Standard laboratory protocols for SARS-CoV-2 characterisation

Basic cell culture protocols are presented, as well as specific protocols for testing SARS-CoV-2 and influenza-positive, or clinical specimens. The protocols include methods such as plaque assays, virus titration, antibody-based detection methods, virus neutralisation assays, as well as protocols to perform sequencing and PCRs. This handbook also highlights the variability between protocols used in different institutes, and points out different ways of performing the assays at appropriate points. However, it is not possible to show the entirety of this variability within the scope of this handbook. Furthermore, an adaptation of the protocols may be necessary upon establishment.

Updates in this report include:

• Replacement of the general cell culture protocol (2.1). Updated version now also includes cultivation advice
  for VeroE6 TMPRSS cells.
• Replacement of the amplicon sequencing on the MinIon (2.5.1).
• Replacement of the virus neutralisation test for SARS-CoV-2 (2.6.3). The updated version contains minor changes.
• Added a protocol for virus neutralisation test for SARS-CoV-2 with staining (2.6.4).