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00.073.0.01.024.00.048. Sindbis virus, isolate R2

Cite this publication as: ICTVdB Management (2006). 00.073.0.01.024.00.048. Sindbis virus, isolate R2. In: ICTVdB - The Universal Virus Database, version 4. Büchen-Osmond, C. (Ed), Columbia University, New York, USA

Cite this site as: ICTVdB - The Universal Virus Database, version 4. http://www.ncbi.nlm.nih.gov/ICTVdb/ICTVdB/

Table of Contents

Isolate Description

Isolate designation: R2.
Isolation date: not specified.
Location: Sindbis health district, 30 miles N of Cairo; Nile delta; Egypt.

Host of Isolate and Habitat Details
Source of isolate: mosquito (Culex univittatus).
Virus was isolated from adults.

Collection and Isolation Details
Virus was isolated by unknown.

Reference to Isolation Report
Taylor RM et al.(1955), Amer. J. Trop. Med. Hyg. 4, 844.

Biocontainment Level

Distribution of this virus falls under quarantine restrictions. It is recommended to handle this virus at the biocontainment level BSL-2.

Classification

This is a description of an invertebrate or vertebrate virus at the isolate level with data limited to classification details. If you have primary data on this virus, please submit them to ICTVdB using the online data entry systems or contact the ICTVdB management.

ICTVdB Virus Code: 00.073.0.01.024.00.048. Virus accession number: 73051924.
NCBI Taxonomy Identifier Taxon ID: 11034.

Name, Synonyms and Lineage

Virus is assigned to the genus 00.073.0.01. Alphavirus in the family 00.073. Togaviridae; not assigned to an order.

Virion Properties

Symptoms in the host are well established and the causative agent is determined.

Distinct viral structures are visible in thin sections of infected tissue. Particles contain nucleic acid which is encapsidated. Size and shape of virus has been determined by electron microscopy.

Virion Properties

Morphology

Virions consist of an envelope and a nucleocapsid. During their life cycle, virions have not been observed outside a cellular environment and have a cell-associated cycle and occur in one phenotype only. Virus capsid is enveloped (with a tight fitting membrane by a single layer envelope. Virions mature naturally by budding through the membrane of the host cell and are 70-80 nm in diameter. The envelope surrounds one nucleocapsid. Surface projections are distinctive glycoprotein spikes composed of two virus proteins forming heterodimers that are embedded in a lipid bilayer and cover the surface evenly. Surface projection proteins are formed by proteins, designated E1 and E2. Host ribosomes are not seen inside the envelope. A regular capsid structure is present. Capsid/nucleocapsid is round and exhibits icosahedral symmetry (T=4). The nucleocapsid is isometric and has a diameter of about 40 nm. Capsids appear round.

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 52 x 106. Virions have a buoyant density in sucrose of 1.22 g cm-3. The sedimentation coefficient is 280 S20w. Virion infectivity is inactivated and destroyed by heating for 10 min above 56°C. Under in vitro conditions virions are stable when stored at 4°C; inactivated; stable. Virions are sensitive to treatment with organic solvents and detergents. The infectivity is reduced after exposure to irradiation.

Nucleic Acid

The genome is monomeric; not segmented and contains a single molecule of linear, positive-sense, single-stranded RNA. The genome is infectious. The complete genome is about 11703 nucleotides long. Sequence can be accessed from GenBank. The RNA is partially sequenced, sequenced region is 340 nucleotides long and encodes 6K, C, E1, E2, E3, nsP1, nsP2, nsP3, nsP4, p62. Sequence has the accession number
[U62449]. The 5'-end of the genome has a methylated nucleotide cap. The 3'-terminus has no long non-coding region. The 3'-terminus has a poly (A) tract. Each virion contains a single copy of the genome; a full length copy.

GenBank records for nucleotide sequences; complete genome sequences.

Proteins

Proteins have been characterized and functions are assigned to them.

The viral genome encodes structural proteins and non-structural proteins. Virions consist of 6 structural protein(s) located in the envelope (E1, E2, E3), nucleocapsid (C) (6k, p62). The viral envelope contains 3 integral membrane proteins.

Structural Proteins: Envelope proteins E1, E2 and E3 have been sequenced. E1, a fusion protein is 439 amino acids long. Protein E2 is 423 and E3 is 63 amino acids long. Nucleocapsid protein C has also been sequenced and is 275 amino acids long.

Non-Structural Proteins: Virus-coded non-structural proteins have been identified by sequence analysis and 4 non-structural protein(s) are found. The virus codes for enzymes and replication-associated proteins; an RNA-dependent RNA polymerase. In addition to the polymerase, the virus codes for enzymes such as helicase, protease, replicase, and synthetase. The non-structural proteins are thought to be involved in capping of viral RNAs, initiation of negative strand RNA synthesis, processing of non-structural proteins, in RNA replication, the formation of a replicase complex for the minus strand synthesis, and the synthesis of the plus strand; function in the cytoplasm of infected cells; polymerase nsP4. Polymerase has been sequenced. Non-structural protein nsP1 has been sequenced and a function assigned. The protein is a replication-associated protein. Non-structural protein nsP2 has been sequenced and a function assigned. The protein is a replication-associated protein. Non-structural protein nsP3 and nsP4 have been sequenced and a function assigned.

Lipids

Lipids are present and located in the envelope. Virions are composed of 30% lipids by weight. The lipids are of host origin and composition depends on the cell in which the virus replicates and are derived from host cell membranes. Viral membranes include phosphatidyl ethanolamine, phosphatidyl choline, phosphatidyl serine, cholesterol, and sphingomyelin. Lipids are essential for infectivity.

Carbohydrates

Carbohydrates are found in virions; are present as glycoproteins.

Genome Organization and Replication

Virions attach to receptors located on the surface of cell membrane, enter host cells by fusion with, or endocytosis of the viral envelope.

The process of intracellular uncoating of virions is understood. Virus uncoating occurs in the cytoplasm; the viral nucleocapsid is delivered to the cell cytoplasm.

By itself, genomic nucleic acid is infectious.

Infection and Replication: Virus replication is initiated by the insect host. In the vertebrate host 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.

Transcription: The 5' ends of mRNAs are capped. The 3' ends of mRNAs possess a poly (A) tract.

Translation: The genome replicates in the cytoplasm.

Antigenicity

The virus is serologically related to all viruses in the genus Alphavirus. Antigenic determinants may be found on envelopes, spikes, and nucleocapsids and correspond to each of the major structural proteins, structural glycoproteins, and non-structural proteins; correspond to each of the major virion proteins C, E1, E2, E3, nsP1, nsP2, nsP3, nsP4. 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 neutralization, hemagglutination inhibition, and complement fixation. Antigenic specificity of the virion can be determined by neutralization tests, or hemagglutination inhibition tests, or complement fixation tests, or ELISA tests, or immunofluorescence assays. In gel-diffusion tests antisera display cross-reactivities among different members of the taxon.

Serological relationships between different members are very close. Cross-reactivity is found. Cross-reactivity between isolates of the same species and species, but not genera. Protective immunity is induced in the form of neutralizing antibodies. The virus serves as an efficient immunogen. These preparations produce antibodies. The virus induces antibodies with distinct reactivities to the subtype-specific determinants, or type-specific determinants, or serogroup-specific determinants, or complex-specific determinants, or genus-specific determinants. The virus induces the formation of neutralizing antibodies, or hemagglutination inhibiting antibodies, or complement-fixing antibodies. Antibody response that is protective against infection is usually directed against virion glycoproteins, or virion surface proteins. The virus serotype is determined by a serum neutralization test; using monoclonal antibodies. Antigenic distances between individual species, expressed as serological indices, are correlated with the degree of sequence difference in their coat protein. Species that are serologically interrelated have antigenic homologies with different isolates of the same virus species and species of the same serogroup. Species in the genus are related antigenically. They are sharing some epitopes in the structural proteins, or in the non-structural proteins. The virus is closely related to other viruses of the SIV-complex (Ross River Virus, Semliki Forest Virus, O'nyong-nyong Virus, Middelburg Virus) and related to all other alphaviruses. Classification of members of this taxon is based on their sequence homologies. Reliable virus detection and identification can be achieved by serological tests, or PCR techniques, or using specific primers.

Diagnostics and Reference Collections

The best tests for diagnosis are PCR, neutralization, IgM, IgG, Elisa, Hi, CF, IFA.

Biological Properties

Natural Host

Virus infects during its life cycle arthropod and vertebrate hosts. Virus has an enzootic cycle and is transmitted from arthropod vector to birds, arthropod vector to competent reservoir host, and arthropod vector to vertebrate host, but neither vertical nor horizontal transfer of the virus between the vertebrate hosts has been observed. Domain Viral hosts belong to the Domain Eucarya.

Domain Eucarya
Kingdom Animalia.

Kingdom Animalia
Phylum Arthropoda and Chordata.

Phylum Arthropoda
Subphylum Hexapoda; Class Insecta; Subclass Pterygota (winged insects), Order Diptera.

Phylum Vertebrata
Subphylum Vertebrata; Class Mammalia.

Class Mammalia Order Primates and Rodentia;
Family Hominidae.
Virus infects Homo sapiens (human).

General Symptoms in Animals Infection can affect the nervous system, musculo-skeletal system, and dermis, mucosa or epithelium. General symptoms include fever, or rashes. Lesions are found in nerve tissue.

Severity and Occurrence of Disease

Host: Signs and symptoms may vary, but are usually faint.

Host 2: Any kind of small rodents. The infection is not clinically expressed (for adult animals). Infection is apparent (Sindbis is not a serious pathogen for adult vertebrates). Signs and symptoms may vary, but are usually faint (for adult animals).

Host 3: Birds. Infection is apparent. The infection is not clinically expressed. Signs and symptoms may vary, but are usually faint.

Host 4: Under natural conditions virus infects subhuman primates. Infection is apparent (Sindbis is not a serious pathogen for adult vertebrates). The infection is not clinically expressed. Signs and symptoms may vary, but are usually faint.

Transmission and Vector Relationships

Virus is transmitted by a vector in a direct manner. Virus is transmitted by mechanical inoculation; through an injection; not transmitted by contact between hosts.

Vector Transmission:
Virus is transmitted by arthropods, by insects of the order Diptera, family Culicidae, Culicinae (culicine mosquitoes). Virus is retained when the vector moults; replicates in the vector.

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

Experimental Hosts and Symptoms

Under experimental conditions susceptibility to infection by virus is found in many families.

Host:
Experimental host is susceptible to infection mice.

Diagnostic Hosts

For virus isolation the most commonly used test animals are suckling mice, chicken embryo, duck embryo; cell lines or tissue cultures are chicken embryo cell cultures. Virus has been propagated in experimental animals and developing embryo.

Maintenance and Propagation Hosts

Most commonly used maintenance and propagation host species are suckling mice. Virus is propagated in embryonated eggs chicken, duck.

Assay Hosts

Host: Most commonly used species for assaying the virus are suckling mice.

Pathology

Virus can be best detected in nervous system.

Histopathology: Histopathologic lesions are found in brain. Virions are found in the cytoplasm. Primary histological changes include inflammation and necrosis.

Geographical Distribution

Geographical distribution of the virus is probably restricted. The virus spreads in Eurasia, Central Asia, East Asia, and Australasia and Pacific Islands. The virus is known to occur in temperate regions, subtropical regions, and tropical regions; viral host lives in the atmosphere. The viral host is found in a populated environment. The virus occurs in Australia, Bangladesh, Czech Republic, Egypt, India, Israel, Jordan, Lebanon, Libya, Malaysia, Russian Federation, and Thailand.

Ecology, Epidemiology and Control

A fact sheet on this virus is available from the www.microbiology.wustl.edu/sindbis/sin_genes

References

Norder H, Lundstr JM, Kozuch O and Magnius L (1996). Genetic relatedness of Sindbis virus strains from Europe, Middle East and Africa Virology In press.

PubMed References. Pathogen description www.microbiology.wustl.edu/sindbis/sin_genes



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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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