Lab Manager | Run Your Lab Like a Business

In Focus

a microscopic view of pathogens found through environmental testing
photo provided by lab manager

Environmental Monitoring of Pathogens is Key to Effective Management of Current and Future Outbreaks

The efficacy of monitoring air and wastewater for viruses and other pathogens during public health crises has been repeatedly demonstrated, and feasibility is greater than ever


Environmental sampling to monitor pathogens in the air and wastewater during outbreaks or pandemics allows for more rapid, informed decisions in managing public health crises. Though such monitoring has been put in practice prior to this, the COVID-19 pandemic has spotlighted the need to establish standardized procedures.


Recent research has underpinned the importance of considering aerosols as a route for transmission in the case of airborne viruses and other pathogens. A more thorough understanding of this transmission route is needed, however, and public health guidelines and monitoring systems have been slower to catch up.

One reason for this is that air-sampling has historically been more challenging than sampling surfaces leading to a relative void in research and data, though the process has been simplified in recent decades with newer technology.

Gelatine filters, which are ideal for air-sampling, have been a tried and tested method for three decades1 and are routinely used in environmental monitoring during pharmaceutical manufacturing. They offer retention rates equivalent to HEPA filters (up to 99.8 percent) in a water-soluble format. The filter matrix is dissolved in a small volume of water or buffer, along with any particles or pathogens suspended on it, that can then be moved directly into qPCR workflows with minimal loss, providing better recovery results than other detection methods.

Over the last two decades, air sampling has been used successfully to identify sources in other disease outbreaks and in animal husbandry. For example, airborne transmission of Middle East respiratory syndrome coronavirus (MERS-CoV) was identified as a likely route after air sampling in a South Korea MERS isolation ward confirmed viable MERS-CoV contamination of the air2.

Efficacy of air sampling for SARS-COV-2 surveillance has been demonstrated in numerous studies around the world examining hospital e.g.3 and public settings. One major consideration when sampling air is level and type of air exchange in the test setting—the suitability of air monitoring procedures for SARS-COV-2 in both indoor settings with isolated airflow (cinemas) and large, semi-outdoor settings with high air exchange rates (mosque) was demonstrated in a comparative study4 . Protocols have been further applied to testing the efficacy of portable and static-installation air cleaners in terminating viruses.

Real-time surveillance of outbreaks requires flexibility to deploy testing where and when it is needed and the sensitivity to detect low viral counts. Modern portable units like Sartorius’ Airport MD8 offer the ability to effectively and efficiently sample any high-traffic, high-contamination risk area, including hospitals, public transport, train stations and airports, and potential sources like dense gatherings and barns.


Monitoring wastewater is a key tool for pathogen detection and surveillance. To reduce the limits of detection, viruses, viral particles, and genomic material must be concentrated from water samples prior to extraction and quantification—this can be achieved efficiently by ultrafiltration. Filtration units on the market, such as Vivaspin® and Vivaflow®, offer efficient concentration from initial sample volumes of 100 µL up to several liters. Vivaspin® ultrafilters (with 50 kDa MWCO PES membranes) were used for concentration of wastewater samples before qPCR detection of SARS-CoV-2 RNA in an early study that established increased presence of the virus in wastewater prior to clinical case numbers rising5 .

While demonstrably effective for localized monitoring of pathogens, a lack of consistency in air and wastewater sampling protocols makes larger-scale comparisons and datasets difficult to achieve. Establishing effective and consistent sampling protocols will assist both research and monitoring efforts, enabling more rapid, informed public health measures in response to outbreaks of pathogens.


1. Sartorius. covid-19-air-monitoring/detecting-airborne-influenza-virus-a (1990) Detecting Airborne Influenza Virus A

2. Kim, S. H. et al. 2016. Extensive Viable Middle East Respiratory Syndrome (MERS) Coronavirus Contamination in Air and Surrounding Environment in MERS Isolation Wards. Clin. Infect. Dis. 63, 363–369. DOI: 10.1093/cid/ciw239. 

3. Chan, V. W. M. et al. 2020. Air and environmental sampling for SARS-CoV-2 around hospitalized patients with coronavirus disease 2019 (COVID-19). Infect. Control Hosp. Epidemiol. 41, 1258–1265. DOI: 10.1017/ICE.2020.282. https://pubmed.ncbi. 

4. Victorio, Y., Utama, R., Scherwing, C. & Arakel, E. (2021) Validation of an Airborne SARS-CoV-2 Surveillance System in a Controlled Space, Cinema, and Mosque in Indonesia

5. Trottier, J. et al. 2020. Post-lockdown detection of SARS-CoV-2 RNA in the wastewater of Montpellier, France. One Heal. 10, 100157. DOI: 10.1016/J.ONEHLT.2020.100157.

To learn more, visit: