Rapid WGS of SARS-CoV-2 and respiratory viruses for disease surveillance using nanopore sequencing

当前的COVID-19大流行需要先进的诊断分析方法，这些方法可以在全球许多实验室中快速部署，既可以进行COVID-19诊断检测，也可以由公共卫生机构对人群内部和人群之间的疾病进行监测和监测。迄今为止，我们和其他人已经开发并部署了多种快速抗原检测试剂盒，用于使用定量实时PCR或下一代测序（NGS）进行COVID-19诊断检测。Nonacus计划测试和验证一种新的、高度快速的全基因组测序文库制备方法，用于用纳米孔测序对病毒基因组进行测序。随着大流行的不断发展，在样本附近（分散）准确实时监测病毒突变并在短时间内获得有效信息至关重要。这对了解疫情的发展和传播，指导防控工作和疫苗研究尤为重要。该方法将提供第一种商业化的方法，并且比目前用于SARS-CoV-2全基因组测序（WGS）的纳米孔方法更快、成本更低、通量更高。此外，作为技术验证的一部分，我们将更广泛地验证该技术，而不仅仅是针对SARS-CoV-2，并将开发该技术作为泛呼吸道病毒WGS筛选技术，以便在未来的任何病毒爆发中使用该技术，并且我们可以在监测环境中使用单一方法更好地了解呼吸道病毒在人群中传播。这笔拨款将使我们能够在已经开展SARS-CoV2工作的两个临床实验室验证该方案之前，在Nonacus实验室对SARS-CoV-2 WGS库准备产品进行最终验证和优化工作。为了进一步用SARS-CoV-2验证该方法，我们将开始工作，并对泛呼吸病毒产品进行早期验证。该项目及其将商业化的产品是创新的，因为在纳米孔测序方面，目前还没有现有的商业上可获得的快速、低成本、高度复用的COVID-19 /呼吸道病毒WGS工作流程或产品。此外，现有的开源协议，如ARTIC，虽然性能令人满意，但比我们计划的更长、更复杂、更昂贵，而且缺乏更高复用的能力。我们预计该结果将成为首个商业上可用的快速低成本全基因组测序方法，通过纳米孔测序对SAR-CoV-2\进行测序。

The current COVID-19 pandemic requires advanced diagnostics assays which can be rapidly deployed across many laboratories, globally and to allow for both diagnostic COVID-19 testing but additionally a for surveillance and monitoring of the disease within and between populations by public health institutions.To date ourselves and others have developed and deployed multiple rapid antigen testing kits for diagnostic COVID-19 testing using both quantitiative real time PCR or indeed next generation sequencing (NGS).Nonacus plan to test and validate a novel and highly rapid Whole Genome Sequencing library preparation approach for sequencing Viral genomes with nanopore sequencing.With the continuous development of the pandemic, accurate real-time monitoring of virus mutations in close proximity (decentralised) to samples and obtaining effective information in a short period of time is critical. It is particularly important to understand the development and spread of the epidemic, guide prevention and control work, and vaccine research.This method will provide the first commercially available method and a more rapid, lower cost and higher throughput advancement to current nanopore methods being used for whole genome sequencing (WGS) of SARS-CoV-2\.Additionally as part of the technology validation we will validate the technology more broadly than just for SARS-CoV-2 and will develop the technology out as a Pan- Respiratory-Viral WGS screening technology, such that for any future viral outbreaks the technology could be used and also so that we can in the surveillance setting better understand using a single method what respiratory virus' are spreading in the population.This grant will enable us to undertake final validation and optimisation work for the SARS-CoV-2 WGS library prep product within the Nonacus lab before validating this protocol within 2 clinical laboratories already undertaking SARS-CoV2 work.Further to validating the method with SARS-CoV-2 we would then start the work up and early validation of a Pan-Respiratory-Viral product.This project and the product which will be commercialised from its work is innovative as there is no existing commercially available rapid and low cost, highly multiplexed COVID-19 / respiratory virus WGS workflow or product ahead on nanopore sequencing. Further the existing open source protocols such as ARTIC while performing satisfactorily suffer with being longer, more complex and much more expensive than we have planned and also lack capacity for higher multiplexing.We expect the outcome to be the first commercially available rapid and low cost whole genome sequencing methodology by nanopore sequencing for SAR-CoV-2\.