Porcine circovirus type 2 (PCV2) genotyping in Austrian pigs in the years 2002 to 2017

Abstract

Background: Eight different PCV2 genotypes with varying prevalence and clinical impact have been described so far. PCV2 infection is still widespread among the vaccinated population and several experimental studies have clearly demonstrated that there is no induction of a 100% cross-protective immunity between the PCV2 genotypes. Hence, PCV2a-based vaccines may be ineffective. In this longitudinal study, the PCV2 genotype and haplotype evolution in Austria in the years 2002 to 2017 was investigated by phylogenetic analysis of 462 bp-long sequences of the capsid protein gene (ORF2). The obtained findings may be of practical relevance for the future development of vaccination strategies.

Results: One hundred thirty four of a total of 161 formalin-fixed and paraffin wax-embedded samples could be sequenced successfully. There was no significant influence of storage time on sequencing success or quality. PCV2a (8.2%), PCV2b (77.6%), PCV2d (13.4%), and PCV2g (0.8%) were found. PCV2d was first detected as early as in 2004. PCV2g was described once in 2009. Both global PCV2 genotype shifts were observed. PCV2a occurred with a low prevalence during the first study years only in samples from non-vaccinated swine herds and was gradually replaced by PCV2b until 2011. PCV2b was the most prevalent genotype over the whole study period and was detected in samples from vaccinated and non-vaccinated herds. During the last two study years, the prevalence of PCV2d increased, although at this point almost all herds were vaccinated. The haplotype diversity was high, but the nucleotide diversity was low. Especially for genotype PCV2b, an increase in haplotype diversity could be described during the first study years.

Conclusion: Extensive PCV2a-derived vaccination resulted in a reduction of prevalence and in a stabilization of genotype PCV2a, whereas genotypes PCV2b and PCV2d evolved as a consequence of natural and vaccination-induced selection. An ongoing virus circulation may be the result of reduced vaccine-induced protection.

Keywords: Genotype shift; Genotypes; Haplotypes; Porcine circovirus type 2.

Fig. 1

Maximum likelihood tree constructed with 105 capsid protein gene sequences. The tree is constructed from sequences of the present study (acc. no. MN150551-MN150684) and 32 representative PCV2 sequences of different genotypes (PCV2a labeled blue: acc. no. AF201305, AY424401, EU148507, EU386606, FJ483938, KP231099; PCV2b labeled red: acc. no. AY256457, DQ218419, EU545549, HQ591367, JN382175, KY806030, KY806064; PCV2c labeled turquoise: acc. no. EU148503; PCV2d labeled green: acc. no. JN006448, JF683408, JX912915; PCV2e labeled violet: acc. no. KT795288; PCV2f labeled orange: acc. no. HQ591381, KT369067, LC004746, LC004749, LC008134, MG739618; PCV2g labeled pink: acc. no. AY713470, DQ151643, JX948768, KP420197; PCV2h labeled brown: GQ449669, KC514969, KM042403, MH465473). NC_001792 served as outgroup. The tree with the highest log likelihood (− 3808.33) is shown. The percentage of trees in which the associated taxa clustered together is shown next to the branches (1000 replicates, in %)

Fig. 2

Number of PCV2 sequences and haplotypes per genotype per year. The columns represent the numbers of PCV2 sequences per genotype per year (PCV2a – dark blue, PCV2b – dark red, PCV2d – dark green, PCV2g – pink) and the number of PCV2 haplotypes (HT) per genotype per year (PCV2a – light blue, PCV2b – light red, PCV2d – light green, PCV2g – rose)

Fig. 3

Median-joining networks of PCV2a, PCV2b and PCV2d classified according to the year of detection (see legend). The numbers of mutation steps are indicated in red numbers next to the branches. Branches without numbers represent mutation steps of one. A. PCV2a. Except of one haplotype, which is constituted of three samples, all haplotypes are constituted of one sample. The haplotypes are separated by one to 26 mutation steps from the main haplotype. B. PCV2b. One very common haplotype is shared by 34 individuals. Seven haplotypes are constituted of two to nine samples. Most haplotypes are constituted of one sample separated by one to two mutation steps from the main haplotype. Two further clades can be distinguished and the associated haplotypes are separated by up to twelve and 23 mutation steps, respectively, from the main haplotype. C. PCV2d. Except of three haplotypes, which are constituted of two to four samples, all haplotypes are constituted of one sample. The haplotypes are separated by one to two mutations steps from the main haplotype