New Paper (Other): A dynamic nomenclature proposal for SARS-CoV-2 to assist genomic epidemiology

[adebali]

Title: A dynamic nomenclature proposal for SARS-CoV-2 to assist genomic epidemiology

General Information

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

Link: https://www.biorxiv.org/content/10.1101/2020.04.17.046086v1

What is the paper's Manubot-style citation?

Citation: doi:10.1101/2020.04.17.046086

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

• lineage
• evolution
• nomenclature

Please note the publication / review status

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

Which areas of expertise are particularly relevant to the paper?

• [x] virology
• [x] epidemiology
• [x] biostatistics
• [ ] immunology
• [ ] pharmacology
• [x] other: evolution

[adebali]

Summary

Suggested questions to answer about each paper:

• What did they analyze?

The authors analyzed the SARS-CoV-2 genome sequences through phylogenomics. They assigned hierarchical clusters based on the phylogeny of the genomes.

• What methods did they use? Multiple sequence alignment (MAFFT), phylogenetic tree construction with IQTREE2 with GTR+Γ model along with ultrafast bootstrapping with 1000 replicates.

• Does this paper study COVID-19, SARS-CoV-2, or a related disease and/or virus? SARS-CoV-2

• What is the main finding (or a few main takeaways)? A nomenclature proposal for universal lineage assignments based on phylogenetics.

• What does this paper tell us about the background and/or diagnostics/therapeutics for COVID-19 / SARS-CoV-2?

Genome sequencing is routinely done in clinics to understand (i) the evolution, (ii) genetic diversity and (iii) transmission routes of the virus. This task is computationally challenging as it requires a massive amount of genomics work including multiple sequence alignment and phylogenetic tree generation. Rather than running long pipelines for each virus isolate, lineage assignment can be performed easily through a well-established web server and nomenclature agreed with the consensus. This paper proposes lineage nomenclature along with a web server that can be easily used by non-experts.

• Do you have any concerns about methodology or the interpretation of these results beyond this analysis?

Further classifications (new lineages and sub-lineages) will possibly be needed in the future. How authors will manage the regular updates is not clear. Also, how the pangolin webserver quickly assigns lineages is unclear. There is no detail given regarding this methodology.

Any comments or notes?

Pangolin is a useful tool that should be mentioned in this comprehensive review.