eDNA to eRNA: From Fish Ecology To Surveillance Of Human Disease
Researchers continue to push the boundaries and limitations of the eDNA technology, repurposing eDNA techniques to detect human eRNA, particularly in aquatic environments!
August 26, 2021
In part 1 of this eDNA series we examined how environmental DNA is detected in aquatic or soil samples weeks or months after the organism has passed through. In part 2 we discussed why filtration is chosen rather than precipitation as the preferred method in the sample prep stage prior to eDNA extraction and which filter material is best.
In part 3 of the eDNA blog series, we delve into the rapidly evolving world of eDNA. Once a tool used predominately within the field of ecology, its breadth of applications has recently exploded and will no doubt continue to grow rapidly in the foreseeable future. In fact, most recently, researchers have begun to repurpose eDNA techniques to detect eRNA in human wastewater. These genetic tools are being employed to better understand and monitor the SARS-CoV-2 virus driving the current global COVID-19 human pandemic (1). SARS-CoV-2 viral shedding in fecal matter takes place in infected individuals, regardless of whether that individual is symptomatic, and its detection in human wastewater provides a sensitive early-warning system for the spread of COVID-19 in communities.
Sterile Conditions, Single-use and Re-use
Because RNA is a less stable molecule than DNA, eRNA does not persist in the environment as long as eDNA, so researchers have to be more streamlined in their collection and filtration approaches. The speed and manner in which they filter become critical. Sterility is also a concern in the field, as well as ease of use. In fact, when Majanevaet al., 2018 carried out a comparative study to look at the two different material types of filters on eDNA yield, they chose Pall’s 0.2 µm PES and Pall’s 0.45 µm MCE filters attached to a 300mL reservoir, sterile and individually packed making them incredibly easy to use in the field (2) (see figure 1).
Figure 1: Pall’s 300ml MicroFunnel™ Filter Funnel Overview. Supports a variety of membranes (mixed cellulose ester, polyethersulfone and modified polyethersulfone membrane in 0.2-0.8 µm pore sizes.)
The location of eDNA or eRNA sampling can influence workflow process changes in order to streamline the collection of water samples at remote or inconvenient sites, e.g., remote tropical river locations. Robson et al., 2016 made several modifications to their decontamination and ﬁltering eDNA protocols to maximize efﬁciency when working in the tropics (3). To reduce processing and decontamination times, the researchers switched from a magnetic filter funnel to Pall’s smaller, less expensive 300ml MicroFunnel™ filter funnel (Figure 1), with 0.8 µm Metricel® black, gridded membrane (made of hydrophilic modified PES, individually bagged and gamma irradiated) for each sample. Where these funnels can be re-used for months, the costs were then significantly reduced. According to Robson et al., their smaller size and stackable nature make our Micro Funnel filter funnel ideal for remote ﬁeldwork where space is limited” (3).
Similarly, in the eRNA filtration world, re-use protocols have recently been developed. Wastewater surveillance technology relies on the use of viral concentration, often via ultrafiltration devices such as the Pall Jumbosep™ centrifugal device, to validate the presence of viral shedding into community sewage systems. Scientists recently showed that the sample reservoir and filtrate receiver unit of the Jumbosep device could effectively be sanitized and re-used, resulting in an economic and environmental advantage.
With a full range of filtration devices, filters, funnels, manifolds, and the Sentino® field-friendly portable pump, Pall continues to support the development of high sensitivity workflows to address the problem of extremely low concentrations of eDNA or eRNA in water samples. Incorporating sterile filtration with expeditated filtration rates and reduced filter clogging into eDNA and eRNA workflows ultimately will help the much-needed standardization in the eDNA and eRNA space.
To learn more about how additional Pall products have been integrated into eDNA workflows by the scientific community, please read the Scientific Brief: The Importance of Filtration in the eDNA World
This was the final of a three-part series on the emerging and exciting field of eDNA. You can find the previous posts in the series here:
- Wu F et al. (2020) SARS-CoV-2 titers in wastewater are higher than expected from clinically confirmed cases. mSystems 5: e00614 –20
- Majaneva, M., Diserud, O.H., Eagle, S.H.C. et al. (2018) Environmental DNA filtration techniques affect recovered biodiversity. Sci Rep 8, 4682
- Robson, H.L.A., Noble, T.H., et al. (2016). Fine-tuning for the tropics: application of eDNA technology for invasive fish detection in tropical freshwater ecosystems. Molecular Ecology Resources
- Decontamination of Jumbosep™ Centrifugal Devices used for Concentrating Viral Particles in Testing of Wastewater Samples. Pall Technical Bulletin, 2020