As South Africa went into its Covid-19 lockdown on March 27, one person died in Western Cape and confirmed cases climbed above 1,000. Professor Cheryl Cohen of the National Institute for Communicable Diseases (NICD) said the outbreak was now reaching the stage of local transmission and of clustered and community transmission where it is no longer a majority-imported disease.

The World Health Organisation (WHO) categorises the coronavirus and the disease it causes – Covid-19 – into four categories: Stage 1, which is imported by travellers; Stage 2, which is clustered transmission; Stage 3, which is local transmission, and Stage 4, widespread community transmission.

The good news is that surveys by the NICD show Covid-19 has not yet seeped into the public health sector in great numbers (though one of the people who died did so in a public hospital in Western Cape) and is not showing up in two significant surveys run by the organisation.

South Africa’s first cases, reported from March 5, were imported largely from Europe and later from the US and other countries. Local transmissions (Stage 3) started on March 18, along with analysis of the Free State infections, which confirmed the cluster phase, also imported by travellers from the US and Israel but which by yesterday had infected a total of 44 people in the province.

Gauteng, Western Cape and KwaZulu-Natal have the highest numbers, driven by the fact that people who travel by air are most likely to be in these three provinces. The viral effect is now clear in those provinces.

At 1,000 positive tests, South Africa is on the cusp of community transmission.

“The difficulty is in how you make that assessment. The concern is that, because of the nature of this illness, there is already some low level of community transmission,” said Cohen.

The WHO has said as Covid-19 becomes generalised into the community, communication of confirmed cases can slow down from the daily accounting to less frequent information as testing is deepened and results take longer to come through.

South Africa is still reporting daily but, as the data media collective MediaHack website reveals, the data being provided is no longer as detailed. This includes data on geographic spread, gender and age.

The two people who died in the Western Cape were relatively young, bucking the trend of most risk for the elderly and those with co-morbidities, which can include diabetes, respiratory diseases, asthma and cardiac conditions.

(South African erroneously stated two persons had died. They later amended this to one  – a young nurse passed away while waiting for test results, which came back negative after she had died. – Ed)

The NICD, which started preparing for and managing the Covid-19 outbreak early in January, has used systems it developed to track flu and pneumonia outbreaks to track and trace how this novel virus is spreading.

The institute uses a network of GPs who survey (by consent) patients who present with symptoms like a fever or cough to trace the annual flu seasons.

“They reveal increased cases (of Covid-19) with no contact with travellers,” said Cohen. “The database of test sites (called sentinel sites) for pneumonia surveillance suggest “public sites are not showing it yet – it (Covid-19) is not really penetrating into public health sites as per the survey”, says Cohen.

That is no reason to rest on laurels. “It is good but because of (the nature of the virus), it is circulating and will reach those systems. We know it from the nature of the disease. If we don’t act decisively there will be more cases there.”

It was important, she said, that South Africa is ramping up testing significantly and described the lockdown as the best medicine for this stage of an epidemic.

Reducing contact slows the spread of the virus and the rate at which cases go up will be slower, which means South Africa’s health system will be more likely to cope. That’s why, said Cohen, the lockdown is so important: a drop in contacts has a directly proportional relationship to a drop in infection rates.

Asked why mortality had been low prior to March 27, Cohen said it was because of the stage of the epidemic in South Africa. “A percentage of patients will get very ill and will die.”

The majority of cases have been in people who travelled and who were assumed to be healthier and younger. But once the infection becomes a generalised community infection it can spread to the most vulnerable places and people in South Africa, making containment very difficult.

The National Health Laboratory Service (NHLS) said on Wednesday 25 March that it would expand its capacity from an existing six laboratories to nine by next month.

It also said it had 18 state-of-the-art machines that would improve volumes and turnaround times. It had more than 180 “GeneXpert analysers” across all provinces and test kits would arrive from the US in April.

These tests can be processed in 45 minutes, said CEO Kamy Chetty in a media release. The smaller machines are mobile, which will be necessary as South Africa moves from imported infections to community infections – a much larger pool of infections.

The NHLS also has six mobile laboratories that have already been deployed. It is widely accepted that part of South Africa’s plan to flatten the viral curve of Covid-19 will require wider testing.

“With all the sites functional, the NHLS has the capacity to process 5,000 samples in 24 hours,” the organisation said in a statement. DM