Kemri Lab

A researcher tests samples for Covid-19.

| Brian Ongoro | AFP

Kemri warns of 16 new coronavirus variants in Kenya

What you need to know:

  • In total, there are now 20 variants in circulation in Kenya, four having been discovered in March last year.
  • One of the four variants first reported during the Kemri’s initial sequencing has mutated and is now raising concern among the team of researchers.

Experts have warned that 16 new variants of the coronavirus could be silently spreading in Kenya.

The scientists from the Kenya Medical Research Institute (Kemri) said the variants of the virus that causes Covid-19 are entirely different from those detected in the UK and South Africa.

In total, there are now 20 variants in circulation in Kenya, four having been discovered in March last year. One of the four variants first reported during the Kemri’s initial sequencing has mutated and is now raising concern among the team of researchers.

Unique to Kenya

And although Kemri termed the findings preliminary, the investigators explained that there is one particular variant, whose samples were collected in Taita-Taveta County, that is unique to Kenya and is yet to be detected elsewhere else in the world.

Dr Charles Agoti, a Kemri researcher and principal member of the team of investigators that reported the findings on Tuesday evening, however, said the vast majority of mutations are often insignificant and have little impact.

He, however, clarified, that it is too soon to say with certainty how — or if at all — the new variant will impact the disease pattern in the country, adding that more tests need to be done.

Kenya’s cases of Covid-19 have been on a downward trajectory, with less than 150 cases reported over the past one week.

But health experts warn this could be a calm before another storm.

Silently spreading

Kemri scientists now say the new variant they picked up in Taita-Taveta could be silently spreading.

Using data drawn from nasal genome specimens of 205 people in eight counties (Nairobi, Kajiado, Kilifi, Taita-Taveta, Tana River, Mombasa, Kwale and Lamu) between June and October, the team identified 16 circulating variants.

The team noted that those seen to be dominating in the number of infections are four which were first seen in early analysis. However, one of the four variants has developed a new mutation which is raising concerns.

“What is strange about the four lineages is that they have become more widespread compared to when they were first detected in the earlier analysis we reported,” explained Dr Agoti.

Genome sequencing is the process of determining the fingerprint of an organism and is done in a science laboratory.

Genome sequencing

Since March last year, Kemri scientists have sequenced close to 500 genomes, with 205 done between June and October, with the most recent samples collected at the onset of the second wave.

To get a clearer picture of the mutations in Kenya, the investigators on Tuesday said they will sequence 400 samples between January and February in multiple sites across the country. 

“It’s like staring at different shots of the same picture to see the differences,” Dr Agoti noted.

Since its discovery in December 2019, the SARS-CoV-2 virus, which causes Covid-19, has undergone multiple changes in its intrinsic nature.

Recently, however, the global scientific community has put the world on alert over the fast pace at which two distinct variants have been spreading.

"If you take the number of infections confirmed in Kenya and look at their genetic make-up, you will find that a huge number have two to three changes that don't alter the overall behaviour of the virus,” Dr Agoti expounded.

Whereas the two strains (first reported in the UK and South Africa) are yet to be identified, scientists have detected a definitive amino acid change, one designated as D80A (meaning change of the amino acid at position 80 of the spike protein from aspartic acid to alanine), in 14 samples collected in Taita-Taveta County. 

“The virus carrying this change seems to have caused quite a significant number of infections in Taita. We have not seen this variant anywhere elsewhere in the world,” explained Dr Agoti, adding that the team could not immediately establish if the genetic change has any significance on how adaptable the virus can be.


 According to experts, mutations can result in a new “lineage” of the virus, which is not the same as a new strain.

However, by tracking these lineages, scientists can determine how fast a virus is spreading through communities or populations.

A lineage like the Taita-Taveta one can dominate a certain population either because it was the first to “arrive” (known as founder effect) or is fitter than the other lineages in circulation.

 “For this particular case we don’t know if it was the founder effect or it was fitter.”

 Once in a while, however, a virus mutates in a way that either helps it survive, reproduce, or even cause severe disease.

 If this happens, the viruses carrying these new mutations can then increase faster due to natural selection, explained Dr Agoti.

Viruses like the coronavirus that causes Covid-19 tend to mutate faster because they have low ability to fix errors when their genetic material is copied to make virus particles inside infected cells.

So, every time a virus replicates, there is a chance of a mutation occurring.

UK variant

This is what seems to be happening with the variant that has rapidly spread across the UK, known as B.1.1.7/501Y.V1, and a similar but different variant recently identified in South Africa as B.1.315/501Y.V2.

Both variants contain a change within the spike protein, called the N501Y mutation, which is thought to improve the virus’s ability to bind to human cells, making it more infectious.

A variant is a form or version of something that differs in some respect from other forms of the same thing or from a standard.

Neither of the highly infectious variants has been detected in the country so far.

However, the team did not rule out the possibility that they could be circulating, saying “genomic surveillance across Africa is very limited and, therefore, introduction and spread in Africa cannot be ruled out”.

In fact, the Kemri team noted that the N501Y mutation was found in a 43-year-old asymptomatic patient from Lamu, but said the mutation was not as significant as in the Taita-Taveta cases.

 “The significance of this is uncertain, since subsequent sampling does not suggest that viruses with this mutation have expanded,” the team said in a policy brief released by the institute.

Experts across the world have been tracking changes to the "spike" of the virus, which gives it its distinctive shape.

More transmissible

This is because any major changes to the spike protein make the virus more transmissible and render drugs and vaccines less effective, meaning they would have to be updated.

The genetic changes can also render diagnostic tools ineffective, therefore requiring modification, noted Dr Agoti.

“If these changes occur in areas where diagnostic tools have been deployed, then laboratories would need to update them. Similarly, if these changes begin to affect vaccine efficacy, then the vaccines would need to be tweaked,” he added.

Pfizer-BioNTech has said its Covid-19 vaccine will likely be effective against the variants that have been reported thus far.

In a new study conducted by scientists from Pfizer and the University of Texas Medical Branch at Galveston, the Pfizer vaccine proved to be effective on strains with the N501Y mutation.

While changes in the UK variant are unlikely to weaken the effectiveness of the current vaccines, scientists say there is a chance that those in the South African variant may do so to some extent, especially because vaccination is yet to begin in many African countries. This effect may, however, be extremely rare.

Besides the UK and South Africa, Japan’s National Institute of Infectious Diseases on Sunday said it had detected a new variant in four travellers arriving from Brazil.

There is also a suspected new strain in the US.

Although scientists are looking into whether the mutation emerged in patients with weaker immune systems who had prolonged infections, giving the virus the opportunity and time to evolve in a way that enables it to spread faster, the World Health Organisation notes that “how and where SARS-CoV-2 VOC 202012/01 originated is unclear”.