Kenya needs to revamp its genome sequencing to pick Covid variants early, expert advises

Kenya needs to analyse its coronavirus variants circulating in the country and check if they are covered by the available vaccines, a virologist has advised.

South Africa Monday announced that it would temporarily suspend using Oxford-AstraZeneca vaccine (commonly referred to as AZ or AstraZeneca) and instead deploy ones by Johnson and Johnson and Pfizer-BioNTech after a study showed that the AstraZeneca shot was not effective in preventing mild to moderate illness from the variant dominant in the country.

Although Dr Moses Masika, a virologist at the University of Nairobi, noted that for now it would be premature for the country to follow South Africa’s steps and pause the use of AZ vaccine, he said there was need to do deep local investigations to understand the extent of the spread of the variants dominant in South Africa (B.1.351 also called the 501Y.V2) and United Kingdom (named B117).

“We should appreciate that the two countries are experiencing a somewhat different trajectory in terms of numbers and most likely circulating variants,” he said in an interview with the Nation.

However, despite the low numbers, there is need to confirm how far the variant might have spread beyond the three cases. Kenya Medical Research Institute had planned to sequence 400 samples between January and February in multiple sites across the country to ascertain the extent of the spread of new variants. Results of this data are yet to be announced.

“My concern is that we have not characterised the strains circulating locally very well. The number we have sequenced so far is very small, about 500 out of more than 100,000 cases. We should sequence more genomes to know which strains are here and whether any of them poses a problem,” said Dr Masika, adding that for now, “I would not strike it [the vaccine] out of the list for Kenya yet, since we do not have any evidence to support such a decision,” he explained.

The country has identified sporadic cases of the South African variant, with the latest reported in a truck driver detected in Lunga Lunga in Kwale County following sequencing of 60 samples early this year. According to acting director-general for health Patrick Amoth, test results of contacts of the said driver have since turned negative and therefore there was no evidence the two strains are active in Kenya.

Dr Amoth said even though the B.1.351 (also called the 501Y.V2) variant, predominant in South Africa, is more transmissible, Kenya has not recorded any upsurge of cases, which so far stand at 102,048 as of Tuesday.

He however issued a high alert to counties near points of entry directing them to reactivate their rapid response teams, a day after four British troops at the Nanyuki base tested positive for Covid-19, weeks after arriving from the UK. It is not yet clear if they tested positive for the B117 variant or not. In the letter dated Monday February 8, Dr Amoth explained that a rapid increase in the number of cases will put more strain on healthcare resources, lead to more hospitalisations, and potentially more deaths.

“In view of the above, it is necessary to all counties and particularly those with official points of entry and international borders to bolster surveillance to minimise importation of the new variants and institute strong response systems to quickly contain cases in the event that they are detected in-country,” reads the letter in part.

These developments come as the country is awaiting its first shipment of vaccines targeted to innoculate about 1.25milllion frontline workers including Healthcare workers, the elderly and people with underlying disease which puts them at risk of developing severe Covid-19.

Based on the South African data, In light of recent news about AstraZeneca, the Coalition for Epidemic Preparedness Innovations (Cepi) released a statement saying – in the context of viral settings without this variant – the vaccine offers protection against severe disease, hospitalisation, and death.

"This means it is vitally important now to determine the vaccine’s effectiveness when it comes to preventing more severe illness caused by the B.1.351 variant," CEPI said in a statement.

CEPI is one of the partners of the Covid-19 Vaccines Global Access (Covax) facility, which has allocated Kenya 4.2million doses of the vaccine. AstraZeneca’s vaccine is a key two-dose jab heavily relied on by countries like Kenya as well as many other African countries because it is easy to transport, store and distribute, given that it can be stored in a standard fridge within temperature varying from 2-8 degrees. The other vaccine that African countries are banking on is the Janssen (a subsidiary of Johnson and Johnson) vaccine because it has been found to be 66 per cent effective when administered as a single dose.

But unlike South Africa which has the options to pause AstraZeneca and opt for Janssen and Pfizer’s vaccine (the latter requires complex ultra-cold conditions for storage and transportation), Kenya and other East African countries have limited options. In fact, in the East African region, Rwanda is the only country that met the required conditions that warranted an allocation of about 102,960 doses of Pfizer’s jabs.

In an analysis, submitted as a pre-print prior to peer-review publication, a two-dose regimen of the AstraZeneca vaccine known as ChAdOx1 nCoV-19 provided minimal protection against mild to moderate infection caused by 501Y.V2 coronavirus variant first identified in South Africa in mid-November 2020.

Clinical trial data are important for the drug and medical device development processing pharmaceutical companies to examine and evaluate the efficacy and safety of the new medical product in human volunteers. This data is a staple resource for most health and medical research and is either collected during the course of ongoing patient care or as part of a formal clinical trial program.

Prior to widespread circulation of the variant found to be more contagious, the vaccine was found to be about 75 per cent effective, researchers said.

However, in a later analysis based mostly on infections caused by the new variant, there was only a 22 per cent lower risk of developing mild-to-moderate Covid-19 compared to those given a placebo. Although researchers said the figure was not statistically significant, due to trial design, it is well below the benchmark of at least 50 per cent regulators have set for vaccines to be considered effective against the virus.