An updated phylogeography and population dynamics of porcine circovirus 2 genotypes: are they reaching an equilibrium?

Abstract

Introduction: Porcine circovirus 2 (PCV2) emerged more than three decades ago as one of the most impactful pathogens in the swine industry. Despite being a DNA virus, one of the hallmarks of PCV2 is its high evolutionary rate, which has led to the emergence of different genotypes, each exhibiting varying degrees of evolutionary success. Current knowledge suggests the occurrence of three main waves of genotype dominance, alternating over time (i.e., PCV2a, PCV2b, and PCV2d), alongside less prevalent genotypes. However, although PCV2d is currently the most common genotype nowadays, the others continue being circulating in the pig population.

Methods: The present study reconsidered the epidemiological and evolutionary patterns of PCV2 genotypes using phylodynamic analyses, benefiting from an almost 10-fold increase in ORF2 sequence availability compared to previous studies. Additionally, a phylogeographic analysis was performed to investigate viral dispersal patterns and frequency, and the selective pressures acting on the capsid protein were estimated and compared among genotypes.

Results: While successive emergence of major genotypes was confirmed, this study extends previous findings by revealing subsequent prevalence fluctuations of PCV2a and PCV2b after their initial decline. This evolutionary process may represent an example of balancing selection, specifically negative frequency-dependent selection, where a genotype fitness diminishes as it becomes more common, and vice versa. Variations in genotype- or clade-specific immunity-affected by the local prevalence of viral groups-combined with the periodic introduction of strains that have independently evolved in different regions, may have led to fluctuations in the population dynamics of major genotypes over time. These fluctuations were associated with ongoing evolution and variations in the capsid amino acid profile.

Discussion: These findings have profound implications for future control strategies. Although PCV2d remains the most prevalent and widespread genotype, other genotypes should not be neglected. Control strategies should thus target the entire PCV2 population, with a focus on fostering broader and more cross-protective immunity.

Keywords: evolution; genotypes; phylodynamic; phylogeography; porcine circovirus 2 (PCV2); selection.

Figure 1

Violin plot depicting the posterior probability estimation of tMRCA and evolutionary rate calculated for different genotypes. For major genotypes, the results obtained from the analysis of the Country-year and Balanced datasets are also reported.

Figure 2

PCV2 population dynamics plot: the left graph illustrates the mean relative genetic diversity (Ne x t) of major PCV2 genotypes, represented by a solid line, while the shaded area indicates the 95% highest posterior density (HPD) interval. In the right panel, the same representation is applied to depict all PCV2 genotypes studied. Where applicable, comparisons between the Country-year and Balanced datasets are shown using different line styles.

Figure 3

Plot depicting the proportion of lineages over time: this figure illustrates the proportion of lineages over time for PCV2a, PCV2b, and PCV2d, based on the analysis of maximum clade credibility (MCC) trees annotated with the reconstruction of ancestral states (i.e., continents). Different geographic areas are represented by distinct color coding. The results derived from the Country-year dataset are shown on the left panel, while those from the Balanced dataset are displayed on the right panel.

Figure 4

Plot depicting the dN-dS ratios of individual genotypes (upper panel) and differences among genotypes (lower panel) at various capsid positions: this figure presents the dN-dS ratios for individual PCV2 major genotypes (color-coded) in the upper panel and the differences among these genotypes in the lower panel (color-coded), focusing on different capsid positions. The plot also overlays the relative surface accessibility (RSA), calculated using the NetSurfP-2.0 server, represented by a gray area. The surface accessibility threshold is set at 25%, as predefined by the software.

Figure 5

Quaternary structure of PCV2: this figure illustrates the quaternary structure of PCV2, highlighting sites under significant episodic diversifying selection as detected by MEME. These sites are color-coded in red, green, and blue for PCV2a, PCV2b, and PCV2d, respectively, on the viral surface of different capsid proteins. In the right panel, the same positions are highlighted on both the external (upper image) and internal (lower image) surfaces of three contiguous capsids. The ribbon structure, also color-coded to correspond with the selection sites, is displayed transparently in the background.

Figure 6

Quaternary structure of PCV2: this figure illustrates the quaternary structure of PCV2, highlighting sites under significantly different selective pressure among genotypes as detected by contrast-FEL. These sites are color-coded in red, green, and blue for PCV2a vs. PCV2b, PCV2a vs. PCV2b, and PCV2b vs. PCV2d, respectively, on the viral surface of different capsid proteins. In the right panel, the same positions are highlighted on both the external (upper image) and internal (lower image) surfaces of three contiguous capsids. The ribbon structure, also color-coded to correspond with the selection sites, is displayed transparently in the background.