How countries are using genomics to help avoid a second coronavirus wave
Scientists in New Zealand, the United Kingdom and other places are using sequence data to track new infections as lockdowns ease.
Clare WatsonJune 11, 2020
Credit: Lisa Maree Williams/Getty
As many countries emerge from lockdowns, researchers are poised to use genome sequencing to avoid an expected second wave of COVID-19 infections.
Since the first whole-genome sequence of the new coronavirus, SARS-CoV-2, was shared online on 11 January, scientists have sequenced and shared some 32,000 viral genomes from around the world. Such a vast amount of data has allowed researchers to trace the origin of COVID-19 outbreaks in their countries and pinpoint when community transmission occurred1.
Now, countries that have successfully suppressed infections are entering the next phase of the COVID-19 pandemic — where there’s a risk of new cases appearing as social restrictions ease. Researchers say that genomics will be crucial to quickly track and control these outbreaks. Studies already show that outbreaks tend to be shorter and smaller when genomics is used to help contact tracing2.
“When there are few cases, genomics can very quickly tell you what you’’re dealing with and therefore guide precision interventions,” says Gytis Dudas, a consulting bioinformatician at the Gothenburg Global Biodiversity Centre in Sweden.
Several places are particularly well placed to do that because they invested in genome sequencing early in the pandemic and have a relatively small numbers of cases. Researchers in New Zealand, and at least one state in Australia decided that they would aim to sequence most coronavirus genomes in their country or state.
As SARS-CoV-2 spread around the world, distinct lineages began to form as viruses circulating in different regions gradually evolved. By comparing sequences, researchers can quickly rule out possible lines of transmission if two sequences don’t match, or link together cases that do.
Scientists in the United Kingdom, the United States and other countries are also sequencing SARS-CoV-2 from a large proportion of cases there, but because their epidemics are still ongoing and case numbers are high, genomics is being used to monitor spread and help identify the source of some cases where contact tracing fails. But such interventions depend on broad sampling, and so in places where diagnostic testing is limited, there will also be gaps in the genomic data.
Fast off the mark
Before the first reported case arrived in Australia from Wuhan, China, on 19 January3, researchers at a laboratory in Melbourne that usually investigates outbreaks of food-borne illness started preparing to sequence SARS-CoV-2 genomes in the state of Victoria.
“We said, let’s just sequence every positive case we get,” says Torsten Seemann, a bioinformatician at the Microbiological Diagnostic Unit Public Health Laboratory based at the Peter Doherty Institute for Infection and Immunity in Melbourne.
So far, Seemann’s team has sequenced three-quarters of the state’s roughly 1,700 cases4, thought to be the most comprehensive sequencing coverage in the world for an infectious-disease outbreak. By comparison, researchers working on the 2014–16 West Africa Ebola epidemic sequenced 5% (1,610 samples) of all infected cases5 in just under 3 years.