Kenya now in position to test for new coronavirus

Tuesday March 3 2020

Health CS Sicily Kariuki and Foreign Affairs CS Monica Juma.

Health CS Sicily Kariuki and Foreign Affairs CS Monica Juma give an update on the coronavirus national preparedness in Kenya's capital Nairobi on February 6, 2019. The country now has the capacity to tests samples for the virus. FILE PHOTO | NATION MEDIA GROUP 

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Two new testing facilities have been set up in Kenya to test for the coronavirus. Up to Tuesday, all samples taken from people suspected of having the virus had been sent to South Africa.

Laboratories at the National Influenza Centre hosted at the National Public Health Laboratories and Kenya Medical Research Institute (Kemri) will begin testing samples, Acting Director-General of Health Patrick Amoth said.

“We received the kits on Sunday and will now be able to test for 2019-nCoV,” Dr Amoth told Nation.

Equipping the laboratories also means that the country will no longer need to ship out samples, as the two labs can compare their results, Dr Amoth added.

Coronaviruses are named for the crown-like spikes on their surfaces. Seven coronaviruses are known to infect humans. Most cause mild to moderate respiratory symptoms and are among the viruses associated with causing the common cold. Until now, the country was unable to confirm whether any of the seven people suspected to have the virus was infected as laboratories lacked the “reagent kits” necessary to identify the coronavirus, officially designated 2019-nCoV.

The virus - previously unknown to science - has been causing severe lung disease in China and has also been detected in other countries. People are known to have died and the outbreak shows no sign of stopping soon.


The new coronavirus arriving on the scene, leaving patients with pneumonia, is always a worry and health officials around the World Health Organization (WHO) have declared a global emergency, to try and contain the outbreak and ascertain if it something far more dangerous. As a result, there has been a global rush to set up diagnostic capabilities in different countries, particularly in developing countries, with hopes of averting a global pandemic.

Testing for a novel pathogen is not as simple and straightforward because the laboratory test kits have to be newly developed and confirmed to be working well. The new coronavirus was only discovered in December 2019 in Wuhan China (2019-nCoV) whereby the Chinese laboratory had to describe its genetic make-up to confirm it is a new virus.

Confirmatory testing for such new viruses requires a sophisticated molecular test called PCR (polymerase chain reaction), which identifies the virus in a sample using specific ribonucleic acid (RNA) sequence referred to as probes, that are exact match to the virus, explains Dr Ahmed Kalebi a Consultant Pathologist and Group CEO of Lancet Group of Laboratories.

“The specific probes used in ordinary clinical setting for molecular tests on other viruses such as HIV have been developed over years and go through a long elaborate process of approval before they are manufactured for commercial use in regular laboratories and can be easily purchased by laboratories in the form of reagent kits from manufacturers,” he said.

However, for the 2019-nCOV, once the RNA sequence was published in January, only a few laboratories in the rest of the world could quickly produce their own in-house probes to test, of which the Centers for Disease Control (CDC) in Atlanta USA was among the first to do so and offered to share their probes with other reference laboratories worldwide.

The FDA in USA last week gave an exception for the probes to be used without the need for regulatory check and with the WHO announcing the 2019-nCoV a global emergency, various countries worldwide are now setting up to run the test in-country.

“Setting up the laboratories to test was not a difficult to-do process since local research and reference laboratories already have the equipment to run molecular PCR assays but the missing ingredient was the probes which are now available locally, thus the test can be done within the country through the Ministry of Health reference laboratories” added Dr Kalebi.

This means that unlike the 48 to 72 hours waiting time for results, any samples that will require to be tested for 2019-nCoV will only take 24 to 48hours.

A week ago, only two laboratories in Africa (South Africa and Senegal) could diagnose the novel coronavirus that originated in China and is rapidly spreading around the world. As of Sunday, the World Health Organization (WHO) expected every nation in Africa to be able to diagnose the disease.

So far seven people in Mombasa and Nairobi counties have been tested for coronavirus (2019-nCoV) with all confirmed as negative. Further, the Ministry of Health was following up some suspected cases in Kitui and Kiambu counties. But as of yesterday evening, Dr Amoth said there were no new suspected cases.

Kenya had been identified as one of the 13 top priority countries in the region, which due to their direct links or high volume of travel to China need to be particularly vigilant for the novel coronavirus.

But this rush is being slowed by a desperate need for virus samples necessary to validate the tests.

“Without vital diagnostic capacity, countries are in the dark as to how far and wide the virus has spread and who has coronavirus or another disease with similar symptoms,” WHO chief Tedros Adhanom Ghebreyesus told a news conference in Geneva on Monday.

As of early Monday, there had been 40,235 confirmed cases reported in China and 909 deaths, as well as 319 cases in 24 other countries, including one death.

Quick and accurate diagnosis of infectious disease is a critical tool to manage outbreaks. As the number of people infected with the novel coronavirus, 2019-nCoV, grows and the death toll multiplies, many labs and commercial entities have ramped up their work developing diagnostic tests, while others have jumped into the fray by providing test reagents.

Most of the testing is being done by public health laboratories. Last week, CDC announced it had developed a new laboratory test kit for use in testing patient specimens for 2019 novel coronavirus (2019-nCoV). The test kit is called the “Centers for Disease Control and Prevention 2019-Novel Coronavirus Real-Time Reverse Transcriptase (RT)-PCR Diagnostic Panel or RT-PCR 2019-nCoV.”

Researchers are also working to develop antibody tests that can tell whether someone has been exposed to the virus. They could help answer how broadly this virus has spread, and whether there are milder cases not being detected, Dr. Mike Ryan, head of the WHO emergency program, told reporters.

WHO has activated a network of 15 referral laboratories that can support national efforts in confirming new cases, and has identified 168 labs globally with the technology to diagnose the virus. Technicians must be trained to run the tests locally to avoid delays associated with having to send them to centralised labs.