echemi logo
Product
  • Product
  • Supplier
  • Inquiry
    Home > Biochemistry News > Microbiology News > The Institute of Microbiology, Chinese Academy of Sciences, etc. build an artificial intelligence-based new coronavirus virtual mutation assessment and early warning system

    The Institute of Microbiology, Chinese Academy of Sciences, etc. build an artificial intelligence-based new coronavirus virtual mutation assessment and early warning system

    • Last Update: 2021-11-05
    • Source: Internet
    • Author: User
    Search more information of high quality chemicals, good prices and reliable suppliers, visit www.echemi.com

    With the continued global epidemic control of the new coronavirus, the genome of the new coronavirus continues to mutate during the epidemic
    .

    So far, with the joint efforts of scientific and technical personnel around the world, more than 4 million viral genomes have been sequenced and multiple viral genome databases have been constructed
    .

    These databases (such as GISAID), on the basis of collecting and displaying data, include functions such as virus typing and traceability analysis, and provide important information for the monitoring and tracking of the global epidemic
    .

    However, with the in-depth study of mutation, the functional impact of mutation has gradually become the focus of attention
    .

    At present, a variety of mutant strains with enhanced infectivity, including Alpha, Beta, and Delta, have been found in many countries and regions around the world, especially the amino acid mutations accumulated at key sites, which have greatly changed the immunological characteristics of the virus.
    , Which increases the risk of virus immune escape, may reduce the protection of existing vaccines, antibodies, drugs and other epidemic control methods, affect the applicability of nucleic acid diagnostic reagents, and pose a severe challenge to the prevention and control of epidemics
    .

    Therefore, the existing basic database that mainly collects and displays data has been unable to meet the needs of future epidemic prevention and control.
    There is an urgent need for a virus mutation risk assessment and early warning system based on big data.
    The impact of mutations will be systematically evaluated and interpreted, so as to implement more accurate and effective epidemic prevention and control strategies
    .

    Recently, the Ma Juncai/Hu Songnian team from the Institute of Microbiology of the Chinese Academy of Sciences, in cooperation with Peking University and the Computer Network Information Center of the Chinese Academy of Sciences, released the "New Coronavirus Variation Assessment and Early Warning System" (SARS-CoV) in the international academic journal Nucleic Acids Research.
    -2 Variations Evaluation and Prewaning System), referred to as VarEPS database
    .

    VarEPS is the world's first system for multi-dimensional risk assessment and early warning of known and virtual variants in the SARS-CoV-2 genome
    .

    The database starts from the perspectives of genomics and structural biology, based on the evaluation of the frequency of mutation sites, from the difficulty of nucleotide mutations, the difficulty of amino acid substitutions, the impact of mutations on the secondary structure of proteins, and the mutations caused by single amino acid mutations.
    ACE2 and neutralizing antibody binding free energy changes are used for multi-dimensional evaluation of mutations, and comprehensive analysis of the effects of known mutations and potential virtual mutations on the function of the virus
    .

    On this basis, the system uses an artificial intelligence classifier algorithm to effectively group mutant strains in terms of transmission and affinity for neutralizing antibodies, and realizes risk assessment and early warning based on virus sequences
    .

    The system can not only be used as a tool for global virus mutation monitoring and tracking, but also based on virtual mutation and risk assessment models, providing effective reference information for precise prevention and control of new mutant strains and antibody vaccine design
    .

    The current analysis results based on this system provide an important decision-making basis for accurately and efficiently responding to the SARS-CoV-2 outbreak, as well as technical reserves for responding to other sudden infectious public health events
    .

    The above-mentioned research results were published online on Nucleic Acids Research on October 11th.
    Sun Qinglan and Shu Chang senior engineers of the Institute of Microbiology, Chinese Academy of Sciences Microbiology Resources and Big Data Center are the co-first authors of the paper
    .

    Researcher Hu Songnian of the State Key Laboratory of Microbial Resources Preliminary Development, Institute of Microbiology, Chinese Academy of Sciences, Special Research Assistant Gao Shenghan, Researcher Ma Juncai of the National Microbiology Science Data Center, and Senior Engineer Wu Linhuanzheng are the co-corresponding authors of the paper
    .

    This research has obtained the national key research and development plan new coronavirus mutation detection and functional impact analysis [2021YFC0863300], the Chinese Academy of Sciences Strategic Leading Science and Technology Special (Class A) Comprehensive Big Data Sharing and Service Platform for Biological Genetic Resources [XDA19050301], Chinese Academy of Sciences Research projects: Capacity building of the Chinese Academy of Sciences Microbiological Science Data Center [WX145XQ07-01], Chinese Academy of Sciences Strategic Biological Resources Network Project [KFDZ-SW-219], National Natural Science Foundation of China BRICS International Cooperation Project SARS-CoV-2 Genome Sequencing and COVID -19 Funding support for epidemiology and mathematical modeling research
    .

    The database is open and free to global users through the National Microbial Science Data Center NMDC, and can be freely accessed on .

    The functional interface of VarEPS system consists of five main parts: "virus and mutation", "binding ability evaluation", "primer efficacy evaluation", "statistics" and "analysis tools"
    .

    Among them, "Virus and Variation" displays in tabular form including lineage, single nucleotide polymorphism (SNP) number, and nucleotide and amino acid variation information, and provides all relevant mutations and primer evaluation results for each virus sequence Separate page
    .

    The "Binding Ability Evaluation" section allows users to query by the location of the mutation's gene, lineage, and antibody binding site.
    The results are displayed in the form of a table of the multi-dimensional risk assessment results of each known mutation and all virtual mutations, calculated and displayed Data such as antibody affinity, binding stability to ACE2, risk of amino acid substitution, and time of first and last detection
    .

    The "Primer Efficacy Evaluation" section can evaluate the effect of each mutant strain on the effectiveness of RT-PCR primers, and provide information about the corresponding strains affected
    .

    Paper link: https://academic.
    oup.
    com/nar/advance-article-abstract/doi/10.
    1093/nar/gkab921/6389500 Figure 1.
    Variation Assessment and Early Warning System (VarEPS) portal features
    .

    The researchers showed the global distribution of genome sequences in time frame and geographic location, and listed the risk level and frequency of feature variation of each pedigree.
    Users can directly submit sequences for variation analysis on the homepage
    .

    Figure 2.
    ACE2 binding stability and antibody affinity risk level of key mutations in the S-RBD region
    .

    The researchers calculated the risk level of reduced affinity of the variant to 15 neutralizing antibodies, and the risk level of reduced antibody affinity and increased ACE2 binding stability was ranked from 0 to 2
    .

    It also provides the frequency of these variants over time
    .


    This article is an English version of an article which is originally in the Chinese language on echemi.com and is provided for information purposes only. This website makes no representation or warranty of any kind, either expressed or implied, as to the accuracy, completeness ownership or reliability of the article or any translations thereof. If you have any concerns or complaints relating to the article, please send an email, providing a detailed description of the concern or complaint, to service@echemi.com. A staff member will contact you within 5 working days. Once verified, infringing content will be removed immediately.

    Contact Us

    The source of this page with content of products and services is from Internet, which doesn't represent ECHEMI's opinion. If you have any queries, please write to service@echemi.com. It will be replied within 5 days.

    Moreover, if you find any instances of plagiarism from the page, please send email to service@echemi.com with relevant evidence.