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S T Nichol

Publications and source records attributed to S T Nichol.

At least 73 records · Page 4Linked to original sources
PubMed1995

Fatal illness associated with a new hantavirus in Louisiana.

A fatal case of hantaviral illness occurred in Louisiana, outside of the range of P. maniculatus, the rodent reservoir for Sin Nombre virus. Hantavirus RNA and antigens were detected in patient autopsy tissues, and nucleotide sequence analysis of amplified polymerase chain reaction (PCR) products identified a newly recognized unique hantavirus, provisionally named Bayou virus. Prominent features of the clinical illness are compatible with hantavirus pulmonary syndrome (HPS), but several features such as renal insufficiency and intraalveolar hemorrhage are more compatible with hemorrhagic fever with renal syndrome (HFRS), a disease associated with Eurasian hantaviruses.

Antigens, Viral↗
PubMed1995

Detection and sequence confirmation of Sin Nombre virus RNA in paraffin-embedded human tissues using one-step RT-PCR.

Sin Nombre virus (SNV) is the causative agent of hantavirus pulmonary syndrome (HPS). SNV RNA can be detected in fresh or frozen autopsy tissue samples by reverse transcriptase polymerase chain reaction (RT-PCR), and virus antigens can be identified by immunohistochemistry. A method was developed for demonstration of SNV RNA in formalin-fixed, paraffin-embedded tissues by RT-PCR. Virus genomes were detected in 8 of 12 (66.7%) fixed human tissue samples that were positive by immunohistochemistry, and RT-PCR prior to tissue fixation. By comparison with nucleotide sequences determined previously in fresh or frozen tissues of the same patients, identical genomic sequences were obtained, proving the authenticity of the PCR products. The study demonstrates that detection of SNV RNA in formalin-fixed, paraffin-embedded archival tissue by RT-PCR is feasible. This method allows retrospective studies on the phylogenetic epidemiology of SNV in North America.

Base Sequence↗
PubMed1995

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.

Animals↗
PubMed1995

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.

Amino Acid Sequence↗
PubMed1995

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.

Animals↗
PubMed1995

Genetic characterization of a human isolate of Puumala hantavirus from France.

PUU90-13 is a strain of Puumala (PUU) virus (family Bunyaviridae: genus Hantavirus) isolated from a human in northeastern France (Rollin et al., 1995). This report describes the full-length sequences of the small (S) and medium (M) genomic RNAs of PUU90-13. The terminal sequences of both the S and M genomic RNAs were found to be conserved and imperfectly complementary. The S RNA of PUU90-13 is 1847 nt in length and contains the nucleocapsid (N) protein gene and a potential overlapping open reading frame (ORF-2) previously described in other hantaviruses. Statistical analysis of the third base substitution frequency in the N ORFs of PUU90-13 and other PUU viruses suggests that the ORF-2 is functional. The M RNA is 3681 nt in length and encodes the glycoprotein precursor. Both genomic segments share the highest degree of nucleotide and amino acid sequence identity with PUUBerkel, a PUU virus from Germany. Phylogenetic analyses of sequences from both segments indicate that PUU90-13 occupies a distinct Western European PUU virus lineage that it shares with PUUBerkel. Both PUU90-13 and PUUBerkel lack a potential N-linked glycosylation site found on the G2 glycoprotein of other PUU viruses.

Amino Acid Sequence↗
PubMed1995

Complete genetic characterization and analysis of isolation of Sin Nombre virus.

This study reports completion of the genetic characterization of the entire genome of Sin Nombre (SN) virus (NMH10) detected in autopsy tissues from a patient who died of hantavirus pulmonary syndrome (HPS). The large (L) genome segment was found to be 6,562 nucleotides in length and encoded a putative L polymerase that was 2,153 amino acids in length. No evidence of segment reassortment with other well-characterized hantaviruses was obtained. The sequence of the entire S, M, and L genome segments of SN virus (strain NMR11) isolated from a mouse (trapped in the residence of the patient infected with SN virus [NMH10]) by passage two times in Peromyscus maniculatus and then by five passages in E6 Vero cells was determined and compared with that of the virus detected in autopsy tissues. Only 16 nucleotide differences were detected between the virus genomes, and none of these resulted in virus protein amino acid substitutions. Determination of the exact 5'- and 3'-terminal sequences of all genome segments of SN virus and representatives of other serologic groups in the Hantavirus genus, family Bunyaviridae, showed the existence of conserved nucleotide domains that may be involved in important regulatory mechanisms, such as RNA encapsidation, polymerase binding, and control of transcription and replication.

Amino Acid Sequence↗
PubMed1995

A newly recognized virus associated with a fatal case of hantavirus pulmonary syndrome in Louisiana.

Genetic analysis of virus detected in autopsy tissues of a fatal hantavirus pulmonary syndrome-like case in Louisiana revealed the presence of a previously unrecognized hantavirus. Nucleotide sequence analysis of PCR fragments of the complete S and M segments of the virus amplified from RNA extracted from the tissues showed the virus to be novel, differing from the closest related hantavirus, Sin Nombre virus, by approximately 30%. Both genome segments were unique, and there was no evidence of genetic reassortment with previously characterized hantaviruses. The primary rodent reservoir of Sin Nombre virus, the deer mouse Peromyscus maniculatus, is absent from Louisiana. Thus, the virus detected in Louisiana, referred to here as Bayou virus, must possess a different rodent reservoir.

Base Sequence↗
PubMed1995

Short report: isolation and partial characterization of a Puumala virus from a human case of nephropathia epidemica in France.

Puumala (PUU) virus (Bunyaviridae: Hantavirus), the etiologic agent of nephropathia epidemica (NE), the mid form of hemorrhagic fever with renal syndrome, is enzootic in Europe and has been known to occur in France since 1983. We report the first isolation of PUU virus in France and western Europe from a case of NE acquired in France. The virus was isolated from a serum collected in the acute phase of the clinical course by successive blind passages in Vero E6 cells. Serologic typing using monoclonal antibodies confirmed the identity of the virus as PUU. The sequence of an 832-nucleotide fragment of the virus medium RNA segment obtained by the polymerase chain reaction (PCR) also classified it as a PUU virus. The sequence of this isolate from a human case in France is closely related to the sequence of a PUU virus obtained by the PCR from a German patient.

Adult↗
PubMed1994

Genome structure and variability of a virus causing hantavirus pulmonary syndrome.

A previously unrecognized hantavirus (family Bunyaviridae) has recently been detected and shown to be associated with a severe respiratory illness with high mortality, termed hantavirus pulmonary syndrome (HPS). This disease has now been identified throughout the western United States. We present nucleotide sequence characterization of the three RNA segments composing the HPS virus genome and address the question of the apparent emergence of this highly lethal virus. No evidence of genetic reassortment with previously recognized hantaviruses was found, each RNA segment being unique and approximately 30% different at the nucleotide level to the segments of the closest relative, Prospect Hill virus. These findings, together with the observed extensive genetic diversity of HPS viruses and examples of geographic clustering of distinct virus genotypes, suggest that HPS and associated virus have likely existed undetected for many years. The virus genome M segment was determined to be 3696 nucleotides in length and encode G1 and G2 proteins, 652 and 488 amino acids in length. The S segment was found to be 2059 nucleotides in length and to encode a nucleocapsid protein, 428 amino acids in length. S segment analysis also revealed an unusually long noncoding region with numerous repeats and evidence for a potential NSS protein encoded in an overlapping frame.

Amino Acid Sequence↗
PubMed1994

Characterization of filoviruses based on differences in structure and antigenicity of the virion glycoprotein.

Eight different filovirus isolates, representing major episodes of filovirus hemorrhagic disease, were propagated for structural and antigenetic analyses of their glycoprotein (GP). Carbohydrate analysis revealed that N- and O-glycosylation are features of filovirus GPs. Oligosaccharide side chains differed in their sialylation pattern and seemed to be cell line-dependent. Marburg virus (MBG) isolates are clearly distinguished from Ebola (EBO) and Reston viruses by a lack of terminal sialic acids when propagated in E6 and MA-104 cells. It was also determined that GP-specific antisera failed to show any cross-reactivity between MBG isolates and other filoviruses. These data, together with prior findings, indicate that the genus Filovirus can be divided into a MBG group and EBO group.

Animals↗
PubMed1994

Detection of Muerto Canyon virus RNA in peripheral blood mononuclear cells from patients with hantavirus pulmonary syndrome.

To determine if Muerto Canyon Virus (MCV) RNA is present in the peripheral blood of patients with hantavirus pulmonary syndrome, a reverse transcriptase-polymerase chain reaction (RT-PCR) assay for MCV RNA was used on blood samples from 20 seropositive case-patients. RNA was prepared from peripheral blood mononuclear cells (PBMC) or blood clot (or both) from 19 and from plasma from 11 case-patients. All 12 blood clot, all 13 PBMC, and 8 of 11 plasma preparations produced an MCV amplification product after RT-PCR with primers from the G2 gene. All of 5 PBMC RNA preparations tested were positive using unnested primers in S segment. Nucleotide sequences were determined for 16 G2 amplimers and 4 S segment amplimers, verifying that unique MCV cDNA sequences were amplified. Viral RNA became undetectable in 5 of 7 convalescent samples tested but was present up to day 23 of illness in 2 case-patients.

Base Sequence↗
PubMed1994

Genetic identification of a new Puumala virus strain causing severe hemorrhagic fever with renal syndrome in Germany.

A severe case of suspected hemorrhagic fever with renal syndrome (HFRS) was recently identified in northwestern Germany. A genetic detection assay was designed that identified hantavirus-specific RNA in the patient's clinical specimens by reverse transcriptase-polymerase chain reaction amplification of virus S and M genome segments. Phylogenetic analysis of the nucleotide sequences demonstrated that this virus belonged to the Puumala (PUU) group, with the closest relationship to a PUU isolate from Finland. Within the group, this virus formed a separate lineage. This finding represents the first genetic characterization of a hantavirus causing severe HFRS in Germany. The data suggest that PUU viruses circulating in western European countries are genetically distinct from their northeastern counterparts. Comparison of deduced amino acid sequences demonstrated a loss of a potential N-glycosylation site in the G2 protein compared with other PUU viruses.

Amino Acid Sequence↗
PubMed1993

Punctuated equilibrium and positive Darwinian evolution in vesicular stomatitis virus.

RNA viruses possess the potential for rapid evolution and serve as excellent models to test evolutionary theory. Molecular phylogenetic analysis of the P gene for a larger number of diverse natural isolates of vesicular stomatitis virus reveals no evidence for a molecular clock but instead shows a stepwise evolutionary pattern unlike that ever seen before. Each step out from the tree's ancestral root to terminal branch tips correlates not with time of virus isolation but with a south-to-north geographical progression from Panama to the United States. The grossly unequal rates of change within this single species imply an underlying mechanism at odds with the prevailing notion that neutral changes are the dominating feature of molecular evolution. This is also a demonstration of punctuated equilibrium at the molecular level.

Base Sequence↗
PubMed1993

Genetic identification of a hantavirus associated with an outbreak of acute respiratory illness.

A mysterious respiratory illness with high mortality was recently reported in the southwestern United States. Serologic studies implicated the hantaviruses, rodent-borne RNA viruses usually associated elsewhere in the world with hemorrhagic fever with renal syndrome. A genetic detection assay amplified hantavirus-specific DNA fragments from RNA extracted from the tissues of patients and deer mice (Peromyscus maniculatus) caught at or near patient residences. Nucleotide sequence analysis revealed the associated virus to be a new hantavirus and provided a direct genetic link between infection in patients and rodents.

Animals↗
PubMed1993

Utilization of autopsy RNA for the synthesis of the nucleocapsid antigen of a newly recognized virus associated with hantavirus pulmonary syndrome.

A newly recognized hantavirus was recently found to be associated with an outbreak of acute respiratory illness in the southwestern United States. The disease, which has become known as hantavirus pulmonary syndrome, has an unusually high mortality (64%). Virus isolation attempts have been unsuccessful thus far, resulting in a lack of homologous antigen for use in diagnostic assays. For this reason, a molecular approach was initiated to produce recombinant homologous antigen. The virus nucleocapsid (N) protein was selected, since N has been shown to be a sensitive antigenic target in other hantavirus systems. The N protein open reading frame of the virus S genome segment was synthesized from frozen autopsy tissue by polymerase chain reaction amplification, followed by cloning and expression in Hela cells (vaccinia-T7 RNA polymerase system) and Escherichia coli. N protein-expressing Hela cells served as excellent antigens for an improved indirect immunofluorescence assay. Use of the E. coli-expressed N protein in an enzyme-linked immunosorbent assay improved the sensitivity and specificity when compared with heterologous antigens used previously. Preliminary analysis also indicates that the higher sensitivity could result in earlier detection of infected persons. These data demonstrate that even in the absence of a virus isolate, the necessary homologous antigen can be produced and can serve to improve the detection and diagnostic capabilities needed to combat this newly recognized fatal respiratory illness in the United States.

Amino Acid Sequence↗
PubMed1993

Interferon induction by viruses. XXII. Vesicular stomatitis virus-Indiana: M-protein and leader RNA do not regulate interferon induction in chicken embryo cells.

Several field isolates, strains, mutants, and revertants of vesicular stomatitis virus (VSV), Indiana (IN) serotype, were studied that differed greatly in their capacity to induce interferon (IFN) in aged chick embryo cells. The predicted M-protein amino acid sequence of a wild-type field isolate that induced > or = 10,000 units/ml IFN in chicken embryo cells was identical to that of a wild-type field isolate that induced < 2 units/ml and of a noninducing wild-type laboratory strain. The 47-base plus-strand leader RNA sequences were the same for five IFN-inducing, and eight noninducing independent isolates of wild-type VSV IN. Our data show that the M-protein and plus-strand leader RNA do not of themselves regulate the induction of IFN in this system. Because the capacity of VSV IN to induce IFN resides in virion-associated elements (Marcus and Sekellick, 1987, J. Interferon Res. 7, 269-284), the differences in IFN yield observed with various isolates must result from changes in other virion components that remain to be determined.

Amino Acid Sequence↗