Abstract
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.
Highlights
Porcine circovirus 3 (PCV-3) is a recently identified member of the genus Circovirus
It must be stressed that current knowledge on PCV-3 immunology is very limited and essentially based on comparison with porcine circovirus 2 (PCV-2)
In order to be practical and useful, the PCV-3 classification must not be for its own sake, but should be of help in the interpretation of the underlying viral features and, in the understanding of its epidemiology and potential control measures [21]
Summary
Porcine circovirus 3 (PCV-3) is a recently identified member of the genus Circovirus. Since its first identification in the United States thorough a metagenomics approach [2,3], a remarkable amount of epidemiological and molecular data has been accumulated regarding PCV-3 This virus has been reported in all continents (with Africa and Australia being the only exceptions so far) at moderate to high rates of detection (>10%), depending on the particular study, country, and farm (reviewed in Klaumann et al, 2018 [1]). In order to be practical and useful, the PCV-3 classification must not be for its own sake, but should be of help in the interpretation of the underlying viral features and, in the understanding of its epidemiology and potential control measures [21] Based on these premises, the applicability of a PCV-3 genotyping proposal is evaluated in the present work, offering standardized criteria based on a consensus shared by different research groups operating around the world
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
