SARS-CoV-2 (Coronavirus) Detection Workflow

Thu 5 Mar, 2020

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

In December 2019 the novel SARS-CoV-2 (formerly named 2019-nCoV or commonly named coronavirus) was identified in Wuhan, the capital of China’s province Hubei. Observations show that the virus is capable of spreading from person to person and causes COVID-19 – an acute respiratory disease with incubation periods estimated between 2-14 days. Based on its rapid spreading with more than 87,000 confirmed cases by the beginning of March 2020 the World Health Organization declared the outbreak a public health emergency of international concern.

Electron-microscopical image of SARS-CoV-2


Important facts:

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

Testing induced for:

  • People with acute respiratory symptoms AND stay in risk area
  • Symptomatic people that had contact to people of confirmed COVID-19
  • Negative results despite of strong suspicions for infection require new sampling and PCR analysis

Complete Detection Workflow

Analytik Jena offers a complete workflow from sampling until the final detection of the virus which is only suitable for research purposes. This article gives you detailed information for sampling, extraction and detection.

1. Sample Preparation

According to WHO1:

  • Respiratory material* (nasopharyngeal and oropharyngeal swab in ambulatory patients and sputum (if produced) and/or endotracheal aspirateor bronchoalveolar lavage in patients with more severe respiratory disease)
  • Serum for serological testing, acute sample and convalescent sample (this is additional to respiratory materials and can support the identification of the true agent, once serologic assay is available)

*Modifiable with information on whether upper or lower respiratory material is better for coronavirus detection.

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. 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.

HandlingSample troughputExtraction platformExtraction kit
NameKey features
-Up to 12 samples / 25 mininnuPREP Virus RNA Kit



MiddleInnuPure C16 touchUp to 16 samples / 31 - 84 min
Extraction platform only
innuPREP AniPath DNA/RNA Kit - IPC16
innuPREP Virus DNA/RNA Kit - IPC16 (MDX)*
innuPREP Virus DNA/RNA Kit - IPC16
HighCyBio FeliXUp to 96 samples / 62 - 73 min
Extraction platform + liquid handling
(e.g. preparation of PCR)
innuPREP AniPath DNA/RNA Kit – FX**
innuPREP Virus DNA/RNA Kit - FX
HighKingFisher FlexUp to 96 samples / 60 min
Extraction platform only
innuPREP AniPath DNA/RNA Kit - KFFLX
innuPREP RNA Virus PLUS Kit (MDX) – KFFLX *

* CE IVD kits only available in Germany
** Release planned for 31st March 2020

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 such as:

  • Coronavirus (Strain 2019-nCoV) by Genesig/Primerdesign
  • SARS-CoV-2 detection assay by TIB MOLBIOL
  • RIDA® GENE Novel Coronavirus 2019 RUO Tests by r-biopharm

The PCR set up can be pipetted by a liquid handling platform like CyBio FeliX . Using PCR workstations or cabinets offer maximum safety and minimize contamination risks. Single components such as reverse transcriptase or others are available via Analytik Jena as well. In general all Real-time PCR-based assays can be established on Real-time thermal cycler of the qTOWER3 family provided by Analytik Jena or similar. Implementations of selected assays are in progress and respective information will be provided as soon as available.


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

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