COVID-19 and Coronavirus Plasmids & Resources

The global research community is moving quickly to expand the knowledge and understanding of COVID-19 and related coronaviruses. To assist with this effort Addgene will maintain this plasmid collection page, which highlights plasmids available that may be useful for COVID-19 related research. Additionally, we have linked to collections of open-access articles, protocols, and other resource collections related to COVID-19 that may be of use to scientists.

Background

The Coronavirus Disease-2019 (COVID-19) pandemic is caused by a novel virus strain from the Coronaviridae family called SARS-CoV-2. Scientists have been working at lightning speed to elucidate as much as they can about this novel virus. It is now known that SARS-CoV-2 entry, like that of SARS-CoV and MERS CoV, depends on binding of the viral spike (S) protein to cellular receptors. The cellular receptor for SARS-CoV-2 and SARS-CoV is hACE2, an angiotensin receptor. Another key step is the priming of the S protein by host cell proteases. The S protein of SARS-CoV-2 is primed by the serine protease TMPRSS2.

Image credit: Maya Kostman for the Innovative Genomics Institute

Addgene COVID-19 Resources

The following types of resources can be found on this page:

• SARS-CoV-2 Antibodies: Recombinant monoclonal antibodies that target SARS-CoV-2 nucleocapsid protein.
• SARS-CoV-2 Plasmids: Plasmids that are available or coming soon containing SARS-CoV-2 sequences.
• SARS-CoV Plasmids: Plasmids that are available containing SARS-CoV (SARS classic) sequences.
• Mammalian Targets: Plasmids containing mammalian sequences linked to SARS-CoV-2 infection.
• General Tools: Plasmids expressing Cas12a/Cas13a, Reverse Transcriptases, etc. that may be useful for detection assays and more.
• Pooled Libraries: Pooled libraries of spike protein mutations.
• Research Articles: A list of free access articles on COVID-19 research.
• Protocols: Protocols that may be useful for COVID-19 research.

Antibodies

• Anti-SARS-CoV-2 Nucleocapsid Protein [mBG17] - Clone mBG17, recombinant mouse monoclonal antibody targeting the SARS-CoV-2 nucleocapsid protein (Brian Geiss).
• Anti-SARS-CoV-2 Nucleocapsid Protein [mBG86] - Clone mBG86, recombinant mouse monoclonal antibody targeting the SARS-CoV-2 nucleocapsid protein (Brian Geiss).

Plasmids

SARS-CoV-2 Plasmids

• Many plasmids containing SARS-CoV-2 sequences are now available and more are currently undergoing quality control analysis in our lab and will be made available as soon as possible. For a full list of searchable plasmids, see the table below.
  • SARS-CoV-2 Viral Pseudotyping Collection - This page includes a table of all spike expression plasmids in our collection that are suitable for generating SARS-CoV-2 spike pseudotyped virus. It also lists several luciferase and fluorescent reporter plasmids that have been used for measuring viral entry and activity in neutralization assays and links to popular envelope and packaging plasmids.
  • SARS-CoV-2 Lentiviral preps now available for several SARS-CoV-2 constructs from the Krogan, Pao, Best, and Sheltzer Labs. These preps are distributed as purified viral particles in solution that are suitable for in vitro use. Volume and minimum titers are listed on each item's material page. Actual titers are reported with each shipment.
    
  • Ginkgo Bioworks Plasmid Collection - Addgene has partnered with Ginkgo Bioworks to distribute SARS-CoV-2 plasmids. To read more about this partnership and the plasmids that are available, please see the Ginkgo Bioworks Blog post: Synthesizing DNA to fight coronavirus . The collection contains:
    
    • Plasmids for E. coli and Yeast expression
    • Spike protein constructs for making VSV pseudo virus
    • Mammalian constructs
    • Due to the size and complexity of the collection, all available Ginkgo SARS-CoV-2 plasmids are curated on a separate Ginkgo Bioworks Plasmid Collection page.
  
  
  • SARS-CoV-2 Pooled Libraries - Yeast surface display libraries of Spike (S) Ectodomain and RBD mutants that can be used to identify antibody escape mutants and for comprehensive mapping.

  Some of the following plasmids are available to industry, in addition to academics and nonprofits, and this is denoted in the Industry column below. For more information on ordering from a for-profit entity, please see our Plasmid Distribution to Industry page. The list of plasmids available to industry is continually growing.

  Other Coronavirus Plasmids: SARS-CoV, MERS, BAT-CoV Plasmids

  Due to export control regulations, MERS and SARS-CoV materials are available only in the US at this time.

  Plasmids Encoding Mammalian Genes or Inserts

  Several mammalian genes have been identified as having a key role in coronavirus infection, such as ACE2 and TMPRSS2, which are involved in the entry of SARS-CoV and SARS-CoV-2. Find plasmids related to these genes below.

  For more information on these genes, see the links and references below:

  • ACE2 - (Human Angiotensin Converting Enzyme 2) is the host cell receptor mediating the entry of SARS-CoV and SARS-CoV-2 viruses. (1)
  • TMPRSS2 - a serine protease that primes the SARS-CoV-2 S protein and is involved in virus entry into cells. (2)
  • FURIN - an enzyme that cleaves precursor proteins to a biologically active state. The SARS-CoV-2 S protein contains a potential cleavage site for furin proteases.(3)
  • BSG - (CD147), transmembrane glycoprotein of the immunoglobulin superfamily, binds to the SARS-CoV-2 S protein and is involved in virus entry into cells. (4)
  • Cathepsin L - a cysteine endosomal protease that triggers proteolysis of SARS-CoV Spike protein, activating its membrane fusion function.(5)
  • TACE - (ADAM17) a metalloprotease that cleaves hACE2, potentially increasing viral infectivity.(6)
  • PCP4 - (Purkinje cell protein 4) is involved in beating of airway cilia.(7)
  • Cytokines - SARS-CoV-2 infection induces a cytokine storm response in the body. For a full list of cytokines and related plasmids see our Immunology Resource Guide.

  General Plasmid Tools

  • SHERLOCK and DETECTR - Simple, portable, and inexpensive platforms to reliably detect nucleic acids at the atomolar level. For more information read Addgene's Blog: Finding nucleic acids with SHERLOCK and DETECTR.
    • Feng Zhang's lab at the Broad Institute has utilized the natural RNAse activity of the Cas13 protein to develop and optimize the method termed Specific High Sensitivity Enzymatic Reporter UnLOCKING (SHERLOCK and SHERLOCKv2).
      • The Broad Institute has published information and protocols for utilizing SHERLOCK to detect coronavirus - Enabling coronavirus detection using CRISPR-Cas13: Open-access SHERLOCK research protocols and design resources
      • Find Zhang Lab Cas13a plasmids
      • Additional protocol for using Cas13a (pC013) for detection of SARS-CoV-2: A Scalable, Easy-to-Deploy, Protocol for Cas13-Based Detection of SARS-CoV-2 Genetic Material. Rauch J, et al. bioRxiv 2020.04.20.052159.
    • Jennifer Doudna's lab has utilized Cas12a’s non-specific ssDNA degradation to develop the method termed DNA Endonuclease Targeted CRISPR Trans Reporter (DETECTR).
      • Mammoth Biosciences has published information and protocols for utilizing DETECTR to detect coronavirus - A protocol for rapid detection of the 2019 novel coronavirus SARS-CoV-2 using CRISPR diagnostics: SARS-CoV-2 DETECTR
      • Find Doudna Lab Cas12a plasmids
  • Addgene's full CRISPR guide and summary of CRISPR pooled libraries.
  • FlipGFP-based activity reporter of SARS-CoV-2 main protease Mpro. (Unpublished)
    • A FlipGFP-based activity reporter of SARS-CoV-2 protease Mpro now available from Xiaokun Shu's lab.
  • A rapid, highly sensitive and open-access SARS-CoV-2 detection assay for laboratory and home testing. Kellner, et al. bioRxiv 2020.06.23.166397
    • reverse transcriptase, protease, and Bst polymerase constructs now available from Andrea Pauli's lab.
  • Neutralizing nanobodies bind SARS-CoV-2 spike RBD and block interaction with ACE2. Huo, et al. Nat Struct Mol Biol. 2020 Jul 13.
    • SARS-CoV-2 Nanobodies now available from Ray Owens' lab.
  • Development of CRISPR as an Antiviral Strategy to Combat SARS-CoV-2 and Influenza. Abbott, et al. Cell. 2020 May 14;181(4):865-876.e12.
    • CRISPR tools and reporters now available from Stanley Qi's lab.
  • COVID-19 Diagnostic Toolkit Enzymes. (unpublished)
    • Taq polymerase and MMLV reverse transcriptase expression plasmids from the Drew Endy and Philippa Marrack Labs.
  • Point-of-care testing for COVID-19 using SHERLOCK diagnostics. Joung J, et al. medRxiv 2020.05.04.20091231
    • AapCas12b plasmid from the Abudayyeh-Gootenberg lab.
  • A one-enzyme RT-qPCR assay for SARS-CoV-2, and procedures for reagent production. Bhadra S, et al. bioRxiv 2020.03.29.013342
    • Reverse Transcriptase plasmids from Andrew Ellington's lab.
  • High-surety isothermal amplification and detection of SARS-CoV-2, including with crude enzymes. Bhadra S, et al. bioRxiv 2020.04.13.039941
    • BST-LF expression plasmid from Andrew Ellington's lab.

  Find plasmid tools that may be helpful for COVID-19 research in the table below:

  Do you have a suggestion for plasmids that would be useful for your COVID-19 research? Fill out this Suggest a Plasmid form. If the plasmid has been described previously we will reach out to the lab to ask them to deposit the plasmid with us.

  Pooled Libraries

  • SARS-CoV-2 Spike (S) Ectodomain and RBD Libraries - Libraries of Spike (S) Ectodomain and RBD mutants (Timothy Whitehead).
  • SARS-CoV-2 Spike Receptor Binding Domain Deep Mutation Scanning Library - Library of Spike protein RBD mutations for comprehensive mapping (Jesse Bloom).
  • SARS-CoV-2 Spike Receptor Binding Domain Site-Saturation Mutagenesis Libraries - Libraries of variant Spike protein RBD mutations for comprehensive mapping (Jesse Bloom, Tyler Starr).

  External Resources

  Research Articles

  Many publishers have allowed free access to articles related to SARS-CoV-2 research during the current outbreak:

  • Cell Press Coronavirus Resource Hub
  • COVID-19 SARS-CoV-2 preprints from medRxiv and bioRxiv
  • Elsevier's Novel Coronavirus Information Center
  • The Lancet COVID-19 Resource Centre
  • The New England Journal of Medicine Coronavirus webpage
  • PLOS Journals COVID-19 Collection
  • Science Journals Coronavirus Collection
  • Springer Nature SARS-CoV-2 and COVID-19 Articles
  • Wiley Online Library - Covid-19: Novel Coronavirus Content Free to Access

  Collections of COVID-19 related articles spanning multiple publishers can be found here:

  • ASM COVID-19 Research Registry
  • COVID-19 Open Research Dataset (CORD-19)
  • LitCovid (NCBI/PubMed)
  • Meta COVID-19 Feed

  Protocols

  Protocols relevant to SARS-CoV-2 Research

  • Coronavirus Method Development Community at Protocols.io
  • Addgene's Protocol for RNA Extraction Without A Kit

  More Coronavirus Resources

  • For more research related resources, such as reagents, data, news, and more, please see Ginkgo's Synthetic Biology (and beyond) Community response to COVID-19

  References

  1. ACE2 - Andersen, KG, et al, 2020, Nature Medicine The proximal origin of SARS-CoV-2.
  2. TMPRSS2 - Hoffmann M, et al, 2020, Cell SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor.
  3. FURIN - Andersen, KG, et al, 2020, Nature Medicine The proximal origin of SARS-CoV-2.
  4. BSG - Wang, K et al, 2020, BioRxiv SARS-CoV-2 invades host cells via a novel route: CD147-spike protein .
  5. Cathepsin L - Bosch BJ, et al, 2008, J Virol. Cathepsin L Functionally Cleaves the Severe Acute Respiratory Syndrome Coronavirus Class I Fusion Protein Upstream of Rather than Adjacent to the Fusion Peptide.
  6. TACE - Heurich A, et al , 2014, J Virol. TMPRSS2 and ADAM17 cleave ACE2 differentially and only proteolysis by TMPRSS2 augments entry driven by the severe acute respiratory syndrome coronavirus spike protein..
  7. PCP4 - Kogiso H, et al, 2020, Int J Mol Sci Airway Ciliary Beating Affected by the Pcp4 Dose-Dependent [Ca 2+] i Increase in Down Syndrome Mice, Ts1Rhr.