Molecular Evolution of the Human Enteroviruses: Correlation of Serotype with VP1 Sequence and Application to Picornavirus Classification

Sixty-six human enterovirus serotypes have been identified by serum neutralization, but the molecular determinants of the serotypes are unknown. Since the picornavirus VP1 protein contains a number of neutralization domains, we hypothesized that the VP1 sequence should correspond with neutralization (serotype) and, hence, with phylogenetic lineage. To test this hypothesis and to analyze the phylogenetic relationships among the human enteroviruses, we determined the complete VP1 sequences of the prototype strains of 47 human enterovirus serotypes and 10 antigenic variants. Our sequences, together with those available from GenBank, comprise a database of complete VP1 sequences for all 66 human enterovirus serotypes plus additional strains of seven serotypes. Phylogenetic trees constructed from complete VP1 sequences produced the same four major clusters as published trees based on partial VP2 sequences; in contrast to the VP2 trees, however, in the VP1 trees strains of the same serotype were always monophyletic. In pairwise comparisons of complete VP1 sequences, enteroviruses of the same serotype were clearly distinguished from those of heterologous serotypes, and the limits of intraserotypic divergence appeared to be about 25% nucleotide sequence difference or 12% amino acid sequence difference. Pairwise comparisons suggested that coxsackie A11 and A15 viruses should be classified as strains of the same serotype, as should coxsackie A13 and A18 viruses. Pairwise identity scores also distinguished between enteroviruses of different clusters and enteroviruses from picornaviruses of different genera. The data suggest that VP1 sequence comparisons may be valuable in enterovirus typing and in picornavirus taxonomy by assisting in the genus assignment of unclassified picornaviruses.

Geographic distribution of mitochondrial cytochrome b DNA haplotypes in New Zealand fur seals (Arctocephalus forsteri)

Nucleotides spanning 361 base pairs of the 5′ portion of the mitochondrial cytochrome b gene were sequenced from 16 New Zealand fur seals, Arctocephalus forsteri, representing seven rookeries in three different regions: the east and west coasts of New Zealand, and Western Australia. Five different mitochondrial haplotypes were observed in these novel sequence data for this species. The geographical distribution of the cytochrome b haplotypes was shown to be heterogeneous by three statistical tests. The major finding of this study is the difference between haplotypes found in fur seals from Western Australian rookeries and haplotypes found in fur seals from New Zealand rookeries. The nucleotide sequence difference found in pairwise comparisons among the surveyed individuals is in the range 0.3–0.8%. One individual showed an unexpectedly large sequence divergence (range 3.3–4.2%) from all other fur seals in this study. We compare alternative hypotheses that this individual is a descendant of an ancient maternal lineage which survived a population bottleneck, that New Zealand fur seals exhibit a rather large amount of genetic variability at this locus, or that this particular individual is a hybrid. Western Australian rookeries were extirpated as a result of sealing during the early 1800s. The geographic distribution of mitochondrial cytochrome b haplotypes suggests that the extirpated Australian rookeries were not recolonized by migrants from New Zealand. No genetic division between fur seal populations sampled from the east and west coasts of New Zealand is revealed using this region of the mitochondrial genome as a genetic marker, but we suggest that it should be possible to create a more discriminating test by examining a more variable DNA target such as the mitochondrial control region.

Eleven distinct VH gene families and additional patterns of sequence variation suggest a high degree of immunoglobulin gene complexity in a lower vertebrate, Xenopus laevis.

Lower vertebrate species, including Xenopus laevis, exhibit restricted antibody diversity relative to higher vertebrates. We have analyzed more than 180 VH gene-containing recombinant clones from an unamplified spleen cDNA library by selective sequencing of JH and CH positive clones following iterative hybridization screening with family-specific VH probes, 11 unique families of VH genes, each associated with a unique genomic Southern blot hybridization pattern, are described and compared. Considerable variation in the number of hybridizing components detected by each probe is evident. The nucleotide sequence difference between VH families is as great as, if not more than, that reported in other systems, including representatives of the mammalian, avian, and elasmobranch lineages. Some Xenopus Ig gene families encode alternative amino acids at positions that are otherwise invariant or very rarely substituted in known Igs. Furthermore, variations in complementarity determining region sequences among members of the same gene family and high degrees of DH and JH region complexity are described, suggesting that in at least this lower vertebrate species, the diversity of expressed Ig VH genes is not restricted.