SARS-CoV-2 (Coronavirus) Detection Workflow for research use only

Fri 11 Sep, 2020

Overview of the SARS-CoV-2 (Coronavirus) Detection Process

In December 2019 the novel SARS-CoV-2 (formerly named 2019-nCoV) was identified in Wuhan, the capital of China’s province Hubei. Based on its rapid spreading with more than 105,000,000 confirmed cases by beginning of February 2021 the World Health Organization declared the outbreak a public health emergency of international concern.

Important facts:

SARS-CoV-2: (+) ss-RNA virus
Related to SARS-CoV and MERS-CoV
Detection based on basis of PCR

Analytik Jena offers a broad product portfolio in the field of nucleic acid extraction and PCR or real-time PCR with both extraction kits and the necessary equipment. For research purposes for the detection of SARS-CoV-2 the following workflow is suggested.

1. Sample Collection

In principle, respiratory material such as nasopharyngeal and oropharyngeal swabs are suitable for the detection of respiratory pathogens. For more detailed information, recommendations of the WHO or other institutions should be observed.
Serum can also be used for serological tests, acute and convalescence samples.

2. Nucleic Acid Extraction

Analytik Jena offers a choice of extraction platforms and related extraction kits for extraction of viral RNA from swabs, cell free body fluids (e.g. serum, plasma, cerebrospinal fluid) and more. The product line innuPREP AniPath allows the simultanous extraction of both bacterial and viral DNA and/or RNA from respective starting materials. A detailed overview is shown in the table below.

Handling	Sample throughput	Extraction platform		Extraction kit
Handling	Sample throughput	Name	Key features	Extraction kit
Manual	Low	-	Up to 12 samples / 25 min	innuPREP Virus TS RNA Kit innuPREP Virus DNA/RNA Kit
Automated	Middle	InnuPure C16 touch	Up to 16 samples / 31 - 84 min Extraction platform only	innuPREP AniPath DNA/RNA Kit - IPC16, non-filled innuPREP AniPath DNA/RNA Kit - IPC16 innuPREP Virus DNA/RNA Kit - IPC16, non-filled innuPREP Virus DNA/RNA Kit - IPC16
	High	CyBio FeliX	Up to 96 samples / 62 - 73 min Extraction platform + liquid handling (e.g. preparation of PCR)	innuPREP AniPath DNA/RNA Kit – FX* innuPREP Virus TS RNA Kit 2.0 - FX innuPREP Virus DNA/RNA Kit - FX
	High	KingFisher Flex	Up to 96 samples / 60 min Extraction platform only	innuPREP AniPath DNA/RNA Kit - KFFLX innuPREP RNA Virus PLUS Kit – KFFLX

* Release planned for mid 2021

3. Amplification and Detection

Molecular assays to detect SARS-CoV-2 have been developed and are accessible through the homepage of the WHO. Furthermore, several commercial kits based on real-time PCR
are available. The table below shows all available detection kits which are tested on qTOWER³ and/or qTOWER³ 84.

Company name	Assay name	CE-IVD/ FDA EUA*	Dye/ configuration/ target
Assays detecting SARS-CoV-2
Altona Diagnostic	RealStar® SARS-CoV-2 RT-PCR Kit 1.0 RUO	-	FAM: Color Module 1 (E gene) VIC: Color module 2 (IC) Cy5: Color module 5 (S gene)
BGI Genomics	Real-Time Fluorescent RT-PCR Kit for Detecting SARS-2019-nCoV	-	FAM: Color Module 1 (N-CoV) VIC/HEX: Color Module 2 (IC)
EuroImmun	EuroRealTime SARS-CoV-2	CE IVD (qTOWER³)	FAM: Color Module 1 (ORF1ab and N gene) HEX: Color Module 2 (IC)
Fosun Pharma USA	Fosun COVID-19 RT-PCR Detection Kit	-	FAM: Color Module 1 (ORF1ab) HEX: Color Module 2 (N gene) ROX: Color Module 4 (E gene) Cy5: Color Module 5 (IC)
IDEXX	Water SARS-CoV-2 RT-PCR Test	-	FAM: Color Module 1 (N1 and N2) HEX: Color Module 2 (IC)
Ingentix	ViroReal® Kit SARS-CoV-2 & SARS	CE IVD (qTOWER³)	FAM: Color Module 1 (RdRp) Cy5: Color Module 5 (IC)
Inno-Train Diagnostik GmbH	Covid-19 FluoGene Q	CE IVD (qTOWER³)	FAM: Color Module 1 (N1 gene) VIC/JOE: Color Module 2 (M gene) ROX: Color Module 4 (IC)
Mikrogen	ampliCube Coronavirus SARS-CoV-2	-	FAM: Color Module 1 (E gene) HEX: Color Module 2 (ORF1a) Cy5: Color Module 5 (IC)
Mikrogen	ampliCube Coronavirus Panel	-	FAM: Color Module 1 (MERS-CoV) HEX: Color Module 2 (SARS-CoV,SARS-CoV-2, Bat SARS-like CoV) ROX: Color Module 4 (HCoV) Cy5: Color Module 5 (IC)
Perkin Elmer	SARS-CoV-2 RT-qPCR Reagent kit	CE IVD (qTOWER³)	FAM: Color Module 1 (N gene) HEX: Color Module 2 (ORF1ab) Cy5: Color Module 5 (IC)
Perkin Elmer	New Coronavirus Nucleic Acid Detection Kit	FDA EUA (qTOWER³) FDA EUA (qTOWER³ 84)	FAM: Color Module 1 (N gene) ROX: Color Module 4 (ORF1ab) HEX: Color module 2 (IC)
PrimerDesign	Coronavirus (COVID-19)		FAM: Color Module 1 (RdRp) VIC: Color module 2 (IC)
Procomcure Biotech	PhoenixDx® SARS-CoV-2 IVD	CE IVD (qTOWER³)	FAM: Color Module 1 (E gene) FAM: Color Module 1 (RdRp)
R-Biopharm	RIDA®GENE SARS-CoV-2 RUO	-	FAM: Color Module 1 (E gene) VIC: Color module 2 (IC)
RTA Laboratories	Diagnovital SARS-CoV-2 Multiplex	FDA EUA (qTOWER³) pending	FAM: Color Module 1 (N gene, ORF1ab) HEX: Color Module 2 (IC)
Seegene	Allplex™ 2019-nCoV Assay	-	FAM: Color Module 1 (E gene) HEX: Color Module 2 (IC) ROX: Color Module 4 (RdRP gene) Cy5: Color Module 5 (N gene)
Shimadzu	2019 Novel Coronavirus Detection Kit	-	FAM: Color Module 1 (N1 gene) ROX: Color Module 4 (N2 gene) Cy5: Color Module 5 (IC)
Siemens healthineers / Fast-Track Diagnostic	FTD SARS-CoV-2 Assay (RUO)	-	FAM: Color Module 1 (ORF1ab and N gene) Cy5: Color Module 5 (IC)
SolGent	DiaPlexQ Novel Coronavirus (2019-nCOV) Detection Kit	-	FAM: Color Module 1 (N gene) VIC: Color Module 2 (ORF1a) Texas Red: Color Module 4 (IC)
TIB MOLBIOL	TIB MOLBIOL LightMix® Modular SARS-CoV-2 (COVID19) RdRP	-	FAM: Color Module 1 (RdRP gene) Cy5: Color module 5 (IC)
TIB MOLBIOL	TIB MOLBIOL LightMix® Modular SARS-CoV.2 (COVID19) E gene	-	FAM: Color Module 1 (E gene) Cy5: Color module 5 (IC)
Wells Bio	careGENE™ COVID-19 RT-PCR kit	-	FAM: Color Module 1 (N gene) ROX: Color Module 4 (IC) Cy5: Color Module 5 (RdRp)
Wells Bio	careGENE™ N-Cov RT-PCR Kit	-	FAM: Color Module 1 (E gene) ROX: Color Module 4 (IC)
Assays detecting SARS-CoV-2 mutations
TIB MOLBIOL	TIB MOLBIOl VirSNiP SARS-CoV-2 Spike 501Y	-	FAM: Color Module 1 (SARS Spike 501Y)
Inno-Train Diagnostik GmbH	Covid-19 FluoGene Q N501Y (RUO)	-	FAM: Color Module 1 (N1 gene) VIC/JOE: Color Module 2 (M gene) ROX: Color Module 4 (IC) Cy5: Color Module 5 (S N501Y)
Assays detecting SARS-CoV-2 and Influenza viruses
EuroImmun	EURORealTime SARS-CoV-2/Influenza A/B	CE IVD (qTOWER³)	FAM: Color Module 1 (ORF1ab and N gene) ROX: Color Module 4 (Influenza A) Cy5: Color Module 5 (Influenza B) HEX: Color Module 2 (IC)
Ingentix	ViroReal® Kit SARS Coronavirus & Influenza A/B	CE IVD (qTOWER³)	FAM: Color Module 1 (SARS) VIC: Color module 2 (Influenza A/B) Cy5: Color Module 5 (IC)
Mikrogen	ampliCube Respiratoty Flu & SARS-CoV-2	-	FAM: Color Module 1 (Influenza-A) HEX: Color Module 2 (Influenza-B) ROX: Color Module 4 (ORF1a) Cy5: Color Module 5 (IC) Cy5.5: Color Module 6 (E gene)
R-Biopharm	RIDA®GENE Flu & SARS-CoV-2 RUO	-	FAM: Color Module 1 (Influenza A/B) VIC: Color Module 2 (ICR) ROX: Color Module 4 (E gene) Cy5: Color Module 5 (RdRp gene)

*Please note that products of Analytik Jena GmbH listed here are not explicitly marked as CE IVD and are exclusively intended for research purposes. The validation of the kits was performed by the assay manufacturers themselves on qTOWER devices and was subsequently CE IVD or FDA EUA certified.

The PCR set up can be pipetted by a liquid handling platform like CyBio FeliX . Using PCR workstations or cabinets increases maximum safety and minimizes contamination risks. Single
components such as qPCR Master Mixes and Reverse Transcription MasterMix are available via Analytik Jena as well. In general all Real-time PCR-based assays can be established on the qTOWER³ real-time thermal cycler family provided by Analytik Jena or similar. Information on further commercial qPCR assays for SARS-CoV-2 detection with confirmed compatibility on qTOWER3 devices is available on request.

Automated Pipette Robot - CyBio FeliX

Flexible and fully automatic multi-channel pipetting robot

Learn more: CyBio FeliX

Real-time Thermal Cyclers

High performance DNA amplification and precise quantification

Learn more: qTOWER³

InnuPure C16 touch

Learn more: InnuPure C16 touch

Downloads

Flyer Workflow detection of SARS-CoV-2 (English)

Open PDF

Implementation of SARS-CoV-2 (Coronavirus) detection assays from TIB MOLBIOL on qTOWER³ for research use

Open PDF

Biofoundries and SARS-CoV-2 diagnostics

Watch now

Feedback

Comments (23)

Abhimanyu Pandey – at 07.05.2020

thank you

Reply
- Analytik Jena AG – at 08.05.2020
  
  You are welcome!
  
  Reply
Mustakim,MD,Clin.Path – at 17.05.2020

Thank you,I am User Analytic Jenna PCR labkesda Soppeng From South Celebes Indonesia.

Reply
- Brian Kohn – at 29.06.2021
  
  Dear AnalytikJena Team
  
  we are using a SARS-CoV-2 kit from DNA-Technologies (https://dna-technology.com/) on the qTower which is brand new.
  However we are not getting any Ct values for the samples.
  
  Kindly advise.
  Best wishes
  
  Reply
- Analytik Jena – at 30.06.2021
  
  Dear Mr. Kohn, we have forwarded your request to our Life Science support team, which will contant you as soon as possible.
  
  Reply
Florian Werner – at 18.05.2020

We have also validated our Kylt SARS-CoV-2 Kits on the qTower 384. Very satisfied with the performance and results. (https://www.kylt.eu/de/products/show/more/454)

Reply
Bhuneshwar Behra – at 20.05.2020

Thank you

Reply
Sunil Prasad Lekhak – at 14.06.2020

Dear Sir/Madam

We are trading company in Nepal, specialized in Molecular Diagnostic lab.
Currently we are looking for Fully automated Nucleic acid extraction system and liquid handling system.
I am very much interested in your CyBio Felix system.

Could you please send me technical specifications and Distributor Price for Nepal.

Looking forward to your reply.

Sunil Prasad Lekhak

Life Sciences Solutions Pvt. Ltd.

Reply
- Analytik Jena AG – at 25.06.2020
  
  Thank you for your inquiry. We have forwarded your request to our sales team which will contact you as soon as possible.
  
  Reply
Jazz – at 02.07.2020

I Am looking into doing research for covid kit for salmon , poultry etc sample, can I ask if your kit suitable for animal sample ? What is the price to run a covid test? If the test including extraction and regained as well? Can you quote both ? What is the lead time and shelf life of this ?

Reply
- Analytik Jena AG – at 02.07.2020
  
  Thank you for your inquiry. Our sales team will contact you shortly to answer your questions.
  
  Reply
Mario Schwarzkopf – at 24.07.2020

Hallo, ich Interessiere mich auch für ein Kit mit dem schnellstmöglich das Virus nachgewiese, bzw. ausgeschlossen werden kann. Ich bräuchte alle Gerätschaften, die Notwendig wären um dies für eine Mobile Prüfung zu nutzen. Würde mich über nähere Informationen und Preise freuen.

Beste Grüße
:Schwarzkopf

Reply
- Analytik Jena AG – at 24.07.2020
  
  Hallo Herr Schwarzkopf, wir haben Ihre Anfrage an unser Sales-Team weitergeleitet, welches die genauen Einsatzzwecke und Gegenheiten mit Ihnen abklären wird.
  
  Reply
Sara Sánchez – at 17.08.2020

Cordial saludo,

Quisiera saber si hay un proceso de validación con el kit comercial Molecutech Real Time COVID-19 el cual nos puedan compartir. O si hay opción de hacer una capacitación virtual para la interpretación de los resultados de las corridas realizadas con el qTower 3 y el Kit de Molecutech.

Reply
- Analytik Jena AG – at 19.08.2020
  
  Dear Mrs. Sánchez, right now the kit isn't validated on qTOWER3 yet. Please contact our application specialists at support-ls@analytik-jena.com. I'm sure that you will find an appropriate solution for your setup together.
  
  Reply
Mudhafar – at 11.09.2020

Are SARS-CoV-2 (Coronavirus) Kits from Analyticgena Working with Applied Biosystem 7500 fast Device?

Reply
- Analytik Jena AG – at 14.09.2020
  
  Analytik Jena offers various nucleic acid extraction kits which can be used for the purification of viral RNA such as the SARS-CoV-2. For the subsequent detection via RT real time PCR on the one hand the PCR assay amplifying SARS-CoV-2-specific targets via distinct fluorescent dyes or probes is required. Such SARS-CoV-2 assays are not part of Analytik Jena's product portfolio. On the other hand a real time cycler is needed (which is offered by AJ). The PCR Assay and real time cyclers have to be compatible. The sample preparation via nucleic acid extraction does not affect the real time cycler so it is no problem to do nucleic acid extraction with kits by Analytik Jena and PCR with any cyler such as the Applied Biosystem 7500 fast Device .
  
  Reply
Michael – at 27.10.2020

What cell free body fluid is the “liquor” part? That is from your web site above:

2. Nucleic Acid Extraction
Analytik Jena offers a choice of extraction platforms and related extraction kits for extraction of viral RNA from swabs, cell free body fluids (e.g. serum, plasma, liquor) and more.

Reply
- Analytik Jena AG – at 28.10.2020
  
  The aforementioned body fluid is cerebrospinal fluid. Thank you for the hint! We have corrected the text passage.
  
  Reply
Mary – at 02.12.2020

Dear Sir/ Madam,

We are using the KH medical etraction and detection kits for COVID-19 Virus. We already have the qTower2.0 at our institute but it seems not to give good amplification/ detection curves in the same. should we upgrade it or what could be the problem?

Reply
- Analytik Jena AG – at 03.12.2020
  
  Dear Mary, thank you for reaching out to us. The qTOWER2 should be able to help with your COVID-19 detection. Maybe a software update is all that is necessary. Our Life Science support staff has been contacted to assist you in solving this problem.
  
  Reply
Hue Anh – at 17.05.2021

Dear Sir/ Madam,
For testing Seegene's Allplex™ 2019-nCoV Assay on qTower3, Is color compensation required? If yes, Can I use AJ's Color compensation kit?

Thanks!

Reply
- Analytik Jena GmbH+Co. KG – at 17.05.2021
  
  For reliable results with AllplexTM 2019-nCoV Assay by Seegene a color compensation with the Standard 2 matrix from qPCRsoft 4.1 or qPCRsoft384 1.2 is required.
  
  Reply

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