Aug 1, 2021

Mawazo Writing Africa

Writing about the main

Why Kenya is dragging feet on genomic sequencing for Covid-19

“I would like to know what level of concern might be in my system, but my results only show that I tested positive,” said Nairobi-based senior journalist Zeynab Wandati.

In In an interview on Monday, Ms. Wandati said she would like to know so that she can get a rough idea of ​​how responsive her immune system is to other variants.

“Not telling patients this is one of the ways Reasons why the government doesn’t have dates. I asked a friend who was in the hospital about his treatment and learned that the medication he was taking was not the same as the one I was receiving, “she said.

” Was with me the infection was mild because I got the first dose of the AstraZeneca vaccine before the virus showed up. My sense of smell is back and I am feeling stronger today, so my next test is on the 23rd and I hope it comes back negative. ”

In Kakamega, a county hospital official confirmed that they did not have genome sequencing data Variants in the county, although the facility is treating patients from Kisumu, where the Delta variant was widespread.

The reason they said is that the Kenya Medical Research Institute does not send this information to them. < / p>

“We are usually not interested in knowing which variant. When we send samples, we just want to know how many tested positive and how many tested negative, ”the officer explained.

Genome sequencing is a laboratory process used to determine an organism’s fingerprint.

Experts say mutations can lead to a new “lineage” of the virus that is not identical to a new strain, and by following those lineages, scientists can determine how a virus spreads through communities or populations.

For example, lineages such as Taita Taveta may dominate certain populations, either because she “arrived” first (known as the Founder Effect) or was fitter than the rest of the other lineages in circulation.


Dr. Ahmed Kalebi, a consulting pathologist and founder of Lancet Kenya, says that knowing the variant has no direct clinical relevance to the management or treatment of the individual Covid-19 patient.

“That’s because that from a clinical point of view all Covid-19 cases are treated equally depending on the severity of the clinical status regardless of the Covid-19 variant, “he told the nation.

“Also, there is currently no definitive evidence that certain variants cause more cause more serious illness than others in terms of patient treatment.”

Recent genome sequencing data, he said, showed that more than 50 percent of the samples tested showed the alpha and beta variants.

“I would suspect that the delta variant is now mainly in the lake basin and in the western counties as well as in Mombasa and Kilifi, probably also in Nairobi, over 50 percent of the total amount – because that t is the trend around the world where most countries that have similar hubs to our JKIA are now reporting an increase in delta variants, “he said.

” The percentage for each variant is simply the number of the positive samples confirmed by genome sequencing. this particular variant out of 100 positive samples tested. ”

However, the determination of variants is of public interest as certain variants of concern are more contagious or transmissible than others and therefore from a public health perspective for the It is imperative for authorities to know which variants are in circulation.

“This affects the approach to mitigation and containment measures that need to be enforced by the authorities, which would require an increased level, when something like Delta increases, as seen in many countries that have had to take more decisive action in response. ”

Very expensive

A senior official The Department of Health told the Nation on Monday that the government is careful that genomic sequencing data, if made public, will be misused and abused “You can only be sure if you genome sequencing on a large percentage of positive cases, but I’m not sure we’re doing enough to be honest,” the official said .

“Remember, we do targeted testing, not bulk testing. Unless people suspect they are exposed, we don’t do genome sequencing for all positive results because we can’t afford it. ”

For counties, he said, genome sequencing is only done on request and if officials don’t see the need for it, Kemri won’t. He also said that Kenya is using old equipment that cannot keep up with new technologies in other countries.

“A genome test is very expensive and, in fact, much more expensive than a PCR test. In our case, for reasons of cost, we only do what we call sampling the sample, ”said Dr. Kalebi.

Dr. Moses Masika, a virologist, agreed: “Genomic data are compared to. not easy to generate PCR. For this reason, we only sequenced around 1,000 samples out of almost 200,000 positive coronavirus cases. “

Dr. Kalebi suspects, however, that the government is not disclosing the data out of its own interest.

“If, for example, the Delta variant is widespread according to the samples they tested, such results would paint an alarming picture that they would want to downplay as a government, knowing that various countries have taken drastic measures to punish countries with a huge wave of the Delta variant, including banning flights from those countries, “he said.

” The data Keeping these variants under control would therefore be for understandable national strategic reasons. ”