Hands-on time is also minimal, facilitating automation. The approach is highly flexible, allowing the on-demand sequencing of small numbers of samples or scaling up to high-throughput sequencing needs. Midnight is a simple, rapid method of sequencing SARS-CoV-2 genomes at low cost per sample. Both methods employ a PCR tiling approach in which the viral genome is amplified in overlapping sections, maximising coverage across the full genome. There are two methods available for whole-genome nanopore sequencing of SARS-CoV-2: Midnight and ARTIC Classic. Furthermore, the sequencing of full-length immune cell receptor genes via long nanopore reads allows research into the response of the immune system to SARS-CoV-2 infection. Whole human genome sequencing can enable research into what might cause different responses to the virus in different individuals. In addition to investigating the virus itself, nanopore sequencing can be employed to investigate the interactions between SARS-CoV-2 and the infected host. Researchers in Australia and South Korea have performed direct RNA sequencing of the virus, providing insights into the transcriptome of the virus and epigenetic modifications present. This enables base modifications to be preserved and detected in nanopore sequencing data. Nanopore sequencing can also be used to directly sequence RNA, without conversion to cDNA. Preparation of clinical research samples via SISPA (Sequence-Independent, Single Primer Amplification), followed by nanopore sequencing, is an effective method of rapidly identifying unknown and novel infectious agents and generating consensus sequences. This infographic describes some of the approaches available for metagenomic and metatranscriptomic sequencing of SARS-CoV-2 samples. These aim to understand co-morbidity patterns of the disease, and also have the potential to be useful in broader surveillance of outbreaks in a population. Multiple groups are investigating approaches that characterise not only the SARS-CoV-2 virus, but other pathogens or microorganisms present in the sample. View the Community timeline Interested in infectious disease? Visit the Resource Centre to view the latest publications, presentations, and more from scientists using nanopore sequencing to research COVID-19. Starter pack and bundle options are available, providing everything you need to start sequencing, whether you’re new to nanopore sequencing or getting started with SARS-CoV-2 analysis, at low cost per sample. Making use of fast, streamlined library preparation methods, real-time nanopore sequencing and data streaming, and highly scalable nanopore sequencing technology, these workflows enable you to set up SARS-CoV-2 sequencing quickly and easily in your own lab. Their foundational work, and that of Nikki Freed and Olin Silander, form the core of the workflows available for the nanopore sequencing of SARS-CoV-2. Oxford Nanopore have worked closely with the ARTIC Network, who have developed workflows for the rapid preparation and sequencing of SARS-CoV-2 whole genomes in use by scientists around the world. This experience has supported the rapid deployment of nanopore sequencing in the COVID-19 pandemic. The unique features of nanopore technology have enabled its use by the scientific community for the rapid sequencing of pathogens in multiple outbreak situations, including Zika, Ebola, Yellow Fever, and Swine flu. This can help indicate, or rule out, routes of transmission, enable identification and investigation of clusters, and help inform strategies to control the spread of the virus. Determine how strains of the virus are related.These may impact the nature of the disease caused by the virus, or inform future treatment strategies and vaccine design. Quickly identify variants and track their prevalence and distribution.In combination with rapid data sharing across the scientific community, this enables genomic epidemiological analysis, which has become a key part of the global public health response to the COVID-19 pandemic.īy rapidly sequencing and sharing SARS-CoV-2 genomic data, it is possible to: Scientists around the world are using nanopore sequencing to rapidly sequence and analyse SARS-CoV-2 virus genomes. Genomic epidemiology is the study of how variations in the genomes of pathogens, or their hosts, influence health and disease, including how common specific variations are, how they interact with environmental factors, and how they contribute to disease risk.
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