CoughWatch: Meet the South African researchers tracking COVID-19

Mvuyo Makhasi is leading a team tracking the pandemic via a novel digital platform – CoughWatchSA.

  • 23 May 2022
  • 6 min read
  • by Linda Geddes
Mvuyo Makhasi
Mvuyo Makhasi


COVID-19 has shone a light on the importance of disease surveillance: without it, small outbreaks rapidly mushroom into uncontainable ones, requiring blanket restrictions on people’s behaviour to bring them back under control. Surveillance also enables scientists to keep track of which variants of viruses or other disease-causing organisms are circulating, meaning vaccines can be tweaked or drugs altered to keep as many people healthy as possible.

"Within the next five to ten years, I can foresee the establishment of a digital participatory surveillance network in Africa, that would enable us to share trends, compare data between different countries, and carry out analysis at a continental or regional level."

In many countries, surveillance for respiratory diseases such as influenza, respiratory syncytial virus (RSV) and now COVID-19 has traditionally relied on so-called facility-based surveillance. This involves health care staff taking swabs from patients they encounter in hospitals or clinics who meet the diagnostic criteria for an influenza-like illness – such as headache, cough and/or fever – and sending these samples to a laboratory to determine which virus they have.

“Part of our objective is to identify the start and peak of the influenza season based on a number of cases that we identify, and contribute to decision-making about the composition of the seasonal influenza vaccine, by looking at the strains that were identified in the current season,” says Mvuyo Makhasi, a data manager for the National Institute for Communicable Diseases (NICD) in Johannesburg, South Africa. “You can also use the data to potentially identify novel pathogens that may lead to clusters of cases, shaping our public health response to them, and feeding into surveillance efforts at a national and international level.”

Such surveillance is harder in countries where access to medical care is unequally distributed across urban and rural areas, and where testing capacity is limited, such as in many low to middle-income countries. Even in wealthy countries, obtaining a true picture of how many people have a respiratory illness and what their symptoms are is complicated. Those with mild symptoms often choose to treat them at home rather than consulting a health care professional.

There is also a time delay between the development of symptoms and people presenting at health care facilities, which leaves epidemiologists playing a constant game of catch-up with what’s happening on the ground.

“All of these things may lead to a potential under-reporting of cases, while limited testing capacity means that we can’t confirm and diagnose all of those that are reported. This affects our ability to respond to and address those health challenges,” Makhasi says.

Although visiting a clinic may be too difficult or too time-consuming for many, most people do nowadays have access to the internet, either through a computer or a mobile phone. So, Makhasi is piloting what is referred to as a “digital participatory surveillance platform” called CoughWatchSA. Launched in South Africa in March 2022, it will collate and interpret data from thousands of volunteers reporting information about their respiratory symptoms through a weekly online questionnaire.

Makhasi hopes such participatory surveillance could ultimately strengthen African countries’ ability to respond to respiratory diseases across the continent.

“I think that by using technology, we are in a position to get richer data from everyone, which could provide more accurate insights into country- and continent-wide trends, compared to traditional facility-based surveillance, which is more limited in terms of geography and the financial resources available,” he says.

“Also, because you get closer to real-time data, without waiting for people to become ill enough to visit a clinic or be admitted to hospital, it allows you as a public health community to investigate where reports are coming from, and to initiate testing, so that you can confirm which pathogens are in circulation.”

This isn’t the first time that researchers have used participatory surveillance to monitor people’s health. In 2016, Tanzanian researchers piloted a mobile app called AfyaData, which encouraged users to report any health report any symptoms they encountered – the most common being those related to the digestive system. This demonstrated the potential of harvesting close to real-time data from the community, says Makhasi, who started his career in information technology before turning to public health.

Then, during the COVID-19 pandemic, the UK-based ZOE Covid Symptom Study saw up to four million people from around the globe routinely logging their symptoms and vaccination status, with a subset of them offered PCR tests to confirm whether or not they were infected.

A key difference is that participants in the CoughWatchSA study will not incur any mobile data costs as a result of taking part in the weekly survey. Those living in selected suburbs in Gauteng, KwaZulu-Natal and Western Cape provinces, may also request a self-swabbing kit to be delivered to them if they have symptoms of respiratory illness, which will identify whether they are infected with influenza, RSV or COVID-19. The result will be sent to their mobile phones.

Besides knowing what’s causing their symptoms, there are other, indirect, benefits to taking part. “Although there's no direct incentive to individuals, we believe that in getting close to real-time data on cases in the community it will allow us to implement a timelier public health response, which will benefit participants indirectly,” says Makhasi. “We also want to share data about the trends that we identify, as a way of improving awareness about respiratory illnesses, and what’s happening locally. We think it might be of interest for people to understand what is happening in their communities.”

Participants can enrol in the CoughWatchSA by scanning a QR code or clicking a link to CoughWatchSA on the NICD’s website. Having completed the initial enrolment survey, they will be emailed a weekly follow-up questionnaire asking whether they’ve experienced any symptoms that week, when they began, if they’ve changed their behaviour as a result of those symptoms, and what kinds of medical care they’ve sought. Once enrolled, participants are requested to continue reporting their symptoms until the pilot terminates at the end of December.

“We hope that with the data we will have, we can then advocate for more funding to develop this into a long-term surveillance programme,” says Makhasi.

The idea isn’t to replace traditional facility-based surveillance, but to complement it. “One of the limitations of facility-based surveillance is that you aren’t able to quantify the burden of non-medically attended cases. But now in a platform like this, you can systematically and continuously collect patterns of health-seeking behaviours, including which alternative means of care people have accessed, and their impact on the public health support structures that we have,” Makhasi says.

“Access to real-time data will also allow us to identify regional hotspots and to do forecasting, which will be communicated internally, as well as to our participants – providing them with a warning about when to be more vigilant, or to intensify non-pharmaceutical initiatives such as wearing masks, because we’re seeing an increase in the number of cases in their area.”

If successful, Makhasi hopes the approach could be expanded beyond South Africa, potentially to include other infectious diseases such as HIV or gastrointestinal illnesses as well. Doing so, would be particularly beneficial in low-income countries, where establishing a robust network of clinics and laboratories to carry out facility-based surveillance may be costly. By contrast, using a mobile app or online survey to conduct disease surveillance is relatively low cost.

“Within the next five to ten years, I can foresee the establishment of a digital participatory surveillance network in Africa, that would enable us to share trends, compare data between different countries, and carry out analysis at a continental or regional level,” Makhasi says. “We think this could make a huge contribution to pandemic preparedness, and our response to novel pathogens.”