Sequencing Used to Identify Delta, Other Coronavirus Variants
By Angelo Fichera
Posted on August 4, 2021
Researchers use genomic sequencing — not the clinical tests used to diagnose patients with COVID-19 — to identify and track specific variants of the novel coronavirus, SARS-CoV-2, including the highly contagious delta variant. But viral posts try to deny the existence of the variant by misleadingly claiming there is “no ‘Delta Variant’ test.”
The delta variant of the novel coronavirus — now the dominant version of the virus in the U.S. — has presented additional challenges as the country tries to mitigate the spread of COVID-19. The highly contagious variant is responsible for a surge in outbreaks across the country, particularly in areas with low vaccination rates. Vaccines still protect against the variant, especially against serious illness and death, but may be less effective against delta compared to other forms of the virus.
Yet false and misleading claims have recently sought to not only cast doubt on the seriousness of the variant, but question its existence.
One such meme shared on Facebook more than 12,000 times misleadingly asks, “Since there is no ‘Delta Variant’ test, how exactly are people being diagnosed with the ‘Delta Variant’?”
The same question was presented in a July 26 tweet shared by thousands that was posted by Errol Webber, a film producer and Republican who unsuccessfully ran for Congress in California last year. Similar posts have been shared hundreds of times each.
Adding to the misperception, at a White House press briefing July 30, Emerald Robinson, a reporter for the conservative outlet Newsmax, asked, of the delta variant, “How do you test, when — that it’s the dominant strain in the area, when people just test whether they’re COVID positive?”
White House Principal Deputy Press Secretary Karine Jean-Pierre, seemingly perplexed, said “we don’t test it” and that “we listen to public health and scientists, and they tell us that it’s the Delta variant.”
On Twitter, Robinson — who has nearly 400,000 followers — has since misleadingly claimed that “the Biden Administration is unable to provide any proof that Delta variant is real” and later that the administration “has no idea how to test for the Delta variant.”
But the various posts trying to cast doubt on the validity of the delta variant betray a lack of understanding of how variants are being identified and tracked. There is testing to identify delta and other variants, but it’s more sophisticated than the routine clinical testing — often by polymerase chain reaction, or PCR, tests — used to simply determine whether someone has COVID-19.
Dr. Benjamin Pinsky, an associate professor of pathology and medicine at Stanford University, told us in a phone interview that it’s worth first noting that “all the diagnostic tests are capable of detecting the delta variant — they just don’t distinguish it from different lineages.” In other words, the PCR tests do detect the delta variant as SARS-CoV-2.
To do that, scientists use a process called genomic sequencing. As the Centers for Disease Control and Prevention explains, sequencing is a way to decode the genes of a virus to better understand factors such as its spread and evolution.
John Everett, who helps conducts such research at Penn Medicine to understand the virus’ presence in the Delaware Valley, explained it this way: “Research institutions, including Penn, study samples collected from the community by sequencing viral genomes in those samples. We identify mutations in the genomes, compared to the original Wuhan strain, where groupings of specific mutations are used to define viral variants or lineages.”
“We track the relative rise and fall of different lineages which we can break apart by zip code to build a picture of how the different lineages are spreading in our area,” Everett, the bioinformatics director for the University of Pennsylvania lab group behind the research, told us by email.
The group’s data show how the delta variant has rapidly become the main lineage identified in most samples tested from the University of Pennsylvania Health System.
Some findings done through PCR tests can provide insights into the suspected lineage present. For example, the alpha variant — first identified in the United Kingdom in September 2020 — caused PCR failures involving the virus’ S gene, which codes for the surface spike protein, because of the variant’s mutations.
The phenomenon of variants causing test issues is expected, Everett said, which is why PCR tests check against “multiple regions of the viral genome.” That’s “another reason why surveillance is important — to identify mutations in the community which may interfere with tests and adjust the tests as needed,” he said.
Dr. Marie-Louise Landry, director of the Clinical Virology Laboratory at Yale New Haven Hospital, noted that the S gene issue “was only suggestive of alpha” since it was only one of the characteristic mutations of alpha. Sequencing the whole genome, she told us by email, is still needed to confirm that it was indeed the alpha variant.
Pinsky, who is also medical director of the Clinical Virology Laboratory for Stanford Health Care, said his lab runs a second, different PCR test on samples that are positive for SARS-CoV-2 to look for specific mutations that are seen in variants of concern and variants of interest prior to sequencing.
For the delta variant, Pinsky said, what’s known as the L452R mutation is often a telling sign: About 94% of the samples analyzed by his lab that show that mutation are proven to be delta once sequenced, he said. Moreover, about 90% of all positive samples recently sequenced by his lab are delta, he said.
“Delta is certainly not a hoax,” Pinsky said.
And while some of the viral posts online suggest patients are being “diagnosed” with the delta variant, all the experts we consulted said that patients would not be typically informed of the lineage identified — though, in areas with predominantly delta transmission, patients may be able to make inferences.
Dr. Atul Butte noted to us in an email that sequencing analyses “are NOT clinical tests.”
“These sequences are used for public health tracking and epidemiology,” said Butte, a University of California, San Francisco pediatrics and epidemiology professor who also directs the university’s Bakar Computational Health Sciences Institute. “We wouldn’t deliver any different medical care right now, based on whether one variant is present or another.”
Editor’s note: SciCheck’s COVID-19/Vaccination Project is made possible by a grant from the Robert Wood Johnson Foundation. The foundation has no control over our editorial decisions, and the views expressed in our articles do not necessarily reflect the views of the foundation. The goal of the project is to increase exposure to accurate information about COVID-19 and vaccines, while decreasing the impact of misinformation.
Butte, Atul. Professor of pediatrics and epidemiology, University of California, San Francisco. Email to FactCheck.org. 2 Aug 2021.
“CDC’s Role in Tracking Variants.” Centers for Disease Control and Prevention. Updated 17 Jun 2021.
“COVID Data Tracker.” Centers for Disease Control and Prevention. Accessed 3 Aug 2021.
“COVID-19 Vaccine Breakthrough Case Investigation and Reporting.” Centers for Disease Control and Prevention. Accessed 2 Aug 2021.
Everett, John. Bioinformatics director, Bushman Lab, University of Pennsylvania. Email to FactCheck.org. 2 Aug 2021.
Hale Spencer, Saranac. “Meme Trumpets Falsehood About Delta Variant.” FactCheck.org. 9 Jul 2021.
“Karine Jean-Pierre holds White House news briefing.” Rev.com. 30 Jul 2021.
Landry, Marie-Louise. Director, Clinical Virology Laboratory at Yale New Haven Hospital. Email to FactCheck.org. 3 Aug 2021.
“Penn Medicine Surveillance Sequencing of SARS-CoV-2 Variants.” University of Pennsylvania. Accessed 2 Aug 2021.
Pinsky, Benjamin. Associate professor of pathology and medicine, Stanford University. Phone interview with FactCheck.org. 3 Aug 2021.
“Polymerase Chain Reaction (PCR) Fact Sheet.” National Human Genome Research Institute. Updated 17 Aug 2020.
“SARS-CoV-2 Variant Classifications and Definitions.” Centers for Disease Control and Prevention. Updated 3 Aug 2021.
“Statement of Vote | General Election – November 3, 2020.” California Secretary of State’s Office. Accessed 3 Aug 2021.
“Tracking SARS-CoV-2 variants.” World Health Organization. Accessed 3 Aug 2021.
“What is Genomic Surveillance?” Centers for Disease Control and Prevention. Updated 17 Jun 2021.
“White House Daily Briefing.” C-SPAN. 30 Jul 2021.
“Why S-Gene Sequencing is Key for SARS-CoV-2 Surveillance.” Thermo Fisher Scientific. 5 Feb 2021.