Covid-19 testing

A heath worker takes a nose swab from a man for Covid-19 testing. The number of confirmed Covid-19 cases in Kenya has risen to 104,780 after 280 people tested positive.

| File | Nation Media Group

After a year of Covid-19 war, new variants open tougher battlefront

The Centers for Disease Control and Prevention’s medical illustrator's rendition of the Sars-CoV-2 virus that causes Covid-19 is a distinct one – a gray sphere with bright red spines that is instantly recognisable.

It looms behind TV presenters during news updates, is printed on fliers, and scrolls by in tweet after tweet.

The iconic spiked representation of the novel coronavirus has become synonymous with the havoc the disease has wreaked across the world.

Today, March 12, marks a full year since the first Covid-19 case was confirmed in Kenya, as the disease was officially being declared a pandemic by the World Health Organisation (WHO).

It also marks a little over a year since Unicef launched its emergency response to protect children from the fallout of the infections. As vaccination campaigns roll out worldwide — bringing new hope to those devastated by the disease, directly or indirectly — we look back at key moments, and disturbing developments.

A new and deadly virus strikes Wuhan, China

The discovery of severe acute respiratory syndrome coronavirus 2 (Sars-CoV-2) was first reported in Wuhan, the capital of Hubei Province in Central China, on December 31, 2019. By January 23, 2020, the city was on lockdown, and tens of thousands more cases of the Covid-19 reported in the weeks to come. Even before the disease was declared a global health emergency, Unicef had shipped six tonnes of personal protective supplies to health workers on the frontlines in Hubei, China.

For weeks, the mysterious virus that created a global pandemic in just over two months saw numbers of infections and deaths grow rapidly in Europe, even as countries around the world left their borders open, with only China on their radar.

A Nation Newsplex review of the first 621 reported cases revealed that at least 37 countries and Hong Kong — a special administrative territory of China — on five continents, imported Covid-19 cases to Kenya. The UK accounted for the second-highest number (17) and the US’ 15 put it in third place.

China, the epicentre of the pandemic, contributed only two cases — a Kenyan woman from Nyandarua and a man living in Nairobi. Today, about 110,356 cases and 1,898 deaths (as of Wednesday evening) have been recorded in the country.

A year later, most countries have put the worst behind them, aided by aggressive government policies and vaccines.

The country received its first batch of vaccines early last week and has so far vaccinated about 4,000 frontline workers, most of them health professionals.

Rising cases

After a three-month break when the country’s rate of infection and fatalities were on a decline, Kenya is once again experiencing another wave, one that had been predicted by scientists at the Kenya Medical Research Institute (Kemri) through scientific projections early in the year.

The projection shows that by June 1, about 13,700 additional people will be diagnosed with Covid-19 and 116 are likely to die, the scientific paper released January 21 showed.

One of the reasons for this surge is schools reopening in January, which resulted in increased mixing between children, teachers, and parents.

Dr Moses Masika, a virologist at the University of Nairobi’s Department of Medical Microbiology, said: “Over the last year, we have seen that Covid-19 can be controlled using the simple measures that are now like a song on our lips: social distance, wash hands frequently, wear a mask and stay away from people if you are sick.

“We have also seen that anywhere in the world, every time people ignore or slacken in following these prevention measures, Covid sneaks back in. It is not seen immediately, but weeks later,” he says.

Heightened political activity that has seen people gather in large numbers could be one of the reasons the country is now facing a third wave, something that Dr John Nkengasong, the director of the Africa CDC agreed with, saying: “Kenya is a model for fighting Covid through public health measures. And each time you ease restrictions, you get a rebound of infections, It’s like applying brakes on a car, if you press them, the car stops, if you release, it moves.”

New variants fueling Covid spike

But another possibility could also be playing out: that new highly transmissible variants could be driving up infections.

In mid-December, the UK announced it had recorded a new strain of the coronavirus now known as 501Y.V2 (or B.1.1.7). This strain has been reported to be 70 per cent more transmissible than the existing strain (D614G), which had also mutated from the original virus in Wuhan in the country. After this announcement, the WHO reported the presence of this new strain in the Netherlands, Australia, and Denmark.

Barely a week later, South Africa reported yet another new strain dubbed 501.V2 (B.1.351), said to have mutated more than the UK strain and quickly become the most dominant in reported new cases of infection in South Africa.

As of yesterday, the Africa CDC announced that 15 member states had reported the UK variant while 14 had the South African variant. Both of the variants have been reported in Kenya, with Ministry of Health Director-General Patrick Amoth explaining that a team of British soldiers who tested positive for the virus shortly after entering the country in early January were, in fact, infected with the new variant circulating in the UK.

The two variants, coupled with a warning from Kemri in early January that 16 new variants could be silently circulating in Kenya, increase speculation that the third wave being witnessed in the country could be arising from the variants. However, due to the low level of genome sequencing done in the country, Dr Masika says, this cannot be confirmed unless we sequence more samples than we are currently doing.

“Out of about 110,000 confirmed cases, we have only sequenced 686, mainly by a team at Kemri-Kilifi. This means we do not have a clear picture of what variants are circulating in the country,” he says.

Coronavirus is named after the crownlike spikes that protrude from its surface. The virus is enveloped in a bubble of oily molecules, which falls apart on contact with soap.

Like all viruses, the novel coronavirus -- explains Dr Eddy Okoth Odari, a virologist -- is covered with proteins that give it its character and traits. The spike proteins, or S-proteins — the red crown-like spikes in the iconic image — allow the virus to attach to human cells. These are the proteins that make it easy for the virus to rapidly spread.

The virus also has Envelope proteins or E-proteins, represented by scattered yellow crumbs, which help it get into those cells. And membrane proteins, or M-proteins, give the virus its form. It enters the body through the nose, mouth, or eyes, and attaches to cells in the airway that produce a protein called ACE2.

Once in the cells, the coronavirus releases a snippet of genetic material called RNA, which begins making proteins that will keep the immune system at bay and help assemble new copies of the virus.

Dr Odari, a senior lecturer and researcher of medical virology in the Department of Medical Microbiology at the Jomo Kenyatta University of Agriculture and Technology (JKUAT), says the new variants improve the virus’ fitness, meaning that it can bind to the ACE2 receptors better than the original virus.

“When there is increased binding, it means that infectivity of the virus will also increase, therefore, more people are likely to be infected,” notes Dr Odari.

But it is the mutations and receptor proteins of the virus’s capability to reduce the binding capacity of the neutralising antibodies that worries him more. Antibodies are one of the body’s defence mechanisms against infections. Neutralising antibodies not only bind to a virus but also bind in a manner that blocks infection.

When an infection occurs, the body produces both an antibody and a T-cell response. Antibodies are small proteins made by the immune system that stick onto the surface of viruses. Neutralising antibodies can disable the coronavirus.

T-cells on the other hand are a type of white blood cell, which helps to coordinate the immune system and are able to spot which of the body's cells have been infected and destroy them.

“If you were infected in the first wave, your body must have generated certain memory cells and certain neutralising antibodies. These antibodies will remain in the body to protect you from subsequent infection.

“What we are seeing, however, is that if someone was previously infected and then gets the SA or UK variant, theoretically, the protection capability as a result of the first infection during the first wave will not be effective,” explains Dr Odari, adding that this is what is causing fear among scientists because it means that even the people who were already infected are now vulnerable against the new variants, a situation that can take the country back to where it was in July last year.

His fears seem to be backed by new research published in Nature, in the paper, “Antibody Resistance of SARS-CoV-2 Variants B.1.351 and B.1.1.7.” suggesting that the two variants -- first detected in South Africa and the UK, respectively -- show increased resistance to antibody neutralisation in laboratory experiments. The findings suggest that current antibody therapies and vaccines may be less effective against some variants of the virus.

One thing that the experts agree on is that all RNA viruses like Sars-CoV-2 mutate, some more than others. Many of these mutations are insignificant but occasionally, they cause changes in the structure of the virus that may make the virus more lethal.

As it is, all three 501Y variants (B.1.351, B.1.1.7, and P.1 first detected in South Africa, UK, and Brazil respectively) have a common mutation of interest (E484K), which is thought to modify the part of the virus that antibodies target. This enables the variants to escape neutralisation by most of the existing antibodies that worked for previous variants.

So, how can the country deal with a moving target that can so easily change?

The fact that it is spreading fast and has infected so many people across the world within a short time makes it possible for many mutations to occur, notes Dr Masika.

However, although the frequency of different symptoms varies, he adds, no new symptoms resulting from the variants have been noted.

“We can predict but sometimes there's not much we can do to prevent some of the events.”