December 2, 2021
On November 19, scientists at a private lab in Johannesburg called Lancet noted a troubling number of mutations in recently sequenced coronavirus samples. After confirming the pattern in several other local samples, they alerted the national health authorities, who then flagged the variant to the World Health Organization. We now know it as Omicron—a “variant of concern.”
The identification of Omicron is a testament to the importance of broad genomic surveillance. Without the efforts of the South African scientists who identified and reported it, nations would not have been able to prepare for Omicron’s potential impact—and start looking for it themselves. Its detection is a clear sign that genomic surveillance is working and that we must keep supporting it as the pandemic wears on.
This isn’t the last time a new coronavirus variant will emerge—as long as people around the world remain unvaccinated, people will continue to get infected, which will give rise to new variants. As Omicron is illustrating now, no matter where variants are first identified, they can spread across the globe quickly. That’s why it’s essential that all countries do their part in sequencing samples and sharing data.
The U.S. has come a long way in terms of improving its genomic surveillance of the virus, which was widely criticized throughout the pandemic for being too slow and patchy, especially for a country with so many infections and unvaccinated people. In December 2020, the U.S. ranked 43rd among countries sequencing and sharing COVID samples. By April 2021, it had inched up to 33rd. Given the country’s leadership in the Human Genome Project, wrote Case Western Reserve University scientists Dana C. Crawford and Scott Williams in PLOS Genetics this past July, the dearth of U.S. sequencing data during the COVID pandemic is “unbelievable and problematic.”
Crawford, a professor at Case Western’s medical school, told me in an email that when they wrote the article, the U.S. was sequencing fewer samples compared to other countries, its sequencing efforts varied dramatically across states, and there was no national coordinated sequencing pipeline. This “meant that the virus could mutate into a more dangerous form undetected, making it very difficult for public health officials to respond to the new strain before it overwhelms local hospitals,” she says.
But now, says Crawford, the U.S. “is no longer behind other countries in genomic surveillance for SARS-CoV-2.” One reason is that the CDC is now coordinating a genomic surveillance effort that involves samples from all states and territories. At a briefing on Tuesday, CDC director Rochelle Walensky said that 80,000 samples are being sequenced each week—about one in every seven positive samples. The U.S. currently ranks 21st among nations sequencing COVID samples (Iceland, Denmark, and New Zealand are leading the way). Walensky also said at the briefing that the CDC would expand virus surveillance at four of the nation’s busiest international airports: JFK, San Francisco, Newark, and Atlanta. These efforts are supported by $1.7 billion in funding that the Biden administration pledged in April.
There’s still plenty of room for improvement. Crawford points out that the coronavirus sequences from U.S. samples aren’t attached to any clinical data, like information on disease severity and vaccine effectiveness. As a result, the sequences can only tell us about the presence of new strains and changes in their frequency over time, but not the real-world impact of a particular variant. “Knowing the viral sequence is good,” she says, “but without linked clinical data, it is not useful for understanding the likelihood of changing the course of the pandemic.”
Other experts have argued that funding isn’t being used and distributed quickly enough and that sequencing centers need to coordinate more closely. Some have pointed out that sequencing ability is uneven across states, meaning that variants that crop up in low-surveillance areas may be missed. Importantly, sequencing isn’t possible without widespread, fast, and affordable testing, which is still out of reach for many Americans.
Nevertheless, the detection of Omicron in California on Wednesday is proof that the CDC’s surveillance system is working. “The US is now in a position to quickly identify potentially new dangerous strains that may arise in this country, giving us the opportunity to warn other countries about its existence much like South Africa has done with Omicron,” says Crawford. Even after the pandemic, she adds, the U.S. pipeline can “serve as a blueprint for genomic surveillance of other emerging infectious diseases”—so long as there’s continued support for the technology and expertise.
Thanks for reading, and please reach out if you have any questions or comments—I’d love to hear from you.
Stay safe out there,