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APHIS eFile: BRS Applicant Training

BRS Permit Applications (APHIS 2000) in APHIS eFile

• Welcome to APHIS eFile

• Submitting Permit Applications

• Post-Submission Activities

• Managing Compliance
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WELCOME! 

USDA APHIS Biotechnology Regulatory Services 

(BRS) applicants must use APHIS eFile to submit 

permit applications for importation, interstate 

movement, or environmental release of organisms 

developed using genetic engineering.
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WHAT’S NEW?

On March 28, 2022, BRS’ Permit Application was updated in APHIS eFile:

Modernized Web 

Application Interface

Improved 

SOP/Attachment Area

Remodeled XML 

Upload Table

Applications up to 500 Constructs and 250 Locations may be submitted!

PDF generation process updated to output PDFs of all sizes!
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TRAINING OBJECTIVES

This training will teach new and existing BRS applicants how to draft and 

submit BRS applications for review using the updated interface, and perform 

post-submission activities such as editing applications, reviewing permit 

conditions, and submitting compliance reports.
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TABLE OF CONTENTS

Welcome to APHIS eFile

Pages 4 - 11

Submitting Permit Applications

Pages 12 - 20

Post-Submission Activities

Pages 21 - 28

Managing Compliance

Pages 29 - 34

Watch Training Recording Part 1:

https://usda.adobeconnect.com/pikjvu9ygw8w/

Watch Training Recording Part 2:

https://usda.adobeconnect.com/p5pxmosp10ns/
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Welcome to APHIS eFile
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WELCOME TO APHIS EFILE

Account Registration

Pages 8-9

Manage your Account

Page 10

Your Home Tab

Page 11-12

Access your Applications, Authorizations, Permits, etc. 

Page 13

Understanding Applications, Authorizations, Line Items, etc.

Page 14
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WELCOME TO APHIS EFILE

Account Registration

Visit https://efile.aphis.usda.gov/ to create your APHIS eFile account.

Click here to learn more about registration!

To sign up, an identity-verified USDA eAuthentication Account is required.
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WELCOME TO APHIS EFILE

Account Registration

When you register, your contact information 

will import from your USDA eAuthentication 

account. 

Edit your Contact Details to match your 

business address, email, and phone 

number, and confirm. 

If you do not have a USDA eAuthentication 

Account, select Create Account and follow 

the on-screen prompts. 
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WELCOME TO APHIS EFILE

Manage Your Account

Visit My Profile to update Contact 

and Organization information as 

needed. 

Use the Associated 

Organizations tab to: • Adjust your private account 

name. 

• Set up or join a shared 

Organization Account.

• Note that new Organizations 

take a few minutes to 

appear after creation.
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WELCOME TO APHIS EFILE

Your Home Tab

Your Home tab in APHIS eFile 

includes several shortcuts to:

• Start an APHIS application, 

including an APHIS 2000.

• Pre-filtered views of your activity 

in APHIS eFile.

• Links and resources for various 

APHIS programs.
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WELCOME TO APHIS EFILE

Your Home Tab

Your Home Tab also 

contains a link to 

view constructs 

submitted on BRS 

applications. The BRS Construct 

dashboard is linked in 

the Construct card.
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WELCOME TO APHIS EFILE

Access your Applications, Authorizations, Permits, etc. 

Select My Activity to 

access your 

Applications, 

Authorizations, 

Permits, etc.

This area will be blank 

until you create 

applications in APHIS 

eFile. 

Use the Filter to select 

Activity Type or Status to 

further refine your 

results.
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WELCOME TO APHIS EFILE

APHIS eFile Records: Understanding Applications, Authorizations, Line Items, etc.

Applications Authorizations

Line Items

Contains all the details of your application.

APHIS process for reviewing applications 

and issuing permits.

Draft and submit for permit 

authorizations.
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Submitting Permit Applications
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SUBMITTING PERMIT APPLICATIONS

Using BRS’ Permitting Assistant

Page 17-21

Drafting a Web Application

Page 22-24

Using the XML Uploader

Page 25

Drafting and Uploading SOPs

Pages 26-35

Reviewing, Certifying, and Submitting an Application

Page 36

Accessing Application PDFs

Page 37
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SUBMITTING PERMIT APPLICATIONS

Using BRS’ Permitting Assistant

The BRS Permitting Assistant

(BRSPA) is an interactive interface 

that allows applicants to:

• Enter details about their organism 

and activity to determine whether a 

permit is required.

• Quickly initiate a new web-entry 

application.
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SUBMITTING PERMIT APPLICATIONS

Using BRS’ Permitting Assistant

Login to begin the BRSPA

Select APHIS 2000 (Web) 

Application

OR Select the BRSPA card
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SUBMITTING PERMIT APPLICATIONS

Using BRS’ Permitting Assistant

Step 1:

Enter your organism 

details.

Step 2:

Use the attribute filters 

to refine your outcomes.

Step 3:

Add the outcome and 

proceed to the next step 

to confirm your 

selections.
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SUBMITTING PERMIT APPLICATIONS

Using BRS’ Permitting Assistant

Select a Sharing Organization

This determines who can see the 

application, as well as the name of the 

organization on the application.

Select a Responsible Person

This is the name of the applicant who is 

responsible for overseeing compliance 

with permit conditions.
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SUBMITTING PERMIT APPLICATIONS

Using BRS’ Permitting Assistant

Locate the Draft 

Application you intend 

to submit.

Select View Details to 

begin drafting the new 

application.
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SUBMITTING PERMIT APPLICATIONS

Drafting a Web Application

Application Details

• Identify whether your application includes CBI.

• Include details of the dates needed and preliminary organism details.

Organisms

• Review organism details entered in the BRSPA.

• Add/Edit organism details (if needed).

Supplier/Developers

• Information is not required.

• Add CBI claims to contacts after saving for reuse.

Key Application Fields!
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SUBMITTING PERMIT APPLICATIONS

Drafting a Web Application

Locations

• Select and enter the applicable Location Types for your application.

• Provide Agent contact details for each of the locations.

• Add Materials to locations that include destinations.

• Enter your Location Unique ID and include four pairs of GPS coordinates for release 

location.

Key Application Fields!

Constructs

• Add a new construct or use a construct from a previously submitted application 

(in APHIS eFile).

• Provide intended trait and genotype details for each.
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SUBMITTING PERMIT APPLICATIONS

Drafting a Web Application

Identify if your application has CBI.

Key Reminders!

Enter a minimum of four GPS Coordinates.

Add Materials to Destination Location

or Origin and Destination Location type.

Click Save and Next button 

to validate data entry.
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SUBMITTING PERMIT APPLICATIONS

Using the XML Uploader

Some applicants prefer to upload 

XML files to populate the data.

The remodeled XML upload table:

• Shows the latest upload on top.

• Refreshes every 30 seconds to 

show upload statuses.

• Allows up to 25 MB of data to 

be uploaded.

Use Add New File button to 

choose a file for upload.
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SUBMITTING PERMIT APPLICATIONS

Drafting and Uploading Standard Operating Procedures (SOPs)

What is an SOP?

A collection of procedures that describe how an organism developed using genetic 

engineering (modified organism) will be:

• Secured during shipment between contained facilities and movement to/from release 

locations.

• Contained within facilities at origin and destination locations.

• Confined during release into the environment.

• Maintained and disposed of at all locations in a manner that prevents its 

unauthorized release, spread, dispersal and/or persistence in the environment.
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SUBMITTING PERMIT APPLICATIONS

Drafting and Uploading Standard Operating Procedures (SOPs)

SOP Review Pathways

Submit SOP with permit application

Complete and Submit 

Permit Application

Processing of Permit 

Application

Issue or Deny 

Permit Application

Submit permit application at least:

• 45 days before importation or interstate movement is to begin; or

• 120 days before environmental release is to begin.
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SUBMITTING PERMIT APPLICATIONS

Drafting and Uploading Standard Operating Procedures (SOPs)

Submit SOP before permit application (pre-review, this task is not a mandatory requirement).

SOP Complete and Submit 

Permit Application

Processing of Permit 

Application

Issue or Deny 

Permit Application

Submit SOP for Pre-review:

• To BRS.Permits.SOP@usda.gov.

• At least 60 days before intended permit application submission.

Review of SOP

SOP Review Pathways
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SUBMITTING PERMIT APPLICATIONS

Drafting and Uploading Standard Operating Procedures (SOPs)

Formatting Suggestions for an SOP

• File type and naming convention

• <Organization Name>_<Organism Common Name SOP>_<Movement Type>_<Date>.<docx or pdf>.

• High level document description

• Organization name.

• Applicable Movement type(s).

• Applicable modified organism(s) (scientific and common names).

• Confidential Business Information

• If SOP contains CBI, then CBI guidelines must be followed: 

(https://www.aphis.usda.gov/brs/pdf/CBI_Submission_Guidance.pdf)
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SUBMITTING PERMIT APPLICATIONS

Drafting and Uploading Standard Operating Procedures (SOPs)

Data Needs for an SOP

Importation or Interstate Movement

• Secure Shipments of Modified Organisms between Contained Facilities

• Description of material(s) used to support modified organism during shipping.

• Description of packaging material(s).

• Containment of Modified Organisms within Facilities

• Description of how modified organism will be stored and identified.

• Maintenance, Devitalization, and Disposition of Modified Organisms in Containment

• Description of how supporting and packaging materials will be cleaned and disposed.

• Description of maintenance and disposal procedures to prevent release, spread, 

dispersal and/or persistence in the environment. 

• Description of records to demonstrate compliance with SOP and regulations.
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SUBMITTING PERMIT APPLICATIONS

Drafting and Uploading Standard Operating Procedures (SOPs)

Importation or Interstate Movement

• Country and locality where organism was collected, developed, manufactured, 

reared, cultivated, and cultured (as applicable).

Data Needs for an SOP
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SUBMITTING PERMIT APPLICATIONS

Drafting and Uploading Standard Operating Procedures (SOPs)

Environmental Release

• Secure Transport of Modified Organisms to and from Release Locations.

• Confinement of Modified Organisms to prevent Unauthorized Release

• Description of confinement procedures to prevent release, spread, dispersal and/or 

persistence in the environment.

• Maintenance, Devitalization, and Disposition of Modified Organisms in Confinement

• Identification of the Release Site and of the modified organisms.

Data Needs for an SOP
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SUBMITTING PERMIT APPLICATIONS

Drafting and Uploading Standard Operating Procedures (SOPs)

• Country and locality where organism was collected, developed, manufactured, 

reared, cultivated, and cultured (as applicable).

• Termination, Volunteer Monitoring, and Replanting of Environmental Release Sites

• Termination of release.

• Monitoring to prevent unauthorized release, spread, dispersal, and/or persistence 

after trial.

• Replanting after Field Trial Termination and during Volunteer Monitoring.

Environmental Release

Data Needs for an SOP
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SUBMITTING PERMIT APPLICATIONS

Drafting and Uploading Standard Operating Procedures (SOPs)

Resources

• Suggestions for SOPs Submitted for APHIS BRS Permits.

• SOP Templates (before end of FY2022).

Documents

• BRS BQMS page.

• Program components will be updated before end of FY2022.

Biotechnology Quality Management System (BQMS)
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SUBMITTING PERMIT APPLICATIONS

Drafting and Uploading Standard Operating Procedures (SOPs)

Uploading SOPs

• Use the Add SOP or

Attachment button to select a 

file.

• Select Attachment type and 

CBI Version attributes.

• Include equal number of CBIIncluded and CBI-Deleted 

attachments.

• Use Delete button to remove 

incorrect attachments.
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SUBMITTING PERMIT APPLICATIONS

Reviewing, Certifying, and Submitting an Application

Complete Missing Data and Review Submission

Agree to the Terms

Certify and Submit 3

2

1
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SUBMITTING PERMIT APPLICATIONS

Accessing Application PDFs

Application PDF Copies may be accessed 

via the Notes and Attachments section.

• Located at the bottom of the Application 

Details Page.

• Depending on the application’s size, 

these may take time to appear.

• Refresh the folder using the Yellow 

Refresh button.
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Post-Submission Activities
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POST-SUBMISSION ACTIVITIES

Using the My Activity Page

Page 40

Editing a Permit Application

Page 41

Reviewing Permit Conditions

Pages 42

Accessing Permit Copies and Labels

Page 43-46

Request to Amend a Permit

Page 47
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POST- SUBMISSION ACTIVITIES

Using the My Activity Page

APHIS eFile’s My Activity page 

may be used to resume 

applications and access Submitted 

Authorizations. • Use Filters, Search bar, Sort 

and Display options to locate 

Applications and 

Authorizations.

• Home Tab buttons auto-filter 

this view.
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POST - SUBMISSION ACTIVITIES

Editing a Permit Application

Login to APHIS eFile and select the hyperlink from your APHIS email notification.

Update the Sections in Waiting on Customer status, Save, then Submit your revised responses.

Review Action Required table on the Review and Submit section:
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POST - SUBMISSION ACTIVITIES

Reviewing Permit Conditions

Login to APHIS eFile and select the hyperlink from your APHIS email notification

View Conditions to review 

each Condition Description.

Agree or Disagree and 

provide Comments 

(if necessary).

Save each section, then 

Submit your Responses.
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POST - SUBMISSION ACTIVITIES

Accessing Permit Copies and Labels

Login to APHIS eFile 

and select My Activity 

tab.

Select Authorizations

from the Activity Type.

Select Issued from the 

Status filter.
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POST - SUBMISSION ACTIVITIES

Accessing Permit Copies and Labels

Select View Details on the Issued Authorization 

Activity card.

Scroll to the Notes and Attachments section 

at the bottom of the Authorization Detail Page.
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POST - SUBMISSION ACTIVITIES

Accessing Permit Copies and Labels

• If your permit contained CBI, there will be a CBI-Included and CBI-Deleted version in 

the respective folders. 

• If your permit did not contain CBI, your permit may be accessed in the No-CBI folder. 
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POST - SUBMISSION ACTIVITIES

Import labels may also be accessed via the Notes and Attachments Section of an issued 

authorization.

You may also access import labels from the 

attachment in your email from APHIS 

noting your labels are ready.

Accessing Permit Copies and Labels
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POST - SUBMISSION ACTIVITIES

Request to Amend a Permit

Enter the Authorization Number in the Search Bar. Select View Details.

Add an Amendment. Add the Amendment Details.

NOTE: You will need to Certify and Submit the 

application again for the Amendment process. 

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Managing Compliance
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MANAGING COMPLIANCE

Reports and Notices Overview

Page 50

Drafting and Submitting Compliance Reports

Page 51

Drafting and Submitting Compliance Notices

Page 52

Respond to Compliance Incident Proceedings

Page 53

Access Inspection Results Letter

Page 54
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COMPLIANCE

Reports and Notices Overview

REPORT/NOTICE WHEN IS IT NEEDED

Pre-Planting/Release Notice Create a Pre-Planting Notice prior to planting your APHIS approved 

organism.

Planting/Environmental Release Report* Create a Planting Report to notify APHIS that you have planted your 

approved organism.

Pre-Flowering Notice Create a Pre-Flowering Notice before your organism flowers.

Pre-Harvest/Pre-Destruct Notice Create a Pre-Harvest/Pre-Destruct notice before you harvest your 

organism.

Field Test Report* Create a Field Test Report to notify APHIS of the location details for 

your Field Test.

Volunteer Monitoring Report* Create a Volunteer Monitoring Report to notify APHIS of the location 

you are monitoring.

Cleaning (Return to General Use) Notice Create a Cleaning (Return to General Use) Notice to notify APHIS of 

the location, equipment and date of the cleaning.

*Indicates a report that is typically required for issued permits that include release locations.
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COMPLIANCE

Drafting and Submitting Compliance Reports

Enter the Authorization Number in the Search Bar. Select View Details.

Select View/Report/Notices. Select Add to create the applicable Report.

NOTE: Provide Location Details 

including GPS coordinates, Constructs, 

and Supporting Documents to certify 

and submit the report. 

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COMPLIANCE

Drafting and Submitting Compliance Notices

Enter the Authorization Number in the Search Bar. Select View Details.

Select View/Report/Notices. Select Add to create the applicable Notice.

NOTE: Provide the Location Details, 

including Site information, and 

Supporting Documents to certify and 

submit your notice. 

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COMPLIANCE

Respond to Compliance Incident Proceedings

Enter the Authorization Number in the Search Bar. Select View Details.

Select the CI-00XXXX folder. Select the Responsible Party Documents folder.

Select the Upload Arrow to add files to the Authorization.

NOTE: You will receive a message notifying 

you that your files have been successfully 

uploaded. 

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COMPLIANCE

Access Inspection Results Letter

Enter the Authorization Number in the Search Bar. Select View Details.

Select the IN-00000XXXXX folder.

Select the Notice of Inspection 

Results document hyperlink and 

preview/download as needed.

NOTE: You will receive a message notifying 

you an Inspection results letter is available.

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Thank you! 

Questions?
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APPENDIX

System Setup

• Compatible browser – For the best user experience, please use 

Google Chrome. Other available browsers include Firefox, Safari, and 

Edge. APHIS eFile is NOT supported by Internet Explorer.

• Emails – Add the APHIS eFile email at aphis.efile@usda.gov and 

support@salesforce.com to your address book so that any automatic 

emails are not sent to junk.

• Zoom –100%

Contact

If you require technical assistance, please contact:

Help Desk

help@usda.gov

If you require assistance with your applications, please contact:

BRS 

BRS.eFile@usda.gov