New Paper (Other): Learning the language of viral evolution and escape

[marouenbg]

Title: Learning the language of viral evolution and escape

General Information

Please paste a link to the paper or a citation here:

Link: https://science.sciencemag.org/content/371/6526/284

What is the paper's Manubot-style citation?

Citation: @doi:10.1126/science.abd7331

Is this paper primarily relevant to Background or Pathogenesis?

• [ ] Background
• [ ] Pathogenesis
• [x] Methods

Please list some keywords (3-10) that help identify the relevance of this paper to COVID-19

• keyword 1 surveillance
• keyword 2 machine learning
• keyword 3 escape mutations
• keyword 4 Natural Language Processing (NLP)

Please note the publication / review status

• [ ] Pre-print
• [x] New Peer-Reviewed Paper
• [ ] Peer-Reviewed Paper Pre-2020

Which areas of expertise are particularly relevant to the paper?

• [ ] virology
• [ ] epidemiology
• [ ] biostatistics
• [ ] immunology
• [ ] pharmacology
• [x] other: machine learning

[marouenbg]

Summary

Suggested questions to answer about each paper:

• What did they analyze? They predicted the occurrence of escape mutations in the sequence of SARS-CoV-2 and other viruses.

• What methods did they use? Natural Language Processing on the sequences of influenza A hemagglutinin, HIV-1 envelope glycoprotein, and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike glycoprotein.

• Does this paper study COVID-19, SARS-CoV-2, or a related disease and/or virus? This is a prediction of escape mutations in influenza A hemagglutinin, HIV-1 envelope glycoprotein, and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike glycoprotein.

• What is the main finding (or a few main takeaways)? The main novelty of this paper is that it provides a tool to predict novel escape mutations that can promote resistant variants. This tool can be used a prediction tool along with genomic sequence analysis #778, to detect the emergence of escape mutations.

• What does this paper tell us about the background and/or diagnostics/therapeutics for COVID-19 / SARS-CoV-2? This tool confirmed known escape mutations in SARS-CoV-2 spike protein in RBD and N-terminal domain and suggests that they can occur beyond the RBD domain. However, S2 subunit is depleted of any escape potential.

• Do you have any concerns about methodology or the interpretation of these results beyond this analysis? None

Any comments or notes?

Perhaps, the most interesting aspect of this work is the modeling of escape mutations. Escape mutations are defined as mutations that preserve the virus pathogenicity but change the sequence presented to the host to evade detection. This can be modeled in NLP as a problem of finding grammatically correct sentences that carry a different meaning.