Spatio-temporal clustering of African swine fever virus (Asfarviridae: Asfivirus) circulating in the Kaliningrad region based on three genome markers

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Abstract

Introduction. The rapid spread of African swine fever in the Kaliningrad region makes it necessary to use the methods of molecular epidemiology to determine the dynamics and direction of ASF spread in this region of Russia.

The aim of the study was to determine single nucleotide polymorphisms within molecular markers K145R, O174L and MGF 505-5R of ASFVs isolated in Kaliningrad region and to study the circulating of the pathogen in European countries by subgenotyping and spatio-temporal clustering analysis.

Materials and methods. Blood samples from living domestic pigs and organs from dead domestic pigs and wild boars, collected in the Kaliningrad region between 2017 and 2022 were used. Virus isolation was carried out in porcine bone-marrow primary cell culture. Amplicons of genome markers were amplified by PCR with electrophoretic detection and subsequent extraction of fragments from agarose gel. Sequencing was performed using the Sanger method.

Results. The circulation of two genetic clusters of ASFV isolates on the territory of the Kaliningrad has been established: epidemic (K145R-III, MGF 505-5R-II, O174L-I – 94.3% of the studied isolates) and sporadic (K145R-II, MGF 505-5R-II, O174L-I – 5.7%).

Conclusion. The broaden molecular genetic surveillance of ASFV isolates based on sequencing of genome markers is necessary in the countries of the Eurasian continent to perform a more detailed analysis of ASF spread between countries and within regions.

About the authors

Roman S. Chernyshev

Federal Centre for Animal Health (ARRIAH)

Email: chernishev_rs@arriah.ru
ORCID iD: 0000-0003-3604-7161

Postgraduate Student, Reference Laboratory

Russian Federation, Vladimir

Alexey S. Igolkin

Federal Centre for Animal Health (ARRIAH)

Email: igolkin_as@arriah.ru
ORCID iD: 0000-0002-5438-8026

Head of Reference Laboratory

Russian Federation, Vladimir

Andrey R. Shotin

Federal Center for Animal Health (ARRIAH)

Email: shotin@arriah.ru
ORCID iD: 0000-0001-9884-1841

Researcher, Reference Laboratory

Russian Federation, Vladimir

Nikolay G. Zinyakov

Federal Centre for Animal Health (ARRIAH)

Email: zinyakov@arriah.ru
ORCID iD: 0000-0002-3015-5594

Senior Researcher, Reference Laboratory for Avian Influenza

Russian Federation, Vladimir

Ivan S. Kolbin

Federal Center for Animal Health (ARRIAH)

Email: kolbin@arriah.ru
ORCID iD: 0000-0003-4692-1297

Postgraduate Student, Reference Laboratory

Russian Federation, Vladimir

Anastasia S. Sadchikova

Federal Centre for Animal Health (ARRIAH)

Email: sadchikova@arriah.ru
ORCID iD: 0009-0001-0801-2394

Postgraduate Student, Reference Laboratory

Russian Federation, Vladimir

Ivan A. Lavrentiev

Federal Center for Animal Health (ARRIAH)

Email: lavrentev@arriah.ru
ORCID iD: 0009-0003-0552-3812

Postgraduate Student, Reference Laboratory

Russian Federation, Vladimir

Konstantin N. Gruzdev

Federal Center for Animal Health (ARRIAH)

Email: gruzdev@arriah.ru
ORCID iD: 0000-0003-3159-1969

D. Sc. (Biology), Professor, Chief Researcher of the Information and Analytical Center

Russian Federation, Vladimir

Ali Mazloum

Federal Center for Animal Health (ARRIAH)

Author for correspondence.
Email: mazlum@arriah.ru
ORCID iD: 0000-0002-5982-8393

Senior Researcher, Reference Laboratory

Russian Federation, Vladimir

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Supplementary files

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1. JATS XML
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2. Supplementary materials
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3. Fig. 1. Spread of ASF in the Kaliningrad region (2017–2022)

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4. Fig. 2. Multiple nucleotide alignment of genome marker fragments K145R (a), O174L (b) and MGF 505-5R (c) of ASFV isolates obtained by Sanger sequencing

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5. Fig. 3. Distribution of ASFV genotype II variants in the territory of the Kaliningrad region and Eastern European countries based on genetic analysis of markers K145R (a), O174L (b) and MGF 505-5R (c)

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6. Fig. 4. Neighbor-joining dendrogram showing phylogenomic of ASFV isolates from eastern Europe based on clustering analysis

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7. Fig. 5. The pattern of territorial origin and circulation of ASFV in Kaliningrad region based on analyses of published and original data

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Copyright (c) 2024 Chernyshev R.S., Igolkin A.S., Shotin A.R., Zinyakov N.G., Kolbin I.S., Sadchikova A.S., Lavrentiev I.A., Gruzdev K.N., Mazloum A.

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