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

In an interview on Monday, Ms Wandati said she would love to know so that she can get a rough idea about her immune system’s response level vis a vis other variants.

“Not telling patients is part of the reason the government does not have data. I asked a friend who was hospitalised about his treatment and I learnt that the medication he was on was not the same as what I was on,” she said.

“For me the infection was mild because I received the first dose of the AstraZeneca vaccine before the virus showed up. My sense of smell is back and I feel stronger today, so my next test is on the 23rd and I’m hopeful it will be negative.”

In Kakamega, an official at the county general hospital acknowledged that they did not have any genomic sequencing data on existing variants in the county though the facility treats patients from Kisumu, where the Delta variant has been prevalent.

The reason, they said, is that the Kenya Medical Research Institute does not send that information to them.

“We are not usually interested in knowing which variant. All we want to know when we send over samples is how many tested positive and how many tested negative,” the official explained.

Genome sequencing is a laboratory process of determining the fingerprint of an organism.

Experts say mutations can result in a new “lineage” of the virus that is not the same as a new strain, and by tracking these lineages scientists can determine how a virus spreads through communities or populations.

For example, 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.

Variants

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

“This is because, from a clinical perspective, all Covid-19 cases are treated the same depending on the severity of the clinical status regardless of the Covid-19 variant,” he told the Nation.

“Also at present there is no definitive evidence that certain variants cause more severe disease than others in terms of how the patient should be treated.” 

The last genomic sequencing data, he said, showed that more than 50 per cent of samples tested had the Alpha and Beta variants.

“I would suspect that the Delta variant is now above 50 per cent of the total particularly in the lake basin and Western counties, as well as Mombasa and Kilifi, probably Nairobi too – for this is the trend worldwide where most countries that have transport hubs similar to our JKIA are now reporting a delta variant spike,” he said.

“The percentage for each variant simply means the number of positive samples that are confirmed from genomic sequencing to be of that particular variant out of 100 positive samples tested.”

However, determining variants is of public health interest as certain variants of concern are more rapidly infectious or transmissible than others and thus from a public health perspective it is absolutely essential for authorities to know which variants are in circulation. 

“This influences the approach in terms of mitigation and containment measures to be enforced by the authorities whereby a heightened level would be required when there is a spike in a variant such as Delta as seen in many countries who have had to take more decisive actions in response.”

Very expensive

A high-ranking official at the Health ministry told the Nation on Monday that the government is cautious that genomic sequencing data if released can be misused and abused.

“You can only be definite when you are doing genomic sequencing on a huge percentage of the positives cases, but I’m not sure we are doing enough to be honest,” the official said.

“Remember we are doing targeted testing not mass testing. Unless people suspect they are exposed, we are not doing genomic sequencing on all the positives because we cannot afford it.”

For counties, he said, genomic sequencing is only done upon request and if officials see no need for it, Kemri will not do it. He also said Kenya uses old equipment that cannot match what new technologies in other countries are delivering.

“One genomic test is very expensive and in fact far more expensive than a PCR test. In our case because of the costs we only do what we call sampling of the sample,” Dr Kalebi said.

Dr Moses Masika, a virologist, agreed: “Genomic data is not easy to generate as compared to PCR. That’s why we’ve sequenced just about 1,000 samples out of nearly 200,000 positive coronavirus cases.”

Dr Kalebi, however, suspects that the government is reluctant to share the data because of its own interests.

“If, for instance, the Delta variant is rampant according to the samples they’ve tested, such results would portray an alarming picture that as a government they’d wish to downplay for we know various foreign countries have taken drastic punitive measures against countries with a huge wave of the Delta variant, which include banning flights from those countries,” he said.

“So keeping a lid on the data for these variants would be for understandable national strategic reasons.”