Researches have identified that the coronavirus causing Covid-19 has mutated, and presently, there are two variants of the virus as seen from genetic sequencing.
With the World Health Organisation (WHO)’s call on countries to “test, test and test” as part of the strategy to contain the coronavirus pandemic, these new developments in the nature of this virus makes that call more crucial now more than ever.
Initially, Kenya had no capacity to test any suspected cases of Covid-19 and samples had to be flown to South Africa, posing several logistical challenges and delays.
But to the relief of many Kenyans, two main laboratories currently have capacity to test for the SARS-CoV-2, the virus that causes Covid-19. These are the National Influenza Centre and Kenya Medical Research Institute (Kemri) laboratories in Nairobi, Kilifi, Kericho, Kisumu and Busia.
Prof Wallace Bulimu, a research scientist and Kemri’s Rapid Response Team leader explains that the laboratory has the capacity to do the PCR test that identifies certain genetic markers unique to this virus.
“We can even do advanced testing like sequencing, to identify the genetic make-up of this virus, to be compared to the sequence in the database as a confirmatory test or for research,” he says.
The samples are collected by a swab from the nasopharynx (up ones nose) or the oropharynx (down ones throat) where the highest concentration of the virus is. The tip of the swab is dipped into a transport media to transfer it to a lab.
Once collected, the samples are packaged in what is called “triple packaging”, so that in case of any leakage, it is contained in any one of the bags minimising risk to the lab scientists handling the samples.
“The lab scientist will then check the documentation and integrity of the sample under a biosafety cabinet to protect them from any spillage or them contaminating the sample,” Prof Bulimu adds.
Due to the highly-infectious nature of the Covid-19 samples, the lab scientists decontaminate the containers containing the suspected virus with a spray containing chlorine at each and every step of handling it.
Once the sample has been confirmed at the Sample Management and Reception Facility, it is then transferred to the main lab where the actual PCR testing is done.
“At the moment we have manual processes, but the Kemri labs have high-tech digital PCR machines that can process 2,000 samples in a day,” says Buluma.
The Nairobi lab has processed over 150 samples so far, with a turnaround time of four hours, which is very long compared with the high-tech machine that can process every half hour.
The lab scientists handling these samples are donned in full personal protective gear that protects their mucus membranes – eyes, nose, mouth – areas that provide easy access of the virus into the body.
The first step during processing to ‘release’ the RNA from the virus is to deactivate it using an alcohol based disinfectant or a chlorine product. This step, according to Prof Bulimu, is the most dangerous for the scientist.
The Kemri lab scientists, however, have experience in handling dangerous pathogens, the COVID19 samples are no different to the Ebola or influenza viruses for example.
The virus is deactivated while maintaining genetic material that is retrieved to detect the type of virus present in the sample. The sample is then mixed for ten minutes with another chemical that makes it non-infectious.
After that, it is transferred to another tube that ‘traps’ the RNA before it is mixed with an enzyme, reverse transcriptase, to generate a complementary DNA of the virus through a process called reverse transcription.
This DNA is then subjected to three primers that will detect whether the SARS-CoV-2, the causative agent of Covid-19 is present. These are an N-gene, E-gene and a RdRP-gene.
The N-gene detects any strain of coronavirus present in the sample submitted. The E-gene on the other hand picks SARS-like viruses and these include SARS-CoV-1, MERS-CoV and the current SARS-CoV-2.
The RdRP-gene is specific to SARS-CoV-2, the virus in question.
“In a positive result, all three targets will light up, or at least the E and RdRP-genes,” Prof. Bulimu explains.
A negative sample will have none of the three or just the N-gene. An inconclusive sample, which must be repeated will have the N and RdRP-genes only.
The Kemri lab has received samples from the National Influenza Centre for confirmation or validation. Other samples it receives are from Mbagathi’s Isolation Unit and 13 other countries including Somalia, Seychelles, Madagascar and other Oceanic nations.