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    Assay determines the percentage of Omicron, other variants in Covid wastewater

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    Wastewater monitoring emerged amid the Covid-19 pandemic as an effective and noninvasive way to track a viral outbreak, and advances in the technology have enabled researchers to not only identify but also quantify the presence of particular variants of concern (VOCs) in wastewater samples.

    Last year, researchers with the Singapore-MIT Alliance for Research and Technology (SMART) made the news for developing a quantitative assay for the Alpha variant of SARS-CoV-2 in wastewater, while also working on a similar assay for the Delta variant. Previously, conventional wastewater detection methods could only detect the presence of SARS-CoV-2 viral material in a sample, without identifying the variant of the virus.

    Now, a team at SMART has developed a quantitative RT-qPCR assay that can detect the Omicron variant of SARS-CoV-2. This type of assay enables wastewater surveillance to accurately trace variant dynamics in any given community or population, and support and inform the implementation of appropriate public health measures tailored according to the specific traits of a particular viral pathogen.

    The capacity to count and assess particular VOCs is unique to SMART’s open-source assay, and allows researchers to accurately determine displacement trends in a community. Hence, the new assay can reveal what proportion of SARS-CoV-2 virus circulating in a community belongs to a particular variant. This is particularly significant, as different SARS-CoV-2 VOCs — Alpha, Delta, Omicron, and their offshoots — have emerged at various points throughout the pandemic, each causing a new wave of infections to which the population was more susceptible.

    The team’s new allele-specific RT-qPCR assay is described in a paper, “Rapid displacement of SARS-CoV-2 variant Delta by Omicron revealed by allele-specific PCR in wastewater,” published this month in Water Research. Senior author on the work is Eric Alm, professor of biological engineering at MIT and a principal investigator in the Antimicrobial Resistance (AMR) interdisciplinary research group within SMART, MIT’s research enterprise in Singapore. Co-authors include researchers from Nanyang Technological University (NTU), Singapore National University (NUS), MIT, Singapore Centre for Environmental Life Sciences Engineering (SCELSE), and Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER) in Italy.

    Omicron overtakes delta within three weeks in Italy study

    In their study, SMART researchers found that the increase in booster vaccine population coverage in Italy concurred with the complete displacement of the Delta variant by the Omicron variant in wastewater samples obtained from the Torbole Casaglia wastewater treatment plant, with a catchment size of 62,722 people. Taking less than three weeks, the rapid pace of this displacement can be attributed to Omicron’s infection advantage over the previously dominant Delta in vaccinated individuals, which may stem from Omicron’s more efficient evasion of vaccination-induced immunity.

    “In a world where Covid-19 is endemic, the monitoring of VOCs through wastewater surveillance will be an effective tool for the tracking of variants circulating in the community and will play an increasingly important role in guiding public health response,” says paper co-author Federica Armas, a senior postdoc at SMART AMR. “This work has demonstrated that wastewater surveillance can be used to quickly and quantitatively trace VOCs present in a community.”

    Wastewater surveillance vital for future pandemic responses

    As the global population becomes increasingly vaccinated and exposed to prior infections, nations have begun transitioning toward the classification of SARS-CoV-2 as an endemic disease, rolling back active clinical surveillance toward decentralized antigen rapid tests, and consequently reducing sequencing of patient samples. However, SARS-CoV-2 has been shown to produce novel VOCs that can swiftly emerge and spread rapidly across populations, displacing previously dominant variants of the virus. This was observed when Delta displaced Alpha across the globe after the former’s emergence in India in December 2020, and again when Omicron displaced Delta at an even faster rate following its discovery in South Africa in November 2021. The continuing emergence of novel VOCs therefore necessitates continued vigilance on the monitoring of circulating SARS-CoV-2 variants in communities.

    In a separate review paper on wastewater surveillance titled “Making Waves: Wastewater Surveillance of SARS-CoV-2 in an Endemic Future,” published in the journal Water Research, SMART researchers and collaborators found that the utility of wastewater surveillance in the near future could include 1) monitoring the trend of viral loads in wastewater for quantified viral estimates circulating in a community; 2) sampling of wastewater at the source — e.g., taking samples from particular neighborhoods or buildings — for pinpointing infections in neighborhoods and at the building level; 3) integrating wastewater and clinical surveillance for cost-efficient population surveillance; and 4) genome sequencing wastewater samples to track circulating and emerging variants in the population.

    “Our experience with SARS-CoV-2 has shown that clinical testing can often only paint a limited picture of the true extent of an outbreak or pandemic. With Covid-19 becoming prevalent and with the anticipated emergence of further variants of concern, qualitative and quantitative data from wastewater surveillance will be an integral component of a cost- and resource-efficient public health surveillance program, empowering authorities to make more informed policy decisions,” adds corresponding author Janelle Thompson, associate professor at SCELSE and NTU. “Our review provides a roadmap for the wider deployment of wastewater surveillance, with opportunities and challenges that, if addressed, will enable us to not only better manage Covid-19, but also future-proof societies for other viral pathogens and future pandemics.”

    In addition, the review suggests that future wastewater research should comply with a set of standardized wastewater processing methods to reduce inconsistencies in wastewater data toward improving epidemiological inference. Methods developed in the context of SARS-CoV-2 and its analyses could be of invaluable benefit for future wastewater monitoring work on discovering emerging zoonotic pathogens — pathogens that can be transmitted from animals to humans — and for early detection of future pandemics.

    Furthermore, far from being confined to SARS-CoV-2, wastewater surveillance has already been adapted for use in combating other viral pathogens. Another paper from September 2021 described an advance in the development of effective wastewater surveillance for dengue, Zika, and yellow fever viruses, with SMART researchers successfully measuring decay rates of these medically significant arboviruses in wastewater. This was followed by another review paper by SMART published in July 2022 that explored current progress and future challenges and opportunities in wastewater surveillance for arboviruses. These developments represent an important first step toward establishing arbovirus wastewater surveillance, which would help policymakers in Singapore and beyond make better informed and more targeted public health measures in controlling arbovirus outbreaks such as dengue, which is a significant public health concern in Singapore.

    “Our learnings from using wastewater surveillance as a key tool over the course of Covid-19 will be crucial in helping researchers develop similar methods to monitor and tackle other viral pathogens and future pandemics,” says Lee Wei Lin, first author of the latest SMART paper and research scientist at SMART AMR. “Wastewater surveillance has already shown promising utility in helping to fight other viral pathogens, including some of the world’s most prevalent mosquito-borne diseases, and there is significant potential for the technology to be adapted for use against other infectious viral diseases.”

    The research is carried out by SMART and its collaborators at SCELSE, NTU, and NUS, co-led by Professor Eric Alm (SMART and MIT) and Associate Professor Janelle Thompson (SCELSE and NTU), and is supported by Singapore’sNational Research Foundation (NRF) under its Campus for Research Excellence And Technological Enterprise (CREATE) program. The research is part of an initiative funded by the NRF to develop sewage-based surveillance for rapid outbreak detection and intervention in Singapore.

    SMART was established by MIT in partnership with the NRF in 2007. SMART is the first entity in CREATE developed by NRF and serves as an intellectual and innovation hub for research interactions between MIT and Singapore, undertaking cutting-edge research projects in areas of interest to both Singapore and MIT. SMART currently comprises an Innovation Centre and five interdisciplinary research groups: AMR, Critical Analytics for Manufacturing Personalized-Medicine, Disruptive & Sustainable Technologies for Agricultural Precision, Future Urban Mobility, and Low Energy Electronic Systems.

    The AMR IRG is a translational research and entrepreneurship program that tackles the growing threat of antimicrobial resistance. By leveraging talent and convergent technologies across Singapore and MIT, they tackle AMR head-on by developing multiple innovative and disruptive approaches to identify, respond to, and treat drug-resistant microbial infections. Through strong scientific and clinical collaborations, our goal is to provide transformative, holistic solutions for Singapore and the world. More

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      MIT J-WAFS announces 2022 seed grant recipients

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      The Abdul Latif Jameel Water and Food Systems Lab (J-WAFS) at MIT has awarded eight MIT principal investigators with 2022 J-WAFS seed grants. The grants support innovative MIT research that has the potential to have significant impact on water- and food-related challenges.

      The only program at MIT that is dedicated to water- and food-related research, J-WAFS has offered seed grant funding to MIT principal investigators and their teams for the past eight years. The grants provide up to $75,000 per year, overhead-free, for two years to support new, early-stage research in areas such as water and food security, safety, supply, and sustainability. Past projects have spanned many diverse disciplines, including engineering, science, technology, and business innovation, as well as social science and economics, architecture, and urban planning. 

      Seven new projects led by eight researchers will be supported this year. With funding going to four different MIT departments, the projects address a range of challenges by employing advanced materials, technology innovations, and new approaches to resource management. The new projects aim to remove harmful chemicals from water sources, develop drought monitoring systems for farmers, improve management of the shellfish industry, optimize water purification materials, and more.

      “Climate change, the pandemic, and most recently the war in Ukraine have exacerbated and put a spotlight on the serious challenges facing global water and food systems,” says J-WAFS director John H. Lienhard. He adds, “The proposals chosen this year have the potential to create measurable, real-world impacts in both the water and food sectors.”  

      The 2022 J-WAFS seed grant researchers and their projects are:

      Gang Chen, the Carl Richard Soderberg Professor of Power Engineering in MIT’s Department of Mechanical Engineering, is using sunlight to desalinate water. The use of solar energy for desalination is not a new idea, particularly solar thermal evaporation methods. However, the solar thermal evaporation process has an overall low efficiency because it relies on breaking hydrogen bonds among individual water molecules, which is very energy-intensive. Chen and his lab recently discovered a photomolecular effect that dramatically lowers the energy required for desalination. 

      The bonds among water molecules inside a water cluster in liquid water are mostly hydrogen bonds. Chen discovered that a photon with energy larger than the bonding energy between the water cluster and the remaining water liquids can cleave off the water cluster at the water-air interface, colliding with air molecules and disintegrating into 60 or even more individual water molecules. This effect has the potential to significantly boost clean water production via new desalination technology that produces a photomolecular evaporation rate that exceeds pure solar thermal evaporation by at least ten-fold. 

      John E. Fernández is the director of the MIT Environmental Solutions Initiative (ESI) and a professor in the Department of Architecture, and also affiliated with the Department of Urban Studies and Planning. Fernández is working with Scott D. Odell, a postdoc in the ESI, to better understand the impacts of mining and climate change in water-stressed regions of Chile.

      The country of Chile is one of the world’s largest exporters of both agricultural and mineral products; however, little research has been done on climate change effects at the intersection of these two sectors. Fernández and Odell will explore how desalination is being deployed by the mining industry to relieve pressure on continental water supplies in Chile, and with what effect. They will also research how climate change and mining intersect to affect Andean glaciers and agricultural communities dependent upon them. The researchers intend for this work to inform policies to reduce social and environmental harms from mining, desalination, and climate change.

      Ariel L. Furst is the Raymond (1921) and Helen St. Laurent Career Development Professor of Chemical Engineering at MIT. Her 2022 J-WAFS seed grant project seeks to effectively remove dangerous and long-lasting chemicals from water supplies and other environmental areas. 

      Perfluorooctanoic acid (PFOA), a component of Teflon, is a member of a group of chemicals known as per- and polyfluoroalkyl substances (PFAS). These human-made chemicals have been extensively used in consumer products like nonstick cooking pans. Exceptionally high levels of PFOA have been measured in water sources near manufacturing sites, which is problematic as these chemicals do not readily degrade in our bodies or the environment. The majority of humans have detectable levels of PFAS in their blood, which can lead to significant health issues including cancer, liver damage, and thyroid effects, as well as developmental effects in infants. Current remediation methods are limited to inefficient capture and are mostly confined to laboratory settings. Furst’s proposed method utilizes low-energy, scaffolded enzyme materials to move beyond simple capture to degrade these hazardous pollutants.

      Heather J. Kulik is an associate professor in the Department of Chemical Engineering at MIT who is developing novel computational strategies to identify optimal materials for purifying water. Water treatment requires purification by selectively separating small ions from water. However, human-made, scalable materials for water purification and desalination are often not stable in typical operating conditions and lack precision pores for good separation. 

      Metal-organic frameworks (MOFs) are promising materials for water purification because their pores can be tailored to have precise shapes and chemical makeup for selective ion affinity. Yet few MOFs have been assessed for their properties relevant to water purification. Kulik plans to use virtual high-throughput screening accelerated by machine learning models and molecular simulation to accelerate discovery of MOFs. Specifically, Kulik will be looking for MOFs with ultra-stable structures in water that do not break down at certain temperatures. 

      Gregory C. Rutledge is the Lammot du Pont Professor of Chemical Engineering at MIT. He is leading a project that will explore how to better separate oils from water. This is an important problem to solve given that industry-generated oil-contaminated water is a major source of pollution to the environment.

      Emulsified oils are particularly challenging to remove from water due to their small droplet sizes and long settling times. Microfiltration is an attractive technology for the removal of emulsified oils, but its major drawback is fouling, or the accumulation of unwanted material on solid surfaces. Rutledge will examine the mechanism of separation behind liquid-infused membranes (LIMs) in which an infused liquid coats the surface and pores of the membrane, preventing fouling. Robustness of the LIM technology for removal of different types of emulsified oils and oil mixtures will be evaluated. César Terrer is an assistant professor in the Department of Civil and Environmental Engineering whose J-WAFS project seeks to answer the question: How can satellite images be used to provide a high-resolution drought monitoring system for farmers? 

      Drought is recognized as one of the world’s most pressing issues, with direct impacts on vegetation that threaten water resources and food production globally. However, assessing and monitoring the impact of droughts on vegetation is extremely challenging as plants’ sensitivity to lack of water varies across species and ecosystems. Terrer will leverage a new generation of remote sensing satellites to provide high-resolution assessments of plant water stress at regional to global scales. The aim is to provide a plant drought monitoring product with farmland-specific services for water and socioeconomic management.

      Michael Triantafyllou is the Henry L. and Grace Doherty Professor in Ocean Science and Engineering in the Department of Mechanical Engineering. He is developing a web-based system for natural resources management that will deploy geospatial analysis, visualization, and reporting to better manage and facilitate aquaculture data.  By providing value to commercial fisheries’ permit holders who employ significant numbers of people and also to recreational shellfish permit holders who contribute to local economies, the project has attracted support from the Massachusetts Division of Marine Fisheries as well as a number of local resource management departments.

      Massachusetts shell fisheries generated roughly $339 million in 2020, accounting for 17 percent of U.S. East Coast production. Managing such a large industry is a time-consuming process, given there are thousands of acres of coastal areas grouped within over 800 classified shellfish growing areas. Extreme climate events present additional challenges. Triantafyllou’s research will help efforts to enforce environmental regulations, support habitat restoration efforts, and prevent shellfish-related food safety issues. More

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      in Environment

      SMART researchers develop method for early detection of bacterial infection in crops

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      Researchers from the Disruptive and Sustainable Technologies for Agricultural Precision (DiSTAP) Interdisciplinary Research Group (IRG) ofSingapore-MIT Alliance for Research and Technology (SMART), MIT’s research enterprise in Singapore, and their local collaborators from Temasek Life Sciences Laboratory (TLL), have developed a rapid Raman spectroscopy-based method for detecting and quantifying early bacterial infection in crops. The Raman spectral biomarkers and diagnostic algorithm enable the noninvasive and early diagnosis of bacterial infections in crop plants, which can be critical for the progress of plant disease management and agricultural productivity.

      Due to the increasing demand for global food supply and security, there is a growing need to improve agricultural production systems and increase crop productivity. Globally, bacterial pathogen infection in crop plants is one of the major contributors to agricultural yield losses. Climate change also adds to the problem by accelerating the spread of plant diseases. Hence, developing methods for rapid and early detection of pathogen-infected crops is important to improve plant disease management and reduce crop loss.

      The breakthrough by SMART and TLL researchers offers a faster and more accurate method to detect bacterial infection in crop plants at an earlier stage, as compared to existing techniques. The new results appear in a paper titled “Rapid detection and quantification of plant innate immunity response using Raman spectroscopy” published in the journal Frontiers in Plant Science.

      “The early detection of pathogen-infected crop plants is a significant step to improve plant disease management,” says Chua Nam Hai, DiSTAP co-lead principal investigator, professor, TLL deputy chair, and co-corresponding author. “It will allow the fast and selective removal of pathogen load and curb the further spread of disease to other neighboring crops.”

      Traditionally, plant disease diagnosis involves a simple visual inspection of plants for disease symptoms and severity. “Visual inspection methods are often ineffective, as disease symptoms usually manifest only at relatively later stages of infection, when the pathogen load is already high and reparative measures are limited. Hence, new methods are required for rapid and early detection of bacterial infection. The idea would be akin to having medical tests to identify human diseases at an early stage, instead of waiting for visual symptoms to show, so that early intervention or treatment can be applied,” says MIT Professor Rajeev Ram, who is a DiSTAP principal investigator and co-corresponding author on the paper.

      While existing techniques, such as current molecular detection methods, can detect bacterial infection in plants, they are often limited in their use. Molecular detection methods largely depend on the availability of pathogen-specific gene sequences or antibodies to identify bacterial infection in crops; the implementation is also time-consuming and nonadaptable for on-site field application due to the high cost and bulky equipment required, making it impractical for use in agricultural farms.

      “At DiSTAP, we have developed a quantitative Raman spectroscopy-based algorithm that can help farmers to identify bacterial infection rapidly. The developed diagnostic algorithm makes use of Raman spectral biomarkers and can be easily implemented in cloud-based computing and prediction platforms. It is more effective than existing techniques as it enables accurate identification and early detection of bacterial infection, both of which are crucial to saving crop plants that would otherwise be destroyed,” explains Gajendra Pratap Singh, scientific director and principal investigator at DiSTAP and co-lead author.

      A portable Raman system can be used on farms and provides farmers with an accurate and simple yes-or-no response when used to test for the presence of bacterial infections in crops. The development of this rapid and noninvasive method could improve plant disease management and have a transformative impact on agricultural farms by efficiently reducing agricultural yield loss and increasing productivity.

      “Using the diagnostic algorithm method, we experimented on several edible plants such as choy sum,” says DiSTAP and TLL principal investigator and co-corresponding author Rajani Sarojam. “The results showed that the Raman spectroscopy-based method can swiftly detect and quantify innate immunity response in plants infected with bacterial pathogens. We believe that this technology will be beneficial for agricultural farms to increase their productivity by reducing their yield loss due to plant diseases.”

      The researchers are currently working on the development of high-throughput, custom-made portable or hand-held Raman spectrometers that will allow Raman spectral analysis to be quickly and easily performed on field-grown crops.

      SMART and TLL developed and discovered the diagnostic algorithm and Raman spectral biomarkers. TLL also confirmed and validated the detection method through mutant plants. The research is carried out by SMART and supported by the National Research Foundation of Singapore under its Campus for Research Excellence And Technological Enterprise (CREATE) program.

      SMART was established by MIT and the NRF in 2007. The first entity in CREATE developed by NRF, SMART serves as an intellectual and innovation hub for research interactions between MIT and Singapore, undertaking cutting-edge research projects in areas of interest to both Singapore and MIT. SMART currently comprises an Innovation Center and five IRGs: Antimicrobial Resistance, Critical Analytics for Manufacturing Personalized-Medicine, DiSTAP, Future Urban Mobility, and Low Energy Electronic Systems. SMART research is funded by the NRF under the CREATE program.

      Led by Professor Michael Strano of MIT and Professor Chua Nam Hai of Temasek Lifesciences Laboratory, the DiSTAP program addresses deep problems in food production in Singapore and the world by developing a suite of impactful and novel analytical, genetic, and biomaterial technologies. The goal is to fundamentally change how plant biosynthetic pathways are discovered, monitored, engineered, and ultimately translated to meet the global demand for food and nutrients. Scientists from MIT, TTL, Nanyang Technological University, and National University of Singapore are collaboratively developing new tools for the continuous measurement of important plant metabolites and hormones for novel discovery, deeper understanding and control of plant biosynthetic pathways in ways not yet possible, especially in the context of green leafy vegetables; leveraging these new techniques to engineer plants with highly desirable properties for global food security, including high-yield density production, and drought and pathogen resistance; and applying these technologies to improve urban farming. More