Database User Guide

1. Database format
 
The Viropendium Database is designed to provides two main levels of information:
 
  • First-level, general information displayed in the form of a Table
  • Detailed information on specific products in the form of Product files that can be accessed by clicking on a product’s name in the Table
 
1.1 Table
 
First-level information displayed in the Database takes the form of a Table with the following headings:
 
  • Sponsor(s): Main group involved in product development. Note that Product files can also mention co-sponsors and partners also playing a role in product development. 
  • Product: Product name and synonyms (italics)
  • Type of product: Nature of the product, based on the following categories:
    • Vaccine: product used to elicit immune response
    • Immunomodulator: product that can modulate immune response
    • Antibodies: immunoglobulins raised against a particular antigen
    • Inhibitor: product interfering with viral or cellular process(es)
    • Inhibitor & Immunomodulator: product harboring properties of inhibitor and immunomodulator
    • Other: product acting through a mechanism distinct from the above
  • Mode of action: Mechanism of action of products acting as inhibitors:

3A IN:                    
inhibitor of Rhinovirus protein 3A
a-gluco IN:            
alpha-glucosidase I inhibitor
Antisense:             
RNA or DNA molecule which binds to complementary strand of nucleic acid (usually in a target mRNA) to inhibit gene expression
cdk IN:                   
inhibitor of cellular cyclin-dependent kinase
Cyclophil IN:         
inhibitor of cellular cyclophilin
DHS IN:                
inhibitor of cellular deoxyhypusine synthase
DNA Pol IN:
DNA polymerase inhibitor
DOHH IN:
inhibitor of cellular deoxyhypusine hydroxylase
EI:
entry inhibitor
EI/MI:
inhibitor of both viral entry and maturation process
EI/Regul IN:
inhibitor of both viral entry and viral regulatory protein
Encaps IN:
encapsidation inhibitor
HDAC1 IN:
inhibitor of cellular histone deacetylase I enzyme
Hel IN:
helicase inhibitor
Hel-Pri IN:
helicase-promase complex inhibitor
HI-NA IN:
inhibitor of hemagglutinin-neuraminidase enzyme
II:
integrase inhibitor
II/EI:
inhibitor of both integrase enzyme and entry process
II/PIC:
inhibitor of both integrase enzyme and pre-integration complex
Ion IN:
ion-channel forming protein (viroporin) inhibitor
IRES IN:
internal ribosome entry site inhibitor
MI:
maturation inhibitor
Multiple:
more than 2 concurrent inhibitory activities
NA IN:
neuraminidase inhibitor
NcRTI:
nucleoside-competing reverse transcriptase inhibitor
NNRTI:
non-nucleoside reverse transcriptase inhibitor
NNRTI/EI:
inhibitor acting both as NNRTI and entry inhibitor
NRTI:
nucleoside reverse transcriptase inhibitor
NRTI/NNRTI:
mixture of NRTI and NNRTI
NS5A IN:
inhibitor of non-structural NS5A phosphoprotein
PARP IN:
inhibitor of cellular poly-ADP ribose polymerase
PI:
protease inhibitor
PIC IN:
inhibitor of pre-integration complex
PPRTI:
pyrophosphate reverse transcriptase inhibitor
Regul IN:
inhibitor of viral regulatory protein
Release IN:
inhibitor of virion release from infected cells
Ribozyme:
“Ribonucleic acid enzyme”, RNA molecule catalyzing cleavage of target RNA sequences
RNA Pol IN:
RNA polymerase inhibitor
RNAse:
ribonuclease
RT-like IN:
inhibitor of reverse transcriptase-like enzyme
RNAi:
RNA interfering (including siRNA, shRNA, ddRNAi, etc)
SVM:
selective viral mutagenesis
Uncoat IN:
inhibitor of viral uncoating in entry process
Unknown:
mechanism of action not yet determined
Unspecified:
mechanism of action unspecified or undisclosed by sponsor
Zn-f IN:
zinc-finger inhibitor

 

  • Mode of action: Types of vaccines:

    Inactivated vaccine, whole or split virions:

    Suspension of purified whole or split virions (including Influenza virus “subvirion” vaccines), chemically or physically inactivated to remove infectivity, used to elicit immune response

    Live attenuated vaccine:

    		Suspension of live, attenuated virus with limited replication capacity or pathogenicity, including reassortant viruses from the same viral family, used to elicit immune response

    Recombinant protein vaccine:

    Purified viral proteins obtained using genetic recombination and expression vectors, used as protein suspension or added to liposomes, virosomes or VLPs to elicit immune response, with or without adjuvant

    Non-recombinant protein vaccine:

    Purified viral proteins obtained directly from virions or subvirion particles, and used as suspension or added to liposomes or virosomes to elicit immune response with or without adjuvant

    Peptide vaccine:

    Synthetic peptides derived from natural or modified amino acid sequence of viral proteins, used to elicit immune response with or without adjuvant

    Recombinant vaccine, viral expr vector:

    Viral expression vector or chimeric/recombinant viruses (usually from different viral families), used as vaccine to express viral antigens and elicit immune response

    Recombinant vaccine, plasmid expr vector:

    Plasmid expression vector used as vaccine to produce viral antigens and elicit immune response

    Conjugated vaccine:

    Viral protein or peptide chemically bound to another molecule or recombinantly expressed as a fusion protein with exogenous amino acid sequences, used to elicit immune response
     

    Related virus vaccine:

    A distinct virus in the same viral family but with limited replication capacity or reduced pathogenicity is used to elicit immune response

 

  • Viral Family: Name of viral family according to taxonomic criteria, ending with “viridae” (see Viral Taxonomy page for further information)
  • Virus: Virus name. Sometimes, where a product is developed for more than one virus in a single viral family without further precision on the actual virus names, or when a products is developed for closely related viruses in the same viral family, a generic name such as “Herpesviruses” or “Poxviruses” can appear in the grid.
  • Status-1: Current stage of development of the product, including:
    • Research stage (basic science / discovery)
    • Preclinical (assays and animal testing intended to support IND filing)
    • IND filing
    • Clinical stage: Phases I, I/II, II, II/III, III
    • NDA/BLA filing
    • Market
  • Status-2: Additional information and details regarding product’s stage of development
 
Alphabetical order
The default settings of the Table display the products listed by sponsor’s name in alphabetical order in the first column. The order can be reversed by clicking on “Sponsor(s)”. Similarly, the content of all the other columns can also be listed in alphabetical or reverse alphabetical order by clicking on the heading at the top of the column.

 

Display

When using the default "Page View" mode, click on the triangle-shaped cursors at the bottom of the pages (left and right corners) to go to the next pages. You can also select a specific page number by moving the cursor between the "<" and ">" symbols along the dotted line at the bottom of the page.

Alternatively, you can click on "Show or print as a continuous list" at the bottom of the page to see (and print) the Table as a continuous list. This option can also be used when conducting searches in the Database.

1.2 Product files
 
To see all information included in a Product file, click on the product’s name in the Table. A Product file will appear with all the information collected about the product.
 
In Product files, the upper, central section contains general information such as product’s name and synonyms, sponsor and co-sponsor, type of compound and viral indication. When the product is developed for more than one virus, the line “Other virus” indicates the family to which this additional virus target belongs. Clicking on the viral family name in “Other virus” leads to a distinct Product file corresponding to the other indication of the product.
 
The left section contains a summary of the available information along with the structure, chemical formula and molecular weight (available for several compounds). Click on the structure to enlarge it (click outside the enlarged image to go back to the original size).
 
The central section contains most of the information on the product under different sections and sub-sections such as Details, Characteristics, PK Data, Dosage or Route of Administration, Resistance, In vivo and Clinical data, and Activity in vitro. The actual number of sub-sections for a particular product depends on its nature and the information available.
 
The right section contains information regarding the current development Status, some Remarks regarding product or sponsor, and Patent information when available.
 
The information can be saved or printed at will. We recommend “Landscape orientation” as your printer settings for best results.
 
 
1.3 Viewing Options
 
Above the Table, the following options are listed:
 
  • Click here to view the Database User Guide

This leads to the Database User Guide that can be consulted at all time by subscribers.

  • View all available products
This option allows the user to see all the products listed in the Database and some other information that depends on the type of subscription:
    • Custom Access subscribers are allowed to see only the list of products and the viral family names. All the other columns of the Table appear as empty, except for some demo products which are free such as: ChimeriVax-Dengue, Retrovir, P-1946 and Focetria®. Subscribers can click on any product’s name to see a new window showing the cost of the corresponding file. To buy a Product file, they just click on the link “Click here to buy access”, which leads them to the payment site. After a Product file is bought, it becomes part of the list displayed when “View all the products I have access” is selected.
    • Viral Family Access subscribers are allowed to see the list of products and the viral family names, along with the demo products. In addition, they see all the products that correspond to the viral family they have selected. For these products, they see the complete set of information in the Table’s columns and have access to their Product files by clicking on the product’s name in the Table. They can also click at any moment on a product’s name not included in their Viral Family package to see the cost of the corresponding file and decide if they buy it. To buy a Product file, they just click on the link “Click here to buy access”, which leads them to the payment site. After a Product file is bought, it becomes part of the list of products displayed when “View all the products I have access” is selected.
    • Full Access subscribers are allowed to see the complete list of products (including the demo products) with all the information available in the Table’s columns and product files. They have illimited access to the information in the Database and have no need to buy any additional product files.
  • View all the products I have access
This option allows the user to see only the products that have been bought, along with the demo products.
    • Custom Access subscribers will see the demo products along with the product files they have bought, if any.
    • Viral Family Access subscribers will see the demo products along with the products that correspond to the viral family they have selected and any other product files that have been bought, if any.
    • Full Access subscribers will see the complete list of products (including the demo products) with all the information available in the Table’s columns and product files. For these subscribers, there is no difference between “View all available products” and “View all the products I have access”.

 

2. Search options in the Database
 
The Database is designed to provide multiple search options that vary depending on the type of subscription.
 
  • Custom Access subscription, and Viral Family Access subscription:
SEARCH is essentially a basic search module, with the ability to perform searches using just one criterion: either Product name or Viral family name.
  • Full Access subscription:
These subscribers can use the SEARCH module with additional search criteria not available to Custom Access and Viral Family Access subscribers. Also, they can use the ADVANCED SEARCH module which allows single or multiple criteria searches based on Sponsor name, Product name, Product type, Mode of action, Viral family, Virus, and development Status. All these criteria can be combined for highly targeted searches.
 
2.1 Basic SEARCH module
 
This module carries on simple searches using either the Product name or a Viral Family name as search criteria.
 
Simply type the product’s name in the open box, select “Product” as the search criterion in the “Search in” box, and click on the “Go” button. The system will look for the product in the Database and display the corresponding line(s) from the Table. Click on the product name to get access to the corresponding Product file.
 
Note that the system allows you to enter a synonym instead of the more usual (or registered) name. For instance, entering either azt or azidothymidine as the product name will get Retrovir® as the result.
 
If the product name is not listed in the Database, the system will display an empty Table row with the mention “Products: 1-0 (Total 0)”.
 
A basic search can also be performed using a Viral Family name as the search criterion. This is done by entering the Viral Family name in the open box and selecting “Viral family” as the search criterion (“Search in” box). In this case, the system will display all the products corresponding to this viral family name.
 
As noted above, Custom Access and Viral Family Access subscribers can use the basic SEARCH module with only Product name or Viral Family name as search criteria. In the case of Full Access subscribers, the basic SEARCH module has the following set of search criteria enabled: Sponsor(s) / Product / Type of product / Mode of action / Viral family / Virus / Status.
 
Full Access subscribers can also use an additional “All” criterion which allows searches in all fields simultaneously. This provides a much more powerful and flexible tool even if the module remains limited to single-criterion searches. 
 
 
2.2 ADVANCED SEARCH module (Full Access subscribers only)
 
The most distinctive element of the ADVANCED SEARCH module is its ability to perform searches in the Database involving any combination of up to 6 (out of 7) possible criteria: Sponsor(s) / Product / Type of product / Mode of action / Viral family / Virus / Status.
 
Simply click on the ADVANCED SEARCH button to display the 7 search criteria fields. Enter one or more search criteria in the appropriate fields using the drop down boxes, and click on “Go”. The system will look for products matching the search criteria in the Database and display the corresponding line(s) from the Table. Click on the product name to get access to the corresponding Product file(s).