Full genome characterization of porcine circovirus type 3 isolates reveals the existence of two distinct groups of virus strains

Robert Fux,Ellen Kathrin Link,Christine Renken,Christina Söckler,Gerd Sutter,Mathias Ritzmann,Matthias Eddicks,Roman Krejci

doi:10.1186/s12985-018-0929-3

Abstract

BackgroundThe occurrence of the novel porcine circovirus type 3 (PCV3) was reported from the Americas, Asia and Europe. Although this virus was detected in association with various clinical syndromes in pigs, its role as possible swine pathogen remains unclear. PCV3 was detected with high prevalence in Polish farms, but to date no genome sequences were available from European PCV3 strains.MethodsWe collected 1060 serum samples from piglets at the age of 20–24 weeks from 53 farms distributed all over Germany. PCV3 DNA was detected using a real-time PCR and subsequently complete PCV3 genome sequences were obtained after multiply primed rolling circle amplification and sequencing of overlapping PCR products. Phylogenetic analysis was performed by neighbor-joining method and maximum likelihood method.ResultsWe obtained 15 complete PCV3 genome sequences as well as nine partial sequences including the putative ORFs 1, 2 and 3 from PCV3 viremic animals in German pig farms. Phylogenetic analysis of these German as well as 30 full genome sequences received from GenBank divided the PCV3 strains into two main groups and several subclusters. Furthermore, we were able to define group specific amino acid patterns in open reading frame 1 and 2.ConclusionPCV3 is distributed with high prevalence in German pig industry. Phylogenetic analysis revealed two clearly separated groups of PCV3 strains, which might be considered as PCV3 genotypes. Specific nucleotide and amino acid marker positions may serve for easy and fast intraspecies classification and genotyping of PCV3 strains. No correlation between PCV3 variants with their geographical origin was evident. We found the same diversity of PCV3 strains in Germany as in other countries. We hypothesize that PCV3 is not a newly emerging virus in the German pig population. Future studies will have to show, if PCV3 genotype specific biological properties are evident.

Highlights

The occurrence of the novel porcine circovirus type 3 (PCV3) was reported from the Americas, Asia and Europe
By analogy to the Porcine circovirus type 2 (PCV2) field, we identified marker nucleotide and codon positions, which substantiate the definition of the two PCV3 subgroups
We demonstrated that PCV3 is distributed with high prevalence in German pig industry

Summary

Introduction

The occurrence of the novel porcine circovirus type 3 (PCV3) was reported from the Americas, Asia and Europe. This virus was detected in association with various clinical syndromes in pigs, its role as possible swine pathogen remains unclear. High PCV3 prevalence was reported from randomly selected farms of different health status from Poland without association of PCV3 to specific clinical signs [5]. PCV2 is associated with several clinical diseases and syndromes and is responsible for major economic losses in swine industry worldwide [10]. In contrast to PCV1 and PCV2 a canonical start codon (ATG) is missing in ORF1 of PCV3. Similar to PCV3 ORF1 the start codon for ORF3 remains unclear. An alternative initiation codon (TCG, nucleotide (nn) position 1900–1902) would result in a 231 aa protein (ORF3231), whereas a methionine codon (ATG, nn position 62–64) would yield a 177 aa protein (ORF3177) [2]

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