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Why hunting, tracking, analysing and studying SARS-CoV-2 and other pathogens must continue

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Regardless of the pandemic moving into the endemic phase in certain regions, Mary Rodgers, principal research scientist at Abbott and Gregory Orf, senior scientist at Abbott explain to Viveka Roychowdhury the importance of keeping early surveillance detection systems in place as “a threat somewhere is a threat everywhere. Thus accurate diagnosis via testing and effective vaccinations remain the essential combination in keeping case numbers down

Dr Rodgers, in our last interview, in February 2020, we were discussing your team’s discovery of a new strain of HIV called HIV-1 Group M, subtype L and you said, “To end the HIV pandemic, we must continue to outthink this virus”. Do you think we will ever be close to out-thinking the SARS-CoV-2 virus?

Mary Rodgers: We’ve made incredible advances in only two years to build new tests, vaccines and other tools to combat SARS-CoV-2. As immunity continues to increase from infections and vaccinations, we hope to see COVID-19 rates stabilize and become endemic or potentially seasonal like the flu and other respiratory viruses. Going forward, we need to keep up our pandemic defenses through ongoing surveillance, testing and global collaboration between public health, the scientific community and industry to make sure we are continuing to keep pace with SARS-CoV-2 as it evolves.

Part of your work to out-think this virus has been about tracking its mutations as it spreads through the world. Your recently published study in Virus Evolution found significant differences in the mutations in the SARS-CoV-2 variants during Senegal’s first wave in mid-2020 and the second wave in late 2020. As the world comes to terms with the latest SARS-CoV-2 variant, XE, which is estimated to be more transmissible, explain to us the significance of these findings.

Rodgers: Viruses are continuously changing through an accumulation of mutations – they are being tested by nature to make the virus fitter and more adapted to humans. Over time, the right combination of mutations shows up and the pathogenicity or transmissibility of the virus changes. At this point, it can become a variant of concern. 

These studies tell us what to be looking for going forward- what mutation combinations could lead strains to develop into variants of concern because they confer a fitness advantage. We continue to retrospectively study Omicron and other variants to stay a step ahead of this pandemic and new threats.

What are the factors aiding the global spread of infections like SARS-CoV-2?
Rodgers: We live in a more global, interconnected world than ever before. And there are no shortages of pathogens- in fact there are 10 million times more viruses on Earth than stars in the universe. The next virus is just an air flight away. As such, novel disease outbreaks are increasing, driven by factors such as globalisation, climate change, population growth and closer contact between humans and animals. 

Explain to us how Abbott’s app demonstrates this geographic spread, and correlates specific changes in the lineage of the virus to greater transmissibility and severity of regional and global waves of the pandemic.

Gregory Orf: In Senegal, Abbott has an existing surveillance partnership with IRESSEF, the Institut de Recherche en Santé, de Surveillance Epidémiologique et de Formation as part of the Abbott Pandemic Defense Coalition (APDC). We worked with IRESSEF to collect and analyze samples of SARS-CoV-2 from the first two waves of infections in 2020 and early 2021 for this study.

Our findings showed that these Senegalese variants had higher levels of fitness and infectivity from their mutation characteristics; in fact one variant was able to prevent Alpha’s takeover in the country.

Since these variants were more fit, we decided to utilise a special kind of calculation called a phylogeographic analysis. This allowed us to take the genetic data and merge it with air travel data to predict the import of SARS-CoV-2 into Senegal, and its export and dispersal from Senegal to other parts of the world. Including air travel data was important because it adds a layer of information that can help resolve ambiguities that the genetic information alone may leave.

This type of analysis is not new, but it helped us map and better illustrate the travel of these variants’ month-by-month. Of particular importance is that the early variant B.1.416, after emerging in Senegal, was exported to Europe – first to France and Spain, and then onto the UK, Italy, and others. After variant B.1.1.420 was imported from Italy, it was re-exported back to Europe as well as the US, Japan, and Australia.  

These study insights are important because they illustrate for the larger public health and scientific community how far and fast a variant can travel, and which mutations are gaining fitness so we can anticipate what to look for in the next variants of concern.  

This kind of work is the result of the Coalition’s mission to help prevent future viral threats. The APDC is a first-of-its-kind, industry-led global scientific and public health partnership dedicated to improving early detection and rapid response to viral threats. With 14 scientific and public health organisations, the Coalition is actively hunting, tracking, analysing and studying SARS-CoV-2 and other pathogens.

How can these insights from molecular surveillance of SARS-CoV-2 variants help scientists predict future variants and their impact?

Rodgers: Simply looking at a variant’s sequence won’t tell us if it will become a variant of concern- we have to look deeper to understand how that variant performs- its level of fitness, patterns of infection and transmissibility. And that’s what we’ve been learning through our scientific studies. When we dive deeper into factors that drive a strain to become more predominant or to cause more cases, we unravel more of the mystery around SARS-CoV-2.

The argument is that with increasing community spread and some countries already close to approaching the endemic phase, would resources spent on genomic screening be better deployed elsewhere, like on medicine research or increasing hospital beds, etc. How can governments and policy makers best make use of such data while planning pandemic measures like imposition of lock downs, investing in genomic screening of samples, etc?

Orf: Continued genetic screening will remain instrumental for many reasons. First, it informs diagnostic manufacturers like Abbott about how well their tests continue to accurately diagnose cases, and it also informs vaccine manufacturers about how to further tailor or optimize their vaccines as the virus evolves. Regardless of the pandemic moving into the endemic phase in certain regions, accurate diagnosis via testing and effective vaccinations remain the essential combination in keeping case numbers down. Governments and policy makers benefit from the early surveillance detection systems remaining in place to inform our ability to respond rapidly and protect our communities. A good example of this recently was our APDC partners in South Africa alerting the world to the Omicron variant weeks before significant cases of it were seen outside South Africa. This head start gave world governments the chance to prepare, even if the case counts in their own countries were low at the time.

What are the learnings from such global viral surveillance programmes for future infectious disease research and control?

Rodgers: A threat somewhere is a threat everywhere: fighting pandemics requires a multi-sector approach that include governments, academia, international agencies, and industry working together.

That’s why Abbott launched the Pandemic Defense Coalition last year. Global collaboration is needed more than ever to help us prepare for and help prevent future viral threats. The Coalition offers speed because it breaks down global barriers and streamlines sharing of virus information and samples. The quicker an emerging pathogenic threat can be found and characterised, the quicker it can be controlled – we can ensure diagnostic tests are developed to detect the threat and that vaccines and therapeutics are effective in preventing and treating it.

What is the progress on other diseases like HIV, that Abbott’s viral surveillance program is tracking?

Rodgers: We continue our work on hepatitis and HIV today and have expanded our research with our Coalition partners. For example, Abbott is partnering in India with YRG Care in Chennai. We are looking at viral evolution and transmission patterns for diseases including HIV, hepatitis, and SARS-CoV-2, especially in marginalized and transient populations. Our work together can inform test and treat programs to help effectively reduce the incidence and spread of these diseases in and out of the country. We also work together with on virus discovery to mitigate future pathogens of concern.

Many countries do not have the funding or infrastructure for such studies. How will these gaps impact global health and what are the short term solutions?

Rodgers: One of the silver linings of the pandemic is that it created more awareness to gaps in public health and pandemic preparedness. That’s why its critical to maintain global collaboration. No single institution can prepare a country for the next pandemic – we have to work together.

Regular communication is key to the success of these public-private partnerships. Government, industry, and academia work most effectively together to share what they’re learning about infectious disease and emerging public health threats freely.

Finally, in the longer term, we’ll need to build our virus-hunting workforce. The World Health Organization recommends a global ratio of one field epidemiologist for every 200,000 people. Only a fraction of countries has met that goal.

Initiatives like the Training Programs in Epidemiology and Public Health Intervention Network, which Abbott has a fellowship program with, is already training epidemiologists in more than 100 countries, can help. We must build up our pipeline of scientists and infrastructure across the world to raise pandemic defenses everywhere.

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