COVID-19: Evolution of the Diagnostics


Dr Simon Masha (PhD, Microbiologist) | Email:

As I gather my thoughts around this disease (COVID-19), by the time of writing this piece, there are 387,742 cases, 16,782 deaths.

102,404 people have recovered.

Looking at these numbers, we can quickly say that majority of the people who will get the infection will recover.

These numbers are largely based on infections that have occurred in the Western world. Many developing countries have gone on lock down to reduce importation of the virus, which is very commendable, given the fragility of the health systems in developing countries.

Countries will now have to slow down local transmission by accurately diagnosing infected individuals, and proactively doing contact tracing of individuals who have potentially been exposed to the virus. This process can be made faster if the Government decides to publish the names of individuals who have the infection, as those who have been in contact with the infected persons can self-quarantine (but this is a discussion for another day).

Below I summarize my current knowledge with regards to diagnosis of the virus. It is important to note that knowledge about the disease is quickly evolving, and what we know now may quickly change over the current pandemic.

1. What happens if you get COVID-19? What diagnostic tools do we have? Good news is, we can use Nucleic Acid Amplification Technique Tests (NAATs). This detects whether patients actually have the coronavirus RNA. This may be used for individuals who are currently infected since it detects the SARS-CoV-2 itself.

These tests were available from January 2019 and have the ability to differentiate SARS-CoV-2, the causative agent of COVID-19, from other coronaviruses circulating in humans.

By 28th January 2019, China’s National Medical Products Administration had approved diagnostic test kits from five companies, and the number of test kits has kept on going-up.

More good news is that Cepheid, an American company known for diagnostics using the GeneXpert platform, which utilize NAAT, have developed an automated molecular test for the qualitative detection of SARS-CoV-2, the virus that causes COVID-19.

As of 2016, Kenya had installed over 70 GeneXpert machines and currently have slightly in excess of 200 GeneXpert machines distributed across the country, mostly in County and sub-County Hospitals. This unique platform can be used to detect various pathogens, including causative pathogens for Chlamydia, Gonorrhoea, Trichomoniasis, TB, and HIV.

In Kenya, the GeneXpert machines are frequently used for the latter two infections. The new Xpert® Xpress SARS-CoV-2 test can provide rapid detection of the current pandemic, coronavirus SARS-CoV-2, in approximately 45 minutes with less than a minute of hands on time to prepare the sample.

Whilst this is good news, understandably, Cepheid may produce the test cartridges for its American market before it can export to any other country. The Kenyan government should be on the lookout on how they can utilize the wide network of the GeneXpert machines to perform diagnosis faster by engaging all facilities that have the GeneXperts.

NAATs testing will continue to be important to determine who still has the virus from individuals who have been cured. However, diagnosis is slightly more complicated than this.

If you have had COVID-19 and have recovered, the existing test for viral RNA will only tell us you are not infected. A different kind of test, called a serological test, that measures the antibodies your body makes against the virus is required.

The serological test tests our response to the virus rather than the presence of the virus. The serological tests became available in early February. This test will allow scientists to know who has or has had the infection since the antibodies will persist even after virus has been cleared.

What is known so far is all humans have not encountered this virus before, so we are all “immunologically naive,” i.e. we have no natural immunity. This in part explains why the virus has spread so quickly and has become pandemic.

Serological testing will quickly become important as we begin to turn the tide to determine who can go back to work, having already been exposed to the virus and recovered.

From a previous study of coronaviruses, we know that individuals can get re-infected. The difference is that the period of virus shedding is shorter, and fewer people will develop signs/symptoms to the disease.

In summary, there are several diagnostics options. However, in many developing countries, we will continue to rely on a long diagnostic NAAT assay, which take between 4-6 hours, and which requires batching of samples for efficiency. It also requires highly skilled personnel, and expensive equipment to perform the test.

This will slow down the time it takes to get diagnostic results and potentially impact on local transmission. Good news is, rapid NAATs and serological tests are becoming available, and with the potential for being scaled-up, more people will be accurately screened.

All countries that have been successful in combating COVID-19 have done this by scaling up testing, enabling identifying individuals who were mildly ill, as-well as asymptomatic people, and stopping them from spreading the virus.

We have to keep practicing social distancing (or physical distancing) to minimize potential contact with the pathogen, and more importantly increase our hygiene practices to slow down the spread of the virus.

Finally, many thanks to Jack Ma for the donation of various medical supplies. Maybe we should just start considering how “we” can donate financially to ensure more individuals can get tested. In the meantime, until this pandemic runs its course, #StayAtHome!

Dr Simon Masha (PhD) is a Kenyan Microbiologist | Email: