Covid-19: Combining genetics and geography to track SARS-CoV-2 variants

A screenshot of the interactive map created by Dr Orf that shows the spread of the B.1.416 viral lineage in August 2020 to and from Senegal and various parts of the world, especially Europe, in the middle of Senegal’s first Covid-19 wave. — Abbott

It's long been the fear of public health experts that our interconnected world would enable one virulent disease to spread quickly, with devastating effects across the globe.

That fear came to pass with the SARS-CoV-2 virus, which emerged in Wuhan, China, at the end of 2019, and subsequently spread around the world in a matter of months.

Viruses are unique as they are only able to reproduce inside the cells of another living organism.

So, being able to penetrate and make use of the resources of another organism’s body – in other works, infect a host – is crucial to the survival of a viral species.

This is the reason why viruses are able to mutate and adapt so quickly to evade the defences of their host, whether it be a plant, animal or human being.

Therefore, it was no surprise that the original version of the coronavirus rapidly mutated into a number of variants, which in turn have spawned numerous lineages.

A viral variant has one or more mutations that differentiate it from the original virus.

A lineage – which would have mutated further itself – can be traced back to one common viral variant as its ancestor.

University College London Genetics Institute director and professor of Computational Systems Biology Dr Francois Balloux said in an expert opinion provided by the Science Media Centre in the United Kingdom: “Viruses tend to evolve fairly fast with different strains constantly acquiring mutations over time.

“SARS-CoV-2 is no exception to this pattern, with each lineage acquiring two mutations a month on average.”

A mutation is a single change in a virus’ genetic code, which may or may not result in a change in the characteristics of the virus.

As it is essentially a random process, some mutations have resulted in viral variants that are more infectious and/or cause more severe illness than others, while others have no significant clinical impact.

And as we have seen so far, new SARS-CoV-2 viral variants and lineages are still emerging.

Being able to quickly identify and genetically sequence new viral variants, and track them as they spread, is of great importance to inform and implement public health measures.

These include monitoring the accuracy of diagnostic tests, which work based on identifying specific genetic sequences; ensuring both vaccines and treatments remain effective, especially vaccines that work based on specific genetic sequences; and determining the need for non-medical interventions, e.g. wearing face masks in public areas, compulsory testing and travel restrictions.

Across time and space

While many scientists around the world have taken on the task of sequencing SARS-CoV-2 viral samples as part of both national and international surveillance efforts, one group of researchers have taken it a step further by retrospectively combining the genetic information with air travel data.

These researchers from the Abbott Pandemic Defense Coalition decided to focus on Senegal as it has one of the best viral surveillance programmes in West Africa.

Dr Gregory Orf, a senior infectious disease scientist with Abbott Laboratories’ Virus Discovery team in the United States, explains: “This study is broadly in the field of what we would call molecular epidemiology.

“So that is the fusion of the genetic sequencing of the viruses, as well as understanding how the case counts grow or subside, and the geographic spread of – in this case – Senegal.”

He notes that the type of phylogenetic analysis they undertook is not new, but the Abbott researchers were the first to apply it with their partner, the Institute for Health Research, Epidemiological Surveillance and Training (IRESSEF) in Senegal.

“It has helped us better map how that local epidemic in Senegal evolved during the first two waves in the first year of the pandemic,” he says.

Basically, they were able to tackle the question of what particular SARS-CoV-2 viral variants were present in the African nation and how these variants moved in time, as well as geographically, during the period of the study from March 2020 to May 2021.

Knowing the type of public health and travel restrictions put in place to prevent the spread of the virus also allowed them to observe the effects of such measures.

Interesting interplay

As with much of Africa, the initial introduction of the SARS-CoV-2 virus to Senegal was via travellers from Europe, according to the study paper published in the journal Virus Evolution in March (2022).

However, Senegal also “returned” the favour via the dominant viral variants in its first two waves of Covid-19.

The first wave during March to October 2020 was dominated by a “homegrown” lineage descended from the B.1 viral variant, known as B.1.416.

Once restrictions were eased, this B.1.416 lineage hopped on planes to Spain, France and the UK, with Spain and France then contributing to its spread to the rest of Europe.

Subsequently, the B.1.1.420 lineage took over during the second wave of Covid-19 from November 2020 to April 2021.

This lineage originated from Italy, but evolved to become fitter and more transmissible while in Senegal before travelling back out to several other countries, especially in Europe.

Interestingly, the researchers point out that the Alpha viral variant, which was introduced into Senegal around December 2020, never became the dominant variant, unlike in many other countries around the world.

Abbott Laboratories principal research scientist Dr Mary Rodgers notes that one thing they’ve learned from the study is that you can’t always predict what will happen based on just the mutations present in a particular strain.

“We definitely found mutations that we would suspect would be leading to a variant of concern emerging, but they didn’t,” she says.

Dr Orf adds: “In most other countries around the world, Alpha became the predominant variant, and yet in Senegal, it didn’t, because there was a variant that was there that had a similar level of fitness and infectivity (B.1.1.420), and it was entrenched in that country and it sort of resisted the takeover of Alpha.

“And because it had similar infectivity characteristics to Alpha, when it was exported to other countries, it faced the same competition with Alpha, and in the places where Alpha was already entrenched, Alpha was able to resist the Senegalese strain.

“So you have this interplay between two variants that are of similar infectivity, and the one that was predominant already is the one that ended up winning out.”

Dr Orf also managed to integrate all the information into an interactive map that shows the movement of the variants according to time.

The researchers hope that this study, along with other similar research, will help policymakers make appropriate public health decisions.

“It’s like to know what could happen next, you have to have a solid foundational understanding of what happened before.

“And early in the pandemic, we didn’t have that background information, and so, studies like this are really important so that we can serve that need so that the best decisions can be made going forward,” says Dr Rodgers.

Moving forward, the researchers hope to replicate this method in a South American country in the near future.

As the research in Senegal was done before Covid-19 vaccines were available, this next study will also enable them to see how vaccination levels affect the movement of viral variants.

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