South Africa: COVID-19 - Testing to Be Ramped Up and New Tests in Pipeline

South Africa's strategy to defeat COVID-19 (Coronavirus Disease 2019) is to lockdown the country and upscale testing to quickly identify individuals who may have been infected with the SARS-CoV-2 virus.

As the country entered its first day of the 21-day lockdown, Health Minister Zweli Mkhize announced the country's first two deaths from COVID-19. Both deaths were in the Western Cape - one in the public and one in the private health sectors. The number of confirmed cases has also tipped the 1000 mark. Globally over half-a-million people have been infected and around 23 000 have died.

Plan to boost testing capacity

To stem the tide of infections the National Health Laboratory Service (NHLS) is planning to boost testing capacity to 36 000 tests a day by the end of April. According to the NHLS, it is currently testing around 5 000 samples a day.

On Tuesday morning Mkhize said at a media briefing that a total of 12 815 tests had been conducted in the country and that around 10 000 of these were done in private laboratories. If around 5 000 test were conducted each day since then, the total tests conducted should now be well above 25 000.

To meet the 36 000 per day target, the number of testing laboratories will be increased from six to nine by end of next month and the number of mobile laboratories will go up from four to 20.

Globally efforts are continuing to urgently develop new diagnostics and to increase testing capacity to catch positive cases.

Local health experts have argued that for South Africa's lockdown to have maximum impact it must be accompanied by expanded testing, contact tracing and isolation of those who are infected.

In some countries, such as Italy where initial testing was slow, high infection rates have put pressure on health facilities and the primary focus has shifted from testing for possible infection to having enough beds and ventilators for the seriously ill. In South Korea, on the other hand, testing began early and vigorously which together with contact tracing lead to the country bringing its epidemic under control relatively quickly.

The tests we use at the moment

The NHLS uses the current gold standard for testing which is done on viral genetic material taken from nose and throat swabs. The test uses a molecular biology tool called reverse transcription polymerase chain reaction (RT-PCR). It is a high through-put machine and works by extracting the viral genetic information from a patient's sample and "amplifying" the genetic sequence (essentially making more of the genetic material) to create enough of it to test for the virus.

According to Professor Tulio de Oliveira, a geneticist and Director of KRISP - a Research and Innovation Sequencing Platform in KwaZulu-Natal, PCR tests have the advantage of picking up positive cases before a person displays any symptoms. "This is very important especially for health care workers who, if positive for the virus, can self-isolate and prevent the infection from passing onto others." He however warned that with high demand from countries across the globe it would be difficult to get a steady supply of reagent, an ingredient for PCR tests.

Dr Kamy Chetty, Chief Executive Officer of the NHLS, says there is adequate testing capacity and equipment to meet the demand in South Africa. "The NHLS is pursuing various sources of supplies to obtain PCR-based test kits and has a commitment from suppliers that South Africa will be a priority," she said.

Adding to the COVID-19 testing arsenal, Dr Chetty said more than 180 GeneXpert analysers will be made available in all provinces for testing by April. The test kit for the GeneXpert was approved by the United States' drug regulatory body, the FDA last week, and the company has started production. The test kits are due to arrive next month. GeneXpert machines are already being used extensively in the country to test for tuberculosis.

"The advantage, according to the supplier, is that the GeneXpert tests can be processed in 45 minutes, and the smaller machines can be placed in mobile vehicles which makes it ideal for community testing," Dr Chetty says. "It's a pity that this new test kit was not available sooner, as it would have made a huge difference to how testing gets done. We are nevertheless pleased that it will be ready shortly," she added.

Serological tests

Serological tests for COVID-19, not yet available in South Africa, differ from PCR tests in that they look for antibodies rather than for the viruses' genetic material. A positive serological test thus indicates that someone has at some point been infected with SARS-CoV-2, but does not necessarily indicate current infection. PCR tests on the other hand can only tell if someone is currently infected.

Professor De Oliveira said such antibody tests would be useful to find out the percentage of a population that has been infected. "This means that positive health care workers could be released to return to work and presumably become resistant to infection. It also could, in theory, allow areas where a high percentage of the population were infected to be released from lockdown." He added that there is a lot still to understand about the new pathogen. "We currently believe that a person will get infected only once, but we need more data to fully understand the risk of secondary infection."

According to the New York Times, antibody tests are already being used in Singapore, China (which has eight different types of anti-body testing kits) and a handful of other countries. But, they only are just coming to market in the West.

Public Health England, in the United Kingdom said that millions of 15-minute home coronavirus tests will become available to people self-isolating. The test which resembles a pregnancy test, involves pricking a finger to produce a drop of blood, which is then analysed by the device. Delivery, however, will only happen once the rapid test has been thoroughly evaluated.

The test aside, scientists are eager to learn how long COVID-19 antibodies give immunity to people who have developed them. Early evidence suggests that antibodies to coronaviruses may last some time. Antibodies to Middle East Respiratory Syndrome (MERS) and Severe Respiratory Syndrome ARS were still active in humans three years after they were infected.

Potential CRISPR tests

Prominent CRISPR researchers are also working on using this still relatively new gene-editing technique to make faster, more accurate tests. The jury is however still out on whether a CRISPR test for SARS-CoV-2 will be developed in time.

Such a test will work similarly to the PCR test. When and if the viral sequence is found, a protein known as CAS12 binds to the sequence which it then cuts. In the process, it also cuts a 'reporter' molecule, which has been added to the reaction, and which also binds itself to the viral sequence. When cut the molecule releases colour which enables a positive result for SARS-CoV-2 to be visualised as a simple colour change on a test strip.

*Adele Baleta is an independent Science Writer, media consultant and trainer

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