Given the large number of mutations found in the SARS-CoV-2 Omicron variant, experts in South Africa speculate it likely evolved in someone with a compromised immune system
As the SARS-CoV-2 Omicron variant spreads around the United States and the rest of the world, infectious disease experts in South Africa have been investigating how the variant developed so many mutations. One hypothesis is that it evolved over time in the body of an immunosuppressed person, such as a cancer patient, transplant recipient, or someone with uncontrolled human immunodeficiency virus infection (HIV).
One interesting facet in the story of how the Omicron variant was being tracked as it emerged in South Africa is the role of several medical laboratories in the country that reported genetic sequences associated with Omicron. This allowed researchers in South Africa to more quickly identify the growing range of mutations found in different samples of the Omicron virus.
“Normally your immune system would kick a virus out fairly quickly, if fully functional,” Linda-Gail Bekker, PhD, of the Desmond Tutu Health Foundation (formerly the Desmond Tutu HIV Foundation) in Cape Town, South Africa, told the BBC.
“In someone where immunity is suppressed, then we see virus persisting,” she added. “And it doesn’t just sit around, it replicates. And as it replicates it undergoes potential mutations. And in somebody where immunity is suppressed that virus may be able to continue for many months—mutating as it goes.”
Multiple factors can suppress the immune system, experts say, but some are pointing to HIV as a possible culprit given the likelihood that the variant emerged in sub-Saharan Africa, which has a high population of people living with HIV.
Li “was among the first to detail extensive coronavirus mutations in an immunosuppressed patient,” the LA Times reported. “Under attack by HIV, their T cells are not providing vital support that the immune system’s B cells need to clear an infection.”
Linda-Gail Bekker, PhD (above), of the Desmond Tutu Health Foundation cautions that these findings should not further stigmatize people living with HIV. “It’s important to stress that people who are on anti-retroviral medication—that does restore their immunity,” she told the BBC. (Photo copyright: Test Positive Aware Network.)
Omicron Spreads Rapidly in the US
Genomics surveillance Data from the CDC’s SARS-CoV-2 Tracking system indicates that on Dec. 11, 2021, Omicron accounted for about 7% of the SARS-CoV-2 variants in circulation, the agency reported. But by Dec. 25, the number had jumped to nearly 60%. The data is based on sequencing of SARS-CoV-2 by the agency as well as commercial clinical laboratories and academic laboratories.
Experts have pointed to several likely factors behind the variant’s high rate of transmission. The biggest factor, NPR reported, appears to be the large number of mutations on the spike protein, which the virus uses to attach to human cells. This gives the virus an advantage in evading the body’s immune system, even in people who have been vaccinated.
“The playing field for the virus right now is quite different than it was in the early days,” Joshua Schiffer, MD, of the Fred Hutchinson Cancer Research Center, told NPR. “The majority of variants we’ve seen to date couldn’t survive in this immune environment.”
One study from Norway cited by NPR suggests that Omicron has a shorter incubation period than other variants, which would increase the transmission rate. And researchers have found that it multiplies more rapidly than the Delta variant in the upper respiratory tract, which could facilitate spread when people exhale.
Using Genomics Testing to Determine How Omicron Evolved
But how did the Omicron variant accumulate so many mutations? In a story for The Atlantic, virologist Jesse Bloom, PhD, Professor, Basic Sciences Division, at the Fred Hutchinson Cancer Research Center in Seattle, described Omicron as “a huge jump in evolution,” one that researchers expected to happen “over the span of four or five years.”
Hence the speculation that it evolved in an immunosuppressed person, perhaps due to HIV, though that’s not the only theory. Another is “that the virus infected animals of some kind, acquired lots of mutations as it spread among them, and then jumped back to people—a phenomenon known as reverse zoonosis,” New Scientist reported.
Still, experts are pointing to emergence in someone with a weakened immune system as the most likely cause. One of them, the L.A. Times reported, is Tulio de Oliveira, PhD, Affiliate Professor in the Department of Global Health at the University of Washington. Oliveira leads the Centre for Epidemic Response and Innovation at Stellenbosch University in South Africa, as well as the nation’s Network for Genomic Surveillance.
The Network for Genomic Surveillance, he told The New Yorker, consists of multiple facilities around the country. Team members noticed what he described as a “small uptick” in COVID cases in Gauteng, so on Nov. 19 they decided to step up genomic surveillance in the province. One private clinical laboratory in the network submitted “six genomes of a very mutated virus,” he said. “And, when we looked at the genomes, we got quite worried because they discovered a failure of one of the probes in the PCR testing.”
Looking at national data, the scientists saw that the same failure was on the rise in PCR (Polymerase chain reaction) tests, prompting a request for samples from other medical laboratories. “We got over a hundred samples from over thirty clinics in Gauteng, and we started genotyping, and we analyzed the mutation of the virus,” he told The New Yorker. “We linked all the data with the PCR dropout, the increase of cases in South Africa and of the positivity rate, and then we began to see it might be a very suddenly emerging variant.”
Oliveira’s team first reported the emergence of the new variant to the World Health Organization, on Nov. 24. Two days later, the WHO issued a statement that named the newly classified Omicron variant (B.1.1.529) a “SARS-CoV-2 Variant of Concern.”
Microbiologists and clinical laboratory specialists in the US should keep close watch on Omicron research coming out of South Africa. Fortunately, scientists today have tools to understand the genetic makeup of viruses that did not exist at the time of SARS 2003, Swine flu 2008/9, MERS 2013.
It can take up to eight days after onset of symptoms for a person’s immune system to develop antibodies, so serological tests are not designed for diagnosing recent or active infections, stated a Mayo Clinic news story. However, Reuters reported that the availability of serological tests is “a potential game changer” because they could identify people who are immune even if they had no symptoms or only mild symptoms.
“Ultimately, this might help us figure out who can get the country back to normal,” Florian Krammer, PhD, told Reuters. Krammer’s lab at the Icahn School of Medicine at Mount Sinai in New York City has developed a serological test. “People who are immune could be the first people to go back to normal life and start everything up again,” he said.
However, some experts advise that the presence of antibodies is not necessarily a “get out of jail free” card when it comes to the coronavirus. “Infectious disease experts say immunity against COVID-19 may last for several months and perhaps a year or more based on their studies of other coronaviruses, including Severe Acute Respiratory Syndrome (SARS), which emerged in 2003,” reported Reuters. “But [the experts] caution that there is no way to know precisely how long immunity would last with COVID-19, and it may vary person to person.”
Additionally, it is also “uncertain whether antibodies would be sufficient protection if a person were to be re-exposed to the virus in very large amounts,” such as in an emergency room or ICU, Reuters reported.
Serological Survey Studies Get Underway Worldwide
Aside from detecting potential immunity, the World Health Organization (WHO) says serological tests could be useful for widespread disease surveillance and epidemiological research.
In the US, the Vitalant
Research Institute is leading several large serological survey or
“serosurvey” studies in which regional blood centers save samples of donated
blood for antibody testing, Science
reported.
Science also reported on a similar WHO initiative in which six countries will pool data from their own antibody studies. And in the Netherlands, blood banks have begun screening thousands of blood donations for presence of antibodies, Wired reported.
FDA Emergency Use Authorization
On March 16, the federal Food and Drug Administration (FDA) announced that it would allow commercial development and distribution of serological tests that “identify antibodies (e.g., IgM, IgG) to SARS-CoV-2 from clinical specimens” without an Emergency Use Authorization (EUA). The agency noted that these tests are “less complex than molecular tests” used to detect active infections, and that the policy change is limited to such testing in medical laboratories or by healthcare workers at the point-of-care. “This policy does not apply to at home testing,” the FDA reiterated.
“Serological tests can play a critical role in the fight against COVID-19 by helping healthcare professionals to identify individuals who have overcome an infection in the past and have developed an immune response,” said FDA Commissioner Stephen M. Hahn, MD (above with President Trump during a Coronavirus Task Force press briefing), in an April 7 press statement. “In the future, this may potentially be used to help determine—together with other clinical data—that such individuals are no longer susceptible to infection and can return to work. In addition, these test results can aid in determining who may donate a part of their blood called convalescent plasma, which may serve as a possible treatment for those who are seriously ill from COVID-19.” (Photo copyright: CNBC.)
FDA Issues First EUA for Rapid Diagnostic Test
Cellex Inc., based in Research Triangle Park, N.C., received the first EUA for its qSARS-CoV-2 serological test on April 1. As with other rapid diagnostic tests (RDTs) under development, the qSARS-CoV-2 test detects the presence of immunoglobulin M (IgM) and immunoglobulin G (IgG) antibodies in human blood. The biotechnology company’s RDT can be used to test serum, plasma, or whole-blood specimens, stated Cellex, and can produce results in 15 to 20 minutes.
The FDA has authorized use of the antibody test only by laboratories certified under CLIA to perform moderate and high complexity tests. Cellex has set up a COVID-19 website with information about the qSARS-CoV-2 test for clinical laboratories, patients, and healthcare providers.
Other Serological Tests Under Development
Mayo
Clinic Laboratories announced on April 13 that it is ramping up
availability of an internally-developed serological test. “Initial capacity
will be 8,000 tests per day performed at laboratory locations across Mayo Clinic,” stated the announcement.
“Testing will be performed 24 hours a day, and Mayo Clinic Laboratories is working
to ensure turnaround time is as close as possible to 24 hours after receipt of
the sample.”
Emory University in Atlanta announced on April 13 that it will begin deploying its own internally developed antibody test. Initially, testing will be limited to 300 people per day, comprised of Emory Healthcare patients, providers, and staff members. Eventually, testing will be “expanded significantly,” said Emory, with a goal of 5,000 tests per day by mid-June.
RDTs are typically qualitative, meaning they produce a
positive or negative result, stated the Center for Health Security. An ELISA
test “can be qualitative or quantitative,” noted the Center, but it can take
one to five hours to produce results.
A third type of serological test—the neutralization assay—involves infecting a patient’s blood with live coronavirus to determine if antibodies exist that can inhibit growth of the virus. The test takes three to five days in a level 3 biosafety laboratory to produce results. The Straits Times reported on one laboratory in Singapore that developed a neutralization assay to trace the source of COVID-19 infections that originated in Wuhan, China.
Serological testing is another important tool clinical
laboratories and epidemiologists can use to fight and ultimately defeat the
COVID-19 pandemic and is worth watching.
Asian locales reacted swiftly to the threat of COVID-19 by leveraging lessons learned from previous pandemics and making use of serology testing in aggressive contact tracing
America’s healthcare leaders in government, hospitals, clinical pathology, and medical laboratories can learn important lessons from the swift responses to the early outbreaks of COVID-19 in countries like Taiwan and South Korea and in cities like Singapore and Hong Kong.
Strategies such as early intervention, commitment to tracing contacts of infected people within two hours, quarantines, and social distancing all contributed to significantly curtailing the spread of the latest coronavirus pandemic within their borders, The New York Times (NYT) reported.
Another response common to the efforts of these countries and cities was the speedy introduction of clinical laboratory tests for SARS-CoV-2, the novel coronavirus that causes coronavirus disease 2019 (COVID-19), supported by the testing of tens of thousands of people in the earliest stages of the outbreaks in their communities. And that preparation and experience is paying off as those countries and cities continue to address the spread of COVID-19.
‘We Look at SARS as the Dress Rehearsal’
“Maybe it’s because of our Asian context, but our community
is sort of primed for this. We will keep fighting, because isolation and
quarantine work,” Lalitha
Kurupatham, Deputy Director of the Communicable Diseases Division in
Singapore, told the NYT. “During peacetime, we plan for epidemics like
this.”
Clinical laboratory leaders and pathologists may recall that Hong Kong was the site of the 2003 severe acute respiratory syndrome (SARS) epidemic. About 8,096 people worldwide were infected, and 774 died from SARS, according to the World Health Organization (WHO). In Hong Kong, 299 died out of 1,755 cases. However, Singapore had just 238 cases and 33 deaths.
To what does Singapore attribute the country’s lower
COVID-19 infection/death rate today?
“We can look at SARS as the dress rehearsal. The experience was raw, and very, very visceral. And on the back of it, better systems were put in place,” Jeremy Lim, MD, Co-Director of the Leadership Institute for Global Health Transformation at the National University of Singapore, told TIME.
“It’s a mix of carrots and sticks that have so far helped us. The US should learn from Singapore’s response and then adapt what is useful,” Lim added.
Singapore Debuts Serology Testing for COVID-19 Tracking
As microbiologists and infectious diseases doctors know, serology tests work by identifying antibodies that are the sources of infection. In the case of COVID-19, these tests may have aided in the surveillance of people infected with the coronavirus.
This is one lesson the US is learning.
“CDC (Centers for Disease Control and Prevention) has developed two serological tests that we’re evaluating right now, so we can get an idea through surveillance what’s the extent of this outbreak and how many people really are infected,” Robert Redfield, MD, CDC Director, told STAT.
The graphic above, which is based on data from the federal Centers for Disease Control and Prevention, illustrates how contact tracing is accomplished. “We believe this is the first time in the world where these particular tests have been used in this context of contact tracing,” Danielle Anderson, PhD, Scientific Director, Duke-NUS Medical School ABSL3 Laboratory, told Science. (Graphic copyright: CDC/Carl Fredrik Sjöland.)
‘Leaving No Stone Unturned’
As of March 27, Singapore (located about 2,374 miles from
mainland China with a population of 5.7 million) had reported 732 COVID-19
cases and two deaths, while Hong Kong had reported 518 cases and four deaths.
According to Time, in its effort to battle and treat
COVID-19, Singapore took the following steps:
Clinical laboratory testing for COVID-19 of all
people presenting with “influenza-like” and pneumonia symptoms;
Contact tracing of each infected person,
including interviews, review of flight manifests, and police involvement;
Using locally developed test to find antibodies
after COVID-19 clears;
Ran ads on page one of newspapers urging people
with mild symptoms to see a doctor; and
Government paid $100 Singapore dollars per day to
quarantined self-employed people.
The Singapore government’s WhatsApp account shares updates on the coronavirus, and Singapore citizens acquire wearable stickers after having their temperature checked at building entrances, Wired reported. The article also noted teams of healthcare workers are kept separate in hospitals—just in case some workers have to be quarantined.
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Meanwhile, in Hong Kong, citizens donned face masks and
pressured the government to respond to the COVID-19 outbreak. Officials subsequently
tightened borders with mainland China and took other action, the NYT reported.
Once the COVID-19 genetic sequence became available, national medical laboratory networks in Singapore, Hong Kong, and Japan developed their own diagnostic tests, reported The Lancet, which noted that the countries also expanded capacity for testing and changed financing systems, so people would not have to pay for the tests. In Singapore, the government pays for hospitalization as well, noted The Lancet.
Lessons Learned
The US has far less experience with pandemics, as compared to the Asian locales that were affected by the H1N1 influenza (Spanish Flu) of 1918-1920 and the H5N1 influenza (Avian Flu) of 1957-1958.
And, controversially, National Security Council (NSC) officials in 2018 discontinued the federal US Pandemic Response Unit, moving the NSC employees into other government departments, Associated Press reported.
According to the March 26 US Coronavirus Task Force’s televised
news conference, 550,000 COVID-19 tests have been completed nationwide and
results suggest 86% of those tested are negative for the disease.
The fast-moving virus and rapidly developing story are placing
medical laboratory testing in the global spotlight. Pathologists and clinical laboratory
leaders have a unique opportunity to advance the profession, as well as improving
the diagnosis of COVID-19 and the health of patients.
By taking early measures to combat the spread, the country had a medical laboratory test for COVID-19 available as early as Jan. 24, and was able to focus medical laboratory testing on the most at-risk individuals
With the Coronavirus disease 2019 (COVID-19) outbreak dominating headlines and medical laboratories under growing pressure to increase testing capacity, Taiwan’s rapid response to the pandemic could provide a critical model for other countries to follow.
Given its proximity to mainland China—just 81 miles—and the large number of individuals who frequently travel back and forth between the countries, Taiwan was at risk of having the second-highest number of imported COVID-19 cases, according to a model developed by researchers at Johns Hopkins University and the University of New South Wales Sydney. News reports indicate that, each year, about 60,000 flights carry 10 million passengers between Taiwan and China.
Data from Taiwan’s Centers for Disease Control (CDC) and Central Epidemic Command Center (CECC) indicate that the country has managed to contain the outbreak thanks to these aggressive actions.
As of March 19, Taiwan’s CECC reported a total of 108 laboratory-confirmed COVID-19 infections. That compares with 81,155 in China, 41,035 in Italy, and 10,755 in the US, according to data compiled by the Center for Systems Science and Engineering at Johns Hopkins University. When the World Health Organization (WHO) reports on the number of COVID-19 cases by country, it includes the number of COVID-19 cases from Taiwan under the totals for the People’s Republic of China. WHO made this decision several years ago, under pressure by China to not recognize Taiwan as an independent nation.
The World
Population Review website says Taiwan’s population is about 23.8 million.
But its infection rate is low even on a per capita basis: Approximately 45
infections per million population, compared with 6,784 in Italy, 564 in China,
and 326 per million in the US.
The JAMA authors noted that Taiwan was prepared for
an outbreak after its experience with the severe
acute respiratory syndrome (SARS) pandemic in 2003, which also originated
in China.
Timeline of COVID-19 Outbreak at the Earliest Stages
Taiwan apparently learned a lesson about preparedness from
the SARS outbreak the rest of the world did not and that enabled the tiny
nation to respond immediately to the novel Coronavirus threat.
The country’s efforts began on Dec. 31 with inspections of
flight arrivals from Wuhan. “When there were only a very few cases [of
COVID-19] reported in China, [Taiwanese health authorities] already went onto
every airplane that came from Wuhan,” C. Jason Wang,
MD, PhD, an Associate Professor of Pediatrics and Director of the Center for Policy, Outcomes, and
Prevention at Stanford University and lead author of the JAMA
report, told Vox.
“Health officials came on the airplane and checked people for symptoms,” he
added.
Travelers who had recently visited Wuhan and displayed
symptoms of pneumonia were quarantined at home for 14 days. Taiwan’s
CDC reported that quarantined individuals were being tested for the
2019-nCoV coronavirus (later renamed to SARS-CoV-2)
soon after it was identified. The CECC, activated in January to coordinate the
government’s response, reported the first confirmed imported case on Jan. 21.
On Jan. 24, their
CDC announced that testing for the virus was being performed at the CDC and
eight designated hospitals. Testing included samples from physicians around the
country. As of Feb. 17, daily testing capacity was about 1,300 samples, the JAMA
authors reported.
Wang told Vox that aggressive measures to identify
and isolate at-risk individuals at the earliest stages reduced the volume of clinical
laboratory tests that had to be performed. “Here in the US and elsewhere, we’re
now seeing community spread,” he said. “It’s probably been here for a while.
And so now we’re trying to see, ‘Oh, how many people should we test?’ Then, you
really need to have a very large capacity in the beginning.”
“I think the US has enormous capacity that’s currently not being used,” C. Jason Wang, MD, PhD (above), Associate Professor of Pediatrics and Director of the Center for Policy, Outcomes, and Prevention at Stanford University and lead author of the JAMA report, told Vox. “We have big tech companies that really could do a lot, right? We ought to get the big companies together. Get the governors together, get the federal government agencies to work with each other, and try to find innovative ways to think about how to best do this. We’ve got the smartest people here in the US because they come from everywhere. But right now, those are untapped resources. They’re not working together. And the federal government, the agencies, they need to collaborate a little more closely.” (Photo copyright: Stanford University.)
More Actions by Authorities
The JAMA report supplementary materials notes a total of 124 actions taken by Taiwanese authorities between Jan. 20 and Feb. 24 to contain the outbreak. In addition to the border inspections, quarantines and testing, they included integration of data between the country’s National Health Insurance Administration and National Immigration Agency, so authorities, and later hospitals, could identify any patient who had recently traveled to China, Hong Kong, or Macau.
The steps also included:
An escalating series of travel restrictions,
eventually including suspension of most passenger flights from Taiwan to China,
as well as a suspension of tours to Hong Kong or Macau.
Use of government-issued cell phones to monitor
quarantined individuals.
Fines for individuals breaking the 14-day home
quarantine.
Fines for incoming travelers who failed to
provide accurate health information.
Fines for disseminating false information or
rumors about the epidemic.
Fines and jail sentences for profiteering on disease-prevention
products.
Designation of military camps and other
government facilities for quarantine.
Nationwide disinfection of universities,
colleges, and public spaces around schools.
The government also took aggressive action to ensure
adequate supplies of surgical masks, including stepped-up manufacturing, export
bans, price limits, and a limit of one to three masks per purchase.
The JAMA authors noted that government officials issued daily press briefings to educate the public about the outbreak. Communication efforts also included public service announcements by Taiwan Vice President Chen Chien-jen, a trained epidemiologist.
A poll taken in Taiwan on Feb. 17 and 18 indicated high approval ratings for officials’ response to the crisis.
The JAMA authors also noted some “challenges” in the
government’s response. For example, most real-time public communication was in
Mandarin Chinese and sign language, leaving out non-Taiwanese citizens in the
country. And the cruise ship Diamond Princess, later found to have infections
on board, was allowed to dock near Taipei and disembark passengers. There are
also questions about whether similar policies can be sustained through the end
of a pandemic.
Still, “well-trained and experienced teams of officials were
quick to recognize the crisis and activated emergency management structures to
address the emerging outbreak,” the JAMA authors wrote. “Taiwan is an
example of how a society can respond quickly to a crisis and protect the
interests of its citizens.”
One noteworthy difference in the speedy response to
recognition of a novel coronavirus in Taiwan, compared to recognition of the
same novel coronavirus in the United States, was the fast availability of
clinical laboratory tests for COVID-19 in Taiwan.
Pathologists and clinical laboratory professionals here in
the US are frustrated that their skills and talents at developing and
validating new assays on an accelerated timeline were not acknowledged and
leveraged by government officials as they decided how to respond to the
emergence of the novel coronavirus now called SARS-CoV-2.
Scientist described the speed at which SARS-CoV-2’s full sequence of genetic material was made public as ‘unprecedented’ and medical labs are rushing to validate tests for this new disease
In the United States, headlines scream about the lack of
testing for the novel Coronavirus
disease 2019 (COVID-19). News reporters ask daily why it is taking so long
for the US healthcare system to begin testing large numbers of patients for
SARS-CoV-2, the virus that causes COVID-19. Yet, pathologists
and clinical
laboratory scientists know that new technologies for gene sequencing
and diagnostic testing are helping public health laboratories bring up tests
for a previously unknown new disease faster than at any time in the past.
At the center of the effort to develop accurate new assays
to detect SARS-CoV-2 and help diagnose cases of the COVID-19 disease are medical laboratory
scientists working in public health
laboratories, in academic medical centers, and in research labs across the
United States. Their collective efforts are producing results on a faster
timeline than in any previous discovery of a new infectious disease.
For example, during the severe
acute respiratory syndrome (SARS) outbreak in 2003, five months passed
between the first recognized case of the disease in China and when a team of
Canadian scientists cracked the genetic code of the virus, which was needed to
definitively diagnose SARS patients, ABC
News reported.
In contrast, Chinese scientists sequenced this year’s
coronavirus (originally named 2019-nCoV) and made it available on Jan. 10,
2020, just weeks after public health officials in Wuhan, China, reported the
first case of pneumonia from the unknown virus to the World Health Organization
(WHO), STAT
reported.
Increases in sequencing speed enabled biotechnology
companies to quickly create synthetic copies of the virus needed for research. Roughly
two weeks later, scientists completed sequencing nearly two dozen more samples
from different patients diagnosed with COVID-19.
Molecular biologist Kristian Andersen, PhD (above right, with graduate students who helped sequence the Zika virus), an Associate Professor in the Department of Immunology and Microbiology at Scripps Research in California and Director of Infectious Disease Genomics at Scripps’ Translational Research Institute, worked on the team that sequenced the Ebola genome during the 2014 outbreak. He told STAT that the pace of sequencing of the SARS-CoV-2 coronavirus is “unprecedented.” (Photo copyright: Scripps Research.)
Lower Sequencing Costs Speed COVID-19 Diagnostics Research
Additionally, a significant decline in the cost of genetic synthesis is playing an equally important role in helping scientists slow the spread of COVID-19.In its coverage of the SARS-CoV-2 outbreak, The Verge noted that two decades ago “it cost $10 to create a synthetic copy of one single nucleotide, the building block of genetic material. Now, it’s under 10 cents.” Since the coronavirus gene is about 30,000 nucleotides long, that price reduction is significant.
Faster sequencing and cheaper access to synthetic copies is
contributing to the development of diagnostic tests for COVID-19, an important
step in slowing the disease.
“This continues to be an evolving situation and the ability to distribute this diagnostic test to qualified medical laboratories is a critical step forward in protecting the public health,” FDA Commissioner Stephen M. Hahn, MD, said in an FDA statement.
However, the Washington Post soon reported that the government-created coronavirus test kits contained a “faulty component,” which as of February 25 had limited testing in the US to only 426 people, not including passengers who returned to the US on evacuation flights. The Post noted that the nation’s public health laboratories took “the unusual step of appealing to the FDA for permission to develop and use their own [laboratory-developed] tests” for the coronavirus.
“This is an extraordinary request, but this is an extraordinary time,” Scott Becker,
Parallel efforts to develop and validate tests for COVID-19
are happening at the clinical laboratories of academic medical centers and in a
number of commercial laboratory companies. As these labs show their tests meet
FDA criteria, they become available for use by physicians and other healthcare
providers.
Dark Daily’s sister publication, The Dark Report just published an intelligence briefing about the urgent effort at the clinical laboratory of Northwell Health to develop both a manual COVID-19 assay and a test that can be run on the automated analyzers already in use in the labs at Northwell Health’s 23 hospitals. (See TDR, “Northwell Lab Team Validates COVID-19 Test on Fast Timeline,” March 9, 2020.)
Following the FDA’s March 13 EUA for the Thermo Fisher test,
Hahn said, “We have been engaging with test developers and encouraging them to
come to the FDA and work with us. Since the beginning of this outbreak, more
than 80 test developers have sought our assistance with development and
validation of tests they plan to bring through the Emergency Use Authorization
process. Additionally,” he continued, “more than 30 laboratories have notified
us they are testing or intend to begin testing soon under our new policy for
laboratory-developed tests for this emergency. The number of products in the
pipeline reflects the significant role diagnostics play in this outbreak and
the large number of organizations we are working with to bring tests to
market.”
Pharma Company Uses Sequencing Data to Develop Vaccine in
Record Time
Even as clinical laboratories work to develop and validate diagnostic tests for COVID-19, drug manufacturers are moving rapidly to develop a COVID-19 vaccine. In February, Massachusetts-based biotechnology company Moderna Therapeutics (NASDAQ:MRNA) announced it had shipped the first vials of its potential coronavirus vaccine (mRNA-1273) to the National Institute of Allergy and Infectious Disease (NIAID) for use in a Phase One clinical trial.
“The collaboration across Moderna, with NIAID, and with CEPI [Coalition for Epidemic Preparedness Innovations] has allowed us to deliver a clinical batch in 42 days from sequence identification,” Juan Andres, Chief Technical Operations and Quality Officer at Moderna, stated in a news release.
The Wall Street Journal (WSJ) reported that NIAID expects to start a clinical trial of about 20 to 25 healthy volunteers by the end of April, with results available as early as July or August.
“Going into a Phase One trial within three months of getting the sequence is unquestionably the world indoor record,” NIAID Director Anthony Fauci, MD, told the WSJ. “Nothing has ever gone that fast.”
There are no guarantees that Moderna’s coronavirus vaccine
will work. Furthermore, it will require further studies and regulatory
clearances that could delay widespread distribution until next year.
Nonetheless, Fauci told the WSJ, “The only way you
can completely suppress an emerging infectious disease is with a vaccine. If
you want to really get it quickly, you’re using technologies that are not as
time-honored as the standard, what I call antiquated, way of doing it.”
In many ways, the news media has overlooked all the important
differences in how fast useful diagnostic and therapeutic solutions for
COVID-19 are moving from research settings into clinical use, when compared to
early episodes of the emergence of a new infectious disease, such as SARS in
2003.
The story the American public has yet to learn is how new
genetic sequencing technologies, improved diagnostic methods, and enhanced
informatics capabilities are being used by researchers, pathologists, and
clinical laboratory professionals to understand this new disease and give
healthcare professionals the tools they need to diagnose, treat, and monitor
patients with COVID-19.
