Research On Real-time Identification And Traceability Analysis Of Pathogens Based On High-throughput Sequencing

Over the past few years,emerging infectious diseases have occurred frequently throughout the world.The prevention and control of epidemics has become the focus of work to address public health issues in countries all over the world.High-throughput sequencing technology has been widely used in epidemic prevention and control in recent years,and has played an important role in the identification and traceability of pathogenic microorganisms.However,there is still a gap in high-throughput sequencing data analysis tools and technical processes with real-time and intelligent characteristics that are suitable for infectious epidemic samples.This study utilizes bioinformatics methods,according to the characteristics of the high-throughput sequencing platform,the characteristics of massive genome data,and the process requirements for the identification and traceability of pathogenic microorganisms,database optimization,process improvement and software compilation were carried out.In this study,a real-time identification software for pathogens was designed(software copyright registration number: 2021SR0842694).The software can read and process sequencing raw data in real time during the operation of the second-generation high-throughput sequencing platform,perform species classification and generate automatic reports,and provide the second-generation high-throughput sequencing platform with the function of analyzing while sequencing.Therefore,while ensuring the total amount and quality of sequencing data,Illumina Mi Seq sequencing with the sequencing strategy of PE300 only needs 20% to 25% of the time required for complete sequencing to identify the main species of the sample,effectively improving the efficiency of massive data processing.At the same time,with severe acute respiratory syndrome coronavirus 2(SARS-Co V-2)as the object template for traceability research,based on the sequence data submitted by the public data platform,a localized SNP(single nucleotide polymorphism)database was established and optimized.On the premise of retaining the effective information of genetic diversity,the data volume was greatly compressed,and the reading speed of the database was improved.Based on the SNP database,an analysis method using pathogenic microorganism sequences for rapid traceability was established.It took less than one minute from inputting pathogenic sequences to outputting traceability results,providing a new traceability tool for revealing the potential transmission process of pathogenic microorganisms.The software,database and technical methods produced in this study have been successfully applied to the analysis of new coronavirus mutant strains,which reflects the value potential of related tools in actual epidemic prevention and control.Its popularization and application will effectively improve the speed of identification and traceability analysis of pathogenic microorganisms in future epidemics,and provide support for timely control of infectious disease epidemics.