viruses coming to taibnet

ICTVdB the Universal Virus Database of the International Committee on Taxonomy of Viruses

Taichung Aug 2008

Viruses in 臺灣 : How can ICTVdB facilitate the construction of a

virus database in TaiBNET?

Viruses coming to TaiBNET

Cornelia Büchen-OsmondAustralian National University

Columbia University

http://en.wiktionary.org/wiki/%E8%87%BA

http://en.wiktionary.org/wiki/%E7%81%A3


Taichung Aug 2008

How did we learn about viruses

• symptoms known since thousands of years

– as devastating diseases

• in humans (small pox, polio)

• in animals (foot-and-mouth disease)

– in plants

• tulip color breaking (potyvirus)

• grapevine chrome mosaic (comovirus)


Taichung Aug 2008

How old are viruses?

determination of true age of viruses

• no fossils to determine

• genome sequence mutation, pair-wise comparison

• phylogenetic tree analysis

– ~1% decade in potyviruses

• molecular clock says old

– potyvirus in Australia introduced ~ 60,000 years

– dsDNA animal virusesmuch older


Taichung Aug 2008

Virology began with plant pathology

Mosaic disease in tobacco plants


Taichung Aug 2008

110 years of virology

• In 1892 the Russian scientist Iwanowski recognized that an infectious agent passing through a filter with a pore size of less than 250 nm was responsible for the mosaic disease affecting tobacco plants.

• Beijerinck was the first who associated the term virus with the filterable infectious agent in tobacco plants. – he proposed that a virus was a culturable

contagium vivum fuidum which multiplied in close association with the host's metabolism and was distributed in phloem vessels together with plant nutrients

– his theory was in stark contradiction to the prevailing germ theory based on the metabolic pattern of bacterial diseases

– only in the mid 1930’s the true nature of viruses was revealed as nucleoproteins


Taichung Aug 2008

110 years of virology

• The first filterable infectious agent isolated from animals was the Foot-and-mouth-disease virus reported by Loeffler and Frosch in 1898

• By the beginning of the twentieth century, the concept of viruses as agents of human disease was established when Reed and Carroll recognized Yellow fever virus (Panama Canal)

• Bacterial viruses were discovered independently in 1915 by Twort and by d'Hérelle in 1917 who coined the term bacteriophage, meaning "bacteria eater," to describe the agent's bacteriocidal ability .


Taichung Aug 2008

Discovery of the causative agent• The cause of smallpox was understood much

later– 1886 “elementary bodies” visualized in LM

– 1925 multiplication of poxvirus in cultured cells and chick embryo chorioallantoic membranes (Parker and Nye; Goodpasture)

– 1935 purification and chemical composition of vaccinia virus (Smadel & Hoagland)

– 1943 EM of negatively stained particles (Ruska, Siemens)

– 1954 EM thin sections of virus-infected cells (Morgan)

– 1967 RNA polymerase in infectious particles

– 1974 structure of poxvirus genome

– 1994 complete genome sequence of Variola virus


Taichung Aug 2008

What is a virus

• viruses are found in all forms of life

– subcellular entities consisting of• protein capsids• may have a lipid envelope• nucleoprotein/genome

– dsDNA, ssDNA, dsDNA-RT, dsRNA, ssRNA, ssRNA-RT

– totally dependent on the host

• for genome transcription and replication

• for assembly, maturation and egression


Taichung Aug 2008

Virus infection is host specific

– they can only infect a specific host• one or more host families

• species specific

– they can have a high mutation rates

– they can recombine

– they can acquire genes from the host

– they can transfer genes

Although much reduced forms of life, viruses are master explorers of the evolutionary space and are perhaps even a driving force in evolution and speciation.


Taichung Aug 2008

Classification of OrganismsTraditional Taxonomy

• based on morphology (using the naked eye and handheld lens)

• currently attempting to use molecular data (resulting in unclear relationships)

Virus Taxonomy

• based also on morphology (using EM, x-ray diffraction and crystal structure)

• currently mainly using genomic sequence data


Taichung Aug 2008

Early Classification Systems

• In 1927 the need for a system of virus nomenclature and classification was recognized

• Initially the classification scheme was based on plant, animal, and bacterial viruses

• The earliest efforts to classify within a host group were based on

– common pathogenic properties (symptoms)

– common organ tropisms (liver, leaves etc)

– common ecological and transmission characteristics

• Viruses causing hepatitis were simply lumped together as “the hepatitis viruses”

• This approach is still retained in the International Code of Diseases in which all virus diseases causing hepatitis are still lumped together under one basic code


Taichung Aug 2008

Taxonomic Virus Properties

Since the founding of ICTV (1961) the taxonomic status of a virus has been defined by

• Virion properties– morphology– genome, protein, carbohydrates and lipids

• Genome organisation and replication– metabolic interaction between virus and host– sequence annotations

• Biological properties– host range and vectors– cyto- and histopathology (disease expression)– transmission, epidemiology,

geographic distribution


Taichung Aug 2008

Taxonomy of emerging viruses

• 2 virus families24 floating genera 16 plant virus groups

• 38 virus families138 genera/groups

• 1 order50 families164 genera

• 3 orders56 families233 genera



1971 1st Report

1990 5th Report

1995 6th Report

2000 7th Report

2005 8th Report

2008 ICTVweb


Taichung Aug 2008

Virus nomenclature

The International Committee on Taxonomy of Viruses

• rules on classification and nomenclature

• does not accept Linnaean style binomial nomenclature(genus name followed by species name)

• recognizes taxonomic levels of Order, Family, Subfamily, Genus and Species with standardized Latinized endings

• includes host, symptom, and/or location in species names

• italicizes only a species name ending with “virus”


Taichung Aug 2008

Examples of virus species names species name: Tobacco mosaic virus Alt. name: Tobacco mosaic tobamovirusvirus name: Tobacco mosaic virus

species name: Cercopithecine herpesvirus 1synonym: Herpesvirus simiae (early attempt for true binomial

nomenclature)virus name: Cercopithecine herpesvirus 1

species name: Tomato yellow leaf curl Sardinia virussynonym: Tomato leaf curl virus-Sardiniasynonym: Tomato leaf curl virus - Sardiniasynonym: Tomato leaf curl virus - Spainsynonym: Tomato leaf curl virus – Sardinia [Spain]


Taichung Aug 2008

ICTV-online since 2007

• a new database maintained by ICTV

• each year, after final approval by all ICTV members, the latest Master Species list will be published online by ICTV

• links to the ICTVdB “ Index of Viruses” and virus descriptions


Taichung Aug 2008

ICTV-online entry for White spot syndrome virus first reported in shrimp aquaculture from Taiwan in 1992.

This entry is based on ICTVdB “Index of Viruses”

and this year updated by ICTV


Taichung Aug 2008

Index of Viruses in ICTVdBFamily Names in Taxonomic (genomic) Order


Taichung Aug 2008

ICTVdB uses a decimal code to uniquely identify each virusThe decimal code

• gives every virus in ICTVdB a unique “IP number”

• indicates its taxonomic status and level

• serves as a link within the whole database

• serves as a surrogate accession number in ICTVdB on the web and as hyperlink from other databases e.g., NCBI and SWISS-PROT or taxonomic databases such as Species2000 and GBIF

• records changing taxonomic decisions by ICTV expert Study Groups, but retains old codes to chart the history of virus taxonomy


Taichung Aug 2008

The decimal code in ICTVdB

IsolateIsolate 00.103.0.01.001.00. 003.

The decimal code for White spot syndrome virus indicates its taxonomic context

SpeciesSpecies

FamilyFamily 00.103.

SubfamilySubfamily 00.103.0.

GenusGenus 00.025.0.01.

Nimaviridae

…virales

….virinae

Whispovirus

White spot syndrome virus

WSSV-1-TW (1992)

00.103.0.01.001.

00.OrderOrder

http://cals.arizona.edu/pubs/general/resrpt1997/aquaculture.html


Taichung Aug 2008


Taichung Aug 2008

Virus descriptions in ICTVdB


Taichung Aug 2008

Interoperability in ICTVdB

• Interoperability is achieved in descriptions – via decimal code within ICTVdB – from other databases to ICTVdB

• on species level and above via

– NCBI TaxID to retrieve nucleotide sequences, genomes and PubMed references

• below species level via– sequence accession numbers– specific accession codes to

• Databases: CDC, VIPERdB, VIDEdB, DPV (CMI/AAB)• Catalogs: ATCC, DSMZ, d’Herelle • Publications: ProMed, journals


Taichung Aug 2008


Taichung Aug 2008

and ICTVdB lists are the accepted world standard for virus names


Taichung Aug 2008

ICTVdB in DELTA Format

• three basic flat files plus many directives– character list (> 3000 questions to describe a virus) – specification file (specifies types of characters and

dependencies)– Items file (coded data of >4000 virus descriptions)

• dependencies make characters applicable or inapplicable, depending on choice and correspond to tables in relational databases

• character list can be translated into other languages, including Chinese

• easy transport of data set from – one language to another

– one database to another

The new ICTVdB platform will be in a relational database format using MySQL


Taichung Aug 2008

Regional data sets

• virus descriptions on isolate level with links

– to species/genus level descriptions

– to fact sheets

– to sequence data

– to host databases

– to distribution maps for virus, host, vector

– to images of virus, host vector

– to references


Taichung Aug 2008

Viruses of Plants in Australia • DELTA formatted database

• regional data on viruses

– on hosts and agronomic impacts

– introduction to Australia

• distribution in Australia

• extensive host lists

• on the WWW since 1992

• links to generic descriptions


Taichung Aug 2008

Before viruses are entered in TaiBNET we need to have: • prepare lists of viruses in Taiwan

– in humans

– in agriculture

– in husbandry

– in aquaculture

– in nature

– in all forms of life

• obtain data from taxonomic hierarchy tree in ICTV or GBIF

• prepare short descriptions of isolate data

• customize links to ICTVdB and genomic databases


Taichung Aug 2008

Current ICTVdB DELTA SystemThe current system is based on the DELTA format (DEscription Language for TAxonomy). At its core, Delta is based on linear lists of information (flat files) which specify taxa and their defining characteristics. The Delta system has been engineered to uniquely suit the needs of the worldwide taxonomic community and is used for the classification of plants, animals, viruses, etc... Unfortunately, this taxonomic format and the associated software are no longer being developed. Updates to the Delta database require a highly trained curator with an in depth knowledge of the system. Publication of the database to the web is done using a mixture of specialized programs, scripts and hand editing. As a result the web-based ICTVdB is actually a set of static web pages which must be regenerated each time data are released.

Interactive virus identification is currently through the Windows application Intkey. Intkey is the interactive taxonomic keying system that is shipped with Delta. It allows a user to identify an organism by successive pruning of taxa. As details are entered about the organism, the number of taxa matching the specified information is listed. This is a valuable tool but the lack of cross-platform compatibility (Windows only) is a major complaint.

Isolate data, describing viruses found around the world, are submitted through EntVir, a MySQL database system feed by PHP-based forms which also must be regenerated each time the database is published. Isolate data ultimately ends up as an email that is imported into the Delta system manually. In the current system, all isolate review and database entry is handled through a single curator.


Taichung Aug 2008

Proposed ICTVdB System

The proposed replacement architecture utilizes a relational database (MySQL) where the flat files have been translated to their equivalents in a relational database schema. The relational database will capture the taxonomic hierarchy, descriptive data for taxa, and isolate descriptions. Users will interact with the MySQL database through a custom web application with the following functions:

Browse - A taxonomic tree will be used to navigate through viral taxa. This will allow visual browsing of the taxonomic hierarchy. Viruses will also be indexed by name, host and genome organization.

Query - A basic search will allow users to query the taxonomic hierarchy, virus names and other data. The stand-alone IntKey application will be replaced by an advanced search function with a flexible system of forms and search refinement.

Data Entry - An improved data entry system will be used to keep the ICTVdB up to date and to make data entry as simple as possible. Until this system is fully functional, the current EntVir system will remain in place.


Taichung Aug 2008

Proposed System

The proposed replacement architecture utilizes a relational database (MySQL) where the flat files have been translated to their equivalents in a relational database schema. The relational database will capture the taxonomic hierarchy, descriptive data for taxa, and isolate descriptions. Users will interact with the MySQL database through a custom web application with the following functions:

Browse - A taxonomic tree will be used to navigate through viral taxa. This will allow visual browsing of the taxonomic hierarchy. Viruses will also be indexed by name, host and genome organization.

Query - A basic search will allow users to query the taxonomic hierarchy, virus names and other data. The stand-alone IntKey application will be replaced by an advanced search function with a flexible system of forms and search refinement.

Data Entry - An improved data entry system will be used to keep the ICTVdB up to date and to make data entry as simple as possible. Until this system is fully functional, the current EntVir system will remain in place.


Taichung Aug 2008

The database will be populated with data from several sources:

One time conversion of current Delta format flat files to the database Annual taxonomy and nomenclature updates from the ICTV executive committee

Virus annotations made by Curators

Contributors submission of virus isolates

An important feature of the revised system is the concept of decentralized data entry and review. Isolate submission will be reviewed by the Head Curator and/or other specialists with knowledge of particular viral families. These Curators will be given the ability to review Pending isolate submissions for correctness and approve them for transfer from a Pending status to Approved isolates for release in the next ICTVdB version. Curators will be volunteers and will have the ability to decline to review isolates, in a manner similar to the peer review system used by journals. Yearly updates to the taxonomy will be made using the Master Species List maintained by the ICTV. The Master Species List contains the current description of virus taxonomy down to the species level and is updated, as needed, by the ICTV executive committee (EC). Decentralization is expected to greatly improve the accuracy and speed of the ICTVdB update process.

viruses coming to taibnet

Documents

term virus

mouthdisease virus

sections of virus

virus database

concept of viruses

true nature of viruses

filterable infectious

yearsdsdna animal viruses