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Open AccessArticle

Genotyping Porcine Circovirus 3 (PCV-3) Nowadays: Does It Make Sense?

Department of Animal Medicine, Production and Health (MAPS), Padua University, 35020 Legnaro, Italy
Vitalant Research Institute, San Francisco, CA 94118, USA
Department of Laboratory Medicine, University of California, San Francisco, CA 94118, USA
Institute for Infectious Diseases and Zoonoses, Department for Veterinary Sciences, LMU Munich, 80539 Munich, Germany
Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, USA
MOE Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
MOA Key Laboratory of Animal Virology and Department of Veterinary Medicine, Zhejiang University, Hanghou 310058, China
Departament de Sanitat i Anatomia Animals, Facultat de Veterinària, UAB, 08193 Bellaterra, Spain
UAB, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
OIE Collaborating Centre for the Research and Control of Emerging and Re-emerging Swine Diseases in Europe (IRTA-CReSA), 08193 Bellaterra, Barcelona, Spain
Author to whom correspondence should be addressed.
Viruses 2020, 12(3), 265;
Received: 31 January 2020 / Revised: 20 February 2020 / Accepted: 25 February 2020 / Published: 28 February 2020
(This article belongs to the Special Issue Endemic and Emerging Swine Viruses)
The discovery of a globally distributed porcine circovirus (Porcine circovirus 3; PCV-3) has led to intense research activity and the production of a large amount of molecular data. Different research groups have proposed several, not always concordant, genotypes for this virus. While such categories could aid an easier interpretation of PCV-3 molecular epidemiology, any classification, to be useful in practical settings, must be univocal and of help in the understanding of underlying biological features and epidemiology. Based on these premises, the possibility of defining PCV-3 genotypes was evaluated on the broadest available dataset of PCV-3 complete genome (n = 357) and open reading frame 2 (ORF2, n = 653) sequences. Genetic distance and phylogenetic clustering were selected as the main objective criteria. Additional factors, including the number of within-cluster sequences, host and geographic clustering, concordance between different genomic regions, and analysis method were also taken in account to generate a classification that could be effectively applied in research and diagnostic settings. A maximum within-genotype genetic distance of 3% at the complete genome and 6% at the ORF2 levels, bootstrap support higher than 90%, and concordance between analysis methods allowed us to clearly define two clades which could be potentially defined as genotypes. Further subdivision was not suggested due to the absence of a meaningful association between PCV-3 and its biological/epidemiological features. Nevertheless, since one of the clades included two strains only, thus far we formally propose the definition of only one PCV-3 genotype (PCV-3a). The established criteria will allow us to automatically recognize other genotypes when more strain sequences are characterized. View Full-Text
Keywords: PCV-3; genotypes; classification; ORF2; genome PCV-3; genotypes; classification; ORF2; genome
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    Doi: 10.5281/zenodo.3630784
    Description: Supplementary data 1. List of the accession numbers of the sequences used in the present study. Relevant metadata are also reported. Supplementary figure 1. Maximum likelihood phylogenetic tree based on the ORF2 sequences. The tree nodes have been colour coded based on the respective bootstrap support.
MDPI and ACS Style

Franzo, G.; Delwart, E.; Fux, R.; Hause, B.; Su, S.; Zhou, J.; Segalés, J. Genotyping Porcine Circovirus 3 (PCV-3) Nowadays: Does It Make Sense? Viruses 2020, 12, 265.

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