In the process of pathogen identification, it is an accurate and effective strategy to compare the samples under test with the genome databases of known pathogens. Alibaba Cloud Genomics Service (AGS) supports quick comparison of metagenome sequencing data. This topic describes how to use AGS to perform virus sequencing.
Prerequisites
Background information
Coronavirus SARS-CoV-2 RNA (hereinafter referred to as COVID-19) can be detected in the upper or lower respiratory tract with a few weeks after the onset of the disease. At present, many types of RT-PCR kits are available to diagnose COVID-19. RT-PCR tests are cost-effective and can provide feedback within a short period of time. However, due to factors such as virus concentration and kit quality, RT-PCR tests are prone to false negatives. Multiple tests are required for confirmation, and only one specific virus can be checked at a time.
Metagenomic next-generation sequencing (mNGS) for pan-pathogen detection directly extracts a certain proportion of nucleic acid fragments (including a large amount of human nucleic acids and a small amount of microbial nucleic acids) from clinical samples for sequencing, data comparison with database engines, and bioinformation analysis. This enables unbiased identification of pathogenic microorganisms. This technology has made great contributions to the early detection and accurate sequencing of COVID-19.
Compared with RT-PCR tests, mNGS testing requires longer detection periods but provides higher accuracy. It can check multiple virus types at a time and monitor the mutations that may occur during the transmission of viruses. This allows you to enhance the prevention and control of viruses. Clinically, it is advisable to check suspected patients again, especially those who cannot be diagnosed by fluorescent quantitative PCR. This further improves the accuracy of test results and effectively prevents false negatives caused by virus mutations. After the genome of the pathogen is identified and updated in databases, the pathogen can be accurately detected by comparing nucleic acid sequences.
AGS supports quick comparison of mNGS data. It can complete the comparison of 3.2 billion base pairs (22 million reads) of an alveolar sample and the reference sequence of known pathogen genomes (including COVID-19, 39 BetaCov RNAs, and 9,334 known viruses) within 60 seconds. It also allows you to upload custom virus libraries to compare with samples under test. You only need to create an Object Storage Service (OSS) bucket and run AGS commands to complete the entire comparison process. AGS provides reports about high-quality alignments of reads and supports detection of multiple pathogen types. This provides solid data support for researches on the protein and mutations of COVID-19.
Genome sequencing service providers, disease control centers, hospitals, universities and research institutes, and pharmaceutical companies are all welcome to apply for trial.
Preparations
Examples of rna-mapping
Click Use AGS to test rna-mapping viruses to watch a video tutorial of how to use AGS CLI to test rna-mapping viruses.