Genetic diversity in the yellow head nidovirus complex

Penaeus monodon shrimp collected from across the Indo-Pacific region during 1997–2004 were screened for the presence of yellow head-related viruses. Phylogenetic analyses of amplified ORF1b gene segments identified at least six distinct genetic lineages (genotypes). Genotype 1 (YHV) was detected only in shrimp with yellow head disease. Genotype 2 (GAV) was detected in diseased shrimp with the less severe condition described as mid-crop mortality syndrome and in healthy shrimp from Australia, Thailand and Vietnam. Other genotypes occurred commonly in healthy shrimp. Sequence comparisons of structural protein genes (ORF2 and ORF3), intergenic regions (IGRs) and the long 3′-UTR supported the delineation of genotypes and identified both conserved and variant structural features. In putative transcription regulating sequences (TRSs) encompassing the sub-genomic mRNA 5′-termini, a core motif (5′-GUCAAUUACAAC-3′) is absolutely conserved. A small (83 nt) open reading frame (ORF4) in the 3′-UTR of GAV is variously truncated in all other genotypes and a TRS-like element preceding ORF4 is invariably corrupted by a A > G/U substitution in the central core motif (5′-UU(G/U)CAAC-3′). The data support previous evidence that ORF4 is a non-functional gene under construction or deconstruction. The 3′-UTRs also contain predicted 3′-terminal hairpin-loop structures that are preserved in all genotypes by compensatory nucleotide substitutions, suggesting a role in polymerase recognition for minus-strand RNA synthesis.