Scientists monitor new mutation of the Delta variant 

Mashujaa Day

Revellers enjoy time off at the Jomo Kenyatta Public Beach on Mashujaa day on October 20, 2021. Many Kenyans preferred to stay indoors due to the hard economic times occasioned by Covid-19. 

Photo credit: Wachira Mwangi | Nation Media Group

What you need to know:

  • Last week, the government relaxed the restrictions after the country controlled its fourth Covid-19 wave.
  • Ministry of Health is keenly monitoring the spread of the AY.4.2 sub-variant through genomic surveillance.

A new coronavirus descendant related to the Delta variant, called AY.4.2, is being closely monitored by scientists in the US, UK, Russia and Israel.

The news came a day after Kenya relaxed its Covid-19 rules by lifting the dusk-to-dawn curfew, increasing gatherings in areas of worship to two-thirds, and allowing entertainment joints to operate between 5pm and 11pm like the pre-lockdown era.

Last week, the government relaxed the restrictions after the country controlled its fourth Covid-19 wave.

Acting Director General of Health Patrick Amoth on Thursday said although Delta remains the dominant variant circulating in the country, the ministry is keenly monitoring the spread of the AY.4.2 sub-variant through genomic surveillance.

“Remember the progress the UK made in their vaccination but you see the situation they are now grappling with because of this sub-variant. We are keenly looking at it because it can easily disrupt our vaccination programme,” said Dr Amoth.

Coronavirus has continued to mutate and change as it has spread across the globe in the last two years. The most concerning new variant of the coronavirus is an offshoot of the Delta variant called AY.4.2. It is currently spreading in the UK and has confirmed presence in US, Russia, and Israel.

Virus mutation

Though still rare, scientists are anxiously tracking the sub-variant, which in the UK has been found to be responsible for a growing proportion of Covid-19 cases. Although AY.4.2 has only recently been recognised by virologists who follow the genetic evolution of Delta, it already accounts for almost 10 per cent of UK cases. 

Prof Walter Jaoko, director of Kavi Kenya AIDS Vaccine Initiative (Kavi) institute of clinical research, said it is too early to know what the changes in the spike protein enable the new virus subtype to do in the human body. 

“There is a lot we still do not know and nobody knows if the changes on the two sites of the spike protein make it do, for example, make the sub-variant more aggressive in transmission, causing severe disease or enables it to escape immune response,” said Prof Jaoko, a professor of medical microbiology and tropical medicine.

One of the key biological characteristics of the severe acute respiratory syndrome (SARS)-CoV-2, the virus that causes Covid-19, is the presence of spike proteins that allows the virus to penetrate host cells and cause infection.

This spike protein is the focus of most Covid-19 vaccines as it is the part of the virus that enables it to enter human cells. Mutations to the spike protein lead to questions about the vaccine because the three leading jabs — Pfizer, Moderna, and Oxford/AstraZeneca — all train the immune system to attack the spike.

For a virus mutation to be classified as a variant of concern (VoC), scientists check for three things: Whether the variant is more transmissible, causes severe disease compared to existing variants like Alpha, Beta, Gamma, and Delta, or it escapes immunity developed either naturally from infection or vaccination, explained Prof Omu Anzala, a virologist and microbiologist at Kavi.

Variant under investigation

While many different AY lineages of the Delta variant have been documented to date, AY.4.2 has caught the attention of virus-watchers around the world recently because it has two changes located on the viral spike protein, which could perhaps give it some advantages. But it is unclear if that is the case yet.

“So far, from the information I have seen from the UK, there is a high likelihood that Delta Plus does not escape natural or vaccine immunity, but this is a matter still under investigation,” Prof Anzala said.

AY.4.2, which has not been assigned a Greek letter by the World Health Organisation (WHO) and listed by the UK as a variant under investigation (VUI), has garnered global attention from the infectious disease community due to its two changes located on the viral spike protein, which could perhaps give it some advantages.

So, with all the unknowns, should Kenya worry? “In Kenya, we are not able to tell whether the sub-variant is already in the country or not because we do not do enough genomic sequencing. There are a lot of ifs yet to be answered,” noted Prof Jaoko.

Prof Anzala, however, noted that due to the country’s significantly low vaccination levels, the emergence of this new subtype is not only a cause of worry globally but also locally. As of October 22, data from the Health Ministry shows that only 5.2 per cent of adults in the country have been fully vaccinated.

Experts are now calling on Kenyans not to drop their guard despite the country recording low daily infections and deaths.

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