Sewer monitoring to track COVID-19 in developing countries: a case study in Brazil

Liberty Square in Belo Horizonte, Minas Gerais, Brazil. Filipefrazao /

A project in Belo Horizonte aims to ensure wastewater monitoring for the SARS-CoV-2 virus covers vulnerable communities, offering lessons for developing countries.


The first patient with symptoms of COVID-19 was reported in Brazil on 25 February 2020, later confirmed to be infected with the new coronavirus (SARS-CoV-2). The evolution of the COVID-19 epidemic curve was delayed compared with Europe in particular, but cases began increasing at an alarming rate at the beginning of May.

Brazil is plagued with enormous social inequality, and a huge percentage of the population live under conditions of vulnerability, not serviced by water supply or sewerage systems. Approximately 35 million Brazilians do not have access to treated water and 100 million people do not have access to sewage collection.

Such appalling sanitation conditions may aggravate the situation during the pandemic, at a time when limited clinical testing leaves health authorities in the dark when it comes to understanding how the virus is circulating in Brazilian communities.

Monitoring the occurrence of the new coronavirus in the influent of sewage treatment plants (STPs) has been shown to be a powerful surveillance tool for infectious diseases, and could be relevant for COVID-19 surveillance, with early successful examples in the Netherlands, Australia, France, and the USA (see ‘More information’ in accompanying article).

This approach may be even more relevant for developing countries such as Brazil, but only if sewage monitoring also contemplates different points in the sewerage network. In developing countries, it is very usual that a significant portion of the sewage generated does not reach STPs. Testing only at treatment plants would make it impossible to extrapolate sewage monitoring data to the whole population. The authors consider this the most suitable strategy for countries with limited sewage treatment infrastructure, such as Brazil.

Figure 1: Sampling from
a manhole, using an
automatic sampler

Monitoring the sewage: a case study in Brazil

A pioneering initiative in Brazil is taking this need into account. It is being led by the Brazilian National Water Agency (ANA) and the National Institute of Science and Technology (INCT) on Sustainable STPs (coordinated by the Federal University of Minas Gerais, Belo Horizonte), in partnership with the Minas Gerais Institute for Water Management (IGAM), the Sanitation Company for Minas Gerais (COPASA), and the Minas Gerais Department of Health (SES).

The project aims to map the occurrence, abundance and circulation of SARS-CoV-2 in the city of Belo Horizonte, located in the southeast of Brazil, with a population of approximately two million people (six million people in its metropolitan area).

The design of the monitoring plan considered the collection of sewage samples not only at the inlet and outlet of the STPs. Sewage is being monitored on the basis of regions within the city, with hot spots being monitored also.

Identification of sewage collection points was based on the following guiding principles: homogeneous spatial distribution of sampling points, covering the two watersheds in the city; influence of hospitals, considering their possible higher viral load because of the presence of patients with suspected and confirmed cases of COVID-19; health vulnerability index, covering a broad spectrum of social classes; and the presence of and accessibility to the sewerage network for sample collection.

Regarding the population not served by sewers, sampling would still be feasible if taken from open or closed drains that carry both runoff water and raw sewage. However, monitoring such points brings more complexities and would only be feasible during the dry season.

A total of 24 samples are being collected on a weekly basis, including 10 raw sewage samples from each of the two watersheds, two effluent samples from the main STPs in each watershed, and two samples from the main streams of those watersheds. These stream samples are being collected immediately upstream from treated effluent discharge points.

Samples are collected using automatic samplers and then kept refrigerated (Figure 1). Detection and quantification of SARS-CoV-2 is being performed by RT-qPCR following the US CDC protocol. Figure 2 shows the distribution of sampling points, with the identification of the watersheds and regions of the city that tested positive and negative for the presence of the virus during the first six weeks of monitoring. Nearly half of the regions being monitored are vulnerable zones of the city.

Appeal of the initiative

The project has been mapping SARS-CoV-2 in the sewers of Belo Horizonte since 13 April 2020, with seven sampling campaigns concluded up to 29 May. Dynamic maps are being developed to show trend curves (growth or decrease) of the number of people infected by the virus. Preliminary results indicate stronger virus circulation in regions that include neighbourhoods with greater social vulnerability. These maps are being updated weekly for the different areas of interest in the city, and then made available to the State Health Department.

As in other wastewater-based epidemiology projects being carried out elsewhere for COVID-19, there are uncertainties and challenges that need to be addressed. These include developing the appropriate methodology for estimating the number of infected individuals based on viral RNA concentrations in sewage, and understanding the rate of decay of RT-qPCR signal for SARS-CoV-2 in sewage with the higher temperatures and surfactant concentrations typical in developing countries. A further issue is gathering and applying reliable COVID-19 diagnostic data where testing is very limited.

Even so, the authors believe the study will make important contributions to the epidemiological monitoring of COVID-19 in the city, particularly regarding early detection of the occurrence of the virus in specific regions of the city. This may serve as an alert for the need for urgent, regional action by health authorities. It can also contribute to chronological monitoring of the impact of pandemic control measures, including social isolation, identifying the regions where they were more or less effective (measured, respectively, by the decrease or increase in the number of cases and the concentrations of the virus in the sewer). In the latter, there would be an alert to the need to strengthen recommendations for social isolation, hand washing, etc.

After the most critical period of the pandemic, the monitoring plan will be expanded to also include collection and analysis of sewage samples in other hot spots in the city, such as airports, bus stations and schools. Hot spots in the most vulnerable regions (e.g. slums) could be sampled as well, to give an idea of the community health in places not served by sewage collection.

Figure 2: Map with the location of monitoring points
and their respective catchment areas, highlighting the
regions with positive (in red) and negative (in green)
virus detection in the fifth week of monitoring

Another important contribution of the study is that it is serving as a pilot project, the principles of which are being used as a basis for replication in other Brazilian cities. All steps related to the development and validation of guidelines have been disseminated and made available to other institutions in Brazil. The dissemination strategy includes the publication of technical weekly bulletins and a series of open webinars. The first webinar, on 22 May 2020, was attended by more than 700 people from all over the country and from Italy, France, Mexico and Colombia.


Center for Disease Control and Prevention. 2019-Novel coronavirus (2019-nCoV) Real-time rRT-PCR panel primers and probes. (accessed 02 April 2020).