Our Response to COVID-19: Publishing AI-Derived Experimental Data and Reagent Insights for COVID-19 R&D Efforts

Update: As of April 9th, we added more reagents for SARS-CoV2 studies, bringing the total to:

• 113 antibodies
• 231 protein products
• 45 assay kits

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As a science-first organization, we’re committed to leveraging our AI technology and people to fight the COVID-19 pandemic. In particular, we’re conducting a deep analysis using our AI technology to identify novel reagents to study the virus, as well as to surface relevant experimental design insights.

Researchers are working around the clock to identify drugs to treat the infection and vaccines to prevent it. Studying the virus without the proper reagents and experimental data is extremely challenging. As a global leader in AI-assisted experimental design, our team has prioritized the following initiatives to enable and accelerate this critical research:

1. Collecting new reagents and publications: We’re curating, processing, and documenting all new publication data and reagents specifically associated with SARS-CoV-2/COVID-19
2. Repurposing existing reagents: We’re performing an in silico analysis of existing antibody, RNAi, and protein reagents to find those that can be repurposed
3. Mining data for insights: We’re using targeted data mining strategies to identify pertinent publications and extract relevant experimental data from them

To ensure we get this data in the hands of researchers as soon as possible, we’ve created a temporary data-sharing version, as it will take a few weeks to incorporate this data into our platform. We are making these data available to the entire scientific community, immediately, free of charge through this link:

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 * Disclaimer: the intent of this article is not in any way to endorse the commercial products listed here, but to create a centralized resource page for the ease of tracking research tools that will advance the R&D efforts against COVID-19. BenchSci does not receive any commissions or fees from vendors whose products are featured here or on our platform.

COVID-19

The sudden outbreak of a viral pneumonia, known as the coronavirus disease 2019 (COVID-19), has rapidly increased in epidemic scale since it first appeared in Wuhan, China, in December 2019. On March 11th, 2020, the World Health Organization (WHO) declared the COVID-19 outbreak as a pandemic, meaning that the virus has the potential to spread to all countries on the globe. To prevent the spread of COVID-19 and to treat those who are affected, several pharmaceutical companies and academic institutions have increased their R&D efforts to develop diagnostic tests (Roche, Partners Healthcare), vaccines (Moderna, GSK, Sanofi) and drug treatments (Janssen, Regeneron).

Collective research efforts in 2020 identified a novel coronavirus, named as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), as the cause of COVID-19, and the virology of SARS-CoV-2 has since been elucidated. While this is a critical step towards developing vaccines and drug treatments for COVID-19, there is also a need for optimal reagents that can be used in the drug and vaccine development process. To assist with the ongoing R&D efforts, we’ll be tracking the available reagents for SARS-CoV-2, as well as the associated publication data, by protein targets in this article.

The virology of SARS-CoV-2

SARS-CoV-2 is an enveloped, positive sense, single stranded RNA virus, meaning that the virus can be directly translated into proteins in the host cell, and is susceptible to lysis by detergents such as soap. SARS-CoV-2 belongs to the betacoronavirus genera, and one third of its genome encodes four main structural proteins: spike glycoprotein (S), envelope (E), nucleocapsid (N), and membrane (M) proteins, with the rest of the genome being translated into non-structural proteins that form the replicase transcriptase complex (RTC) for viral replications. To date, commercially available reagents are exclusively for the structural proteins of SARS-CoV-2, which we’ll describe in more detail in each section below.

SARS-CoV-2 Detection Assays
Assay Type	Number of Products	Number of Vendors
ELISA	8	3
Lateral Flow Assay	9	5
qPCR	17	8

View the full list of SARS-CoV-2 detection kits

Spike glycoprotein (S)

The spike glycoproteins are located on the surface of the virus, and have been found to be a critical component for viral entry into the host cell by binding to angiotensin-converting enzyme 2 (ACE2) receptors. The viral entry occurs through membrane fusion, as well as clathrin-dependent and -independent endocytosis. Once inside the cell, the S protein utilizes a N-terminal signal sequence to gain access to the endoplasmic reticulum (ER).

View the full list of reagents for the S protein

 

Nucleocapsid protein (N)

Nucleocapsid is the viral unit without the envelope and the membrane proteins. While we do not yet fully understand the function of nucleocapsid for SARS-CoV-2, based on our understanding of SARS-CoV-1, it likely tethers the viral genome to RTC, and subsequently packages the encapsulated genome into viral particles.

View the full list of reagents for the N protein

 

Envelope protein (E)

The viral envelope protein fuses with the host cell membrane to facilitate SARS-CoV-2 entry into the host cell. Outside of the cell, the envelope protein also protects the virus from the host’s immune system, and thus it plays a crucial role in the pathogenesis of SARS-CoV-2.

View the full list of reagents for the E protein

 

In addition to tracking the latest reagents available for SARS-CoV-2, over the next two weeks, we will be performing additional analyses for insights on how these reagents can be used in the research efforts for COVID-19 diagnoses, vaccines, and treatments.

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