COVID-19: Africa's sequencing lag

There are hundreds of variants of SARS-CoV-2, the coronavirus that causes COVID-19 infections.

The variants are split into many lineages on an ancestral tree, like related families, with branches of mothers and fathers, children, cousins, aunts and uncles, from the As to the Bs, the Cs, Ds, G, K, L, M, P, [...] Y and Z.

They are all related. But it is virtually impossible to stay on top of every single one.

We've seen that most recently with a new Variant of Interest (VOI), thought to have come out of Central Africa called B.1.620. 

Its oldest known so-called ancestor was detected in Cameroon.

Some say variant B.1.620 has traveled from Central Africa to Europe. It may well have originated somewhere else, in Europe for instance, and traveled in the opposite direction to Cameroon.

But as two authors of a first major international study into B.1.620 have told DW, the variant's origin is not really the point. At least, not for now, because we really can't tell where it originated until more of the virus gets sequenced. 

You sequence a virus' genome to work out its characteristics — how it spreads and infects people — and you need to do that at speed as and when outbreaks occur locally, so that scientists can track the variants via a global database when they spread.

But many African countries are not sequencing enough of the virus, although there are initiatives to improve the situation.

What makes B.1.620 interesting?

B.1.620 has been detected in Lithuania, France, Germany, Spain, Belgium and the Central African Republic, with evidence of what the researchers call "ongoing local transmission."

It is "quite rare outside of Africa and it's not attracting a lot of attention at the moment," says the study's corresponding author, Gytis Dudas, a researcher at the Gothenburg Global Biodiversity Centre in Sweden.

The European Centre for Disease Prevention and Control (ECDC) told DW in a statement Wednesday that "the highest number of detections [were currently] in Lithuania (77 cases), France (40), and Germany (29)."

The ECDC says B.1.620 has also been detected in the Czech Republic, Ireland, Norway, and Portugal. It's also been detected in North America. 

"The likely region of origin is Central Africa, but this is still uncertain," say experts at the ECDC.

The ECDC classifies B.1.620 as a Variant of Interest.

It has certain mutations that are found in other variants, which have gone on to become Variants of Concern.

Those mutations include E484K, P681H, and S477N, as well as several so-called "deletions" in the virus' spike protein.

The virus uses the spike protein to attach itself to human cells, infect us and spread.

What would make B.1.620 a Variant of Concern (VOC)?

"B.1.620 might become a VOC if there's strong evidence to suggest, for instance, an increased transmission advantage, or a change in immune responses [to the virus]," says Dudas.

There is a good chance, then, that B.1.620 will become a VOC.

It is already showing signs of faster transmission — it moves faster, infecting more people, quicker — and that's linked to its ability to "escape" human immune responses. Which is in part because of the mutation known as E484K.

"We can be quite certain that B.1.620 is very likely to be able to evade a lot of neutralizing antibodies that [we have] built up against other strains of the virus that don't have the mutations that this strain has," says Dudas.

The E484K mutation is present in VOCs, such as B.1.351, the South African variant, and P1, the so-called Brazilian variant. It is found in variants detected in the UK, Nigeria, the Philippines, Colombia, Russia, and the US.

"But showing a transmission advantage is extremely difficult. It takes a lot of data and often that's data from countries, where the sequencing data and the medical data can be linked very well," says Dudas.

Getting sequencing data for B.1.620 out of Central Africa, on the other hand, has been difficult.

Why do we need more sequencing?

Scientists tend to say we should be sequencing between 5% and 10% of all SARS-CoV-2 infections.

That may not seem like a lot, but the scientists in this study say it's a manageable amount and significant enough to track how a variant is progressing.

African countries, however, lag behind. Ahidjo Ayouba, a research director at IRD, France's sustainable development research institute, estimates that African countries have sequenced just 10% of about 1.5 million sequences shared at GISAID, and initiative for data sharing.

"That's across all African countries," says Ayouba, who co-authored the study on B.1.620. "Most of those sequences come from South Africa. Some African countries have only shared about 10 or 20 sequences. That's not enough to understand the circulation of different viruses in different countries."

But Ayouba knows the situation locally, first-hand.

"People just don't have enough sequencing machines. Many African countries don't have enough trained people," he says.

With more sequencing, you learn more about a virus' dynamics — how it's changing, spreading, crossing borders, and when. And the sooner you sequence it, the quicker you can catch it.

"Given the limited number of sequences we have from Central Africa, all we know is that the oldest ancestor of B.1.620 is from Central Africa, namely, Cameroon," says Ayouba. "We need more sequencing in Cameroon and other parts of Africa to understand the dynamics of this variant [over] time."

Ayouba is engaged in a knowledge transfer program with one of three authorized sequencing institutes in Cameroon. He's helped train a researcher at his own lab in Montpelier and together they will spend a few weeks sequencing the virus there, locally and in real-time.  

Why are some mutations so common?

Researchers say that the E484K mutation "crops up quite often" and that that seems to be because of our own immune response to the virus.

There seem to be particular areas of the spike protein that our immune systems prefer to target, as a means of neutralizing — or stopping — the virus. One of those virus "sites" happens to be the "484" site.

Because so many people have had the disease around the world, and many more are being vaccinated, it is "very easy," says Dudas, for the virus to change that one little part. 

But Dudas says it's still worth getting vaccinated.

"Our immune response doesn't just target that one area," he says. "We target multiple areas of the spike protein and even though we might not be able to prevent an infection or a re-infection, vaccines will still protect us from severe symptoms and very often death as well."