A rapid genomics strategy could speed up identification of changes in the genetic code of SARS-CoV-2, helping identify the source of COVID-19 cases.
Although the viral sequence has been available since February 2020 (see BioNews 1033), the SARS-CoV-2 virus can accumulate mutations over time making it difficult to track the source of initial infection in some COVID-19 cases. To date, the standard sequencing method would determine 100-150 nucleotides at a time, taking around a day to sequence the complete viral genome, but researchers at the University of New South Wales, in Sydney, Australia have developed a protocol to make use of a new sequencing technology, known as nanopore.
'Every time the SARS-CoV-2 virus passes from person to person, it may make copying errors that change a couple of its 30,000 genetic letters. By identifying this genetic variation, we can establish how different cases of coronavirus are linked – to know where a case was potentially picked up from and who they may have given it to,' said the first co-author Dr Rowena Bull, an associate professor from the Kirby Institute for Infection and Immunity.
Nanopore sequencing gets its name from the way long DNA molecules pass through a hole or 'nanopore' in a membrane, and can determine the complete SARS-CoV-2 viral genome in four hours. The short turnaround was possible because the genetic code of SARS-CoV-2 is 30,000 nucleotides long.
Nanopore predates COVID-19 but has not been widely adopted because its accuracy is not as well studied as older technologies. The study, published in Nature Communications, addressed that issue by analysing 157 SARS-CoV-2-positive patient samples and reported a 99 percent accuracy in determining genetic variants between cases. The researchers believe that using nanopore technology could improve SARS-CoV-2 surveillance by allowing point-of-care genomic testing.
'Nanopore devices are cheaper, faster, portable and don't require the lab infrastructure needed by current standard pathogen genomics tools,' said the senior author of the study Dr Ira Deveson, from the Garvan Institute of Medical Research. 'We hope our validation of this protocol will help other public health teams around the world adopt this technology.'