Diversity and evolution of a newly emerged North American Type 1 porcine arterivirus: analysis of isolates collected between 1999 and 2004

European-like Type 1 porcine reproductive and respiratory syndrome virus (PRRSV) isolates, known as North American (NA) Type 1 PRRSV, appeared in United States (U.S.) swine herds in 1999. Their diversity and evolution were studied over a five-year period by constructing phylogenetic trees using nsp2 and ORF5 sequences of 20 NA Type 1 isolates, including the only known isolate from Hawaii. All but two of the isolates possessed the same 51-nt deletion in nsp2, suggesting a clonal origin. Parsimony and distance analysis showed that viruses could be placed into two distinct sub-clades, which were similar for both nsp2 and ORF5. An incongruity between the two trees identified one isolate, 04-41, as the product of recombination. Recombination analysis using SimPlot identified a break point located downstream of the nsp2/3 junction. Results from this study suggest that NA Type 1 PRRSV in the U.S. is a well-established and rapidly evolving group. However, the forces driving genetic diversity and separation are complex and remain to be elucidated.