные полиморфизмы в геномах вирусов клещевого энцефалита и Западного Нила при тройной природной инфекции у садовой камышовки (Acrocephalus dumetorum)Single nucleotide polymorphisms are typical for tick-borne encephalitis and West Nile viruses during triple natural mixed infections in Blyth’s reed warbler (Acrocephalus dumetorum)https://orcid.org/0000-0002-8237-457XПономареваЕ. П.PonomarevaE. P.

р. п. Кольцово, Новосибирская область

Koltsovo, Novosibirsk Region,

ponomareva_ep@vector.nsc.ruhttps://orcid.org/0000-0003-1275-171XТерновойВ. А.TernovoiV. A.

р. п. Кольцово, Новосибирская область

Koltsovo, Novosibirsk Region

https://orcid.org/0000-0002-2782-8364ПротопоповаЕ. В.ProtopopovaE. V.

р. п. Кольцово, Новосибирская область

Koltsovo, Novosibirsk Region

https://orcid.org/0000-0001-6150-370XТупотаН. Л.TupotaN. L.

р. п. Кольцово, Новосибирская область

Koltsovo, Novosibirsk Region

https://orcid.org/0000-0002-0229-321XЛоктевВ. Б.LoktevV. B.

р. п. Кольцово, Новосибирская область; Новосибирск

Koltsovo, Novosibirsk Region; Novosibirsk

Государственный научный центр вирусологии и биотехнологии «Вектор» РоспотребнадзораРоссияState Research Center of Virology and Biotechnology “Vector”Russian FederationГосударственный научный центр вирусологии и биотехнологии «Вектор» Роспотребнадзора; Федеральный исследовательский центр Институт цитологии и генетики Сибирского отделения Российской академии наукРоссияState Research Center of Virology and Biotechnology “Vector”; Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of SciencesRussian Federation202605032026301117125Copyright © Пономарева Е.П., Терновой В.А., Протопопова Е.В., Тупота Н.Л., Локтев В.Б., 20262026Пономарева Е.П., Терновой В.А., Протопопова Е.В., Тупота Н.Л., Локтев В.Б.Ponomareva E.P., Ternovoi V.A., Protopopova E.V., Tupota N.L., Loktev V.B.This work is licensed under a Creative Commons Attribution 4.0 License.https://vavilov.elpub.ru/jour/article/view/4987

Вовлечение различных видов диких птиц в формирование природных очагов вирусов клещевого энцефалита (ВКЭ) и Западного Нила (ВЗН) обеспечивает быстрое распространение этих ортофлавивирусов в различных географических районах и формирование новых природных очагов данных инфекций. Однако роль популяционной вариабельности ВКЭ и ВЗН в формировании природных очагов, возможность появления (селекции) новых вирусных вариантов, патогенных для человека, в этих природных очагах остаются еще недостаточно изученными. Цель настоящего исследования – оценить популяционную гетерогенность геномов ВКЭ сибирского и дальневосточного генотипов и ВЗН, которые были одновременно выделены из тканей одной особи садовой камышовки (Acrocephalus dumetorum), отловленной в природных ландшафтах пригорода Томска. С этой целью были использованы методы выделения вирусных штаммов на различных культурах клеток в сочетании с анализом полных вирусных геномов полученных изолятов, определенных методами традиционного и высокопроизводительного секвенирования (NGS). Консенсусные полногеномные нуклеотидные последовательности вирусов получали секвенированием по Сэнгеру и сравнивали с последовательностями, полученными методом NGS, с однонуклеотидными заменами (single nucleotide variant, SNV) 2 % и выше, в  пределах изучаемой популяции. Обнаруженный однонуклеотидный полиморфизм (SNP) ассоциировался как с синонимичными, так и несинонимичными нуклеотидными заменами преимущественно локализующихся в генах неструктурных белков ВКЭ и ВЗН. При этом возможных рекомбинационных событий в геномах изолированных ортофлавивирусов обнаружить не удалось. Результаты показали, что изоляты ВЗН Tomsk/bird/2006/A4, ВКЭ PT12 и PT122, выделенные из A. dumetorum, представлены гетерогенными вирусными популяциями, в которых обнаруживаются множественные SNV, возникающие с частотой от 1.75 до 19.88 % для ВЗН и от 2.08 до 23.73 % для ВКЭ. Для большинства выявленных SNP найдены аналогичные нуклеотидные замены в геномах уже известных штаммов ВКЭ и ВЗН, что может свидетельствовать о важной роли этих SNV-спектров в вирусной адаптации и обеспечении генетического и фенотипического разнообразия этих вирусов в природе.

Wild bird species contribute significantly to the rapid geographic dissemination of tick-borne encephalitis viruses (TBEV) and West Nile virus (WNV), facilitating the establishment of new natural foci of these orthoflaviviruses. However, the impact of TBEV and WNV population variability on shaping these foci, as well as the potential emergence of new human-pathogenic viral variants, remain underexplored. This study aimed to assess the genetic heterogeneity of TBEV (Siberian and Far Eastern genotypes) and WNV, isolated simultaneously from the tissues of a single garden reed warbler (Acrocephalus dumetorum) collected in the suburbs of Tomsk. The methods of viral strain isolation on various cell cultures were used in combination with a whole-genome analysis of isolates through traditional and high-throughput sequencing (NGS) methods. Consensus full-genome nucleotide sequences of the viruses were obtained by Sanger sequencing and compared with those obtained by NGS, with single nucleotide substitutions (single nucleotide variants, SNVs) accounting for 2 % or higher within the population under study. Our findings revealed single nucleotide polymorphisms (SNPs) associated with both synonymous and non-synonymous nucleotide substitutions, primarily located within the non-structural protein genes of TBEV and WNV. Notably, recombination events were not detected in the genomes of isolated orthoflaviviruses. The WNV isolate, Tomsk/bird/2006/A4, and the TBEV isolates, PT12 and PT122, obtained from A. dumetorum, exhibited heterogeneous viral populations, with SNVs ranging in frequency from 1.75 to 19.88 % for WNV and from 2.08 to 23.73 % for TBEV. Most identified SNPs shared similar nucleotide substitutions in the genomes of already known strains of TBEV and WNV, suggesting that these SNVs could play a crucial role in viral adaptation and underscore the genetic and phenotypic diversity of these viruses in nature.

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The authors declare that there are no conflicts of interest present.