A letter from the EC-funded Framework 6 research project on Porcine Circovirus Diseases published in the Veterinary Record on June 28 proposes an elegant methodology based on the proportion of nucleotide sites at which two sequences being compared are different (p-distance). This value is found by dividing the number of nucleotide differences by the total number of nucleotides compared. The potential cut-off values to distinguish different genotypes are established through the construction of a p-distance/frequency histogram.

Using this technique three genotypes PCV2 have been identified and named PCV2a, PCV2b and PCV2c. The prototype viruses AF055392 (Stoon-1010) for PCV2a; AF055394 (48285) for PCV2b and accession number EU148503 for PCV2c have all been based on the first sequences recorded in the GenBank (http://www.ncbi.nlm.nih.gov). These prototype viruses were all isolated and sequenced by members of the EU PCVD consortium. PCV2a and PCV2b genotype viruses have been recovered from PMWS cases worldwide. There is some evidence that PCV2a genotype viruses predominated on pig farms with and without PMWS from 1997 until 2003 and that PCV2b strains have been more common in outbreaks of PMWS from 2004, although not in all countries. The only PCV2c genotype viruses have been recovered from Denmark during the 80s when PMWS was not present or at least had not been identified.

The PCVD project management team, lead by Prof Gordon Allan, warned against complacency: “Porcine Circovirus Diseases continue to be a major problem on many pig farms worldwide and although significant progress has been made in understanding the virus there are still gaps in our understanding which the virus continues to exploit. Virus elimination remains a distant dream but the excellent response to vaccination raises serious unanswered questions about the sub-clinical effects of the virus and the duration that these have been affecting pig production.” The Framework 6 PCVD project has published its 2008 newsletter that updates on progress in a number of key areas of investigation into the interaction between PCV2 and pigs. The Consortium continues to make good progress as it draws this EU Framework 6 programme of research to a conclusion in early 2009.

There is a strong belief that the new convention on naming can only assist rapid progress in unlocking the secrets of the Circovirus diseases that have decimated pig production worldwide.