A private jet, the crimson “A” of the University of Alabama painted on its tail, lifted off from Tuscaloosa, Ala., around daybreak Saturday with extraordinary cargo: cellular debris collected from the nose of Nick Saban, the football coach.

Three days earlier, Saban had announced that he had tested positive for the coronavirus. Now, still in isolation hours before second-ranked Alabama was to play third-ranked Georgia, Saban knew the specimen aboard the plane was his diagnostic lifeline to the sideline. If a laboratory in Mobile, Ala., reported that the sample was negative for the virus, Saban, who had asserted that he had no symptoms and had repeatedly tested negative after his initial result, would be allowed to leave isolation a week early and coach in the prime-time game.

And so it was. Hours after a final negative result — and with no small help from a rule change that Southeastern Conference leaders approved six days before the positive test that shocked Alabama — millions of people watched on television as Saban led the Crimson Tide to a 41-24 victory.

The episode underscored two aspects of the response to the virus: Even the most rigorous tests — in this case a polymerase chain reaction, or P.C.R., widely considered the gold standard of infectious disease diagnostics — can falter. And, more than seven months into the nation’s coronavirus crisis, access to testing remains inconsistent, except among America’s elite.

While tests remain scarce in many communities, and too expensive to allow some leagues and universities to compete this fall, they have more than once helped break a prominent figure out of isolation.

“It’s a reminder of the stark disparity between the haves and have-nots,” said Dr. Ashish Jha, dean of the Brown University School of Public Health.

Alabama’s football program is clearly one of the haves. Anchored by one of the most celebrated brands in college football — the university claims 17 national championships, including five during Saban’s tenure, now in its 14th season — Alabama’s athletic department is among the country’s wealthiest. Bryant-Denny Stadium just had a $107 million renovation, and Saban is to earn more than $9 million for this season.

As the pandemic has strained athletic finances on campuses nationwide, it has, in some ways, put Alabama’s resources and football obsession on greater display. The SEC, for instance, requires its football teams to be tested at least three times a week under a protocol that hinges almost entirely on P.C.R. testing, one of the most accurate and expensive techniques on the market. But Alabama opted for daily screenings of its football players and coaches.

Early last Wednesday afternoon, Saban learned that one of his P.C.R. tests, which had been processed at a local laboratory, had come back positive. He headed home, oversaw practice via Zoom and held a news conference from afar, saying he had been “very surprised” by the result. (Alabama declined to comment beyond Saban’s public remarks and the statements the athletic program issued last week.)

With the case count around the football complex low — only Saban and the university’s athletic director tested positive, according to Alabama — and Saban an evangelist for masks and physical distancing, people in Tuscaloosa and elsewhere wondered whether that Wednesday test was flawed.

P.C.R.-based tests for the virus hunt for specific stretches of genetic material, which they can copy repeatedly until their targets reach detectable levels. That makes it easy to identify the virus, even when it is scarce, and difficult to mistake something else for the pathogen. But as with any procedure, mistakes are possible.

Differences in the way the test samples are handled, processed and analyzed can upend results. Pressure to speed up the turnaround time for results could also make it harder to keep machines running in tiptop shape, or to ensure consistency from test to test.

“The most likely culprit was probably some sort of contamination,” possibly from a nearby sample that came from someone who actually had the virus, said Sarah Jung, the scientific director of clinical microbiology at Children’s Hospital Colorado. “This is detecting things we can’t see. That makes it all the more difficult.”

Mishaps are also bound to happen during a flood of tests. Alabama’s athletic department has said little about its testing throughout the pandemic, but the football program is administering at least 120 screenings a day, Saban suggested on ESPN on Saturday. The SEC’s 14 athletic programs are collectively running thousands of P.C.R. tests every week.

“It’s a game of numbers,” Dr. Jung said. “I’m not saying it’s inevitable, but when groups like this test a lot, the chances for a situation like this to occur increase.”

Even under ideal circumstances, the best products will occasionally fail, Dr. Jha said.

“There is not something that is 100 percent perfect,” he said. “That’s why you do confirmatory tests.”

Alabama swiftly began its investigation into Saban’s positive result. There were medical reasons to try to confirm the result, but urgent football ones, too.

Less than a week before Saban said he had tested positive, the SEC’s chancellors and presidents had approved an update to the league’s medical protocols. Under the new policy, an asymptomatic person like Saban who tested positive for the virus could take another P.C.R. test within 24 hours. If that test yielded a negative result, the person could take two more P.C.R. tests, each separated by 24 hours. If all three results were negative, the player, coach or staff member could return to athletics.

The Coronavirus Outbreak ›

Words to Know About Testing

Confused by the terms about coronavirus testing? Let us help:

    • Antibody: A protein produced by the immune system that can recognize and attach precisely to specific kinds of viruses, bacteria, or other invaders.
    • Antibody test/serology test: A test that detects antibodies specific to the coronavirus. Antibodies begin to appear in the blood about a week after the coronavirus has infected the body. Because antibodies take so long to develop, an antibody test can’t reliably diagnose an ongoing infection. But it can identify people who have been exposed to the coronavirus in the past.
    • Antigen test: This test detects bits of coronavirus proteins called antigens. Antigen tests are fast, taking as little as five minutes, but are less accurate than tests that detect genetic material from the virus.
    • Coronavirus: Any virus that belongs to the Orthocoronavirinae family of viruses. The coronavirus that causes Covid-19 is known as SARS-CoV-2.
    • Covid-19: The disease caused by the new coronavirus. The name is short for coronavirus disease 2019.
    • Isolation and quarantine: Isolation is the separation of people who know they are sick with a contagious disease from those who are not sick. Quarantine refers to restricting the movement of people who have been exposed to a virus.
    • Nasopharyngeal swab: A long, flexible stick, tipped with a soft swab, that is inserted deep into the nose to get samples from the space where the nasal cavity meets the throat. Samples for coronavirus tests can also be collected with swabs that do not go as deep into the nose — sometimes called nasal swabs — or oral or throat swabs.
    • Polymerase Chain Reaction (PCR): Scientists use PCR to make millions of copies of genetic material in a sample. Tests that use PCR enable researchers to detect the coronavirus even when it is scarce.
    • Viral load: The amount of virus in a person’s body. In people infected by the coronavirus, the viral load may peak before they start to show symptoms, if symptoms appear at all.

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