Tracking COVID-19 Variants

Image created using MesoCraft 3D-modeling software (nanovis.kaust.edu.sa)

Interactive platform produced by KAUST researchers helps track virus mutations and their spread

MINISTRY OF HEALTH

“I fully support using KAUST’s CovMT to monitor SARS-CoV2 mutations of concern at both the national and the international level, as part of a robust public health strategy going forward.”

Abdullah M. Asiri, Deputy Minister of Health Tracking how the SARS-CoV-2 virus mutates is a pressing concern for public health officials around the world. As of early May 2021 – nearly 14 months into the COVID-19 pandemic – more than 1.6 million unique virus isolates had been identified by scientists, and the list only continues to grow. Virologists have been working around the clock to sequence virus genomes as variants evolve and spread. This global effort has generated vast and daunting amounts of data that most researchers and public health officials do not have time to sift through.

Making this data both accessible and easy to understand and visualize is therefore key to successfully navigating the pandemic, and can help public health officials and policymakers keep track of the most worrying mutations – especially those in the receptor binding domain of the spike protein that enables the virus to infiltrate human cells. Computational science can help, and a team led by KAUST Senior Computational Bioinformatician Dr. Intikhab Alam and his colleagues has developed COVID-19 Virus Mutation Tracker (CovMT), a free, interactive platform to show how the virus is changing and spreading over time. CovMT was developed out of an initiative launched by Distinguished Professor of Bioscience Takashi Gojobori, who is also the acting director of KAUST’s Computational Bioscience Research Center.

Dr. Alam has been leading the development of the platform, which gathers daily data on newly sequenced genomes from GISAID, an initiative that collates genetic sequences and the related clinical and epidemiological data about the SARS-CoV-2 virus from various parts of the world. At present, the interactive platform has genome mutation data for more than 1.6 million virus isolates, which it organizes into groups of generic

TAKASHI GOJOBORI Distinguished Professor of Bioscience and Acting Director of the Computational Bioscience Research Center

CovMT CAN BE ADAPTED FOR OTHER INFECTIOUS DISEASES LIKE MERS-COV AND THE INFLUENZA VIRUS IN THE FUTURE.

virus clades, lineages and more specific mutation sets called “mutational fingerprints”. CovMT then provides interactive graphics to help visualize the data in a user-friendly format. Users of the platform can track the evolution of the virus at the global, continental or even country-specific level; for example, the tracker shows which SARSCoV-2 clades are present on which continents. It also indicates which countries are providing sequencing data, and the local and foreign mutations present in each country. helps scientists identify where a virus with a mutational fingerprint was first detected, as well as the countries to which it eventually spread. Since GISAID provides patient data on the disease severity status for some samples, the tracker can also predict the disease severity of virus isolates that have similar mutational fingerprints but are otherwise lacking patient data.

For example, the tracker shows that the B.1.1.7 variant – which acquired a specific mutation in its spike protein called N501Y that led to a rapid rise of infections in the UK in the fall and winter of 2020 – has also acquired the E484K mutation. This mutation is particularly worrying because it helps SARS-CoV-2 slip past the body’s immune defences and could reduce vaccine effectiveness against the B.1.1.7 variant. The researchers are also closely monitoring other concerning mutations, including L452R, which is spreading in the US and India, and N501T, which is prevalent in Oman, the UAE, Egypt and Jordan.

The researchers are now working on a Saudi-specific version of the tracker for the Saudi Center for Disease Prevention and Control to track new mutations in the Kingdom. The country and the region have some catching up to do in terms of virus genome sequencing, although recent efforts have enabled CovMT to trace the emergence of the UK (B.1.1.7) and South African (B.1.351) variants in the UAE.

Increased virus genome sequencing at the national level will be required to keep track of any new variants in the Kingdom. The team also believes that a consortium comprising government and health care stakeholders from across the GCC would help, and KAUST is prepared to take a leadership role in regional collaboration.