Leading health and academic organizations in the United Kingdom area combining research talents to create a map of the spread of COVID-19 based on whole-genome sequencing. The COVID-19 Genomics UK Consortium (COG-UK), aims to quickly sequence patient samples from confirmed COVID-19 cases in the United Kingdom and share that information to help the UK respond to the current pandemic and other potential pandemics in the future. The UK government announced a £20 million investment in the project on Monday.
A notable addition to the effort is a team from the University of Birmingham, led by Nick Loman, Ph.D., professor of Microbial Genomics and Bioinformatics in the Institute of Microbiology and Infection, whose lab is known for fusing cutting-edge sequencing with microbial genomics. His team brings capabilities of sequencing genomes of the virus in less than 24 hours using nanopore sequencing. With nanopore sequencing, a single molecule of DNA or RNA can be sequenced without the need for PCR amplification.The importance of this method is that it works well even when only miniscule amounts of virus are present in the sample
The consortium’s efforts are designed to provide valuable epidemiological information revealing the chains of the transmission of the SARS-CoV-2 virus responsible for the COVID-19 outbreak. Within the U.K. the researchers are eager to use the information to help understand the role international travel into the U.K. has played compared with local spreading within regions of the country.
Addition of the University of Birmingham to the effort brings unique advantages. The university is home to two initiatives: ARTIC and CLIMB. The CLIMB project, which recently secured funding for a further five years with the CLIMB-BIG-DATA project, will provide the data analysis pipelines, computing and storage capacity required to analyze the large genome datasets produced by the consortium, as well as facilitating national and international research capabilities.
The ARTIC project is a collaborative project developing protocols and methods for real-time viral genome sequencing, now with a project focused on COVID-19. The project is built around nanopore sequencing, in part developed by the University of Birmingham and Oxford Nanopore Technologies. ARTIC has already participated in previous major viral outbreaks, including Ebola and Zika. In January, researchers from the University of Birmingham released this method for sequencing coronavirus to other researchers globally, built on work previously used to trace those epidemics. The sequencing protocol is built on direct amplification of the SARS-CoV-2 virus using tiled, multiplexed primers, described in a paper led by Loman’s team at the University of Birmingham.
“The government’s investment is well-timed to accelerate the pace of viral genome sequence production and ensure this information is openly available to epidemiologists and virologists worldwide,” Loman said. “This will provide an unprecedented real-time view of COVID-19 virus evolution.”