Comparative sequence analyses of sixteen reptilian paramyxoviruses

Viral genomic RNA of Fer-de-Lance virus (FDLV), a paramyxovirus highly path ogenic for reptiles, was reverse transcribed and cloned. Plasmids with sign ificant sequence similarities to the hemagglutinin-neuraminidase (HN) and p olymerase (L) genes of mammalian paramyxoviruses were identified by BLAST s earch. Partial sequences of the FDLV genes were used to design primers for amplification by nested polymerase chain reaction (PCR) and sequencing of 5 18-bp L gene and 352-bp HN gene fragments from a collection of 15 previousl y uncharacterized reptilian paramyxoviruses. Phylogenetic analyses of the p artial L and HN sequences produced similar trees in which there were two di stinct subgroups of isolates that were supported with maximum bootstrap val ues, and several intermediate isolates. Within each subgroup the nucleotide divergence values were less than 2.5%, while the divergence between the tw o subgroups was 20-22%. This indicated that the two subgroups represent dis tinct virus species containing multiple virus strains. The five intermediat e isolates had nucleotide divergence values of 11-20% and may represent add itional distinct species. In addition to establishing diversity among repti lian paramyxoviruses, the phylogenetic groupings showed some correlation wi th geographic location, and clearly demonstrated a low level of host specie s-specificity within these viruses. (C) 1999 Elsevier Science B.V. All righ ts reserved.