Olena Shmahalo/Quanta Magazine

Genomic surveillance of the SARS-CoV-2 virus can help control the current pandemic and prevent future ones. But the process is marred by insufficient data and geographic inequities.

Puja Changoiwala | Quanta Magazine | June 28, 2021

Back at the beginning of the COVID-19 pandemic, before the disease had even drawn the attention of much of the world, researchers in China and Australia mapped the genome of the coronavirus isolated from one of the first patients in the Wuhan outbreak. This first genetic blueprint of the SARS-CoV-2 virus was publicly released soon after, on January 10, 2020. The disclosure of that genome, and others that soon followed, guided the vigorous international scientific response to the pandemic, including the timely development of diagnostic tests, surveillance strategies, vaccines and other new tools for managing the outbreak.

As a report by the World Health Organization (WHO) noted, because technology can now read the genome of a virus sample from a patient in just a few hours, “for the first time, genomic sequencing in real time has been able to inform the public health response to a pandemic.” All the successes that countries have had in coping with the pandemic are built on measures arising from our knowledge of its viral genome.

Yet the need to collect information about the SARS-CoV-2 genome is far from over. “It is too early to conclude how and when the pandemic will end,” said Meng Ling Moi, deputy director of the WHO Collaborating Center for Reference and Research on Tropical and Emerging Viral Diseases. Although numbers are dropping, more than 2.5 million new infections and more than 64,000 deaths were reported in the week before June 22, with significant increases in many countries. Health authorities attribute the strength and persistence of the pandemic to highly contagious variants of the virus that are spreading around the globe.

Genomic sequencing remains the foundational tool for understanding how the virus is evolving, and how our defenses against it need to adapt. In the hands of skilled researchers, genomic data can spell out the deepest secrets of the coronavirus, including epidemiological behaviors that patient data alone cannot capture.

Because of the singular importance of sequencing, in an online news conference last December, Tedros Adhanom Ghebreyesus, the director-general of the WHO, called on countries to step up their SARS-CoV-2 sequencing efforts. The European Commission followed suit a few weeks later, asking EU member states to sequence at least 5% — but preferably 10% — of positive test results from COVID-19 patients. The Centers for Disease Control and Prevention (CDC) also set a target of 5% for the United States in February.

Yet countries are still falling far short of these goals, according to the Global Initiative on Sharing Avian Influenza Data (Gisaid), which manages the most widely used global repository of SARS-CoV-2 genomic data, and other sources. Almost 180 million confirmed COVID-19 infections have been reported globally, but only about 2,042,000 viral genome sequences — from barely more than 1% of the total cases — have been submitted. Rates of sequencing are improving in many countries, but not fast enough. The numbers are particularly alarming for the countries with the most infections: The U.S. has sequenced 1.7% of its 33.2 million cases, while Brazil, with almost 18.2 million infections, and India, with 30.1 million, have sequenced only about 0.1% of their caseloads.

Medical researchers worry that insufficient knowledge of how COVID-19 is changing could disastrously deepen and drag out the pandemic. “The more large gaps in our knowledge of the variants circulating globally, the more likely we are to miss the evolution of an important variant and find ourselves taking backward steps in the fight to control the pandemic,” said Justin O’Grady, who was until recently deputy director of the COVID-19 Genomics UK Consortium (COG-UK) and is now senior director of translational applications at Oxford Nanopore.

If the factors currently holding back viral surveillance are not addressed, there could be more uncontrolled viral outbreaks in our future. “If there are large ‘blind spots’ to virus sequencing surveillance, then with a fast-spreading infection, you cannot prevent pandemics,” said David Haussler, scientific director of the Genomics Institute of the University of California, Santa Cruz. “For this reason it is essential that virus genomes be sequenced everywhere in the world and that information be shared immediately.”

Read more: “A Lack of COVID-19 Genomes Could Prolong the Pandemic