Transcript Slide 1

Viruses coming to TaiBNET
Viruses in 臺灣 : How can ICTVdB
facilitate the construction of a
virus database in TaiBNET?
Cornelia Büchen-Osmond
Australian National University
Columbia University
Taichung Aug 2008
ICTVdB the Universal Virus Database of the International Committee on Taxonomy of Viruses
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
ICTVdB the Universal Virus Database of the International Committee on Taxonomy of Viruses
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 viruses
much older
Taichung Aug 2008
ICTVdB the Universal Virus Database of the International Committee on Taxonomy of Viruses
Virology began with plant pathology
Mosaic disease in tobacco plants
Taichung Aug 2008
ICTVdB the Universal Virus Database of the International Committee on Taxonomy of Viruses
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
ICTVdB the Universal Virus Database of the International Committee on Taxonomy of Viruses
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
ICTVdB the Universal Virus Database of the International Committee on Taxonomy of Viruses
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
ICTVdB the Universal Virus Database of the International Committee on Taxonomy of Viruses
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
ICTVdB the Universal Virus Database of the International Committee on Taxonomy of Viruses
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
ICTVdB the Universal Virus Database of the International Committee on Taxonomy of Viruses
Classification of Organisms
Traditional 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
ICTVdB the Universal Virus Database of the International Committee on Taxonomy of Viruses
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
ICTVdB the Universal Virus Database of the International Committee on Taxonomy of Viruses
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
ICTVdB the Universal Virus Database of the International Committee on Taxonomy of Viruses
Taxonomy of emerging viruses
1971
1st Report
1990
5th Report
1995
6th
2000
2005
2008
Taichung Aug 2008
Report
•
2 virus families
24 floating genera
16 plant virus groups
•
38 virus families
138 genera/groups
•
1 order
50 families
164 genera
•
3 orders
56 families
233 genera
•
3 orders
73 families
287 genera
•
5 orders
84 families
314 genera
7th Report
8th Report
ICTVweb
ICTVdB the Universal Virus Database of the International Committee on Taxonomy of Viruses
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
ICTVdB the Universal Virus Database of the International Committee on Taxonomy of Viruses
Examples of virus species names
species name: Tobacco mosaic virus
Alt. name:
Tobacco mosaic tobamovirus
virus name: Tobacco mosaic virus
species name: Cercopithecine herpesvirus 1
synonym:
Herpesvirus simiae
(early attempt for true binomial nomenclature)
virus name: Cercopithecine herpesvirus 1
species name: Tomato yellow leaf curl Sardinia virus
synonym:
Tomato leaf curl virus-Sardinia
synonym:
Tomato leaf curl virus - Sardinia
synonym:
Tomato leaf curl virus - Spain
synonym:
Tomato leaf curl virus – Sardinia [Spain]
Taichung Aug 2008
ICTVdB the Universal Virus Database of the International Committee on Taxonomy of Viruses
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
ICTVdB the Universal Virus Database of the International Committee on Taxonomy of Viruses
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
ICTVdB the Universal Virus Database of the International Committee on Taxonomy of Viruses
Index of Viruses in ICTVdB
Family Names in Taxonomic (genomic) Order
Taichung Aug 2008
ICTVdB the Universal Virus Database of the International Committee on Taxonomy of Viruses
ICTVdB uses a decimal code to
uniquely identify each virus
The 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
ICTVdB the Universal Virus Database of the International Committee on Taxonomy of Viruses
The decimal code in ICTVdB
The decimal code for White spot syndrome virus
indicates its taxonomic context
00.
Family
00.103.
Subfamily
00.103.0.
Genus
00.025.0.01.
Species
00.103.0.01.001.
Isolate
Taichung Aug 2008
…virales
Order
Nimaviridae
….virinae
Whispovirus
00.103.0.01.001.00. 003.
White spot syndrome virus
WSSV-1-TW (1992)
ICTVdB the Universal Virus Database of the International Committee on Taxonomy of Viruses
Taichung Aug 2008
ICTVdB the Universal Virus Database of the International Committee on Taxonomy of Viruses
Virus descriptions in ICTVdB
Taichung Aug 2008
ICTVdB the Universal Virus Database of the International Committee on Taxonomy of Viruses
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
ICTVdB the Universal Virus Database of the International Committee on Taxonomy of Viruses
Taichung Aug 2008
ICTVdB the Universal Virus Database of the International Committee on Taxonomy of Viruses
Taichung Aug 2008
ICTVdB the Universal Virus Database of the International Committee on Taxonomy of Viruses
and ICTVdB lists are the accepted world standard for virus names
Taichung Aug 2008
ICTVdB the Universal Virus Database of the International Committee on Taxonomy of Viruses
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
ICTVdB the Universal Virus Database of the International Committee on Taxonomy of Viruses
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
ICTVdB the Universal Virus Database of the International Committee on Taxonomy of Viruses
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
ICTVdB the Universal Virus Database of the International Committee on Taxonomy of Viruses
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
ICTVdB the Universal Virus Database of the International Committee on Taxonomy of Viruses
Current ICTVdB DELTA System
The 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 crossplatform 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
ICTVdB the Universal Virus Database of the International Committee on Taxonomy of Viruses
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
ICTVdB the Universal Virus Database of the International Committee on Taxonomy of Viruses
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
ICTVdB the Universal Virus Database of the International Committee on Taxonomy of Viruses
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.
Taichung Aug 2008
ICTVdB the Universal Virus Database of the International Committee on Taxonomy of Viruses