OTUs Updated February 11, 2020

Overview

The Virtool OTU reference is a fully editable and tracked collection of viruses, viral isolates, and their genome sequences. The data in the virus reference is used to identify potential viral infections in Illumina libraries derived from your samples.

Concepts

An OTU (organization taxonomic unit) typically represents a single pathogen species. References are composed of a set of related OTUs.

An OTU must contain one or more isolates and each isolate must have one or more sequences attached to it.

Here is the structure of a single viral OTU containing one isolate and its sequences:

- OTU | Apple Mosaic Virus
    - Isolate | Isolate 1
      - Sequence 1 | NC_003464
      - Sequence 2 | NC_003465
      - Sequence 3 | NC_003480

Browse OTUs

The OTUs that belong to a Virtool reference can be easily browsed and edited. To start browsing member OTUs for a given reference:

Navigate to the references list by clicking on References in the main navigation bar. References list

Select the reference of interest by clicking on it. We will look at Banana Viruses here. Banana Viruses reference

Navigate to the OTUs tab to view the OTUs that belong to the reference. Banana Viruses OTUs

Click on an OTU item to view its detail page. ABTV Detail

In the virus database browser, you can:

  • find viruses by their names or abbreviations using the search bar
  • view only viruses modified since the last index build

Create an OTU

Creating a new OTU for a given reference requires only a name. You can optionally provide an abbreviation like those commonly used for viruses.

Start by clicking under the OTUs tab to bring up a dialog for creating OTUs. “Create OTU button

The OTU creation dialog will appear. Enter a name and abbreviation for the new virus. “Create OTU dialog

Save the new OTU. It should now appear in the list of OTUs for this reference. “New OTU in modified state”

Navigate to the newly created OTU by clicking on it. Notice that there is a warning indicating that the OTU is not ready for primetime. New OTU detail

Edit an OTU

The name or abbreviation for an OTU can be made after its creation.

Navigate to the detail view for the OTU you want to edit. Bad Banana Detail

Click on the icon in the top-right of the view to show the edit dialog. Note that you will not see this icon if you don’t have modification rights on the parent reference. Edit dialog

Change any of the fields and click Save. We will change the abbreviation in this example. Edit dialog changes

Remove an OTU

Navigate to the detail view for the OTU you want to delete. Remove OTU

Click on the top next to the OTU name. A dialog box like the one below will show up to confirm the deletion of the OTU. Confirm removal of OTU

Click Confirm to permanently remove the OTU from the parent reference. The OTU will be removed from the OTUs list and the index must be rebuilt to accomodate this change. Remove OTU

Add an Isolate

Isolates are how sequence data are organized within the virus record. To maintain continuity with virus sequence records in Genbank, isolates in Virtool are identified by a source type and source name. These two fields are concatenated to form the isolate’s name.

Examples of source types are: isolate, genotype, and culture.

Examples of source names are: A, Canada, 8801-VLH, or anything really.

Click on the virus entry. “Virus detail empty”

Take note of the red notification at the top of the page. This indicates that the virus cannot be used in analyses until the listed issues are corrected.

Click on Add Isolate to the right of the Isolates heading to bring up a dialog for creating isolates. “Isolate creation dialog”

Notice that the Isolate Name field changes with the other two fields. This will be the display name for the isolate.

However, note: 
  • both fields are optional and the isolate name will be Unnamed if they are both empty
  • in a single virus, multiple isolates can have the same name
  • administrators can add new source types to the isolate

Save the changes by clicking Save. The new isolate appears in the isolate editor. “Virus detail with one empty isolate”

Edit an Isolate

Click on the OTU whose isolate you would like to edit. We will use TMV in this example. Edit TMV

To edit an isolate, click on next to the isolate. A dialog box will show up like the one below. Dialog box for editing an isolete

Make the necessary changes to the isolate and click Save. Edited Isolate

The new changes will be displayed on the detail view page of the OTU. New changes to OTU name displayed

Remove an Isolate

Click on the isolate from the TMV you would like to delete. Delete new isolate

Click on the next to the isolates name. A dialog box like the one shown below will show up. Confirm removal of isolate

Click Confirm to permanently delete the isolate. The isolate should now be removed from the Isolates list. Isolate is removed from list

Fetch a GenBank Sequence

Sequences are members of isolates. Many isolates will only have one sequence. If the virus in question is multipartite, more than one sequence would be assigned to each isolate.

Click near the Sequences heading to bring up a dialog for creating sequences. “Sequence addition dialog”

Fill out the form fields. The Host field is optional. You can pull sequence records from GenBank by entering a valid GenBank accession in the Accession field and clicking . “Populate sequence addition dialog”

Save the new virus. It will appear in the isolate editor. “Populated virus detail view”

Click on the sequence entry to expand it and view all the data associated with the sequence record. Sequence Record

Edit a Sequence

To edit a sequence, click on the next to the sequence entry. An Edit Sequence dialog will appear as shown below. Edit sequence dialog box

In this dialog we can choose to change the name of the host, give the sequence a different name, and alter the sequence by adding/removing base pairs. For this example, we will add the host name and remove the first three letters of the sequence. Edit sequence

Click Save after making the edits. Notice these changes have been applied on the sequence record. Updated sequence record

Remove a sequence

Click on the next to the isolates name. A dialog box like the one shown below will show up. Confirm removal of isolate

Click Confirm to permanently delete the isolate. The isolate should now be removed from the Isolates list. Isolate is removed from list

Schemas

Add a Segment

To add a segment of a particular OTU, click the blue Schema tab. Schema Overview

Under this tab, click Add Segment. A dialog box such as the one below will show up. Add Segment

Give the segment a name and select the Molecule Type and then hit Save. Add Segment

This newly added segment will be displaed under the Schema tab. Schema Overview 2

Edit a Segment

To edit a segment, click on . Edit Segment

We can edit both the name of the segment or the Molecule Type in this dialog box. We will change the molecule type. Edited Segment

The changes made will be displaed under the Schema tab. Schema Overview 3

Remove a Segment

Click on the next to the segment you would like to delete. A dialog box like the one shown below will show up. Confirm removal of segment

Click Confirm to permanently delete the segment. The segment should now be removed from the Schema list. Schema Overview

History

Under this tab a user can track down every change that has been made to an OTU. Built Changes are not reversible, but you can reverse Unbuilt Changes by clicking on the button.

Each change causes the virus’s version to increase by one and is recorded with a timestamp and the user’s name.

See more information about history.