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Clinical Laboratories and Pathology Groups

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More Countries Are Now Capable of Genome Sequencing and Contributing to Global COVID-19 GISAID Database than Ever Before

GISAID hosts a vast, open database of genomic sequences of SARS-CoV-2 coronavirus samples, and medical laboratory scientists in countries across the globe are contributing

Clinical laboratories around the world have been contributing to the global scientific community’s database of knowledge about SARS-CoV-2, the coronavirus that caused the COVID-19 pandemic, and its variants, through an ingenious and crucial network known as GISAID. This cooperative sharing of the coronavirus’ genetic data (now four million genomic sequences strong) has greatly contributed to understanding the spread of infections and progress obtained in developing effective treatments and vaccines.

Headquartered in Munich, Germany, GISAID, which stands for Global Initiative on Sharing Avian Influenza Data, was created in 2008 during the Avian Influenza (Bird Flu) pandemic. The GISAID initiative promotes “the rapid sharing of data from all influenza viruses and the coronavirus causing COVID-19. This includes genetic sequence and related clinical and epidemiological data associated with human viruses, and geographical as well as species-specific data associated with avian and other animal viruses, to help researchers understand how viruses evolve and spread during epidemics and pandemics,” according to the GISAID website.

Clinical pathologists are likely familiar with GISAID. The initiative has become an indispensable tool for researchers battling SARS-CoV-2. GISAID allows scientists and organizations worldwide to upload genetic sequences of COVID-19 samples. Those sequences can then be used in research for treatments, vaccines, and to track emerging variants. The information is invaluable, freely available, and represents the collaborative efforts of scientists around the world in the fight against COVID-19 and other infectious diseases.

An article published in The World, titled, “From Congo to Chile, Small Labs Are Playing a Growing Role in Global Understanding of COVID,” noted that more than four million genomic sequences have been submitted as of October 15, 2021. The more countries around the world that submit sequences to GISAID, the more understanding scientists have of how the virus is mutating. And, as the cost of performing genomic sequencing declines, the number of countries submitting genomes of SARS-CoV-2 to GISAID is rising.

How GISAID Ensures Contributors Receive Credit for Their Work

One of the reasons that GISAID has been so successful in gathering data is that it requires anyone who uses data downloaded from the massive database to give credit to the person or organization who uploaded it. In other words, if a scientist in the United Kingdom (UK) does breakthrough research using genomes that were originally uploaded to GISAID by a scientist in the Congo, the UK scientist must credit the work of the scientist from the Congo.

Other genomic databases do not have this requirement and genetic researchers are often hesitant to share information due to fear their work will be co-opted by others. According to The World, scientists in lower income countries are particularly vulnerable to having their work appropriated.

Even worse is having one’s work appropriated, used to create a product, and then not being given access to that product.

Christian Happi, PhD

“Unfortunately, we’ve seen also the situation whereby people have leveraged that data and created the solution and refused to share the solution with those that shared the data,” virologist Christian Happi, PhD (above), who directs the African Center of Excellence for Genomics of Infectious Diseases (ACEGID) at Redeemer’s University in Nigeria, told The World. “And that is definitely going to roll back this whole open data sharing and access principle.” Happi is also a Visiting Scientist in the Department of Immunology and Infectious Diseases at Harvard’s T.H. Chan School of Public Health. (Photo copyright: Pius Utomi Ekpei/AFP/News 24.)

That is why GISAID’s policy of giving credit is so important, as molecular biologist Francine Ntoumi, PhD, told The World. “This means that we are going to participate in the game. We are able to say what is circulating. You are no more an observer and I think it makes a difference.” Ntoumi is Founder and Executive Director of the Congolese Foundation for Medical Research (CFMR) in the Republic of Congo, a lecturer in Immunology at Marien Ngouabi University, and Associate Professor and Head of a Research Group at the Institute of Tropical Medicine at the University of Tübingen, Germany.

The guarantee that credit will be given softens some of those fears and explains why the GISAID database is so vast, and increasingly contains sequences from scientists in Africa, South American, and other places where genomic sequencing was not widespread prior to the pandemic. Information from all over the world is crucial for scientists monitoring the mutations of the SARS-CoV-2 coronavirus.

Criticisms of GISAID

The fact that more countries are contributing to the GISAID database is certainly a positive, but the non-profit is not without its critics. There have been complaints about the lack of transparency, and some researchers claim to have had their access denied to the data without any explanation.

An article published in Science reported that “Scientists live in fear of losing access to the GISAID database.”

One scientist who requested anonymity told Science, “I am so tired of being scared all the time, of being terrified that if I take a step wrong, I will lose access to the data that I base my research on. [GISAID] has that sword hanging over any scientist that works on SARS-CoV-2.”

In response to these criticisms, GISAID said in a statement, “Any individual who registers with GISAID and agrees to the GISAID terms of use will be granted access credentials. … On rare occasions, GISAID has found it necessary to temporarily suspend access credentials to protect the GISAID sharing mechanism,” The World reported.

The strict sharing rules may be necessary to encourage researchers in lower income countries to contribute their genomic data on SARS-CoV-2. Charles Rotimi, PhD, a geneticist at the National Human Genome Research Institute (NHGRI), told Science, “To make scientists, especially from developing countries, more comfortable—making sure that they are recognized in the work that they are doing—sometimes you have to create an extra layer [of protection].”

GISAID has certainly accomplished much in its assembling four million SARS-CoV-2 genetic sequences. The initiative’s efforts have contributed to a substantial increase in the number of countries around the world that now have gene sequencing capabilities.

This is another illustration for clinical laboratory managers and pathologists of how continual technology advances in gene sequencing equipment and data analysis software make it significantly cheaper, faster, and more accurate to do genetic sequencing. This was not true, just a few years ago.

—Dava Stewart

Related Information:

From Congo to Chile, Small Labs Are Playing a Growing Role in Global Understanding of COVID

Africa CDC Ramps Up Training on SARS-CoV-2 Genomics and Bioinformatics

The Cost of Sequencing a Human Genome

Critics Decry Access, Transparency Issues with Key Trove of Coronavirus Sequences

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

Molecular Diagnostics Laboratory in a Suitcase Travels to Farms to Test Livestock

New molecular point-of-care testing systems already being tested in several African countries

Pathologists will be interested to learn that sophisticated point-of-care molecular diagnostics testing is now being done on livestock in farms. This is a giant leap forward for point-of-care testing, as there are now commercially available suitcase-sized devices used to perform molecular diagnostic tests for avian flu in livestock. These molecular testing systems are undergoing trials in Africa, primarily Sudan and Kenya.

Development of the devices was partially funded through a joint project of the International Atomic Energy Agency (IAEA) and the Food and Agriculture Organization (FAO). The organizations are concerned about trans-boundary animal diseases that, like the avian flu, can cross from one species to another. These agencies funded research to develop molecular diagnostic methods to rapidly identify such diseases. The avian flu test is the first to make use of this new molecular technology.