key: cord-0707051-ryhrhpx7
authors: Alam, Intikhab; Radovanovic, Aleksandar; Incitti, Roberto; Kamau, Allan A; Alarawi, Mohammed; Azhar, Esam I; Gojobori, Takashi
title: CovMT: an interactive SARS-CoV-2 mutation tracker, with a focus on critical variants
date: 2021-02-08
journal: Lancet Infect Dis
DOI: 10.1016/s1473-3099(21)00078-5
sha: 1dd1c673033581c6a7c33e0a58ca8222f83a2400
doc_id: 707051
cord_uid: ryhrhpx7

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An important feature of CovMT system is about Mutation Fingerprints (MFs). We defined Mutation Fingerprints (MFs) as the set of mutations present in the general population with a frequency above 0.005%. This information provides a more specific representation of all synonymous and nonsynonymous mutations found in an isolate of SARS-CoV-2 to facilitate more specific geographic tracking of variants and project COVID-19 severity information. For completeness we include GISAID lineage as well as lineage information.

Location, date of sampling, and patient disease severity information, where available, are summarized for an MF related to a set of isolates, see supplementary information. The geographic origin status of an MF is considered foreign for a country if the earliest found location linked to its MF is not in that country. We categorize patient disease severity status, labeled evidence.host, as either asymptomatic, symptomatic mild, symptomatic severe, deadly, or unknown. When there are isolates represented by the same MF but without evidence.host, we impute the disease severity status as evidence.MF. In this way, we are able to project evidence.host based patient disease severity status from available ~7% to ~20% of isolates worldwide (see global COVID-19 severity information as an interactive circular graph or an interactive MF table with timeline graphs). Taking the example of South African triple mutant, B.1.351, around 345 unique MFs are available. Here, patient disease severity information is available for at least 22 MFs, shown as symptomatic mild, one of such MFs appeared in the UK.

Here we explain Mutation Fingerprint (MF) taking the example of the South African triple RBD mutation variant (K417N, E484K and N501Y) now detected in the UK, as highlighted in the Figure S1 A, with an associated timeline of isolates shown in Figure S1 B, and spread to other countries (lineage B.1.351 highlighted) in Figure S1 C, below. The MFs are more specific as they are able to capture additional mutations not yet defined in known clades or lineages. This allows to group all SARS-CoV-2 isolates with exactly the same set of mutations in to one MF. Such an MF can then be exploited to track associated variants. Furthermore, an MF allows to assign disease severity information if one of the isolates in a MF group are available with original disease severity information, we call evidence.host.

A.

C. Figure Mutations associated with an MF are recorded in a specific format, we call MF Signature, where all detected mutations for each gene are kept together, separated by a delimiter, "|". For each gene, an MF signature shows the name of the gene or INTGEN for intergenic mutations, followed by the count of mutations and coordinates at the protein level as well as genome level, as shown below for the MF related to above shown MF ID: All MFs are available for exploration at CovMT webpage: https://www.cbrc.kaust.edu.sa/covmt/index.php?p=world-variants All MFs are available for exploration at CovMT mutant variant table (1). As an example, to search for the triple RBD mutant, one can use the text mentioned above, highlighted in yellow, and search the MF signature field in MF table (1).

We added section on mutation history for RBD mutations e.g. for N501Y see Figure 1C , or link 2 below, to show connections among first seen date, last seen date, country of isolate sampling and lineage information. Link 3 below shows a dashboard for RBD mutations worldwide.

Tracking of the UK variant shows, see Figure S2 , that it can now be detected in over 50 countries. Lastly, the following table shows important SARS-CoV-2 Isolates with lineage B.1.1.7, which appear to have acquired additional RBD mutation E484K (light color) and in one case a mutation K417N (dark color).

Table S1. List of isolates with lineage B.1.1.7 showing mutation E484K or K417N 1