OXFORD NANOPORE MIDNIGHT PROTOCOL PORTABLE

The ability to deliver a viral genome sequence in under 10 hours provides health authorities real-time data on the same day the sample is taken. This process, now known as the Midnight protocol because it sequences in 1200-base pair sections, was described by Freed, et al., in a 2020 study published in Biological Methods & Protocols.

More specifically, research assays such as the Midnight Panel that sequence the viral genome in bigger sections (i.e., in 1200-base-pair sections with the Midnight protocol rather than 400-base-pair sections with the ARTIC protocol), coupled with rapid enzymatic preparation of the DNA for sequencing, allow researchers to conduct faster, cheaper, and more even sequencing across the viral genome, requiring fewer reads to accurately capture the entire sequence. In instances like this, an ultrafast NGS method to sequence SARS-CoV-2 provides a major benefit. Real-time genome sequencing has enabled health authorities to identify the source of outbreaks in real-time and monitor the spread. Additionally, in some countries such as New Zealand, real-time genome sequencing (patient swab to uploaded genome in under 10 hours) is routinely used in instances of Covid-19 community transmission. However, there is always a desire to make these methods faster, less expensive, and easier to perform. The fast, low-cost, and high-throughput ARTIC Covid-19 protocol has become the most ubiquitous method for sequencing SARS-CoV-2. Since then, the ARTIC Network has spawned multiple NGS protocols in response to outbreaks such as the Zika virus in Brazil and Covid-19. They work with governments and WHO to facilitate fast and accurate diagnosis and evidence-based containment measures. The ARTIC Network is comprised of genomic epidemiologists looking to develop next-generation sequencing (NGS) tools for viral sequencing during outbreaks to generate actionable epidemiological data in real-time. It was during this same outbreak that the ARTIC Network was formed. This work indicated that there were frequent transmission events occurring between Sierra Leone and Guinea. The kit’s utility was validated when the team moved several times and discovered that there were actually two distinct lineages of the Ebola virus circulating in Guinea. The set-up allowed for a rapid sequencing protocol that delivered results within 24 hours of sample collection.

OXFORD NANOPORE MIDNIGHT PROTOCOL PORTABLE

Additionally, the team used a rapid, inexpensive, portable DNA sequencer from Oxford Nanopore, called a MinION, that enabled real-time DNA sequencing. Resources for NGS were thin on the ground at the outbreak sites, so Dr Quick deployed his Lab-in-a-Suitcase, which includes portable isolation cabinets built from repurposed hydroponics tents to recreate sterile lab conditions that minimized sample contamination. The ARTIC routeįor example, during an outbreak of hemorrhagic fever spread by the Ebola virus in West Africa in 2015, Dr Joshua Quick from the University of Birmingham flew from the UK to Guinea to try to track virus evolution in real-time. Although we have monitored mutations in other viruses for decades, many challenges remain. Rapid identification of new mutations that increase the transmissibility, immunity, and/or infection severity of the virus is vital for Covid-19 control, both now and in the future. However, there are, to date, 10 variants of concern or interest being tracked by the World Health Organization (WHO), with many more being monitored in specific regions, such as in Europe and the US. Remarkably, this is a relatively slow mutation rate for a virus, and many of these mutations are neutral or don’t seem to change the way the virus functions.

More than 12,000 mutations have arisen in the SARS-CoV-2 virus since it was discovered in late 2019. When many people are infected, the number of opportunities for these rare, beneficial mutations grow, which means that multiple viral variants can emerge. Unfortunately, these random changes can sometimes result in improved viral traits, such as the ability to bind and infect human cells better. Most of the time, these changes do nothing.

“Viruses evolve - that’s a fact of life”, says Dr Nick Downey (NGS collaborations lead, Integrated DNA Technologies), Dr Nikki Freed (Auckland Genomics, University of Auckland, New Zealand) and Dr Olin Silander (School of Natural and Computational Sciences, Massey University, New Zealand) in this DDW exclusive.Įvery time a virus replicates itself, there is a small chance that a change or mutation can occur in the genome.

Oxford nanopore midnight protocol