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

当前的新冠肺炎大流行需要先进的诊断分析方法，可以在全球许多实验室快速部署，不仅可以进行新冠肺炎诊断测试，还可以用于公共卫生机构对人群内部和人群之间的疾病监测。到目前为止，我们和其他人已经开发和部署了多个快速抗原检测试剂盒，用于使用实时定量聚合酶链式反应或甚至是下一代测序技术进行新冠肺炎诊断测试。Nonacus计划测试和验证一种新的、快速的全基因组测序库制备方法，用于使用纳米孔测序对病毒基因组进行测序。随着疫情的不断发展，对样本附近(分散)的病毒变异进行准确实时监测并在短时间内获得有效信息至关重要。尤其重要的是了解疫情的发展和传播，指导预防和控制工作，以及疫苗研究。该方法将提供第一种商业化的方法，以及比目前用于SARS-CoV-2全基因组测序(WGS)的纳米孔方法更快、更低成本和更高吞吐量的进步。此外，作为技术验证的一部分，我们将不仅对SARS-CoV-2进行更广泛的技术验证，并将开发出作为泛呼吸-病毒WGS筛选技术的技术，这样，对于未来的任何病毒爆发，这项技术都可以使用，也使我们能够在监测环境中使用单一方法更好地了解哪些呼吸道病毒正在人群中传播。这笔赠款将使我们能够在NONACUS实验室内承担SARS-CoV-2 WGS文库准备产品的最终验证和优化工作，然后在已经进行SARS-CoV-2工作的两个临床实验室内验证该协议。进一步验证该方法与SARS-CoV-2，我们将启动泛呼吸道病毒产品的工作和早期验证。该项目和产品将从它的工作是创新的，因为现有的商业上没有快速和低成本的，高度复合的新冠肺炎/呼吸道病毒WGS工作流程或纳米孔测序产品。此外，现有的开放源码协议，如ARTIC，虽然执行情况令人满意，但存在着比我们计划的更长、更复杂和更昂贵的问题，并且缺乏更高复用的能力。我们预计结果将是第一个用于SAR-CoV-2的商业可用的快速、低成本的纳米孔全基因组测序方法。

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\.