Alarming COVID variants show vital role of genomic surveillance

https://www.nature.com/articles/d41586-021-00065-4

15 January 2021
David Cyranoski

2021 is shaping up to be the year of COVID-19 variants. In the past two months, scientists have identified several fast-spreading variants that have prompted government restrictions in many countries — and new variants are being detected more frequently.

The pandemic has ushered in an era of genomic surveillance in which scientists are tracking genomic changes to a virus at a speed and scale never seen before. But surveillance is patchy globally, particularly in the United States, which has the world’s largest COVID-19 outbreak, and in many low- and middle-income countries. Scientists warn that worrying variants are probably spreading undetected in these regions.

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The United States has been less successful in getting genomic epidemiology up and running — despite the May launch of a programme called SPHERES, which enlisted national and local health laboratories, private companies and academic institutions to deliver genomic sequences to public-health response teams.

The effort has not evolved into a national system, and individual academic laboratories do most sequencing rather than the country’s large genomic centres, says Nathan Grubaugh, an epidemiologist at Yale University in New Haven, Connecticut.

As a result, genomic coverage overall is low. The number of SARS-CoV-2 genomes that the United States has shared on GISAID is less than 0.3% of its total number of COVID-19 infections. That compares with nearly 5% for the United Kingdom, 12% for Denmark, and almost 60% for Australia (see ‘Global surveillance’). A new variant in the United States would probably be detected quickly in certain states that have lots of active sequencing labs, such as New York and Washington, but would take a while in places that don’t, says Grubaugh. This is a problem because the more a virus circulates, the more opportunities it has to change.

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The situation could improve with incoming US president Joseph Biden, says Grubaugh. “I am hopeful that the new administration will tap into the expertise within SPHERES to help develop a national system,” he says.

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