New COVID-19 dashboard shares data on how well diagnostic tests perform against variants

Key contributors to PATH’s COVID-19 diagnostics platform, from left to right: Lorraine Lillis, scientific program officer for diagnostics; Neha Agarwal, associate director for diagnostics, and Olivia Halas, program coordinator for diagnostics. (PATH Photos)

While all eyes are on the COVID-19 vaccine, the more dangerous variants of the virus are becoming increasingly dominant.

In Washington state, the United Kingdom variant, or B.1.1.7, and two closely related variants first identified in California have been quickly overtaking other strains. While the state has only rough estimates of the relative portion of each variant, the U.K. and California variants each make up roughly one-third of infections. The original virus and other variants comprise the remaining third. Other states are also seeing similar trends.

As the numbers grow, an effort by global health nonprofit PATH is helping to make sure that the most worrisome variants aren’t able to avoid detection.

The Seattle-based organization recently released a tool that pulls together information on the ability of COVID tests to identify infections regardless of which strain a person has contracted. PATH researchers have manually collected data on hundreds of tests from dozens of manufacturers, making it easier for people to evaluate the available diagnostic tools. For the majority of tests, very limited information is available as to how they will perform against variants.

PATH’s dashboard shows the implications of variants on COVID-19 molecular test detection.

The variant-focused database is part of a broader COVID diagnostics platform developed by PATH, with support from the data visualization company Tableau. It includes information on a test’s performance, where it’s made and approved for use, and whether it’s commercially available.

PATH, an organization working on health equity issues worldwide, developed the platform primarily for use by governments and policymakers, and particularly those in lower-income countries.

While much of the attention in the U.S. has been directed at American infection and vaccination rates, health experts remind people that COVID is a global concern. The original virus and many of the most problematic variants emerged outside of U.S. borders. It’s crucial that other countries are able to track and protect against the disease for the sake of their own residents and for the control of COVID worldwide.

“COVID is not going away. It’s highly suspected that’s going to become an endemic virus similar to the flu,” said Lorraine Lillis, PATH’s scientific program officer for diagnostics. “So we are going to need diagnostics to continuously monitor, diagnose and just see what it’s doing.”

The Washington state Department of Health is sequencing COVID-19 cases to track the dominance of troubling variants. That includes B.1.1.7 (the U.K. variant) and two variants from California with similar mutations: B.1.427 and B.1.429. The samples that are sequenced are not meant to precisely capture the mix of variants in the state. (DOH Image, click to enlarge)

The PATH researchers hope that their work will help highlight smaller, lesser-known diagnostics manufacturers to bring diversity to the market, and that it will encourage test makers to share data on their performance against variants.

There are two approaches for testing for COVID: rapid antigen tests that perform something like a pregnancy test, searching for pieces of the virus; and molecular tests that use PCR (polymerase chain reaction) to detect even small amounts of the virus’s genetic material.

By the end of March, the U.S. Food and Drug Administration had identified four molecular tests “whose performance could be impacted” by mutations found in some of the variants of concern. The tests contain multiple targets to guard against this sort of issue, so they should still catch positive cases. But with so many tests available and more coming on the market, it can be difficult to know which work best.

“There’s just a lot of confusion around this,” said Neha Agarwal, PATH’s associate director for diagnostics. “We did not see any kind of data aggregator built, and so we just felt the need to fill that gap.”

In addition to the diagnostic tests, researchers also take a subset of positive COVID samples and sequence the virus’s entire genetic code, which is how they can identify which variant is present and identify new mutations.

Washington state is a leader in sequencing, scrutinizing nearly 11% of the positive COVID samples in March. While the samples chosen for sequencing are not meant to perfectly represent the mix of variants in the state, it’s still easy to see that the variants are expanding over time. The B.1.1.7 variant, for example, was present in only 3.5% of the cases sampled in early to mid-February. By late March, it was responsible for 35.5% of sequenced infections.

Compared to the original COVID virus, B.1.1.7 is roughly 50% more transmissible and likely to cause more severe infections. Early research suggests that vaccines should still perform well against it.

“The tests are so far addressing the variants concern, [but] it’s still something you have to be vigilant with,” Lillis said. “These viruses, they can mutate so easily. Whenever you develop a test you want to be able to detect as many variants as possible.”

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