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00.026.0.01.044. St. Louis encephalitis virus

Cite this publication as: Calisher, C.H. (2003). 00.026.0.01.044. St. Louis encephalitis virus. In: ICTVdB - The Universal Virus Database, version 4. ICTVdB Management, The Columbia University, Oracle, AZ, USA

Cite this site as: ICTVdB - The Universal Virus Database, version 3. http://www.ncbi.nlm.nih.gov/ICTVdb/ICTVdB/

Table of Contents

Isolation Details

Isolation date: 1933.
Location: St. Louis; Missouri; the United States of America.
Source of isolate: human.
Virus was isolated by Muckenfuss, R.S., Armstrong, C., and McCordock, H.A.; the United States of America.
Reference: Muckenfuss, R.S., Armstrong, C., and McCordock, H.A. (1933) Encephalitis: Studies on experimental transmission Publ. Hlth. Reports. 48:1341-1343.

Classification

This is a description of an invertebrate and vertebrate virus at the species level with data on all virus properties from morphology to genome, replication, antigenicity and biological properties.

ICTVdB Virus Code: 00.026.0.01.044. Virus accession number: 26001044. Former Virus Code: 26.0.1.2.4.07.; former accession number: 26012407.
NCBI TaxID: [11080].

Biocontainment Level

Health authorities recommend to handle this virus at the biocontainment level BSL-3.

Name, Synonyms and Lineage

ICTV approved acronym: SLEV. Virus is an ICTV approved species. Virus is assigned to the genus 00.026.0.01. Flavivirus ; assigned to the family 00.026. Flaviviridae ; not assigned to an order.

Virion Properties

Introduction

Symptoms in the host are well established and the causative agent is determined. Distinct viral structures are visible in thin sections of infected tissue and nucleic acid of virions is encapsidated. Size and shape of virus has been determined by electron microscopy.

Virion Properties

Morphology

Virions have a complex construction and consist of an envelope and a nucleocapsid. Virions are enveloped by a detergent sensitive lipoprotein before leaving the host cell. Virions are spherical and 50 nm in diameter. The envelope surrounds one nucleocapsid and has surface projections. The surface projection proteins are antigenic which exhibit hemagglutinin activity. Surface projections form ring-like subunits and are 7 nm in diameter. Host ribosomes are not seen inside the envelope. A regular capsid structure is present. Capsid/nucleocapsid is round and exhibits icosahedral symmetry. The nucleocapsid is isometric. The capsid shells of virions are composed of a single layer. The capsid surface structure does not reveal a regular pattern with distinctive features and is maintained using conventional electron microscopy. The capsomer arrangement is not distinct. Nucleocapsid contains a nucleoprotein complex.

Virion populations are comprised of particles of uniform size. Capsids all have the same appearance and only one species is recovered in preparations.

Physicochemical and Physical Properties

The molecular mass (Mr) of virions is 60 x 106. Virions have a buoyant density in sucrose of 1.19 g cm-3. There are 5 sedimenting component(s) found in purified preparations (of mosquitoes). The thermal inactivation point (TIP) is at 40°C. Although the titer is dependent on the host, the decimal exponent (DEX) of the dilution end point is usually around dependent on host in which titrated. Virion infectivity is decreased with increasing temperature and destroyed by heating for 30 min above 56°C. Under in vitro conditions virions are stable when stored at -70°C (stability decreases with increasing storage temperature); inactivated in acid environment of pH 1-3; relatively stable in alkaline environment of pH 7-9. Virions are sensitive to treatment with lipid solvents, decrease of 4.0 DEX after treatment with detergents, ether, trypsin, chloroform, heat, and ß-propiolactone as compared with control treatment. The infectivity is reduced after exposure to irradiation.

Nucleic Acid

The Mr of the genome constitutes 6% of the virion by weight. The genome is monomeric; not segmented and consists of a single molecule of linear positive-sense single-stranded RNA. The genome is infectious. Minor species of genomic nucleic acid are not found; non-genomic nucleic acid are not found in virions. The complete genome is about 11000 nucleotides long. Sequence can be accessed at EBI-EMBL, GenBank, and DNA Data Bank of Japan; the RNA has been partially sequenced and complete sequence is 11000 nucleotides long and has the accession number [M16614] (strain MSI-7 (listed at NCBI as MSI.7 and EBI as MS1-7), translated from cDNA of the clones pA3 and p to viral RNA). The sequenced region is 4673 nucleotides long and encodes a polyprotein in a single continuous open reading frame. The mRNAs of the complete cds encode capsid, membrane, envelope and nonstructural proteins (NS1, NS2a, NS2b, NS3). The 5'-end of the genome has a cap. The 5'-terminus has no poly (C) tract. Each virion contains a single copy of the genome.
Reference(s) to sequence databases at GenBank and specialty databases: nucleotide sequences; complete genomes. Medline ID: [87122172].

Proteins

Proteins constitute about 66% of the particle weight; have been identified and been characterized and functions are assigned to them. Particles are made up of a single polyprotein encoding 10 proteins. The viral genome encodes structural proteins and non-structural proteins. Virions consist of 3 structural protein(s) located in the envelope (E protein), membrane (M in mature virions; prM in immature virions), capsid (C protein).

Structural Proteins: Envelope protein E has a molecular mass of (51-)55(-60) kDa (mass estimates vary) and is the product of the polyprotein which synthesizes all structural and non-structural proteins. Envelope protein has been sequenced and a function assigned; sequence has the accession number [P09732] (for genomic polyprotein of strain MSI-7 (listed at NCBI as MSI.7 and SWISS-PROT as MS1-7)); is an attachment protein and a fusion protein. During post-translational processing envelope protein has not been cleaved. Envelope protein M, in mature, prM in immature virions is a membrane protein. During post-translational processing envelope protein has not been cleaved. Nucleocapsid protein C; is binding to the genomic RNA and forming a ribonucleoprotein complex; has not been cleaved.

Non-Structural Proteins: Virus-coded non-structural proteins have been isolated and 7 non-structural protein(s) are found. The virus codes for an RNA-dependent RNA polymerase. In addition to the polymerase, the virus codes for enzymes such as helicase, proteinase, methyl-transferase (RNA triphosphatase). The non-structural proteins are thought to be involved in capping of viral RNAs and in RNA replication. Non-structural protein NS1 is the product of the polyprotein that contains all proteins, has been sequenced and a function assigned. The protein is coded from the RNA of a continuous single ORF; sequence has the accession number [P09732]; a small protein with unspecified function. Non-structural protein NS2A, as well as NS2B, NS4A and NS4B, has been sequenced and a function assigned. The protein is small hydrophobic proteins, suggesting a possible membrane related function. Non-structural protein NS3. Non-structural protein has been sequenced and a function assigned. The protein is a protein that may play a role in the viral RNA replication and possesses protease and helicase activity. Non-structural protein NS5; has been sequenced and a function assigned. Its role is a protein that may play a role in the viral RNA replication.

Lipids

Lipids are present and are located in the envelope. Virions are composed of 17% lipids by weight. The composition of viral lipids is known. The lipids are of host origin and are derived from host cell membranes. Lipids are essential for infectivity (by intact virion).

Carbohydrates

Carbohydrates are found in virions; constitute 9% of virion dry weight; are present as glycoproteins, or glycolipids. Carbohydrate composition in the virion is host-dependent. Enzymes involved in the glycosylation process are virus coded.

Genome Organization and Replication

Virions attach the integral viral envelope proteins to specific receptors located on the surface of cell membrane.

By itself, genomic nucleic acid is infectious.

Infection and Replication: Virus replication is initiated by the insect host (certain hematophagous arthropods); occurs in the midgut and proceeds to salivary glands. In the vertebrate host virus replication occurs in the liver, various organs and tissues. Replication is not restricted to a particular tissue or organ of the host. Although severity of illness depends on route and dose, the majority of infections are subclinical, or mild. Infection does not involve a noncytocidal productive infectious cycle. Infected cells continue to grow slowly (arthropod cells), or do not continue to grow (cells of mammalian origin). Host cell DNA synthesis continues (arthropod cells), or is down-regulated (cells of mammalian origin). Host cell RNA and protein synthesis continues (arthropod cells), or is down-regulated (cells of mammalian origin).

Transcription: The transcription mechanism of the viral genome has been fully investigated. The virus codes for 1 ORF. Initiation of transcription involves removal of cap-structure. The viral genome is transcribed from the viral sense strand by a semi-conservative mechanism from the 5' end by virion-associated enzymes.

The viral genome is transcribed by a viral polymerase into 1 mRNA(s). A single viral mRNA is transcribed in a unidirectional coding arrangement; viral mRNA(s) is/are synthesized from the genome length negative-stranded RNA template.

The 5' ends of mRNAs are capped. The 3' ends of mRNAs do not possess a poly (A) tract.

Virus proteins are encoded by mRNAs that are unique and direct translations of the viral template.

Coding Strategy of Segment 1: RNA has a unidirectional coding strategy and contains 1 ORF, the open reading frame that encodes structural and non-structural proteins. Genome encodes 3 structural proteins, namely membrane proteins, envelope glycoproteins, and capsid protein termed M, E, and C. Structural proteins are encoded in a single continuous ORF. Sequence encodes 7 non-structural proteins, namely polymerase and helicase.

Translation: The genome replicates in the cytoplasm. Replication does not involve a reverse transcription step. The parental genome serves as template for RNA replication. Replication is independent of host nuclear functions. Genome replication involves RNA-directed RNA synthesis; occurs through a single stranded replicative intermediate and is unidirectional. At an early stage, templates are involved in the synthesis of a full-length RNA replication.

Virions are not dependent on a helper virus for replication.

Maturation: The mature virus is found in the host cell cytoplasm of the nervous system and brain tissue, or liver. Nucleocapsids are enveloped in the cytoplasm. Virions mature by exocytosis of the cytoplasmic vesicles in the cytoplasm.

Release: Mechanism of release is known. Infected cells produce virions. Host cells remain intact (arthropod cells), or disintegrate (mammalian cells). Virus is released from host cell by exocytosis. Virus is released from host cell upon death; by lysis. Virus is shed into the gut lumen (arthropods). The virus envelope is acquired from the host cell during the maturation process in the cytoplasm. Envelope lipids are derived from intracellular membranes.

Antigenicity

The virus is serologically related to all viruses of the genus Flavivirus. Antigenic determinants may be found on virion surfaces, envelopes, and nucleocapsids that correspond to each of the major structural proteins, structural glycoproteins, and non-structural proteins. Although different antigenic determinants have different specificities, the antigenic determinants are in general type-specific. Antigenic determinants that possess type-specific reactivity are found on the E protein. The type-specific antigenic determinants are involved in antibody mediated neutralization and hemagglutination inhibition. Antigenic determinants that possess serogroup-specific reactivity are found on the nucleocapsids. The serogroup-specific antigenic determinants are involved in antibody mediated complement fixation. Antigenic specificity of the virion can be determined by neutralization tests, hemagglutination inhibition tests, complement fixation tests, ELISA tests, RIA tests, and immunofluorescence assays. In gel-diffusion tests antisera display cross-reactivities among different members of the taxon.

Serological relationships between different members are found. Cross-reactivity is found between species, but not genera. Protective immunity is induced in the form of neutralizing antibodies. Serological reactions are often complicated by sensitivity of virions to salts. Virions are usually satisfactorily stabilized for use as antigens or immunogens by fixation with glutaraldehyde. The virus serves as an efficient immunogen when animals are infected with whole or disrupted virus particle preparations. These preparations produce antibodies. The virus induces antibodies with distinct reactivities to the type-specific determinants, serogroup-specific determinants, complex-specific determinants, and genus-specific determinants. The virus induces the formation of neutralizing antibodies, hemagglutination inhibiting antibodies, and complement-fixing antibodies. Antibody response that is protective against infection is usually directed against virion surface proteins. The serotype is defined by E protein. The virus serotype is determined by a serum neutralization test, a cross-protection neutralization of infectivity, and ELISA; using monoclonal antibodies. Antigenic distances between individual species, expressed as serological indices, are correlated with the degree of sequence difference in their surface glycoprotein (E). Species that are serologically interrelated have antigenic homologies with different isolates of the same virus species, species of the same serogroup or complex, and serogroups of the same genus. Although the degree of antigenic specificity varies with the degree of relatedness, the antigenicity is distinct from (all flaviviruses, however related). All species in the genus are related antigenically. They are sharing some epitopes in the structural proteins and in the envelope proteins. The virus forms a serological continuum with some clusters around other viruses of the Japanese encephalitis complex. Serological analyses show close interrelationship between viruses originating from the same continent, the same geographic region, different continents, and different geographic regions. The virus is closely related to other viruses of the Japanese encephalitis complex and related to all other flaviviruses. Antigenic variations occur sporadically. Classification of members of this taxon is occasionally based on their antigenic properties and based on their sequence homologies (, the principal means of classification). All flaviviruses share at least some (usually considerable) sequence homology.

Diagnostics and Reference Collections

The best tests for diagnosis are neutralization, hemagglutination-inhibition, complement-fixation, ELISA. Antisera are commercially available from American Type Culture Collection, or W.H.O. regional reference centers.

Vaccines

Vaccines are not available.

Biological Properties

Natural Host Range

Virus infects during its life cycle arthropod and vertebrate hosts. Virus has an enzootic cycle and is transmitted from its arthropod vector to birds and its arthropod vector to an incidental incompetent host (dead end host). Viral hosts belong to the Domain Eucarya.

Domain Eucarya
Kingdom Animalia.

Kingdom Animalia
Phylum Arthropoda (hematophagous arthropods), or Chordata (various birds and mammals).

Phylum Arthropoda
Subphylum Hexapoda; Class Insecta (usually mosquitoes); Order Diptera.

Phylum Chordata
Subphylum Vertebrata; Class Aves and Mammalia.

Class Mammalia
Order Marsupialia (opossums), or Chiroptera, Rodentia, and Primates;
Family Didelphidae: Didelphinae, Philander opossum (Gray Four-eyed Opossum) [TaxID 9272];
Family Hominidae; virus infects Homo sapiens (human).

Host details on isolation Virus was isolated from an adult insect.

Signs and Symptoms

Natural hosts and symptoms

General Symptoms in Animals
Infection can affect the gastrointestinal system, nervous system, and dermis, mucosa or epithelium. General symptoms include headache, or photophobia, or pyrexia, or stiff neck, or uncoordination. Lesions are found in nerve tissue, or liver, or brain. Signs and symptoms include hepatitis or liver dysfunction; meningitis, seizures, encephalitis.

Severity and Occurrence of Disease

Host 1: Infection is apparent. Although disease expression is dependent on dose, infection is usually acute. The infection is clinically expressed; disease has the name encephalitis and is listed in the classification of International Disease Code (ICD-10) with the designation [A83.3]. Signs and symptoms may vary, but are usually mild, severe only sometimes. Prevalence of viral infection is seasonally dependent, incidences of virus infection are usually observed in summer and autumn, during a wet season followed by a dry season. Contagiousness is not observed.

Transmission and Vector Relationships

The virus is transmitted by a vector (mosquitoes) from infected arthropod to vertebrate in a direct manner and in an indirect manner. Transovarial transmission has been demonstrated in colonized Culex pipiens complex mosquitoes originally collected in Memphis, Tennessee, and McLeansboro, Illinois. The virus is transmitted by mechanical inoculation (under laboratory conditions); not transmitted by contact between hosts. Viral transmission by vectors is frequent (during epizootics).

Vector Transmission: The virus is transmitted by arthropods; insects of the order Diptera; family Culicidae, Culicinae (culicine mosquitoes); mosquitoes. The principal natural vector(s) are Culex pipiens, Culex tarsalis, Culex quinquefasciatus, and Culex nigripalpus. The virus is transmitted in a persistent manner; replicates in the vector; does not require a helper virus for vector transmission.

Non-Vector Transmission: The likelihood of viral transmission by respiratory, by faecal-oral route, by direct contact, through sexual contact, by parenteral transmission, through blood or blood products, congenital (germ line) transmission, transplacental transmission, perinatal transmission is nil.

Experimental Hosts and Symptoms

Under experimental conditions susceptibility to infection by virus is found in many species and many families (birds, mammals).

Host 1: Experimentally infected hosts mainly show symptoms of forming antibodies, viremia and death.

Cell lines or tissue cultures susceptible to virus infection:

Symptoms include cytopathic effects.

Diagnostic Hosts

For virus isolation the most commonly used test animals are suckling mice; cell lines or tissue cultures are Vero cells, chick embryo cells, C6/36 cells. Virus has been propagated in experimental animals, or cell culture.

Maintenance and Propagation Hosts

Most commonly used maintenance and propagation host species are suckling mice, Vero cells, C6/36 cells. Cell lines or tissue cultures used for propagating virus are Vero cells, C6/36 cells. Virus is propagated in embryonated eggs chicken, duck. Virus is propagated in embryonated eggs by inoculating the amnion.

Assay Hosts

Host 1: Most commonly used species for assaying the virus are Vero cells, suckling mice.

Pathology

The virus can be detected best in the nervous system; brain tissue.

Histopathology: Primary histological changes include necrosis.

Cytopathology: Inclusion bodies in the host cell are found in the cytoplasm.

Geographical Distribution

Geographical distribution of the virus is probably restricted. The virus spreads in North America and South and Central Americas. Location of first isolation is 90 degree longitude (West); 40 degree latitude (North). The virus is known to occur in temperate regions and subtropical regions. The virus occurs in Argentina, Brazil, Canada, Haiti, Jamaica, Mexico, Trinidad and Tobago, and the United States of America.

Ecology, Epidemiology and Control

A fact sheet on this virus is available from the Centers for Disease Control and Prevention (CDC), National Center for Infectious Diseases (NCID) Fact sheet.

List of Strains and Isolates in the Species 00.026.0.01.044.04.204.001. Parton (V-524-001-522); MS1-7 (=MSI.7) (sequenced).

Data Sources and Contributions

A description of the virus is found in database of U.S. Centers for Disease Control and Prevention (CDC), National Center for Infectious Diseases (NCID). This description has been compiled from data presented in the literature, or ICTV Reports. For further information on virus please contact the Subcommittee Chair (see at ICTV webpage ), or the Study Group (SG) chair (see at ICTV web page ), or the ICTVdB Management .

References

PubMed References .

Contributor

Data have been submitted online to ICTVdB on 26-12-01 by
Charles H. Calisher
AIDL, Department of Microbiology
Colorado State University
Foothills Campus
Fort Collins; Colorado; 80523
U.S.A.
Tel: + 1-970-491-2987.
Fax: + 1-970-491-8323.
Email: calisher@cybercell.net.

DELTA - DEscription Language for TAxonomy developed by Dr Mike Dallwitz, Toni Paine and Eric Zurcher, CSIRO Entomology, Canberra, Australia. ICTVdB - The Universal Virus Database, developed for the International Committee on Taxonomy of Viruses by Dr Cornelia Büchen-Osmond is written in DELTA. The virus descriptions in ICTVdB are coded by, or using data from experts in the field of virology or members ICTV. The character list is the underlying code. All virus descriptions are based on the character list and natural language translations are automatically generated and formatted for display on the Web from the descriptions in DELTA-format. The description has been generated automatically from DELTA files. DELTA - DEscription Language for TAxonomy developed by Dr Mike Dallwitz, Toni Paine and Eric Zurcher, CSIRO Entomology, Canberra, Australia.

ICTVdB - The Universal Virus Database, developed for the International Committee on Taxonomy of Viruses (ICTV) by Dr Cornelia Büchen-Osmond, is written in DELTA. The virus descriptions in ICTVdB are coded by ICTV members and experts, or by the ICTVdB Management using data provided by the experts, the literature or the latest ICTV Report. The character list is the underlying code. All virus descriptions are based on the character list and natural language translations from the encoded descriptions are automatically generated and formatted for display on the Web.

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