New tech at Kemri to enable Kenya to mass test for virus

Kenya has overcome a major bottleneck in mass testing for coronavirus, thanks to an innovation by the Kenya Medical Research Institute (Kemri).

In a twist of irony, response to diseases that brought Kenya to its knees in the last decade — Aids, tuberculosis and a brush with the deadly avian flu in 2009 — is what has enabled this breakthrough.

From the current 600 tests per day, the innovation at Kemri will see Kenya process and get results for at least 35,000 samples in 24 hours.

Tracking coronavirus

Kenya will now use the Cobas 6800 or the 8800 HIV viral load machines and the GeneXpert used for point of care testing for tuberculosis. Prof Matilu Mwau, Kemri Busia director, told the Nation that the Cobas machine is able to run as many as 5,000 tests in a day.

“In the unlikely event that we get to that point, we will be ready,” he said in a recent interview.

Health Cabinet Secretary Mutahi Kagwe in his daily updates Tuesday said the ministry will be processing the results faster than usual and will prioritise healthcare workers and people in quarantine.

By yesterday, 4,923 people had been tested as positive cases shot to 172. The Cobas machines are at least in seven government testing centres, including Kemri centres in Busia, Kisumu and Kilifi.

There is one at the Kenyatta National Hospital in Nairobi, the Coast General Hospital in Mombasa and the Moi Teaching and Referral Hospital in Eldoret. Several private labs in the country also own them.

In a previous interview, GeneXpert coordinator Jeremiah Okari told the Nation that the machines especially efficient at detecting pulmonary TB, a respiratory illness like Covid-19.

For the machines to switch from HIV and TB tests to Covid-19, the government through the Kenya Medical Supplies Authority (Kemsa) will order 100,000 special kits from Switzerland, with support from the World Health Organisation (WHO) Emergency Response Centre and the World Bank.

Kemsa Director Jonah Manjari told the Nation that the agency has ordered for the Cobas Sars-CoV-2 machines manufactured by Swiss multinational Roche, a kit that is able to test up to 4,128 patients in a day.

“Roche said they would be here in two weeks from their warehouses, and could be here faster if the clearing is done quickly,” he said.

The GeneXpert uses the Cepheid's Covid-19 test and is able to provide accurate results in 45 minutes. So how will these work?

Using the juice-making analogy, Lancet Laboratories Director Ahmed Kalebi said the Cobas 6800/8800 and the GeneXpert are ‘blenders’ which need ‘sieves’ to make different types of juice.

However, these two ‘blenders’ have ‘sieves’ for making mango juices (testing HIV and TB) but also have the capability to take other sieves for orange juice (test for Covid-19). It is these ‘sieves’ that Kemsa has ordered for: the Sars-CoV-2 and Cepheid's Covid-19 test.

According to Omu Anzala, a member of the national Covid-19 task force and a professor of virology at the University of Nairobi, testing for Covid-19 is currently done on viral genetic material obtained from nose and throat swabs using reverse transcription polymerase chain reaction (RT-PCR).

Respiratory Society of Kenya official Jeremiah Chakaya told the Nation that the “currently available test has a sensitivity of about 70 per cent, implying it will be falsely negative in up to 30 per cent of persons with Sars-CoV2”. To close this gap, Prof Anzala recommends that tests should be “run in triplicates and all of the three have to be positive for a diagnosis to be confirmed”

While there are several challenges that Kenya is experiencing with controlling Covid-19, the government has received praise from the regional health governing bodies for their laboratory capacity.

The Africa Centres for Disease Control and Prevention (Africa CDC) and its American doppelganger raised the alarm that the figures in Kenya, and Africa in general, could be an under-representation due to limited testing capacity.

In a virtual meeting, Africa CDC Director Dr John Nkengasong told the Nation: “Africa does not manufacture its own diagnostics and this has left them at the mercy of procurement delays.”

This revelation comes at a time when evidence is mounting that mass testing, which involves the test-track-and-trace approach, can allow health officials to separate the infected from the healthy and stop the virus from spreading.

The logic behind mass testing is suppression — efforts to reduce the infectivity of a pandemic. Those in the field of tracking diseases call this infectivity R0, or the R-naught.

Testing isolating people who are positive from those who are healthy is targeted to reduce the R-naught to less than one. Studies that have been carried out in Wuhan and other places show that, when unchecked, the R0 of Covid-19 is between 2 and 3, meaning that every infected person infects two to three others.

An R0 of less than 1 indicates that each infected person results in less than one new infection. When this happens, the outbreak will slowly grind to a halt.

The mass testing in Kenya has been hampered by lack of coronavirus test supplies ending in a long wait that has caused serious problems in the fight against the disease.

“Currently, the main gap to be addressed is the supply of reagents. If sample numbers increase, then a possible gap could be human resources for testing,” Kemri said on April 3.

Kenya’s biggest challenge for testing has been contact tracing, identifying then alerting people who have been within the infection range of a person confirmed to have the virus.