*SHOW ICTVdB - character list. Copyright Cornelia Büchen-Osmond. May 2002. All
rights reserved.

*CHARACTER NOTES
#1. give exact isolate designation \b{}not\b0{} the species name
  of the virus which constitutes the items name in the database. To avoid
  duplicate names in the database the isolate designation can also be added to
  the items name. \line{}Example: items name: \i{}Influenza A virus\i0{},
  isolate\i{} \i0{}A/Puerto Rico/8/34 (H1N1) \par{} isolate designation:
  \b{}A/Puerto Rico/8/34\par{}\par{}\b0{}In case of species description, the
  isolate name of the original record should be recorded here. In the following
  questions the date, location and host of the original record should be given.
#2. Please enter the date in the following format: \b{}day\b0{} followed by
  \b{}month\b0{} followed by \b{}year\b0{}, selecting the day and month from the
  next two questions. Enter the appropriate year in the question following the
  month. The date will be assemble from the 3 separate questions to for
  example:\i{} 22 May 2001\b\i0{}. \b0{}
#7. enter the geographic location where the infected host has been first found,
  not the laboratory in which the virus had been isolated. In case of a species
  description, list here the location of the original record. This set of
  questions is seeking the origin and distribution of the virus, not the
  laboratory of isolation which will be addressed in the next set. For example,
  a virus found in imported plant material should be recorded under the country
  from which the infected material originated, NOT the country where the virus
  was isolated. Also do not list the tissues from which the virus has been
  isolated at this point, the target tissue/cell will be addressed later under
  "Biological Properties".
#8. in case of a description on the species level, list here the location of the
  original record, where the virus was first observed.
#9. in case of a description on the species level, list here the location of the
  original record, where the virus was first observed.\par{}
#11. in case of a description on the species level, list here the host of the
  original record, in which the virus was first observed.
#30. List [author] (last_name first_name), [year], [title],
  [journal/bulletin/report/book], [volume], [pages]. If more than one reference
  should be cited, please add a '\b{};\b0{}' (semicolon) before the next
  reference.
#33. traditional (vernacular) grouping of host(s) listed here correspond with
  the ICTV categories. Questions concerning the formal taxonomic grouping of the
  host(s) will be addressed in detail under "Biological Properties", "Natural
  Host Range".
#35. Identify the level of description. The lowest taxonomic level of a
  description is the isolate level. A description can have only one level.
#36. This is a "house keeping" question and will be filled in by the ICTVdB
  management. If data of the particle properties and biological properties are
  known and entered, then a description is considered complete.
#37. Virus Code (VC) is the decimal code used throughout the ICTVdB database and
  is assigned by the ICTVdB management. The VC has the same function as EC for
  enzymes or ID for sequences. A new virus isolate should be submitted to ICTVdB
  in order to be registered with ICTVdB and be accepted by the ICTV Study
  Groups. Therefore ICTV has proposed that virus isolates must be registered in
  the ICTVdB before the data associated with them can be published. This
  proposal will ensure that the scientific community can clearly identify the
  source of the isolate from which data are produced (at present there are
  problems with this) and as more virus isolates are sequenced, the data are
  clearly linked and identified in databases such as GenBank. \par{}\par{}The
  code can change, if the taxon changes its taxonomic position. The old VC will
  be retained and point to the code.
#38. The virus accession number will be generated automatically when entering a
  new description online using EntVir, the data entry system of ICTVdB.
#39. The former virus code number will be entered by the ICTVdB management.
#40. The former virus accession number will be entered by the ICTVdB management.
#41. Go to the web page
  www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg?name=Viruses and search for
  the virus name in question.
#42. the biocontainment manual published by the U.S. National Institutes of
  Health can be found at www.cdc.gov/od/ohs/biosfty/bmbl4/bmbl4toc.htm. Be aware
  that even the most prominent alert lists provided by biocontainment,
  biohazard, biological warfare and others agencies such as the Australia Group
  (www.australiagroup.net/agcomcon.htm\ul{})\ulnone{} or the Office
  International des Epizooties (OIE
  www.oie.int/eng/maladies/en_classification.htm), use a mixture of virus names
  and disease names. The European and Mediterranean Plant Protection
  Organization provides an alert lists for plant viruses and other plant pests
  at www.eppo.org/QUARANTINE/Alert_List/alert_list.html.
#43. Taxon is used as neutral term instead of family or genus, because the
  descriptions in the database can be on any taxonomic level from order down to
  isolate.
#44. Alternative name(s) are valid and found in the literature, however,
  according to ICTV, they are presently not the preferred names.
#46. List synonyms, \i{}i.e.\i0{} names which are no longer valid names or have
  been used in the literature to describe a "new species", which was later found
  to be a geographical race or strain of or identical to a previously described
  species. Include also common names in different languages. If reference(s) are
  available put them in braces (\{ref.\}) after the name. \b{}Do not include
  names of diseases or strains\b0{}.
#47. List only the currently approved acronym. If there is more than one acronym
  list those under the following character.
#51. In 1999 ICTV decided that the descriptions in ICTVdB should be on the
  isolate level. Species descriptions will be generated in future from a
  summation of primary data of isolates. Please list the name of the species to
  which the strain or isolate belongs.
#55. Select the higher taxonomic levels from lists provided in the following
  questions.
#72. Give reference to isolate and \b{}not sequence\b0{} lists.
#73. The following section deals with the submission and evaluation of taxonomic
  proposals to the ICTV and will be a useful account of taxonomic movements and
  historic interest to virus systematists.
#85. Comment on the taxonomic position and list, for example, the characters,
  that define it.
#89. In most cases when obvious symptoms are observed the nature of the agent
  causing the disease has been established. However, sometimes the virus, or
  subviral agent causing the symptoms or disease has not yet been determined.
  The next few questions are designed to separate naked viruses, viroids and
  prions from all other viruses during an interactive identification with
  INTKEY. During a data submission session these questions should be a only be
  considered if the causative agent is not yet known.
#90. virions are infective particles that consist of a genome which is usually
  encapsidated by virus encoded protein(s). In contrast subviral agents consist
  of either a genome plus capsid protein, e.g., satellite virus, but need a
  helper virus for infection or replication, or a genome which will be inserted
  into a capsid provided by the helper virus, e.g., P4 satellites. Viroids are
  unencapsidated, small, circular, single-stranded RNAs, resembling in structure
  mRNA, and replicate autonomously when inoculated into host plants. Prions are
  found in microsomal fractions of infected tissue which contains numerous
  infective membrane vesicles. The rod-like structures found in brain microsomes
  are not infective. To date, no nucleic acid has been associated with prion
  protein.
#96. This question provides synonyms so that a bacteriophage can be termed phage
  instead of virus.
#98. List of structural building blocks that make up a virion or phage and are
  surrounding the nucleic acid. Non-structural proteins, such as enzymes are
  covered later.
#100. The majority of viruses have only one phenotype. \i{}Baculoviridae\i0{}
  have more than one, where \i{}e.g.\i0{} during the extracellular life cycle
  phase virions are enveloped but not during the intracellular phase.
#105. This includes virions occluded by occlusion or inclusion proteins in
  cells, including polyhedrin of \i{}Nuclearpolyhedrovirus\i0{} or granulin of
  \i{}Granulovirus\i0{}, or crystalline protein matrix of \i{}Cypovirus\i0{}.
#116. virions may be (a) rod-shaped: straight, parallel sides, flat ends; (b)
  filamentous: rod-shaped but often curved or flexuous; (c) bullet-shaped:
  straight, parallel sides with \i{}one\i0{} rounded end; (d) ovoid:
  cigar-shaped; (e) spherical: globular and may be slightly pleomorphic; (f)
  isometric: round or angular (never pleomorphic).
#122. For diameter of unenveloped rounded virions or nucleocapsids go to
  question in the section for unenveloped particles. If in doubt whether a
  virion is enveloped or not check value in both locations during an
  identification process.
#124. if you want to code for sizes of unenveloped elongated virions or capsids
  or nucleocapsids go further down to the questions for sizes of capsid. If you
  try to identify a virus using INTKEY and are in doubt during the
  identification process whether a virion is enveloped or not, check for values
  in both locations.
#128. The envelope of \i{}Baculoviridae\i0{} or \i{}Herpesviridae\i0{} can
  contain more than one nucleocapsid.
#135. Surface projections are restricted to particular areas of the envelope
  surface e.g. the neuraminidase or hemagglutinin in \i{}Orthomyxoviridae\i0{}.
#164. Nucleocapsid shapes are classified according to their symmetry.
#167. Shell of virion e.g., single or double capsid and core of
  \i{}Reoviridae\i0{}, or double capsid of \i{}Tectiviridae\i0{}.
#175. Regular surface pattern appears e.g. star-like as in \i{}Astroviridae\i0{}
  or \i{}Caliciviridae\i0{}, wheel-like as in \i{}Rotavirus\i0{}.
#186. Surface projections are restricted to parts of the virion surface e.g. to
  the vertices in \i{}Adenoviridae\i0{}; to one side as the tail-like fibers in
  \i{}Oryctes rhinoceros virus\i0{} (an unassigned virus that was formerly
  thought to be a member of the \i{}Baculoviridae\i0{}).
#245. Although a nucleoprotein complex consists of the genome plus protein, a
  core can have only one or the other.
#259. This is a morphological question and is not concerned with the an
  incomplete genome as long as the shape of the particle is not altered through
  the lack of part of its nucleic acid content, such as the nucleic acid-free
  lipoprotein particles e.g. HBsAg of \i{}Hepadnaviridae\i0{}. The term
  incomplete virus particles refers to faulty assembled capsids forming tubules
  as found in \i{}Reoviridae\i0{}; particles lacking parts of the capsid or
  envelope; empty particles i.e. shells that do not contain a full set of the
  nucleic acid.
#262. Give any helpful hints for a successful EM preparation.
#287. the next 3 questions are a set and have to be considered as one sentence
  that will be put together from the different options in the 2 questions. For
  example, the extent on virion infection is reduced | in crude sap.
#307. This question is similar to the next, but not identical. Plant virologists
  prefer to use tripartite rather than 3 segments, animal virologists generally
  refer to segments or molecules. \i{}Polydnaviridae\i0{} are multipartite
  whereas \i{}Orthomyxoviridae\i0{} have a segmented genome.
#308. The next questions are a set and will read as a sentence. At first glance,
  the questions appear to be in the wrong order starting with the number of
  molecules rather than the nucleic acid type. However in the natural language
  translation it will read \i{}e.g.\i0{} as follows: \i{}The genome is
  tripartite, consists three molecules of linear, positive-sense single stranded
  RNA\i0{}, or \i{}The genome consists of one molecule of circular double
  stranded DNA forming a non-covalently closed circle\i0{}.
#310. supercoiled is a conformation that dsDNA (\i{}Fuselloviridae\i0{},
  \i{}Polydnaviridae\i0{}) or dsRNA (\i{}Phytoreovirus\i0{}) molecules can
  adopt. When boths strands of a ds molecule are covalently colased one of the
  strands becomes over- or under-wound in relation to the other. The torsional
  strain causes the molecules to coil into a characteristic shape. Superhelical
  means the same, but is usually used for the underwound coil.
#316. subgenomic, satellite and host genomic nucleic acids encapsidated in the
  virion are considered minor species.
#330. Many taxa have only a single value recorded. When using this character for
  identification, you should enter a range of values to be sure of encompassing
  the recorded value. If the number of nucleotides is not known, but a molecular
  weight, then calculate the length and enter the rough estimate.
#331. the following 120 characters refer to the different genome segments
  associated with virions having multipartite genomes. This covers repetitive
  questions for up to 15 segments.
#333. If a virus has only one genome segment, this questions seems to be
  redundant, but for the sake of data comparison it should be filled in as well.
#475. The next 4 questions deal with the base ratio of single stranded genomes.
#480. This question applies only to double stranded genomes.
#481. next to the common set of nucleotide bases (A, G, C, T, or U) virus
  genomes can contain unusual nucleotide bases that are i.e. methylated
  derivates of the common nucleotide bases.
#486. terminal redundancy: The presence of identical nucleotide sequences at
  both ends of a nucleic acid molecule which have linear genomes, e.g. T2, T4,
  T7 phages and retroviral genomic RNA
#487. terminal repetition: The presence of nucleotide sequences at both ends of
  a nucleic acid molecule which are either identical (terminal redundancy) or
  are identical but inverted. Inverted terminal repeats are found in the genomic
  DNA of adenoviruses.\par{}palindromic: a segment of double-stranded DNA in
  which the nucleotide sequence of one strand reads in reverse order to that of
  the complementary strand\par{}
#488. reiterated sequences: nucleotide sequences which occur many times in a
  nucleic acid.
#500. If the double stranded DNA is covalently linked, go to the next question.
#555. List [author(s)] (last_name first_name), [year], [title],
  [journal/bulletin/report/book], [volume], [pages]. If more than one reference
  should be cited, please add a '\b{};\b0{}' (semicolon) before the next
  reference.
#557. As in previous sections, the questions start very broad to establish basic
  categories which lead further down to more detailed questions such as sequence
  status and their functions.
#559. Structural and non-structural proteins are dealt with separately. The
  structural proteins are listed according to their location in particle
  structure from the outside in. There are 2-4 sets of questions each for
  envelope, surface membrane, capsid, outer and inner capsid, spikes and fibers,
  tails, core, matrix, tegument, nucleoid and lateral body proteins.
#563. the next 11 questions are a set and form one to several sentences. If you
  code for example |\par{}563:E1 | 564:10 | 565:P | 566:1&2 | 567:P12345 | 568
  :6 | 5691&6 | 570:heamgglutinase activity | 571:1 | 572:2 | it will translate
  into: "Envelope protein | "E1" | has a molecular mass of | "10" kDa | is the
  product of the polyprotein | "P" | has been sequenced and a function assigned.
  | Envelope protein sequence has the accession number | P12345 |. Envelope
  protein is expressed in the | late transcription phase |; its function is |
  attachment protein and forming the viral spikes, | which possess(es)
  "hemagglutinase activity". During post-translational processing envelope
  protein | has been cleaved from the precursor protein | "E" | and
  modifications occur that include | glycosylation".
#564. The molecular mass of a protein is usually very similar to the relative
  molecular mass Mr. In cases where the molecular mass is significantly
  different, please enter the value for Mr in angle brackets before the kDa
  value.
#913. There are 4 types of polymerases: (1) The RNA-dependent RNA polymerases
  bind RNA, which they depend on for a template, and catalyze the production of
  a RNA polymer; (2) the RNA-dependent DNA polymerases are reverse
  transcriptases, as they associate with RNA, but yield in a reverse sense a DNA
  product; (3) the remaining two classes comprise DNA-dependent polymerases,
  each with respective products of DNA and RNA.
#1126. to get around semantics synonyms are introduced. The next 6 questions
  strung together form one sentence. For example: phages | attach | tail | to
  specific receptors | located on | the cell wall.
#1140. the next questions are forming one sentence. i.e., the viral | core | is
  delivered to the cell | nucleus | the site of | mRNA transcription.
#1145. Provide detail which part of the genomic nucleic acid is required for
  infection, or if subgenomic nucleic acids are required.
#1149. satellite virus, is a defective virus which requires a helper virus to
  provide functions necessary for replication. It may code for its own coat
  protein or various other products.
#1157. In cases where more than one host is involved, start with the vector host
  as host 1 and describe the target host as host 2.\line\par{}
#1221. DNA-dependent DNA polymerases (prokaryotes I, II and III; eukaryotes
  alpha, beta and gamma). Enzymes which synthesizes DNA from a DNA template. In
  eukaryotes DNA polymerase alpha is mainly involved in replication of
  chromosomal DNA; DNA polymerase beta is mainly involved in DNA repair; DNA
  polymerase gamma is mainly involved in the replication of mitochondrial DNA.
  In prokaryotes DNA polymerase I is mainly involved in replication of
  chromosomal replication and has both 3'-5' (proof reading) and 5'-3' (excision
  repair in nick translation) exonuclease activities; DNA polymerase II is
  mainly involved in DNA repair due to UV damage; DNA polymerase III is also
  involved in the replication of chromosomal DNA.\par{}\par{}DNA-dependent RNA
  polymerases are enzymes which transcribe RNA from a DNA template. The enzyme
  initiates and terminates at specific sites (promoter regions and termination
  sites). In eukaryotes there are three forms of DNA dependent RNA polymerase, I
  mediating the synthesis of ribosomal RNA, II mRNA and III
  tRNA.\par{}\par{}RNA-dependent DNA polymerase is a synonym for reverse
  transcriptase. An enzyme encoded by retroviruses. Hepadnaviruses and
  caulimoviruses make a DNA copy of a primed RNA molecule. The enzyme is also
  capable of synthesizing DNA from a DNA template.\par{}\par{}RNA-dependent RNA
  polymerase is an enzyme which transcribes RNA from an RNA template. Most RNA
  viruses encode their version of this enzyme. It is frequently found
  encapsidated in viruses with minus-strands or dsRNA genomes.
#1283. the next 42 questions describe the organization and functional units of
  the first or only genome segment. The same questions are repeated twice for
  segment 2 and 3. The questions are sorted into blocks as follows: \line{} (a)
  coding strategy and number of ORFs (3). \line{} (b) functions of the first ORF
  (4)\par{} (c) segment functions as subgenomic mRNA template (2)\par{} (d)
  functions of the second ORF (8)\par{} (e) functions of additional ORF
  (5)\par{} (f) type of translational units (4)\par{} (g) frameshift
  configuration (2)\par{} (h) intergenic regions (5)\par{} (i) poly region, gene
  blocks (4)\par{} (j) terminal regions (2)
#1662. the term domain was introduced by Woese \i{}et al.\i0{} to distinguish
  Archaea from Bacteria in opposition to the Classification of Plants (Whittaker
  (1978) \i{}Five Kingdom System\i0{}). According to Whittaker the Kingdom
  Monera comprises the two Subkingdoms Archaebacteriobionta and
  Eubacteriobionta. See: Patterson, D.J. and M.L. Sogin (1992) \i{}Eukaryotic
  origin and Protistan diversity\i0{}. In: "The origin and evolution of
  prokaryotic and eukaryotic cells" ED. H. Hartman and K. Matsumo, World
  Scientific CO., New Jersey, pp. 13-46.
#1678. The taxonomy is based on the "Taxonomic Outline of \i{}Archaea\i0{} and
  \i{}Bacteria\i0{}" In: Bergey's Manual of Systematic Bacteriology, 2nd Edition
  (http://www.cme.msu.edu/bergeys/).
#1704. The classification of classes and orders of flowering plants is taken
  from A. Takhtajan (1969) Flowering Plants, Origin and Dispersal. Oliver & Boyd
  Edinburgh, pp. 310
#1849. the host can be selected from the following questions
#1862. the character arrangement has changed, but not all records in the
  database have been moved to their new positions to reflect the extended host
  range for arthropods
#1864. the taxonomy in the previous version for ticks was not well developed.
  Some of the question might overlap at present, but will be fixed.
#1873. the taxonomy is based on the fishbase and Species2000
#1921. the reptile taxonomy is based on Species2000 and ITIS
#1927. the bird taxonomy is based on Species2000 and ITIS
#2018. the taxonomy presented here reflect probably not the latest taxonomic
  insight of this group, but is comparable to the presentation found at
  http://www.crru.org.uk/taxonomy.htm.
#2130. Specify tissue or organ in which virus was found; or specify if virus was
  isolated from \i{}e.g.\i0{} leaf sap, or body fluids, secretions or
  excretions.
#2187. In cases where more than one host is involved, start with the vector host
  as host 1 and describe the target host as host 2.
#2294. Dodder (http://www.ext.colostate.edu/pubs/crops/03112.html) is a
  parasitic seed plant, can cause much damage in crop plants by
  \par{}introducing haustoria into the host vascular system.
#2296. contact between hosts includes contact between plants
#2301. Arthropod vectors are listed at
  <http://www.biosis.org.uk/zrdocs/zr_thes/systvoc/hemiptera.html>
#2521. propagation and maintenance host includes laboratory animals or commonly
  used test plants
#2526. assay host includes laboratory animals or commonly used test plants
#2527. this character applies only to plant assay hosts
#2564. List [author] (last_name first_name), [year], [title],
  [journal/bulletin/report/book], [volume], [pages]. If more than one reference
  should be cited, please add a '\b{};\b0{}' (semicolon) before the next
  reference.
#2593. e.g. the GIS longitude degree for Oracle Arizona is -110° 47' 46.1"
  (-110.796126 decimal format). You can check your US GIS for example at
  http://tiger.census.gov/cgi-bin/mapbrowse-tbl\par{}
#2594. e.g. the GIS latitude degree for Oracle Arizona is  32° 36' 1.8"
  (32.600506 decimal format). You can check your US GIS for example at
  http://tiger.census.gov/cgi-bin/mapbrowse-tbl
#2607. Go to the web page www.promedmail.org and pull out the relevant postings
  by using the search facility.
#2618. Include named taxa of only the next lower taxonomic level e.g. if this
  taxon is a genus with no named subgenus, list the species.
#2655. Field corresponds to Herbarium sheet for "The World Information Network
  on Biodiversity"..
#2656. Field corresponds to Herbarium sheet for "The World Information Network
  on Biodiversity".
#2657. Field corresponds to Herbarium sheet for "The World Information Network
  on Biodiversity".
#2659. Field corresponds to Herbarium sheet for "The World Information Network
  on Biodiversity".
#2679. for example: VP1, VP3, VP4 (capsid protein); NS1 (protease)