Genetic diversity of Siberian bovine coronavirus isolates (Coronaviridae: Coronavirinae: Betacoronavirus-1: Bovine-Like coronaviruses)

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Abstract

Introduction. Bovine coronaviruses (BCoVs) are causative agents of diarrhea, respiratory diseases in calves and winter cow dysentery. The study of genetic diversity of these viruses is topical issue.

The purpose of the research is studying the genetic diversity of BCoV isolates circulating among dairy cattle in Siberia.

Materials and methods. Specimens used in this study were collected from animals that died or was forcedly slaughtered before the start of the study. The target for amplification were nucleotide sequences of S and N gene regions.

Results. Based on the results of RT-PCR testing, virus genome was present in 16.3% of samples from calves with diarrheal syndrome and in 9.9% with respiratory syndrome. The nucleotide sequences of S gene region were determined for 18 isolates, and N gene sequences - for 12 isolates. Based on S gene, isolates were divided into two clades each containing two subclades. First subclade of first clade (European line) included 11 isolates. Second one included classic strains Quebec and Mebus, strains from Europe, USA and Korea, but none of sequences from this study belonged to this subclade. 6 isolates belonged to first subclade of second clade (American-Asian line). Second subclade (mixed line) included one isolate. N gene sequences formed two clades, one of them included two subclades. First subclade included 3 isolates (American-Asian line), and second subclade (mixed) included one isolate. Second clade (mixed) included 8 sequences. No differences in phylogenetic grouping between intestinal and respiratory isolates, as well as according to their geographic origin were identified.

Conclusion. The studied population of BCoV isolates is heterogeneous. Nucleotide sequence analysis is a useful tool for studying molecular epidemiology of BCoV. It can be beneficial for choice of vaccines to be used in a particular geographic region.

About the authors

Alexander G. Glotov

Siberian Federal Scientific Centre of Agro-Biotechnologies of the Russian Academy of Science

Email: glotov_vet@mail.ru
ORCID iD: 0000-0002-2006-0196
SPIN-code: 5020-6503

Institute of Experimentally Veterinary Medicine of Siberia and Far East, Doctor of Veterinary Sciences, Professor, Head of Laboratory

Russian Federation, Krasnoobsk, Novosibirsk Region, 630501

Aleksej V. Nefedchenko

Siberian Federal Scientific Centre of Agro-Biotechnologies of the Russian Academy of Science

Email: homeovet@narod.ru
ORCID iD: 0000-0002-4181-4268
SPIN-code: 1583-5776

Institute of Experimentally Veterinary Medicine of Siberia and Far East, Doctor of Veterinary Sciences, Associate Professor, Leading Researcher

Russian Federation, Krasnoobsk, Novosibirsk Region, 630501,

Anton G. Yuzhakov

Federal Scientific Center All-Russian Research Institute of Experimental Veterinary named after K.I. Scriabin and Ya.R. Kovalenko of the Russian Academy of Sciences

Email: anton_oskol@mail.ru
ORCID iD: 0000-0002-0426-9678
SPIN-code: 4870-9610

Candidate of Biological Sciences, Head of Laboratory

Russian Federation, 109428, Moscow

Svetlana V. Koteneva

Siberian Federal Scientific Centre of Agro-Biotechnologies of the Russian Academy of Science

Email: koteneva-sv@mail.ru
ORCID iD: 0000-0003-2649-7505
SPIN-code: 7545-7206

Institute of Experimentally Veterinary Medicine of Siberia and Far East, Candidate of Veterinary Sciences, Leading Researcher

Russian Federation, Krasnoobsk, Novosibirsk Region, 630501

Tatyana I. Glotova

Siberian Federal Scientific Centre of Agro-Biotechnologies of the Russian Academy of Science

Email: t-glotova@mail.ru
ORCID iD: 0000-0003-3538-8749
SPIN-code: 7488-5915

Institute of Experimentally Veterinary Medicine of Siberia and Far East, Doctor of Biological Sciences, Professor, Principal Researcher

Russian Federation, Krasnoobsk, Novosibirsk Region, 630501

Alina K. Komina

Federal Scientific Center All-Russian Research Institute of Experimental Veterinary named after K.I. Scriabin and Ya.R. Kovalenko of the Russian Academy of Sciences

Email: komina.a.k@yandex.ru
ORCID iD: 0000-0002-7173-5501
SPIN-code: 3699-2612

graduate student

Russian Federation, 109428, Moscow

Nikita Yu. Krasnikov

Federal Scientific Center All-Russian Research Institute of Experimental Veterinary named after K.I. Scriabin and Ya.R. Kovalenko of the Russian Academy of Sciences

Author for correspondence.
Email: nick.krasnickoff2011@yandex.ru
ORCID iD: 0000-0001-8148-3080

graduate student

Russian Federation, 109428, Moscow

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2. Fig. 1. Phylogenetic dendrogram based on the bovine coronavirus glycoprotein S gene sequence region. Bootstrap support is indicated near each node of the dendrogram. The strains obtained in this work are marked with a black circle (●). Reference strains are marked with a black square (■). Strains from the GenBank database present in fig. 1 and 2 are marked with a white triangle (∆). For strains from the GenBank database, the name and identification number are indicated. The clade numbers are indicated to the right of the square brackets.

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3. Fig. 2. Phylogenetic dendrogram based on the bovine coronavirus nucleocapsid N gene sequence region. Bootstrap support is indicated near each node of the dendrogram. The strains obtained in this work are marked with a black circle (●). Reference strains are marked with a black square (■). Strains from the GenBank database present in fig. 1 and 2 are marked with a white triangle (∆). For strains from the GenBank database, the name and identification number are indicated. The clade numbers are indicated to the right of the square brackets.

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Copyright (c) 2022 Glotov A.G., Nefedchenko A.V., Yuzhakov A.G., Koteneva S.V., Glotova T.I., Komina A.K., Krasnikov N.Y.

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