Application Snapshot: SARS-CoV-2 Viral RNA Extraction (COVID)

Customers all over the world are using Opentrons to automate viral RNA extraction for SARS-CoV-2 (COVID-19). Here’s how.

NOTE: In addition to basic liquid handling tasks like serial dilution, tube filling, and microplate filling you can also automate a slew of complex wet lab workflows using the Opentrons platform.  

In this snapshot, you will learn how to automate viral RNA extraction for SARS-CoV-2 using Opentrons hardware, software, consumables, and protocols. You will also learn best practices for optimizing your lab’s workflow to automate this assay, which kits have downloadable protocols ready to use, and which customers have already created Opentrons protocols for.

FAQ

Q: Will the Opentrons platform work in my lab?

A: The platform is open-source so any lab can use it, customizable for different workflows, and kit agnostic.

Q: What is the Opentrons COVID-19 Testing Workstation?

A: The Opentrons COVID-19 Testing Workstation processes up to 2,400 samples per day using the Opentrons OT-2 liquid handling robot, hardware modules, and verified labware. It is made of 3 stations that can be used separately or together to tackle different workflows. Station A performs collection tube plating, pre-extraction, and extraction prep, Station B performs RNA extraction, and Station C performs qPCR preparation. You can purchase the entire system, or simply one station to fit into your lab’s existing workflow. Pricing, support, and setup options for each station may differ depending on your lab’s needs.

Q: Do you have Emergency Use Authorization (EUA)?

A: The Opentrons COVID-19 Workstation is compatible with most molecular diagnostic systems, and has been successfully used with both EUA approved diagnostics and CLIA lab developed tests (LDTs).

Q: How long does the full testing workflow take?

A: The full workstation setup takes slightly longer than 5 hours to run the full workflow from end-to-end. Station A takes 1.75 hours, Station B takes 3 hours, and Station C takes 0.3 hours. Station A does pre-extraction as well as extraction prep steps, which add time to the overall process.

Q: What type of kits customers have already used on the robot?

A: While many of our customers use the popular Zymo Quick-DNA/RNA Viral Kit (EUA Letter, Kit Instructions, Protocol), we’ve validated and utilized a wide variety of SARS-CoV-2 RNA extraction and detection kits on the OT-2. Here is a list of SARS-CoV-2 extraction kits that have been automated on the OT-2 by Opentrons customers:

Company

Name

US-FDA EUA

Zymo

Quick-DNA/RNA viral kit

Yes

ThermoFisher

Viral/Pathogen MagMAX Ultra nucleic acid isolation kit

Yes

Beckman Coulter

RNAdvance viral kit

N/A

Omega Biotek

Magbind Viral DNA/RNA kit

N/A

BPG PureBase

Viral RNA kit

N/A

Seegene

Universal Extraction System

Yes

MGI

MGIEasy Nucleic Acid Extraction Kit

N/A

Clean NA

Clean Viral DNA & RNA Kit

N/A

Promega

Maxwell® HT Viral TNA Kit, Custom

N/A

Here a list of SARS-CoV-2 detection kits that Opentrons has automated for customers:

Company

Name

US-FDA EUA

Seegene

Allplex 2019-nCov Detection Assay

Yes

Ab analytica

REALQUALITY RQ-2019-nCoV

N/A

Genematrix 

Neoplex COVID-19 Detection Kit

Yes

Genefinder

COVID-19 Plus RealAmp Kit

N/A

Zybio

SARS-CoV-2 Nucleic Acid Detection Kit

N/A

Thermofisher

TaqPath RT-PCR COVID-19

Yes

YouSeq

SARS-CoV-2 Multiplex qPCR kit

N/A

Co-Diagnostics

Logix Smart Covid-19

Yes

IDT

2019-nCov CDC

N/A

BPG PrimerDesign

Genesig RT-PCR Assay

Yes

Diatheva

COVID-19 PCR Detection Kit

N/A

ABM

GenomeCoV19 Detection Kit

N/A

Certest

Viasure Real Time detection assay

N/A

IDT

WHO/Berlin Assay

N/A

Q: I need to automate a different kit. Can you automate it for me?

A: If you need another reagent kit automated for your lab, our account management, application engineering, and support teams will work with you to automate your kit on our system.

Q: If I already automate my RNA extraction using a Kingfisher or other lab automation solution, can I use Opentrons for just the sample plating/ qPCR steps?

A: The Opentrons platform can be used for all, or any, steps in a COVID-19 qPCR testing stack. However, the qPCR detection step must be performed off the deck of the robot.

Q: If I process saliva tests without extraction steps, can I use Opentrons for just the sample plating/ qPCR steps?

A: Yes! See: the qPCR answer above.

Q: Do I need to know how to code to use the Opentrons platform?

A: No. Opentrons protocols can be created using plug-and-play protocol design tools. Opentrons also has a team of Applications Engineers to help customers build customized protocols.

Q: Can I see a sample protocol?

A: All of our protocols are open-source and free to access in our Protocol Library and on GitHub.

Q: Are other labs using Opentrons to automate viral extraction for SARS-CoV2 testing?

A: Labs all over the world are using the Opentrons platform to automate viral extraction for SARS-CoV2 testing, including:

Q: How much does setup and support cost?

A: Remote setup and support are included. To view all of our support options, please read this post.

Q: Do you ship worldwide?

A: Opentrons ships worldwide.

PROTOCOLS

Zymo Quick-DNA/RNA Viral Kit

Nucleic Acid Purification with Magnetic Beads