Stuart T. Nichol

The complete genome structure and phylogenetic relationship of infectious hematopoietic necrosis virus

Infectious hematopoietic necrosis virus (IHNV), a member of the family Rhabdoviridae, causes a severe disease with high mortality in salmonid fish. The nucleotide sequence (11,131 bases) of the entire genome was determined for the pathogenic WRAC strain of IHNV from southern Idaho. This allowed detailed analysis of all 6 genes, the deduced amino acid sequences of their encoded proteins, and important control motifs including leader, trailer and gene junction regions. Sequence analysis revealed that the 6 virus genes are located along the genome in the 3 to 5 order: nucleocapsid (N), polymerase-associated phosphoprotein (P or M1), matrix protein (M or M2), surface glycoprotein (G), a unique non-virion protein (NV) and virus polymerase (L). The IHNV genome RNA was found to have highly complementary termini (15 of 16 nucleotides). The gene junction regions display the highly conserved sequence UCURUC(U)7RCCGUG(N)4CACR (in the vRNA sense), which includes the typical rhabdovirus transcription termination/polyadenylation signal and a novel putative transcription initiation signal. Phylogenetic analysis of M, G and L protein sequences allowed insights into the evolutionary and taxonomic relationship of rhabdoviruses of fish relative to those of insects or mammals, and a broader sense of the relationship of non-segmented negative-strand RNA viruses. Based on these data, a new genus, piscivirus, is proposed which will initially contain IHNV, viral hemorrhagic septicemia virus and Hirame rhabdovirus.

Molecular epizootiology and evolution of the glycoprotein and non-virion protein genes of infectious hematopoietic necrosis virus, a fish rhabdovirus

Infectious hematopoietic necrosis virus (IHNV) causes a highly lethal, economically important disease of salmon and trout. The virus is enzootic throughout western North America, and has been spread to Asia and Europe. The nucleotide sequences of the glycoprotein (G) and non-virion (NV) genes of 12 diverse IHNV isolates were determined in order to examine the molecular epizootiology of IHN, the primary structure and conservation of NV, and the evolution of the virus. The G and NV genes and their encoded proteins were highly conserved, with a maximum pairwise nucleotide divergence of 3.6 and 4.4%, and amino acid divergence of 3.7 and 6.2%, respectively. Conservation of NV protein sequence (111 amino acids in length) confirms that the protein is functional and plays an important role in virus replication. The phylogenetic relationship of viruses was found to correlate with the geographic origin of virus isolates rather than with host species or time of isolation. These data are consistent with stable maintenance of virus in enzootic foci. Two main IHNV genetic lineages were identified; one in the Columbia River Basin (Oregon, Washington and Idaho), the other in the Sacramento River Basin (California). The first major IHNV outbreak in chinook salmon in 1973 in the Columbia River was genetically linked to importation of virus-infected fish eggs from the Sacramento River where outbreaks in chinook salmon are common. However, the introduced virus apparently did not persist, subsequent virus outbreaks in Columbia River chinook salmon being associated with Columbia River genetic lineages. In general, virus monoclonal antibody reactivity profiles and phylogenetic relationships correlated well.

Glycoprotein evolution of vesicular stomatitis virus New Jersey

A T1 ribonuclease fingerprinting study of a large number of virus isolates had previously demonstrated that considerable genetic variability existed among natural isolates of the vesicular stomatitis virus (VSV) New Jersey (NJ) serotype [S.T. Nichol (1988) J. Virol. 62, 572-579]. Based on these results, 34 virus isolates were chosen as representing the extent of genetic diversity within the VSV NJ serotype. We report the entire glycoprotein (G) gene nucleotide sequence and the deduced amino acid sequence for each of these viruses. Up to 19.8% G gene sequence differences could be seen among NJ serotype isolates. Analysis of the distribution of nucleotide substitutions relative to nucleotide codon position revealed that third position changes were distributed randomly throughout the gene. Third base changes constituted 84% of the observed nucleotide substitutions and affected 89% of the third base positions located in the G gene. Only three short oligonucleotide stretches of complete sequence conservation were observed. The remaining nucleotide changes located in the first and second positions were not distributed randomly, indicating that most of the amino acids coded by the G gene cannot be altered without reducing the fitness of the VSV NJ serotype viruses. Despite these constraints, up to 8.5% amino acid differences were observed between virus isolates. These differences were located throughout the G protein including regions adjacent to defined major antibody neutralization epitopes. Apparent clusters of amino acid substitutions were present in the hydrophobic signal sequence, transmembrane domain, and within the cytoplasmic domain of the G protein. A maximum parsimony analysis of the G gene nucleotide sequences allowed construction of a phylogram indicating the evolutionary relationship of these viruses. The VSV NJ serotype appears to contain at least three distinct lineages or subtypes. All recent virus isolates from the United States and Mexico are within subtype I and appear to have evolved from an ancestor more closely related to the Hazelhurst historic strain than other older strains. The implications of these findings for the evolution, epizootiology, and classification of these viruses are discussed.

The genetic diversity and epizootiology of infectious hematopoietic necrosis virus

Infectious hematopoietic necrosis virus (IHNV) is a rhabdovirus which causes a serious disease in salmonid fish. The T1 ribonuclease fingerprinting method was used to compare the RNA genomes of 26 isolates of IHNV recovered from sockeye salmon (Oncorhynchus nerka), chinook salmon (O. tshawytscha), and steelhead trout (O. mykiss) throughout the enzootic portion of western North America. Most of the isolates analyzed in this study were from a single year (1987) to limit time of isolation as a source of genetic variation. In addition, isolates from different years collected at three sites were analyzed to investigate genetic drift or evolution of IHNV within specific locations. All of the isolates examined by T1 fingerprint analysis contained less than a 50% variation in spot location and were represented by a single fingerprint group. The observed variation was estimated to correspond to less than 5% variation in the nucleic acid sequence. However, sufficient variation was detected to separate the isolates into four subgroups which appeared to correlate to different geographic regions. Host species appeared not to be a significant source of variation. The evolutionary and epizootiologic significance of these findings and their relationship to other evidence of genetic variation in IHNV isolates are discussed.

RNA genome stability of Toscana virus during serial transovarial transmission in the sandfly Phlebotomus perniciosus

We have carried out a T1 ribonuclease fingerprinting analysis of the RNA genomes of Toscana virus isolates from successive generations of an experimentally virus-infected laboratory colony of Phlebotomus perniciosus sandflies. This analysis detected no virus RNA genome changes during transovarial transmission of the virus over 12 sandfly generations (a period of almost 2 years). These results demonstrate that although RNA viruses can exhibit high rates of mutational change under a variety of conditions, Toscana virus RNA genomes can be maintained in a stable manner during repeated transovarial virus transmission in the natural insect host. The implications of these results for insect RNA virus evolution are discussed.

Experimental vesicular stomatitis virus infection of swine: Extent of infection and immunological response☆

Swine, a natural host species for infection by vesicular stomatitis virus (VSV), were infected with VSV-New Jersey (VSV-NJ) serotype virus obtained from a recent field isolate. Tissues collected from the infected pigs were examined for the presence of infective virus, for viral antigens, and/or for viral nucleic acid. Infective virus could be recovered from tissues near the site of infection for as long as 6 days after the primary infection with VSV. However, no infective virus was recovered following hypothermia induced 11 weeks after infection, or following a secondary challenge with virus 22 weeks after initial infection. Immunofluorescence tests for viral antigens and nucleic acid hybridization assays failed to detect viral antigens or nucleic acids in tissues from which no infective virus could be recovered. Titers of serum-neutralizing antibody peaked 3-5 weeks after infection and then fell slightly until the secondary infection which caused a rapid anamnestic response. Peripheral blood mononuclear cells (PBM) tested 3, 5, 8 or 18 weeks after primary infection all produced readily detectable antigen-specific proliferative responses when cultured with VSV. Thus, although direct tests failed to demonstrate persistence of virus after infection, the humoral and cellular immune response remained elevated for months. Infective VSV was not required to stimulate the proliferative response since UV-inactivated VSV was immunogenic in these in vitro tests. Following primary infection, antigen-specific proliferative responses could be stimulated by several strains of VSV-NJ, but not by VSV-Indiana (VSV-Ind) serotype virus. Secondary infection had relatively little effect on the proliferative response to VSV-NJ strains, but it did cause the PBM to gain responsiveness to VSV-Ind.

Antigen-specific proliferative responses to vesicular stomatitis virus following immunization of cattle with inactive virus☆

Peripheral blood mononuclear cells (PBM) from four normal cows with no known exposure to vesicular stomatitis virus (VSV) were cultured with a New Jersey (NJ) serotype (Ogden) VSV that had been UV-irradiated and inactivated. PBM from these animals produced no detectable proliferative response when incubated with varying concentrations of VSV-NJ (Ogden) ranging from 10 ng to 10 micrograms protein/ml. Two of these cows were immunized with an experimental VSV-NJ vaccine and their PBM were tested at various intervals after immunization. PBM tested 14 days after the initial immunization produced readily detectable antigen-specific proliferative responses when cultured with UV-irradiated strains of VSV-NJ. Following a second immunization, lower concentrations of antigen were sufficient to stimulate the proliferative response and the magnitude of the proliferative response was increased. The responsiveness persisted for at least 6 months after these two immunizations. The specificity of the proliferative response was examined by comparing the responses stimulated by one VSV-Ind and four VSV-NJ serotype strains. The PBM from the immunized cows produced proliferative responses that were essentially specific for the VSV-NJ serotype antigens. In dose titrations, the VSV-NJ antigens were 300-1000-fold more effective than was the VSV-Ind antigen. Thus, persistent antigen-specific proliferative responsiveness that is serotype specific can be stimulated by immunizing cattle with an inactivated VSV vaccine.