Scientists at the Kenya Medical Research Institute (Kemri) have warned that distinct variants of the coronavirus, entirely different from those detected in the United Kingdom and South Africa, could be circulating in the country.
Although the findings are preliminary, the investigators say that a particular variant, picked in samples collected in Taita Taveta County, in the southeastern part of the country, is not only unique to Kenya but likely to be spreading elsewhere in the country.
The vast majority of mutations are often insignificant and have little impact, says Dr Charles Agoti, a Kemri researcher and principal member of a team of investigators who reported the new findings released Tuesday.
It is, however, too soon to say with certainty, or by how much, the new variant impacts on the disease pattern in the country until more tests are completed.
Kenya’s cases of Covid-19 have been on a lower trajectory, with less than 100 cases reported over the last one week. However, health experts warn that this may just be a calm before another storm.
Now, the team of scientists from Kemri say that if the results from Taita are anything to go by, the new variant could be silently spreading. Using samples from more than 200 people in eight counties (Nairobi, Kajiado, Kilifi, Taita Taveta, Tana River, Mombasa, Kwale and Lamu) between June and October, the team identified the 16 circulating lineages. Of these, 12 sequences were recorded to be unique.
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Available genomic data drawn from sequencing of 205 nasal genomes specimens sampled from the eight counties between June and October last year identified the 16 circulating lineages.
The team noted that while four variants have continued to predominate infections in the country since the first case was reported in March, the other 12 have not expanded locally to give rise to many cases at least as of October 2020.
“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 which is done in the laboratory. Since the onset of the pandemic in the country, the Kemri team has sequenced close to 500 genomes, with 205 done between June and October. To get a clearer picture of the mutations in Kenya, the investigators on Tuesday said they will be sequencing 400 samples between January and February across multiple sites in the country.
“It’s like staring at different shots of the same picture to see the difference,” Dr Agoti added.
Since its discovery in December 2019, the SARS-CoV-2 virus which causes Covid-19 has undergone multiple changes as per the intrinsic nature of the virus. Recently, the global scientific community has raised concerns and put the world on alert over the fast pace at which two distinct variants have been spreading. The vast majority of mutations are often insignificant and have little impact, said Dr Agoti.
“If you take the number of infections confirmed in Kenya and looked at their genetic make-up, you will find that a huge number have two to three few changes that don’t change the overall behaviour of the virus.”
Whereas the scientists have not identified either of the two strains (first reported in the UK and South Africa), they detected an entirely unique amino acid change, one designated as D80A (change of the amino acid at position 80 of the spike protein from aspartic acid to alanine), in 14 samples collected in Taita Taveta.
“The virus carrying this change seems to have caused quite a significant number of infections in Taita. We have not seen this variant anywhere else in the world,” explained Dr Agoti, adding that the team is also yet to know if the genetic change has any significance on how adaptable the virus can be.
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 a virus spreads through communities or populations. Lineages, like the Taita Taveta one, can dominate in certain populations either because it was the first to “arrive” (known as founder effect) or fitter than the rest of the other lineages in circulation.
“For this case we don’t know if it’s the founder effect or if it was fitter.”
Every 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, viruses carrying these new mutations can then increase in frequency due to natural selection, explained Dr Agoti.
Viruses with an RNA genome like the coronavirus tend to mutate faster because they have less 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 the chance of a mutation occurring.
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 of the variants contain a change within the spike protein, called the N501Y mutation, thought to improve the virus’s ability to bind to our 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 Kenya so far. However, the Kemri 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 the Taita 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 that gives it its distinctive shape. Essentially, they worry about any major changes to the virus’ spike protein because such mutations not only make the virus more transmissible, they can also mean that drugs and vaccines are rendered less powerful and require them to be updated. The genetic changes can also render diagnostic tools ineffective, therefore requiring modification, noted Dr Agoti.
“If these changes are occurring in areas where diagnostic tools have been deployed, then laboratories will need to update their tools. Similarly, if these changes begin to affect vaccine efficacy, then the latter will need to be tweaked,” the lab scientist added.
Pfizer-BioNTech has said that 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 harm the effectiveness of current vaccines, there is a chance those in the South African variant may do so to some extent, say scientists, especially because vaccination is yet to kick-off in many African countries. This effect, however, may be extremely rare.
Besides the UK and South Africa, Japan’s National Institute of Infectious Diseases 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 (WHO) notes that “how and where SARS-CoV-2 VOC 202012/01 originated is unclear.”
Late Jan, early Feb 2020: A new strain with a mutation known as “D614G” emerges, which later becomes the dominant strain of the coronavirus we know today.
November 5, 2020: The ‘Denmark mink variant’ reported as a unique variant to WHO.
December 18, 2020: South Africa’s health authorities announce South African variant, known as B.1.315/501Y.V2
December 14, 2020: UK health officials report to the World Health Organisation that they have detected a new variant of concern known as B.1.1.7/501Y.V1.
January 10, 2021: Japan’s National Institute of Infectious Diseases said it had detected a new variant of the coronavirus in four travellers arriving from Brazil.