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The new crown epidemic is raging around the world, and the advantages of Nanopore sequencing technology and data analysis in the prevention and control of global infectious diseases have fully emerged. The platform has the characteristics of flexible use, easy operation, fast output, and real-time analysis, which provides strong support and guarantee for public health and epidemic prevention and control. This topic provides a detailed analysis of the Midnight kit and overall solution for the whole genome sequencing of the new coronavirus. At the same time, the whole genome sequencing data, technical parameters and customer experience of the new coronavirus were shared.
On March 30th, we invited Dr. Xiang Xingyu from the Hunan Provincial Center for Disease Control and Prevention and Dr. Su Xudong, an expert in the field of Oxford Nanopore Technologies in China , to bring the application of nanopore long-read sequencing technology in the global new crown epidemic and Midnight. Webinar on the Workflow for Covid-19 Whole Genome Sequencing.
schedule
3:00 - 3:05 pm
Opening introduction
Speaker: Su Xudong
3:05 - 3:30 pm
Topic 1: Midnight Kit - SARS-CoV-2 Whole Genome Sequencing Using Oxford Nanopore Technology
◾Application of nanopore sequencing in the global new crown epidemic
◾Midnight New Crown Whole Genome Sequencing Kit Principle, Process, and Data Performance
◾Introduction to the whole genome data analysis process of 2019-nanopore novel coronavirus
Speaker: Su Xudong
3:30 - 4:00 pm
Topic 2: Application of Nanopore third-generation sequencing in the prevention and control of COVID-19 in Hunan Province
◾Routine monitoring of virus mutation in positive specimens of COVID-19
◾ ARTIC shingled amplicon library construction and sequencing method based on the third-generation sequencing platform
◾Sequencing of delta virus using Midnight V1200 library construction method
Speaker: Xiang Xingyu
4:00 - 4:15 pm
question Time
Speakers: Su Xudong, Xiang Xingyu
Speaker introduction
Dr. Xiang Xingyu
Mail:
Xiang Xingyu, male, Chief Technician of the Microbiological Laboratory of Hunan Provincial Center for Disease Control and Prevention, is mainly engaged in the detection, isolation and identification of respiratory pathogens such as influenza, measles/rubella, etc. Undertook a sub-project of the "Thirteenth Five-Year Major Project" and published many papers in both Chinese and English. Participated in the project "Establishment of a pathogen detection platform for fever and respiratory syndrome and discovery of new pathogens" and won the first prize of Hunan Province Preventive Medicine Science and Technology Award (2018). Starting from 2020, it will undertake the genome sequencing and analysis and traceability of the new coronavirus in the province.
Abstract of the speech: Application of Nanopore third-generation sequencing in the prevention and control of COVID-19 in Hunan Province
In order to better carry out epidemic prevention and control work such as novel coronavirus traceability and mutation monitoring, and provide technical support for epidemiological investigation and risk assessment, the Hunan Provincial Center for Disease Control and Prevention purchased Nanopore's Gridion third-generation sequencing platform in 2020. Starting from 2021, the Hunan Provincial Center for Disease Control and Prevention has used the third-generation sequencing platform to carry out routine monitoring of virus variants in positive samples of imported cases, and successively detected variants such as beta, alpha, delta and omicron from inbound flights in the province. Provides a laboratory basis for assessing import risk and virus mutation trends in the province. In addition to routine monitoring, in the July 2021 outbreak in Delta, Hunan Province, we used the ARTIC shingled amplicon library construction and sequencing method based on the third-generation sequencing platform, taking advantage of its advantages of simple operation, high throughput, and short sequencing cycle. , Under the condition of shortage of personnel and equipment, the sequencing and traceability of more than 140 cases in the province was completed with one set of equipment. In the subsequent Delta epidemic in October, we applied the midnight V1200 database construction method, which further shortened the database construction time and improved the convenience of operation. Third-generation sequencing traceability has also been used to rapidly identify false-positive events caused by some vaccine contamination, making epidemiological investigations and event handling more smooth. With the continuous mutation of the virus, the multiplex PCR-based shingled amplicon library construction method also encountered challenges. The continuous increase of variant sites leads to the reduced sensitivity or absence of certain amplicons in the library, for which we are also constantly improving in our work, making adjustments and improvements, and finally obtain a satisfactory result.
Dr. Su Xudong
Field Application Technologist, Oxford Nanopore Technologies
Graduated from Shanghai Jiaotong University with a Ph.D. in Biology
Main technical background
◾ Worked in Hebei Agricultural University to teach microbiology and food safety and MGI to apply high-throughput sequencing technology;
◾ Long-term commitment to pathogenic microorganism detection and epidemiological research;
◾Familiar with high-throughput sequencing technology.
Project Background and Outcomes
◾ Participated in the research of National 863, 973, Natural Science Foundation, National Science and Technology Major Project, and Ministry of Science and Technology Project;
◾Published more than 20 papers in SCI, EI and Chinese core journals.
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