Abstract
Bovine pestiviruses are members of the species Pestivirus A (bovine viral diarrhea virus 1, BVDV-1), Pestivirus B (BVDV-2) or Pestivirus H (HoBiPeV). To date, BVDV-2 isolates/strains have been classified into three subtypes (a-c) by phylogenetic analysis, and an additional subtype (d) has been proposed based on 5' untranslated region (UTR) secondary structures. In a previous study, we identified some BVDV-2 sequences in the GenBank database that could not be classified as subtype a, b or c by phylogenetic analysis of their genomes, UTRs or individual genes. Here, we performed a detailed study of these sequences and assessed whether they might represent a distinct BVDV-2 subtype. Initially, we collected 85 BVDV-2 complete/near-complete genomes (CNCGs) from GenBank and performed a “proof of equivalence” between phylogenetic analyses based on CNCGs and open reading frames (ORFs), which showed that ORFs may be reliably used as a reference target for BVDV-2 phylogeny, allowing us to increase our dataset to 139 sequences. Among these, we found seven sequences that could not be classified as BVDV-2a-c. The same was observed in the phylogenetic analysis of CNCGs and viral genes. In addition, the seven non-BVDV-2a-c sequences formed a distinct cluster in all phylogenetic trees, which we propose to term BVDV-2e. BVDV-2e also showed 44 amino acid changes compared to BVDV-2a-c, 20 of which are in well-defined positions. Importantly, an additional phylogenetic analysis including BVDV-2d and a pairwise comparison of BVDV-2e and BVDV-2d sequences also supported the difference between these subtypes. Finally, we propose the recognition of BVDV-2e as a distinct BVDV-2 subtype and encourage its inclusion in future phylogenetic analyses to understand its distribution and evolution.
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The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request.
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Acknowledgments
PSBO is a graduate student of the Programa de Pós-graduação em Medicina Veterinária, UFSM, and thanks the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) (Brazil) for his scholarship. EFF (process 301414/2010-6) and RW (process 304153/2014-1) were supported by CNPq research fellowships. The research was financed in part by Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), Brazil—Finance code 001.
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Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) and Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)—Finance code 001.
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PBSO performed the amino acid and phylogeny analyses and assisted in the experimental design, interpretation of results and manuscript preparation; JVJr assisted in the analysis of amino acids and phylogeny, experimental design, and interpretation of results and prepared the final version of the manuscript; RW assisted in the interpretation of results and manuscript review; and EFF assisted in the experimental design, interpretation of results, and elaboration and final review of the manuscript and guided the study.
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Supplementary File S1 Accession numbers of the BVDV-2 complete/near-complete genome sequences collected in our study (DOC 56 kb)
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de Oliveira, P.S.B., Silva Júnior, J.V.J., Weiblen, R. et al. A new (old) bovine viral diarrhea virus 2 subtype: BVDV-2e. Arch Virol 167, 2545–2553 (2022). https://doi.org/10.1007/s00705-022-05565-w
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DOI: https://doi.org/10.1007/s00705-022-05565-w