The SARS-CoV-2 tracker uses publicly available sequence data to show how the virus changes and spreads over time. A tracker called CovMT was developed at KAUST and is expected to help researchers and policy makers understand the evolution of viral mutations.
This can affect vaccine development, patient treatment, and enforcement of restrictions.
“When new variants of the SARS-CoV-2 virus emerge, authorities around the world need to know if these or similar variants have invaded their country,” said the computational biologist who designed the CovMT system. Intiherb Alam says. KAUST Computational Biological Science Research Center.
“The World Health Organization has emphasized that all countries should step up their sequencing efforts. With this increase in sequencing, CovMT will bring researchers, the general public and policy makers up to date on their sequencing efforts. We hope to help you explore and evolve country-specific information. Virus mutations and disease severity. “
Published data is downloaded daily from GISAID to CovMT. This is an initiative to collate clinical and epidemiological data associated with gene sequences for SARS-CoV-2 virus in different parts of the world. The CovMT platform processes this data to detect mutations and mutation fingerprints and define clades.
CovMT provides interactive graphics to help you visualize your results in a user-friendly format.
For example, the tracker shows which SARS-CoV-2 clade is on which continent. It also shows the countries that provide SARS-CoV-2 sequencing data and the local and external mutation fingerprints of the viruses present in each country.
The team devised the concept of “mutation fingerprints” to describe virus isolates with the same set of viral mutations. This allows scientists to see where the virus with the mutant fingerprint was first detected and in which country it eventually spread.
Because GISAID contains patient data that correlates viral mutations and mutations with disease severity, trackers of viral isolates with similar mutation fingerprints but lacking patient data You can also predict the severity of the disease.
Trackers show that the B.1.1.7 mutant, which acquired a specific mutation in a peaplomer called N501Y, which led to a rapid increase in infection in the UK in the fall and winter of 2020, also acquired the E484K mutation. I am. This may affect the effectiveness of the vaccine against this variant.
Trackers also show that the 510 virus isolate of the B.1.351 variant has three mutations in the receptor binding region of the peplomer. This area is especially important because mutations can increase the infectivity of the virus. This triple RBD mutant is currently found in South Africa, the United Kingdom and 22 other countries.
“CovMT may be adaptable to other infectious diseases such as MERS-CoV and influenza virus in the future,” said Takashi Gojobori, deputy director of the Computational Biological Sciences Research Center at KAUST, a molecular biologist. Says. He formed the Task Force that developed CovMT.
We are also creating a Saudi-specific tracker for the Saudi Arabia Centers for Disease Control and Prevention. To monitor variants of kingdom concerns, we need to increase country sequencing work. The Saudi Arabia COVID-19 Consortium may be the best option to achieve this. “
Takashi Gojobori, MOphthalmologist and ADirector, Center for Computational Biological Sciences, King Abdullah University of Science and Technology (KAUST)
Alam, me, et al.. (2021) CovMT: An interactive SARS-CoV-2 mutation tracker focused on key variants. Lancet infection.. doi.org/10.1016/S1473-3099 (21) 00078-5..
CovMT may help researchers track the evolution of SARS-CoV-2 mutations
Source link CovMT may help researchers track the evolution of SARS-CoV-2 mutations