CovMT: an interactive SARS-CoV-2 mutation tracker, with a focus on critical variants

The number of confirmed SARS-CoV-2 cases worldwide has now reached around 100 million, with 2·1 million reported deaths¹ and more than 450 000 SARS-CoV-2 genomes already sequenced. It is vital to keep track of mutations in the genome of SARS-CoV-2, especially in the spike protein's receptor binding domain (RBD) region, which could potentially impact disease severity and treatment strategies.2, 3, 4 In the wake of a recent increase in cases with a more infective variant featuring an RBD mutation (N501Y, B.1.1.7) in the UK, countries worldwide are concerned about the spread of this or similar variants. Increasing sequencing efforts and user-friendly mutation tracking systems are needed for timely tracking of SARS-CoV-2 variants.

We developed a COVID-19 virus mutation tracker system (CovMT; appendix) based on SARS-CoV-2 isolate genomes deposited to GISAID to track the worldwide sequencing efforts and the evolution of the mutational landscape of this virus. CovMT, which is updated daily, summarises mutations from more than 450 000 isolates into groups of generic virus clades, lineages, and more specific mutation sets we call mutation fingerprints. These summaries, with metadata of location, date of sampling, and patient disease severity information, when available, at the continent and country levels, are accessible from the main page of the CovMT system (appendix).

CovMT also provides a timeline history of SARS-CoV-2 variants related to mutations in the RBD region of the spike protein. As of the end of January, 2021, the spread of N501Y, B.1.1.7 variants has been detected in SARS-CoV-2 isolate genomes from nearly 60 additional countries using CovMT (appendix). Nonsynonymous mutations in the RBD region have a high potential to be linked to increased binding efficiency, increased infectivity, and the potential to evade antibodies.2, 3, 4 To track all similar variants, we ranked mutations in the RBD region based on their appearance in the number of isolate genomes in CovMT. The CovMT timeline (appendix) shows that N501Y, S477N, N439K, and L452R mutations can now be detected in more than 41 700, 23 300, 9700, and 2000 isolates, respectively. An important RBD mutation, E484K, which probably allows the virus to evade existing antibodies,⁵ was originally recorded in Denmark during March, 2020, and is now on the rise in South Africa⁵ since October, 2020. More than 510 isolates show triple mutations (K417N, E484K, and N501Y, lineage B.1.351) in South Africa, with some isolates now detected in the UK and 22 other countries. We observed that the UK variant (B.1.1.7) has also acquired the E484K mutation (appendix). A more recent variant, P.1, with E484K and N501Y RBD mutations, appeared in four travellers arriving in Japan from Brazil on Jan 2, 2021. The P.1 variant now appears in six other countries. Timelines and lineage history of each of the top ten most common RBD mutations can be explored at CovMT.

With a particular focus on critical mutations in the RBD region of the spike protein, and with an option to seamlessly accrue the clinical metadata, including disease severity, we believe that CovMT will be useful for scientists, the general public, and authorities to explore country-specific information.

This online publication has been corrected. The corrected version first appeared at thelancet.com/infection on March 1, 2021