• Rapid tracking of emerging pathogens or variants of concern of known pathogens is key to stopping the next pandemic, epidemic or outbreak.
  • We need global cooperation to support and improve health surveillance and monitoring systems in countries.
  • Dr. Tulio de Oliveira, the scientist who alerted the World Health Organisation about the Omicron variant proposes setting up a "Global Fund" to support low- and middle-income countries build genomic surveillance capabilities.

The scientific understanding of the coronavirus is constantly evolving along with the virus itself. From when the virus was first discovered until today, the sequencing and sharing of the genetic code has provided an unprecedented view on how the genomes of the pathogen evolve, the encoded genes for proteins necessary for the virus to infect humans, and for the rapid development of vaccines to contain the pandemic.

As the world now faces a new outbreak with COVID-19 Omicron variant, learning to cope with such uncertainty and the global response to it will define the future course of this pandemic.

Repositories of viral genomic sequences and associated data are proliferating globally. The Ebola outbreak in the mid-2010s accelerated the development of genome sequencing which allowed policymakers and scientists to implement appropriate public health measures to contain the outbreak. Also, the research done at the time could assist in future public health decision making.

To strengthen global viral sequencing and surveillance, there is a need to ensure that any new architecture, systems, standards, or access models are informed by technologists, data systems experts, clinicians, diagnostics and therapeutics developers. This would also require streamlining local-to-global public health decision making and strengthening professionals to deliver fast results. Questions of who can access the data, under what conditions, and how the results will serve the public good will need to be addressed.

South Africa and the United Kingdom were the first big countries to implement nationwide genomic surveillance efforts for the COVID-19 virus as early as April 2020. We spoke with Dr. Tulio de Oliveira, Director of the KwaZulu-Natal Research and Innovation Sequencing Platform (KRISP), University of KwaZulu-Natal and the Director of the Centre for Epidemic Response and Innovation at Stellenbosch University.

How global cooperation helped detect the Omicron variant

Professor De Oliveira and his team were the scientists who first alerted the World Health Organization (WHO) and other authorities to the new Omicron variant. He noticed an alarming uptick of COVID-19 related cases in Gauteng Province and initiated an investigation to understand why they were growing. Gauteng had previously had the largest wave of infections relating to the Delta variant. The anomalies in the samples collected were first detected by scientist Alicia Vermeulen at Lancet Laboratories, a member in the surveillance network, which had sent in six genomes of a very mutated virus. It had also been reported in small numbers from Botswana and Hong Kong.

The data was soon uploaded to GISAID, a global repository which promotes the rapid sharing of data from all influenza viruses and the coronavirus causing COVID-19. Professor de Oliveira shortly after discovered and reported the outbreak to the WHO.

Laboratories examine the properties of the virus and the characteristics of its viral growth, then compare them with those of other virus variants. It is then tested how well the virus can be neutralised by antibodies found in the blood of vaccinated or recovered individuals. We still do not know enough about the Omicron variant until studies are concluded with previously infected or vaccinated individuals, but what we know so far about the Omicron variant points to two urgent requirements in our global response:

  • Universal vaccination is still our best bet against severe COVID-19.
  • The global health architecture needs to be strengthened to protect and promote the wellbeing of all people.

“Fast and honest reporting of a new discovery to trigger the necessary global response to an outbreak is the most important factor”, says de Oliveira. “That’s why as soon we became aware of this new mutation, I contacted our Director General of Health (in South Africa), and the WHO. We continued to have many discussions with top scientists in the field who were collecting hundreds of samples from multiple clinics to confirm if this was a small cluster outbreak or widespread in other geographic regions.”

Global cooperation and investment to replicate timely health surveillance and reporting such as in South Africa could ensure early pathogen detection and inform outbreak response.

A global financial support mechanism for data

De Oliveira proposes a “global fund” that would act as a financial mechanism to support federation of data from viral sequencing efforts in certain low- and middle-income countries, especially with breakthrough infections such as witnessed by the Omicron variant.

“Countries like South Africa which have a large population living under the poverty line and a developing economy take a huge hit when faced with a travel ban as an intervention to outbreaks," he says. "Industries now face huge economic damage, and many people are losing their jobs in a country where the unemployment rate is already very high.”

De Oliveira said he feels the travel ban imposed on South Africa and other Southern African nations upon reporting of the Omicron variant might discourage other countries from reporting such discoveries. However, a formalized global financial support mechanism for low- to middle-income countries would motivate them to be quicker and more transparent with the identification of pathogens or variants of global concern.

Timely and transparent sharing of genomic data is critical to avoid future pandemics and that’s why we need a system that could compensate countries that identify and share information that is of global concern.

—Tulio de Oliveira, Network for Genomic Surveillance, South Africa

"Our role as scientists is to protect the world against such risks and we cannot end up in a situation where scientists or governments decide to keep quiet for three or four weeks," he says. "Timely and transparent sharing of genomic data is critical to avoid future pandemics and that’s why we need a system that could compensate countries that identify and share information that is of global concern.

De Oliveira also stresses on the urgency of universal vaccination and urges governments to deliver on their promises to COVAX. This is the only way to rebuild trust in global health cooperation and restrict future outbreaks of COVID-19 and associated economic damage, he says.

A global strategy for pathogen detection

In May 2021, WHO Member States adopted Resolution 74.7 urging countries to increase their capacity to detect new threats through laboratory techniques, such as genomic sequencing. As waves of COVID-19 disease transmission continue, there is global urgency to strengthen genomic surveillance and real-time tracking of pathogens with pandemic and epidemic potential.

Recognizing the global momentum and clear need for stronger cross-cutting pathogen sequencing and bioinformatics, WHO is coordinating the development for this global strategy. The strategy aims to provide a high level vision to strengthen and scale genomic surveillance for quality, timely and appropriate public health actions in local to global systems.

The WHO Director General, Dr. Tedros Ghebreyesus, is advocating for a legally binding treaty to strengthen the global health architecture. The WHO Member States are setting up an intergovernmental negotiating body that will begin negotiations on an international agreement, for there to be a more coherent and equitable response to future pandemics.