Problems of VirologyProblems of VirologyВопросы вирусологии0507-40882411-2097Central Research Institute for Epidemiology1682410.36233/0507-4088-357efobwoORIGINAL RESEARCHESОРИГИНАЛЬНЫЕ ИССЛЕДОВАНИЯResearch ArticleAfrican swine fever virus (Asfarviridae, Asfivirus) strains from the central regions of Russia, carrying variant 5 of the central variable region (CVR), are characterized by tandem duplication in the intergenic region MGF 360-13L – MGF 360-14LШтаммы вируса африканской чумы свиней (Asfarviridae, Asfivirus, African swine fever virus) центральных регионов России, несущие вариант 5 центральной вариабельной области (CVR), характеризуются тандемной дупликацией в межгенном регионе MGF 360-13L – MGF 360-14Lhttps://orcid.org/0000-0003-3239-9004SkorobagatkoDaria A.СкоробагатькоДарья Александровна
Russian Federation

Candidate of Biological Sciences (Ph. D.), Specialist in Department of Genomics and Molecular Biology

канд. биол. наук, специалист направления геномики и молекулярной биологии

d.skorobagatko86@gmail.comhttps://orcid.org/0000-0002-4770-3796TolkovaEkaterina S.ТольковаЕкатерина Сергеевна
Russian Federation

Main Specialist in Department of Genomics and Molecular Biology

главный специалист направления геномики и молекулярной биологии

katerina.tolkova@gmail.comhttps://orcid.org/0000-0002-3366-8184ShepelevaOlga A.ШепелеваОльга Александровна
Russian Federation

Head of the Department of Genomics and Molecular Biology

руководитель направления геномики и молекулярной биологии

o.shepeleva@cherkizovo.comhttps://orcid.org/0000-0002-5630-5247ShapovalovSergey O.ШаповаловСергей Олегович
Russian Federation

Doctor of Sciences in Biology, Head

д-р биол. наук, директор

s.shapovalov@cherkizovo.comCherkizovo Research and Testing Center LLCООО Научно-испытательный центр «Черкизово»23032026711425210112025Copyright ©; 2026, Skorobagatko D.A., Tolkova E.S., Shepeleva O.A., Shapovalov S.O.Copyright ©; 2026, Скоробагатько Д.А., Толькова Е.С., Шепелева О.А., Шаповалов С.О.2026Skorobagatko D.A., Tolkova E.S., Shepeleva O.A., Shapovalov S.O.Скоробагатько Д.А., Толькова Е.С., Шепелева О.А., Шаповалов С.О.https://creativecommons.org/licenses/by/4.0https://virusjour.crie.ru/jour/article/view/16824

Introduction. The high economic losses and the lack of effective and safe vaccines against African swine fever (ASF) indicate the need for further in-depth studies of the virus genome, its changes and the circulation of genetic lineages. Whole genome sequencing of virus isolates is best suited for this purpose.

The aim of the study. Whole-genome analysis of African swine fever virus (ASFV) isolates obtained in the Lipetsk, Penza and Tambov regions in 2016–2021 and identification of additional diversity markers within the genetic lineage.

Materials and methods. Domestic pig tissue samples were analyzed using whole-genome sequencing and Sanger sequencing. The following programs were used for sequence assembly: CLC Genomics Workbench 22, Trimmomatic v. 0.39, SPAdes v. 4.2.0, BWA-MEM v. 0.7.17-r1188 and bcftools v.1. 22. The phylogenetic tree was constructed in MEGA11 based on the alignment in MAFFT v. 7.526 with 67 genomes from GenBank.

Results. Based on the presence of MGF 360-10L III polymorphism, the analyzed isolates belong to the CVR-V variant of the Russia genetic lineage of the Georgia 2007 clade. Based on the order of formation of MGF 360-10L III and CVR-V, any sequences carrying CVR-V belong to the same genetic lineage. A 12-nucleotide insertion CAGTCTATAAGA was detected, forming a tandem duplication in IGR MGF 360-13L – MGF 360-14L, and polymorphisms in IGR C62L – C962R and in genes D1133L and Q706L were proposed as having phylogenetic potential for differentiation ASFV strains in the central regions of Russia.

Conclusion. The proposed new potential diversity markers have a resolving power for ASFV strains from Central Russia.

Введение. Большой экономический ущерб и отсутствие действенных и безопасных вакцин против африканской чумы (АЧС) указывают на необходимость продолжения углубленного изучения генома вируса АЧС, его изменений и циркуляции генетических линий. Для этого наилучшим образом подходит полногеномное секвенирование изолятов вируса.

Цель работы. Полногеномный анализ изолятов вируса АЧС, полученных на территории Липецкой, Пензенской и Тамбовской областей в 2016–2021 гг., и выявление дополнительных маркеров разнообразия в пределах генетической линии.

Материалы и методы. Образцы тканей домашних свиней исследовали с помощью полногеномного секвенирования и секвенирования по Сэнгеру. Для сборки последовательностей использовали программы CLC Genomics Workbench 22, Trimmomatic v. 0.39, SPAdes v. 4.2.0, BWA-MEM v. 0.7.17-r1188 и bcftools v. 1.22. Филогенетическое древо строили в программе MEGA11 на основе выравнивания в MAFFT v. 7.526 с 67 геномами из GenBank.

Результаты. На основании присутствия полиморфизма MGF 360-10L III проанализированные изоляты относились к варианту CVR-V генетической линии «Россия» клады Georgia 2007. Исходя из очередности образования MGF 360-10L III и CVR-V, любые последовательности, несущие CVR-V, принадлежат к этой же генетической линии. Была обнаружена инсерция в 12 нуклеотидов CAGTCTATAAGA, образующая тандемную дупликацию в IGR MGF 360-13L – MGF 360-14L, и предложены полиморфизмы в IGR C62L – C962R и в генах D1133L и Q706L, имеющие филогенетический потенциал для дифференцировки штаммов вируса АЧС в центральных регионах России.

Заключение. Предложенные к использованию новые вероятные маркеры разнообразия обладают разрешающей способностью в отношении штаммов вируса АЧС из Центральной России.

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