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COVID-19 variants are surging in America and scientists are learning the vaccine may not work as well against them. USA TODAY

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New variants of the COVID-19 virus are likely much more widespread in New Jersey than the current official count of 50 confirmed cases, because the state — like most in the U.S. — lacks the capacity to do the complex, labor-intensive testing needed on a large scale, experts say. 

The state laboratory has conducted only 171 genetic sequences of virus samples, less than 1% of the more than 96,000 positive COVID tests registered in New Jersey since health officials announced the state's first confirmed case of the highly contagious B.1.1.7 variant on Jan. 22.

Despite efforts to ramp up sequencing using more private labs, New Jersey finds itself flying blind to the variants' presence — much as state health officials did in the early days of the pandemic last year, when testing was minimal. 

“We can’t sequence every sample, but we need to do more to get a better understanding of how rapidly it's spreading," said Dr. Stanley Weiss, an epidemiologist at Rutgers New Jersey Medical School. "We don’t have that capability right now."

Coronavirus cases along with hospitalizations and other key data have dropped steadily since early January, suggesting that the second wave of the virus is fading.

But Gov. Phil Murphy said last week that the variants present such an unknown threat that he has held off some reopening plans and now recommends wearing two masks, as recommended by the federal Centers for Disease Control and Prevention. 

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The CDC has warned that the B.1.1.7 from the United Kingdom could be the dominant COVID strain as early as next month.

Three major variant strains — B.1.1.7 and ones from Brazil and South Africa — are the product of natural mutations of the virus that originated in China. 

All three have been detected in the U.S. and have shown to spread more easily, which may lead to more cases of COVID-19, more hospitalizations and more deaths, causing concern for public health officials worldwide. Vaccines are believed to work against the variants, though they may not be as potent.

More: South African coronavirus variant found in Long Island resident, Cuomo says

What isn't known is how widely they've spread. 

Only the B.1.1.7 variant has been detected in New Jersey. There were 50 cases as of Friday, with one death attributed to it — a person with "significant underlying conditions," said state Health Commissioner Judy Persichilli.

Dr. Eddy Bresnitz, one of Gov. Phil Murphy's top public health advisers, said last week that the amount of sequencing being carried out is "reasonable." The state lab had done 107 sequences as of Wednesday with 64 pending, Bresnitz said. 

"We are paying attention to it," he said. "We do think it's a big deal. We are doing what we think is appropriate."

But others believe New Jersey just doesn't have the capacity to detect the variants — a process that can be done effectively only by sequencing the entire genome with special machines. The process takes 22 to 26 hours at Hackensack Meridian Health's laboratory — one of the few facilities in the state that can do the work. 

"We don't have a surveillance program in place," said Dr. David Perlin, the chief scientific officer for Hackensack Meridian. "Can we capture variants and assess the threat? Right now it's not coordinated."

In New Jersey, tests for the variant are conducted on COVID specimens from people who have traveled from Brazil or South Africa during the pandemic. Random samples taken at sites across New Jersey are also sent for testing in an effort to determine whether there is community spread. New Jersey has also sent 111 random samples to the CDC for sequencing.

Most sequencing is done at the state Public Health and Environmental Lab in Ewing, but health officials say they are trying to expand that to other public and private facilities.

The Health Department did not have a list of all the commercial labs capable of genetic sequencing but said labs at Princeton, Rutgers and Hackensack Meridian are already doing the work.

New Jersey-based Quest Diagnostics has doubled its ability to sequence samples in the past month to 2,000 a week, the company recently announced. But that's still a small sample compared with the 250,000 to 300,000 regular COVID-19 tests performed in New Jersey each week.

"When variant cases are confirmed, local and state public health officials perform an investigation that includes contact tracing," said Dr. Ed Lifshitz, a communicable disease expert at the state Health Department. "Contacts are notified and advised to quarantine."

Weiss said there is no way to know how prevalent the variants are in New Jersey without more robust sequencing.

“The overall case numbers are nearly useless in terms of informing us of the threat," he said of the 50 confirmed variant cases. "They say nothing about how common it is.”

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New Jersey is not alone. A Washington Post analysis showed that the U.S. had sequenced about 0.32% of its total cases as of late December — ranking it 43rd in the world.

The variants are not a surprise. And like the seasonal flu, COVID-19 will likely have to be managed via different treatments and vaccines that may have to be taken annually as the virus continues to mutate. 

"It's time for us to understand that the vaccine that's being administered now will not be the entirety of the solution," Perlin said. "This is how a highly contagious virus operates."

Scott Fallon covers the environment for NorthJersey.com. To get unlimited access to the latest news about how New Jersey’s environment affects your health and well-being,  please subscribe or activate your digital account today.

Email: fallon@northjersey.com 

Twitter: @newsfallon 

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