Innovating to anticipate outbreaks

In 2022 and 2023, Malawi — a landlocked country in southeastern Africa — experienced outbreaks of cholera, COVID-19, polio, measles, rabies, and anthrax. Such outbreaks represent threats to the general populations, but forcibly displaced people — most of whom, in Malawi, live in a single, overcrowded camp — are especially vulnerable. High population density, limited access to clean water, and under-pressure healthcare facilities all make the emergence and spread of disease more likely. Boosting water, sanitation, and hygiene (WASH) efforts is an important factor in supporting public health, but good data is also critical to identify and respond proactively to outbreaks.

Enhanced surveillance can help UNHCR, the UN Refugee Agency, and national governments to identify outbreaks before they begin and limit their spread — yet limited testing capacity or reluctance to test can severely limit the efficacy of clinical surveillance in camp settings. One potential solution is wastewater-based epidemiology (WBE).

WBE analyses wastewater to understand a given population’s disease burden. It can provide anonymous data about disease prevalence and capture a broad swathe of the community in a single sample. This methodology has been used, for instance, to detect patterns of SARS-CoV-2 prevalence. But it has rarely been used in displacement settings. In 2024, UNHCR set out to test whether it could be used effectively in a non-sewered displacement context — Malawi’s Dzaleka Refugee Camp — to identify the presence of pathogens of concern and improve and accelerate the response.

This proof-of-concept initiative, supported through UNHCR’s Data Innovation Fund, focused primarily on cholera. It demonstrated the potential efficacy of WBE in camp contexts as well developing recommendations for others seeking to deploy it.

The Context

Malawi hosts approximately 56,770 forcibly displaced and stateless people (as at end of 2024). A vast majority of them live in Dzaleka — the only official refugee settlement in the country, which covers 224 hectares and was originally intended to house 12,000 people. “The camp is congested,” says Ernest Chilalika, UNHCR WASH Associate, “which means hygiene practices can be compromised.” For financial and logistical reasons, it is challenging for UNHCR to meet its minimum standards of WASH services in the camp, including key indicators like water access and hygiene support.

Dzaleka is not connected to the sewer system, and the construction of pit latrines close to water sources can contaminate ground water. Additionally, while each health centre in Malawi should cater to a maximum of 20,000 people, the single health centre in Dzaleka is now serving more than 80,000 people, including camp residents and nearby communities.

In March 2022, Malawi confirmed that it was experiencing an active cholera outbreak. By early 2023, when Brandie Shackelford arrived in the country as an Associate WASH Officer, that outbreak was still ongoing. “I was really struck that we only had four cases in the camp diagnosed during the outbreak,” she recalls. This represents an attack rate of 0.008%, compared to 0.17% and 0.29% for Dowa district and Malawi as a whole, respectively.

Brandie wondered if this was cause for celebration or if it was an indication of critical gaps in public health surveillance. To investigate whether WBE could shed light on this question — and ultimately support UNHCR and Malawi’s Ministry of Health to efficiently mobilize and target resources — she and Ernest applied to the Data Innovation Fund.

The Project

The innovation inherent in this project was based on several factors: the application of WBE to a non-sewered displacement setting; the proposed use of local laboratories for the processing and analysis of collected samples; and the use of both polymerase chain reaction (PCR) and culture methodologies to analyze the samples. Leveraging the existing capacity of a local lab to conduct culture was a cost-cutting measure, intended to determine whether this approach would be financially and logistically viable in refugee camps both in Malawi and elsewhere.

At the outset of the project, refugee hygiene promoters, government health workers, and community leaders informed camp residents about its process and aims via house visits, community meetings, local radio, and the camp’s physical notice board. Three volunteers from the community, each of whom were provided with the cholera vaccine, were incentivized and trained to take the samples. Then, in collaboration with health promoters, seven public latrine sites were identified that had enough regular users to capture a large sample of the population and to ensure anonymity, so the results would not stigmatize certain households.

“The value of this is that you’re going to capture segments of the population you wouldn’t catch with clinical testing,” says Brandie, “people who wouldn’t go to the health centre because they don’t want to, or because they’re asymptomatic.”

Over 26 weeks, around 150 samples were taken from the chosen sites. These were sent, via a cold chain, for analysis to the Public Health Institute of Malawi (PHIM) laboratory. For quality assurance, 10% of samples were also independently analyzed by the project’s two primary research partners — Petros Chigwechokha, of the Malawi University of Science and Technology, and Rochelle Holm, of University of Louisville — who had expertise in WBE.

Without the strong partnerships forged with government bodies, academic institutions, implementing partners, and various UNHCR divisions, the project would not have been possible. This work is complex, with many finer details — for instance, selecting which genes to target, to avoid detecting cholera vaccine — having to be rigorously considered. “We knew from the beginning our knowledge gaps,” says Ernest. “[Petros and Rochelle] were the experts — we knew that we could not do it on our own.”