Oxford Nanopore is working with public health laboratories around the world, and researchers in related areas, to support the current COVID-19 pandemic. This includes rapid sequencing of the novel coronavirus SARS-CoV-2, as well as approaches that characterise a broader range of pathogens in a sample.
A large number of scientists from large centralised labs – and also smaller decentralised ones – are now using nanopore sequencing to support rapid data sharing of genomic data. Rapid data sharing has been key to the public health response, and researchers all over the world have been fast to share the genomes they have sequenced on public databases such as GISAID, GenBank or elsewhere. As numbers of cases have increased, laboratories have been building capacity to sequence larger numbers of the genomes, typically progressing from using the MinION device to the GridION device for sequencing.
Sequencing the virus can support ‘genomic epidemiology’- characterising the virus and helping public health authorities to understand the identity of the virus, whether it is changing and how it is being transmitted – all in conjunction with other epidemiological data.
The scientific community has previously developed methods for the rapid, near-sample nanopore sequencing of pathogens in multiple outbreak situations including Zika, Ebola, Yellow Fever and Swine Flu and a range of other pathogens. This experience has supported the rapid deployment of nanopore sequencing for the current outbreak.
Several researchers are also using nanopore sequencing to characterise multiple pathogens that may be present in a sample.
Oxford Nanopore staff are working with the community to support the development and sharing of best practice and protocols for the sequencing of this virus. The company is offering technical support to public health authorities and researchers, and working to understand the needs of these users so that we can continue to provide the most useful support to the community.