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With new variants, will COVID-19 tests still work?

April 9, 2021 by Neha Agarwal, Troy Leader, and Lorraine Lillis

PATH scientists unpack the diagnostic implications of new variants and outline steps the world can take to more effectively surveil the virus.

Man undergoes a COVID-19 swab test. Photo: U.S. Navy Medicine

Over time, genetic variations in a virus can render diagnostic tests ineffective. Photo: US Navy Medicine.

The vaccine implications of new SARS-CoV-2 variants have dominated recent headlines, but one team at PATH is focused on a different set of implications: those for tests used to detect the coronavirus.

“With [current] COVID-19 diagnostics, we were on a time crunch, we had to get something out there,” PATH’s Lorraine Lillis recently told The New York Times. “Normally, diagnostics take a long, long time, and we’d normally challenge them with multiple variants. We’re doing that, but we’re doing it in real time.”

We spoke with Lorraine and other scientists from PATH’s Diagnostic program to answer key questions about SARS-CoV-2 variants, the implications for diagnostic tests, and the future of disease surveillance.

Q: What are coronavirus variants and where do they come from?

“Like all viruses, the coronavirus takes control of cells in its host—infected human beings—and it uses those cells to print more copies of itself,” says Troy Leader, PhD, senior scientific officer in PATH’s Diagnostics program.

“Each new copy of a virus contains tiny copying errors or variations in its genome—hence, variants. Most of these variations are insignificant, but occasionally, one offers a significant evolutionary advantage. It might be harder for immune systems to detect. It might be more transmissible. And quite rapidly, it can become the dominant strain.

“Just look at the explosion of cases in Lusaka earlier this year—that’s a clear example of a new, more transmissible variant taking hold, and that’s why the world has been paying close attention to the genomic surveillance PATH is doing with the University of Zambia.”

Q: With new variants, will current COVID-19 tests still work?

“As you’d expect, the answer depends on the test and the variant,” says Lorraine Lillis, PhD, scientific program officer with PATH’s Diagnostic program.

“For the variants you’ve heard about in the news so far—B.1.1.7, B.1.135, and P.1—most antigen-based tests will continue to work, because most are targeting the N antigen of the virus. And so far, the N antigen remains conserved in these variants.

“For molecular tests, whether or not they continue working will depend on the number and location of genes that the test targets. The new variants have mutations in the S gene that have been found to impact some assays targeting this particular gene. However, if a test is targeting one or more conserved regions other than the S gene, then the test can be presumed to detect these new variants.

“For tests that only target the S gene, we just don’t fully know yet. Additional studies are required.”

Q: This all sounds complicated. How can health officials keep track of what works and what doesn’t?

“It is very complicated,” states Neha Agarwal, associate director of PATH's Diagnostic program, “which is why the PATH team has expanded our COVID-19 Diagnostics Dashboards to shed light on what we know and don’t know about the variants and their impact on testing.

“Our new variant-specific dashboardsone for molecular tests and one for antigen tests—track key variables such as assay multiplicity and gene or protein target sites. And they help users understand which tests are presumed or confirmed to work with three of the most common variants (B.1.1.7, B.1.135, P.1).”

Explore PATH's COVID-19 diagnostic dashboards
Use the dashboards

“Of roughly 70 tests we’ve assessed, only 22 had publicly available manufacturer information on the effectiveness of detecting the B.1.135 variant (initially reported in South Africa), and only 20 for the P.1 variant (initially reported in Brazil and Japan).

Molecular Dashboard with border

A static image of PATH's new variant-specific molecular diagnostic dashboard. To see the live dashboard, click the text links above. Photo: PATH.

“Everyone’s needs are different,” Neha says, “so our dashboard enables each health official to decide for themselves which tests are best suited for their needs, without having to comb through individual product inserts, manufacturer websites, or research studies. We’ve aggregated all the publicly available information in one place.

“So far, the response to the dashboard has been overwhelmingly positive. If we can secure additional support, we hope to continue monitoring mutations and their implications on diagnostic testing.”

Q: If more variants are bound to emerge, how can the world get ahead of the pandemic?

“Basically, we need more of everything,” says Troy. “First and foremost, the world needs more COVID-19 testing in more places, and if possible, with faster results—particularly in countries where diagnostic testing remains limited.

“As Neha and Lorraine explained, the dashboard plays a critical role in helping public officials make informed decisions when procuring tests for their health systems. But upstream of that, an incredible amount of work and global collaboration goes into creating appropriate, quality-assured diagnostics in the first place.

“At PATH, we accelerate the creation of new diagnostics by de-risking development wherever we can. In the case of COVID-19, we’ve created a biorepository of more than 20,000 qualified clinical samples that test developers can use to validate their tests. We’ve also established a standardized benchmarking panel for evaluating antigen test performance.

“But these sorts of efforts need to go far beyond COVID-19 and the work we’re doing at PATH. The world needs more robust disease surveillance systems all-up—including greater capacity for genomic sequencing in more places. It’s not an accident that new SARS-CoV-2 variants were first spotted in places that have the genomic sequencing capacity to search for them.

“In this pandemic and the next, stronger disease surveillance systems will be essential—not only for detecting new variants as they emerge but also to monitor the impact those new variants have on the effectiveness of our efforts against them: whether distancing measures, vaccines, or anything else.”

Q: What is PATH doing to strengthen disease surveillance systems?

“Beyond our work with the dashboard and with diagnostic development, our team is exploring innovative approaches to rapidly expand disease surveillance data on variants and other pathogens in settings with limited clinical testing,” says Troy.

“For example, we’re working on new environmental surveillance approaches that enable characterizing variants within sewage or other environmental samples. This is a fast, accurate, and affordable way to take a snapshot of what is circulating in a community rather than characterizing viruses collected from individual patients.

“We’re also working to strengthen other critical components needed for effective disease surveillance—including working with national and international partners through efforts in our Global Health Security Initiative that support the strengthening of other key health system components, such as the data reporting systems required to collect and leverage disease surveillance information in public health decision-making.”

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