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Could Omicron Variant Have Links to HIV? Infectious Disease Experts in South Africa Say ‘Yes’

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.

In South Africa alone, “2.2 million people are infected with HIV that is undetected, untreated, or poorly controlled,” infectious-diseases specialist Jonathan Li, MD, told The Los Angeles Times. Li is the Director of the Virology Specialty Laboratory at Brigham and Woman’s Hospital in Massachusetts, and the Director of the Harvard University Center for AIDS Research Clinical Core.

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

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.

Stephen Beale

Related Information:

Classification of Omicron (B.1.1.529): SARS-CoV-2 Variant of Concern

Full Transcript: Tulio de Oliveira on “Face the Nation,” December 12, 2021

How South African Researchers Identified the Omicron Variant of COVID

Stanford Researchers Looking at Possible Link Between Omicron COVID Variant and HIV

Did a Collision of COVID and HIV Forge the Omicron Variant?

Omicron: South African Scientists Probe Link Between Variants and Untreated HIV

How HIV and COVID-19 Variants Are Connected

Omicron’s Explosive Growth Is a Warning Sign

The Scientist in Botswana Who Identified Omicron Was Saddened by the World’s Reaction

Did HIV Help Omicron Evolve?

How Did the Omicron Coronavirus Variant Evolve to Be So Dangerous?

Why Fighting Omicron Should Include Ramping Up HIV Prevention

Network for Genomic Surveillance in South Africa (NGS-SA) to Rapidly Respond to COVID-19 Outbreaks

Serological Antibody Tests a ‘Potential Game Changer’ and Next Phase in Efforts to Combat the Spread of COVID-19 That Give Clinical Laboratories an Essential Role

IVD Companies and medical laboratories are developing serological survey testing that will enable them to determine how widespread COVID-19 has become

While medical laboratories gear up for testing to detect SARS-CoV-2—the novel coronavirus that causes the COVID-19 illness—efforts also are underway for expanded use of serological tests that can detect whether an individual’s immune systems has developed antibodies against the SARS-CoV-2 virus, as well as serological surveys that epidemiologists will use to determine the extent of the infection in whole populations.

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.

The Center for Health Security at the Johns Hopkins Bloomberg School of Public Health lists dozens of other serologic tests that are under development, approved for use in other countries, or approved for research or surveillance purposes. Most are rapid diagnostic tests, but some developers are working on enzyme-linked immunosorbent assays (ELISA).

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.

—Stephen Beale

Related Information:

Coronavirus (COVID-19) Update: Serological Tests

Policy for Diagnostic Tests for Coronavirus Disease-2019 during the Public Health Emergency

Advice on the Use of Point-of-Care Immunodiagnostic Tests for COVID-19

Serology-based Tests for COVID-19

FDA Officially Authorizes Its First Serological Antibody Blood Test for COVID-19

Cellex Cleared to Market Antibody Test for COVID-19

What Are Antibody Tests and What Do They Mean for the Coronavirus Pandemic?

Cellex qSARS-CoV-2 IgG/IgM Rapid Test

IgG/IgM Rapid Test Approved by FDA for EUA Use

EDI Novel Coronavirus COVID-19 ELISA Kits

Mayo Clinic Laboratories Launches Serology Testing In Support of COVID-19 Response

Asian Cities, Countries Stand Out in the World’s Fight Against COVID-19, US Clinical Laboratory Testing in the Spotlight

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

It was Singapore where scientists first experimented with serology testing to track the breadth of coronavirus infection in a community, Science reported, adding that the tests are different from the SARS-CoV-2 tests, which analyze genetic material of the virus from a person’s samples. (Dark Daily recently covered such genetic testing in “Advances in Gene Sequencing Technology Enable Scientists to Respond to the Novel Coronavirus Outbreak in Record Time with Medical Lab Tests, Therapies,” March 18, 2020.)

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.

Singapore’s Health Ministry and its Duke-NUS Medical School previously used an experimental serology test for contact tracing the source of 23 COVID-19 cases at a Singapore church, according to Science.

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. 

“Singapore is leaving no stone unturned,” Tedros Adhanom Ghebreyesus, PhD, Director-General of WHO, told TIME.

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.

—Donna Marie Pocius

Related Information:

Tracking the Coronavirus: How Crowded Asian Cities Tackled an Epidemic

What We Can Learn from Singapore, Taiwan, and Hong Kong About Handling Coronavirus

Singapore Claims First Use of Antibody Test to Track Coronavirus Infections

CDC Developing Serologic Tests That Could Reveal Full Scope of U.S. Coronavirus Outbreak

Singapore Was Ready for COVID-19, Other Countries Take Note

Are High-Performing Health Systems Resilient Against the COVID-19 Epidemic?

Trump Disbanded NSC Pandemic Unit That Experts Had Praised

Advances in Gene Sequencing Technology Enable Scientists to Respond to the Novel Coronavirus Outbreak in Record Time with Medical Lab Tests, Therapies

Taiwan’s Containment of COVID-19 Outbreak Demonstrates Importance of Rapid Response, Including Fast Access to Clinical Laboratory Tests

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.

But after the first reports emerged of the infection in Wuhan, China, “Taiwan quickly mobilized and instituted specific approaches for case identification, containment, and resource allocation to protect the public health,” wrote C. Jason Wang, MD, PhD; Chun Y. Ng, MBA, MPH; and Robert H. Brook, MD, ScD, in an article for the Journal of the American Medical Association (JAMA), titled, “Response to COVID-19 in Taiwan Big Data Analytics, New Technology, and Proactive Testing.”

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. 

—Stephen Beale

Related Information:

Taiwan CDC Press Releases about COVID-19

Is Taiwan’s Impressive Response to COVID-19 Possible in Canada?

Taiwan Has Been Shut Out of Global Health Discussions. Its Participation Could Have Saved Lives

Taiwan Has Only 77 Coronavirus Cases. Its Response to the Crisis Shows That Swift Action and Widespread Healthcare Can Prevent an Outbreak

What the U.S. Can Learn from Taiwan’s Response to Coronavirus

What Taiwan Can Teach the World on Fighting the Coronavirus

As Coronavirus Hot Spots Grow, Taiwan Beating the Odds Against COVID-19

They’ve Contained the Coronavirus. Here’s How

How Many Tests for COVID-19 Are Being Performed Around the World?

Advances in Gene Sequencing Technology Enable Scientists to Respond to the Novel Coronavirus Outbreak in Record Time with Medical Lab Tests, Therapies

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.

On Feb. 4, 2020, the US Food and Drug Administration (FDA) issued its first emergency use authorization (EUA) for a diagnostic test for the coronavirus called 2019-nCoV Real-Time RT-PCR Diagnostic Panel. The test was developed by the US Centers for Disease Control and Prevention (CDC).

“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,

Chief Executive of the Association of Public Health Laboratories (APHL), told the Post.

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.”

So far, the FDA has issued a total of seven EUAs:

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.

—Andrea Downing Peck

Related Information:

To Fight the Coronavirus, Labs Are Printing Its Genome

DNA Sleuths Read the Coronavirus Genome, Tracing Its Origins and Looking for Dangerous Mutations

FDA Takes Significant Step in Coronavirus Response Efforts, Issues Emergency Use Authorization for the First 2019 Novel Coronavirus Diagnostic

Coronavirus (COVID-19) Update: FDA Issues Emergency Use Authorization to Thermo Fisher

A Faulty CDC Coronavirus Test Delays Monitoring of Disease’s Spread

Moderna Ships mRNA Vaccine Against Novel Coronavirus (mRNA-1273) for Phase 1 Study

Drugmaker Moderna Delivers First Experimental Coronavirus Vaccine for Human Testing

China Detects Large Quantity of Novel Coronavirus at Wuhan Seafood Market

Scientists Claim SARS Breakthrough

Discovery of ‘Hidden’ Outbreak Hints That Zika Virus Can Spread Silently

Research Use Only Real-Time RT-PCR Protocol for Identification of 2019-nCoV

Interim Guidelines for Collecting, Handling, and Testing Clinical Specimens from Persons for Coronavirus Disease 2019 (COVID-19)

Roche’s Cobas SARS-Cov-2 Test to Detect Novel Coronavirus Receives FDA Emergency Use Authorization and Is Available in Markets Accepting the CE Mark

Hologic’s Molecular Test for the Novel Coronavirus, SARS-CoV-2, Receives FDA Emergency Use Authorization

Emergency Use Authorization (EUA) Information and List of All Current EUAs

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