Borders reopen

Seemann’s team is preparing to use genomic data to help identify the probable origin of new cases that arise as Victoria’s social restrictions ease. Public-health officials will be able to make decisions to control outbreaks much faster than was possible in the first few weeks of the pandemic when there were fewer genomes to compare, he says.

The genomic data will be particularly important when regional travel resumes. Borders for all states in Australia have been closed since March, but new infections are expected when they reopen. Over the past two months, viral genomes will have mutated just enough to tell whether they come from outside the state, researchers say. “As soon as we get the sequence, we’ll be able to tell whether it came across the border or not,” Seemann says.

Scientists in New Zealand have so far sequenced 25% of country’s 1,154 reported cases. They’re aiming for more than 70% to get the most complete picture practically possible, says Joep de Ligt, lead bioinformatician at New Zealand’s Institute of Environmental Science and Research near Wellington, which is sequencing the country’s cases. With every sequence added, researchers are more likely to be able to pinpoint where the next case fits.

But the sequence data is already proving useful in responding to outbreaks, he says. Genomic data have identified links between cases that were missed by traditional contact tracing and have untangled two clusters that were thought to be one.

Community spread

In the United Kingdom, with vastly more cases, the COVID-19 Genomics UK Consortium, which includes research centres and university labs, formed in March. It has so far sequenced 20,000 viral genomes, representing nearly 10% of lab-confirmed cases in the country, says Nick Loman, a bioinformatician at the University of Birmingham who is part of the consortium. He was one of the team that pioneered rapid genomic-surveillance tools during the Ebola outbreak, which are now being used during the COVID-19 pandemic.

The team hasn’t set a target like New Zealand, says Loman, partly because the United Kingdom has so many cases — approaching 265,000 confirmed infections as of 27 May. Instead, they’re aiming to generate a representative sample of sequences from across the United Kingdom that can support epidemiological investigations.

‘Slips through the cracks’

But using genomics as part of the response to an outbreak has limitations, says de Ligt. With SARS-CoV-2, people who experience asymptomatic infections are unlikely to get tested, he says. “There is that real risk that something slips through the cracks.”

Genomic surveillance also relies on widespread diagnostic testing to capture sequences in the first place, says Loman. The United Kingdom was inundated with cases and was slow to ramp up diagnostic testing. “There’s always the possibility that you’ve not sampled some cases,” he says.

Loman notes that global genomic surveillance will be important when international travel resumes.

But the use of genomic analysis to help contact tracing is largely restricted to high-income countries, says Meru Sheel, an epidemiologist at the Australian National University in Canberra. She would like to see genomics considered as a tool for outbreak responses in resource-limited countries in the Asia–Pacific region, as it was in the Democratic Republic of the Congo, Sierra Leone and Guinea during the Ebola outbreak.

Nature 582, 19 (2020)

doi: 10.1038/d41586-020-01573-5

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