J Gen Virol. 2015 Jul;96(Pt 7):1830-41. doi: 10.1099/vir.0.000100. Epub 2015 Feb 23. Global molecular genetic analysis of porcine circovirus type 2 (PCV2) sequences confirms the presence of four main PCV2 genotypes and reveals a rapid increase of PCV2d. Xiao CT, Halbur PG, Opriessnig T.
What are they studying?
To evaluate the phylogenetic relationship of PCV2 strains, 1680 PCV2 open reading frame 2 (ORF2) sequences were compared and analysed using different statistical methods.
How do they study it?
1537 PCV2 ORF2 gene sequences that were published before February 2014 in “GenBank”, a global internet genome database, and 143 additional ORF2 sequences from the Iowa State University Diagnostic Laboratory database (i.e., a total of 1680 ORF2 sequences) were used for phylogenetic analyses of PCV2.
What are the results?
The study confirmed that PCV2 can be divided into 4 major subtypes: PCV2a, PCV2b, PCV2c and PCV2d. Additionally, the authors describe 6 smaller intermediate clades between those subtypes. One of these intermediate clades seems to be limited to Asia. However, the strains of this clade are reported on an ongoing basis, which suggests it can be considered as an active clade. The other intermediate clades only include very limited numbers of strains and can therefore be considered as inactive. They might correspond to small, extinguished groups of strains showing reduced fitness; intermediate, evolving virus strains; or test artefacts. PCV2c seems to be an extinct group of viruses. The affiliation of individual strains to different genotypes and intermediate clades depended sometimes on the statistical model used and on the number of reference strains used for the analysis.
The results further confirm that there have been two major shifts from one subtype to another one: in 2003, before the use of PCV2 vaccines, from PCV2a to PCV2b, and a second shift from PCV2b to PCV2d that in the US, for example, occurred mainly from 2011 to 2014.
Further phylogenetic test suggest that both PCV2b and PCV2d have evolved independently from each other for over 20 years. In addition, there is an ongoing gradual genetic divergence within each subtype. The reason why PCV2 has a high mutation rate and also such a high genetic diversity —atypical for DNA viruses— is not known. The cause of the ongoing emergence of strains and the genotype shifts that have been observed is also unknown. The first shift occurred before the introduction of PCV2 vaccines.
What conclusions are drawn from this work?
This study demonstrates that PCV2 is evolving much faster than other DNA viruses, and its diversity is wider. The swine industry should further monitor the evolvement of PCV and determine its relevance for the control of PCVD.
The view from the field by Enric Marco
We never stop learning and being surprised. We had learned that DNA viruses were much more stable than RNA viruses and, therefore, their evolution was less dynamic. However, it seems not to be like that when it comes to PCV2. Although it has only been know for a few years (the first sequence is from samples of 1967), the truth is this virus has not stopped evolving. Its genotype has not stopped changing, even hough the meaning of this dynamics in practical or applicative terms is not clear.
The conclusions of the article seem to suggest that the greater presence of the PCV2d genotype would be related to the widespread use of the vaccines, since most of its isolates come from samples taken from farms with clinical problems, despite using the vaccine. This coincidence has spread the belief, amongst some groups of veterinarians, that vaccines do not protect equally against all the discovered genetic types of PCV2. I think it is fair to say, however, that at no time does the article state this. In fact, one of its authors has published more than one article demonstrating the effectiveness of commercial vaccines based on the PCV2a genotype over the others, including PCV2d.
It is no wonder that most of the new genotyped isolates come from samples collected in farms with clinical problems , even though their animals are being vaccinated. If there are no problems, there is no need to take samples either. On the other hand, farms with problems are very likely applying the commercial vaccine. When we come accross situations where the pigs present symptoms suggestive of circovirosis, vaccination is the first measure we all apply (even before performing any diagnostic tests). And when vaccination is already taking place, we verify it is being done correctly, since we are surprised vaccines are failing, their efficiency being so high.
The article highlights the power of the current diagnostic tests. These tests allow us to detect small changes in the genome of a virus and, despite their limitations, to even establish a chronological order in the occurrence of those changes, which helps us to establish relations of genetic closeness or remoteness between the different isolates. Unfortunately, the specific relationship between genotype and phenotype is not always known, and this is one such case. Genetic changes may or may not be related to antigenic changes and/or changes in pathogenesis, but for the moment, and in this particular case, we do not know. We will have to wait for science to progress and dispel the doubts we still have about PCV2.