"Well, it's very important for us to know which variant is out there. You know, some of the variants have been linked to increase in transmission of the virus. We don't know if a variant can pop up that can lead to severe disease. So that's why it's very important in order to get ahead of the curve to be able to see which variant is present."
4. Various of lab technicians working with machines that detect COVID-19 in test samples
5. SOUNDBITE (English) Benjamin Pinsky, Stanford Clinical Virology Laboratory, medical director:
"We're doing a targeted PCR based testing to identify the mutations associated with the variants of concern such as the UK, South Africa the Brazil strain, and also the most recently identified California strain."
6. Various of lab technicians working with machines that detect COVID-19 in test samples
7. SOUNDBITE (English) Benjamin Pinsky, Stanford Clinical Virology Laboratory, medical director:
"So a number of them have these mutations that may impact their ability to be neutralized by the antibodies generated from vaccination, so they could impact the performance of the vaccines."
8. Pinsky shows machine that prepares test samples genetic analysis
9. Workers logging test samples before genetic analysis
10. SOUNDBITE (English) Benjamin Pinsky, Stanford Clinical Virology Laboratory, medical director:
"With the identification of the U.K. variant, the U.S. realized that we were quite behind in variant surveillance. And so there has been a concerted effort to get ahead of this and be able to identify these variants earlier on so that we can prepare appropriately."
11. Various of lab technician prepping test samples in vials before genetic analysis
The U.S. fell behind in the race to detect dangerous coronavirus mutations and is only now beginning to really look for them.
The problem has not been a shortage of technology or expertise. Rather, scientists say, it's an absence of national leadership and coordination, plus a lack of funding and supplies for overburdened laboratories trying to juggle diagnostic testing with the hunt for mutations.
Viruses mutate constantly. To stay ahead of the threat, scientists analyze samples for genetic changes, watching closely for ones that might make the virus more infectious or deadly.
But such testing has been scattershot.
Less than 1% of positive specimens in the U.S. are being sequenced to determine whether they have worrisome mutations. Other countries do better - Britain sequences about 10% - meaning they can more quickly see threats coming at them and try to slow or stop them.
In December, the U.S. got a wake-up call when British researchers announced they had identified a variant that seems to spread more easily.
"The U.S. realized that we were quite behind in variant surveillance. And so there has been a concerted effort to get ahead of this and be able to identify these variants earlier on so that we can prepare appropriately," said Benjamin Pinsky, medical director of the Stanford Clinical Virology Laboratory.
The Stanford lab is on the front lines of American efforts to track new strains of coronavirus. The lab each day screens thousands of test samples from around the San Francisco Bay Area.
"When the samples come to the lab, we screen them for COVID and if they're COVID-positive we now proceed to screen them to see if any of these variants are present," said Obadia Kenji, the lab's operations manager.
So far the Stanford lab has detected the presence of the U.K. and Brazil variants while screening the Bay Area samples. It identified a California strain that's responsible for about 30 percent of the region's infections.
"It's very important for us to know which variant is out there. You know, some of the variants have been linked to increase in transmission of the virus," Kenji said.
U.S. scientists have detected nearly 500 cases of a variant first identified in Britain and expect it to become the cause of most of this country's new infections in a matter of weeks. Another worrisome variant tied to Brazil and a third found in South Africa were detected last week in the U.S. and also are expected to spread.
The British variant is more contagious and is believed to more deadly than the original, while the South Africa version may render the vaccines somewhat less effective. The ultimate fear is that a variant resistant to existing vaccines could eventually emerge.
"So a number of them have these mutations that may impact their ability to be neutralized by the antibodies generated from vaccination, so they could impact the performance of the vaccines," Pinsky said.
But widespread genetic surveillance is not just a matter of looking for strains first identified overseas. Potentially worrisome variants have probably formed inside the U.S., too.
After a slow start, public health labs in at least 33 states are now doing the genetic analysis needed to distinguish emerging coronavirus variants. Other states have formed partnerships with university or private labs to do the work. North Dakota, which began sequencing last week, was the most recent to start that work, according to the Association of Public Health Laboratories.
For more than five years, U.S. public health labs have been building up their ability to do genomic sequencing, thanks largely to a federal push to zero in on the sources of food poisoning outbreaks.
At the pandemic's outset, some labs began sequencing the coronavirus right away. And until recently, those labs didn't find anything that raised alarms, experts said.
On top of that, labs continue to have trouble getting needed supplies - like pipette tips and chemicals - used in both gene sequencing and diagnostic testing.
In November, the CDC began to roll out a national surveillance program designed to methodically pull and check specimens to better determine what strains are circulating.