The nucleotide sequence of a 3266 bp region encompassing open reading frames (ORFs) 2 through 7 of the porcine reproductive and respiratory syndrome virus (PRRSV) was determined for 10 isolates recovered from the midwestern United States. Pairwise comparisons showed that genetic distances between isolates ranged from 2.5% to 7.9% (mean 5.8% ± 0.2%) whereas the Lelystad strain from Europe was, on average, 34.8% divergent from US clones. Thus, US and European PRRSV isolates represent genetically distinct clusters of the same virus. ORF 5, which encodes the envelope glycoprotein, was the most polymorphic [total nucleotide diversity (π) = 0.097 ± 0.007] and ORF 6, encoding the viral M protein, was the most conserved (π = 0.038 ± 0.003). The substantial differences in nucleotide diversity among ORFs suggests that the virus is evolving by processes other than simple accumulation of random neutral mutations. In support of this hypothesis, statistical analyses of the nucleotide sequence provided strong evidence for intragenic recombination or gene conversion in ORFs 2,3,4,5 and 7, but not in ORF 6. An excess of synonymous (silent) substitutions was observed in all six ORFs, indicating an evolutionary pressure to conserve amino acid sequences. Taken together, the data indicate that despite intragenic recombination among extant PRRSV isolates, purifying selection has acted to maintain the primary structure of individual ORFs.
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