摘要:
Sequencing is a fundamental tool for the monitoring of virus outbreaks, such as the recent COVID-19 pandemic, in which sequencing was implemented for the original identification of the SARS-CoV-2 virus, to establish variants of concern, and to track transmission routes throughout the different waves. Sequencing platforms continue to become more widely available, given the development of portable, more economical sequencing devices. However, library preparation remains a challenge for the implementation of sequencing in remote locations, as the whole workflow from sample to sequencing library involves several steps that need to be carried out by qualified personnel in a dedicated laboratory. To tackle this issue, our laboratory has collaborated with the National Research Council (NRC-CNRC) to develop an automated workflow for Nanopore library preparation from SARS-CoV-2 clinical samples using the NRC-developed automated microfluidics device, the PowerBlade. The combination of this automated, portable device with portable sequencing technologies, such as those developed by Nanopore, gives us a workflow that can be easily run almost anywhere without the need for a highly experienced technician due to the automation of the workflow. Furthermore, this adaptable technology could be modified and used for identification of other pathogens. In this work, we present a novel Nanopore library preparation protocol suitable for on-chip implementation on the PowerBlade, which was tested against the standard ONT protocol, both on-chip and off-chip. Additionally, we present a performance comparison of on-chip and off-chip ARTIC SARS-CoV-2 PCR.