The technology used to sequence SARS-CoV-2 at record speed early in the COVID-19 pandemic has been successfully tested as a technique to monitor arboviruses and diseases transmitted mainly by mosquitoes. 

In an article published in the journal Microbiology Society, researchers affiliated with Pasteur Institute in São Paulo, Brazil, and the University of São Paulo (USP), in collaboration with colleagues at the University of Birmingham in the United Kingdom, describe the use of the technology to sequence viral RNA and DNA from blood-engorged mosquitoes collected in São Paulo city with the aim of finding out how arboviruses circulate as a basis for predicting future outbreaks of dengue, zika, chikungunya and yellow fever, among other diseases. 

“The study proved the concept that it’s possible to use metagenomics [sequencing the genetic material of all organisms in an environment at the same time without isolating them] to analyze samples from invertebrates. Previously, it was used to analyze samples from vertebrates [such as humans and other primates]. Our protocol can reveal viral diversity and identify mosquito species while also analyzing their feeding habits, and has the potential to extend our understanding of insect genetic diversity and the dynamics of arbovirus transmission,” said Karin Kirchgatter, a researcher at Pasteur Institute (São Paulo) who coordinated the study jointly with Nicholas J. Loman, Professor of Microbial Genomics and Bioinformatics at the University of Birmingham.

The protocol was developed by researchers affiliated with the Brazil-UK Center for Arbovirus Discovery, Diagnosis, Genomics and Epidemiology (CADDE), which is supported by FAPESP. Arbovirus tracking was made possible by adaptation of a rapid metagenomics technique developed during the PhD research of Ingra Morales Claro, who was supported by a scholarship from FAPESP. 

Another key member of the research team was Ester Sabino, a professor at USP. Sabino led the first sequencing of SARS-CoV-2 in Brazil (in March 2020) and genomic analysis of the first cases of infection by the gamma variant in Manaus, the capital of Amazonas state, about a year later (read more at: agencia.fapesp.br/35414). 

“The success of the tracking test was important. It showed that the technology can also be used to investigate arboviruses rapidly and efficiently. The test wasn’t surveillance but the technique will be an important part of it. We also added information of various kinds, such as epidemiological data, as a basis for predicting new outbreaks of disease,” Sabino said.

How it works

Nanopore sequencing allows for real-time analysis of long DNA or RNA fragments. It works on the principle of minute changes in electric current when the nucleotides of a single-stranded DNA molecule are pulled through a nanopore, a tiny hole (on the order of 1 nanometer in internal diameter) that is made up of certain transmembrane cellular proteins. The amount of change in current is characteristic for each nucleotide. The change in the current is directly read, and the sequence is determined by detecting changes in the current specific to the base in question. The results can be compared to genetic sequencing databases to determine the details of interest, such as the species from which the sample was taken. 

“The technique is still expensive. No genetic sequencing technology can be considered low-cost to date. With time and expanding use, the cost will come down,” said Jeremy Mirza, a researcher at the University of Birmingham and first author of the article. He is also affiliated with CADDE.

Real-time metagenomics can be used to detect emerging viruses and unknown pathogens in samples taken from patients, without requiring reagents developed specifically for certain microorganisms, as do conventional tests.

The protocol described in the article identifies vectors, viruses and hosts by means of a portable device that can be used in future to look for pathogens in remote areas. For the first time, it has now been used to identify not just the virus and mosquito species in a sample, but also the contents of the mosquito’s blood meal.

“We tested the technology on samples collected at the São Paulo zoo, a biodiversity hotspot and hence an interesting area for this type of study. The diversity of vectors and blood meal sources is huge. Large numbers of people are continuously on the move there, it’s a stopover for many migratory birds, and it’s also a controlled location with a known number of animals and species. The mosquitoes can be tracked as they move through the zoo on the basis of the blood on which they feed,” Kirchgatter explained.

The samples analyzed in the study came from engorged mosquitoes collected at the zoo in 2015 and had already been analyzed using traditional techniques. “This enabled us to compare the results and the time taken in each stage of the process,” said Lilian de Oliveira Guimarães, second author of the article and a researcher at Pasteur Institute. At the time, she had a postdoctoral scholarship from FAPESP. 

“In 2015, we analyzed each mosquito individually, identifying the species by classical taxonomy, sequencing specific regions of each specimen and comparing the sequences manually. This took weeks. With the new methodology, molecular identification is feasible in real time. It identifies and correlate species and feeding preferences, as well as the viruses present in the insect.” 

According to the authors, the positive results of the arbovirus tracking test open the door to further research and discoveries. Combining information about mosquito genetic diversity and the transmission dynamics of mosquito-borne viruses presents an opportunity to link novel arboviruses to the mosquito vectors of these pathogens. 

“Further, it can be used to identify animals that may be infected by these viruses and point to risks of spillover into human populations,” the researchers note. “The portability of the technology permits discovery of novel arboviruses in remote environments, and the method can form the basis of an early warning detection system by identifying arboviruses before they spread into human populations, providing a system for preempting future arboviral epidemics”.

About São Paulo Research Foundation (FAPESP)

The São Paulo Research Foundation (FAPESP) is a public institution with the mission of supporting scientific research in all fields of knowledge by awarding scholarships, fellowships and grants to investigators linked with higher education and research institutions in the State of São Paulo, Brazil. FAPESP is aware that the very best research can only be done by working with the best researchers internationally. Therefore, it has established partnerships with funding agencies, higher education, private companies, and research organizations in other countries known for the quality of their research and has been encouraging scientists funded by its grants to further develop their international collaboration. You can learn more about FAPESP at www.fapesp.br/en and visit FAPESP news agency at www.agencia.fapesp.br/en to keep updated with the latest scientific breakthroughs FAPESP helps achieve through its many programs, awards and research centers. You may also subscribe to FAPESP news agency at http://agencia.fapesp.br/subscribe.

Climate change presents a formidable global challenge. Developing efficient carbon capture and storage (CCS) technology is an effective way to mitigate climate change. Carbon capture using biomass waste-derived engineered biochar is a promising avenue in CCS technology. However, optimal synthesis of engineered biochar is a time- and resource-intensive process. Researchers have now devised an active learning strategy that accelerates the development of high-performance engineered biochar with enhanced CO₂ uptake.

In a groundbreaking development, researchers have unlocked the potential of biomass waste-derived engineered biochar for unprecedented CO₂ capture, paving the way for advanced climate change mitigation and sustainable waste management solutions.

Despite the recognized benefits of biochar in addressing environmental challenges, its optimal synthesis for enhanced performance has long been hindered by time- and labor-intensive processes. In response to this challenge, a team of experts has unveiled an innovative active learning strategy designed to guide and expedite biochar synthesis while significantly improving its CO₂ adsorption performance.

The research team, led by Prof. Yong Sik Ok, Chair and Program Director of the APRU Sustainable Waste Management Program, collaborated with Prof. Xiangzhou Yuan from Southeast University, Prof. Javier Pérez-Ramírez from ETH Zurich, and Prof. Xiaonan Wang from Tsinghua University. Their approach leverages experimental data to recommend optimal synthesis parameters, focusing on maximizing the narrow micropore volume of engineered biochar—a key factor in its CO₂ adsorption performance. This work, “Active Learning- Based Guided Synthesis of Engineered Biochar for CO₂ Capture,” has been selected as a Front Cover, which is the featured cover in all ACS journal issues.

The active learning strategy was rigorously validated through experimental tests, with data iteratively leveraged for subsequent model training and revalidation. This iterative process, establishing a closed loop, resulted in the synthesis of 16 property-specific engineered biochar samples over three active learning cycles. Impressively, the CO₂ uptake nearly doubled by the final round, showcasing the transformative impact of this data-driven approach.

“The active learning strategy we employed not only expedites the synthesis of engineered biochar but also maximizes its CO₂ adsorption capacities. This innovative approach has the potential to reshape the landscape of biomass waste-derived materials, offering a data-driven workflow for the development of high-performance biochar with broader applications,” says Prof. Ok.

This research introduces a pioneering data-driven workflow that not only accelerates the development of high-performance engineered biochar but also expands its applications as functionalized materials. The breakthrough holds significant promise for addressing climate change and advancing sustainable waste management practices, marking a crucial step towards a more environmentally conscious future.

“The active learning cycles described in our research exemplify our dedication to innovative methodologies. It is through collaboration and a commitment to sustainable practices that we can drive meaningful change, as reflected in our recent publications in leading journals,” says Prof. Yuan.

In addition to publishing key articles in reputed journals, the team’s remarkable research portfolio includes a series of influential publications, each addressing critical issues and proposing innovative solutions:

• “Machine learning for heavy metal removal from water: recent advances and challenges” – Published in ACS ES&T Water (2023, DOI: 10.1021/acsestwater.3c00215) and featured with a Supplementary Journal Cover, this manuscript explores the application of machine learning in addressing the removal of heavy metals from water sources, highlighting recent advancements and challenges in the field.
• “Sustainability-inspired upcycling of waste polyethylene terephthalate plastic into porous carbon for CO₂ capture” – Published in Green Chemistry (2022, DOI: 10.1039/d1gc03600a) and featured with a Front Cover and selected as a Highly Cited Paper (HCP), this paper delves into the upcycling of waste polyethylene terephthalate plastic into porous carbon materials, offering a sustainable solution for CO₂ capture.
• “Sustainable Food Waste Management: Synthesizing Engineered Biochar for CO₂ Capture” – Published in ACS Sustainable Chemistry & Engineering (2022, DOI: 10.1021/acssuschemeng.2c03029) and featured with a Front Cover, this work upcycles food waste into high-performance engineered biochar for CO₂ capture, indicating that a net negative global warming potential could be achieved using food waste-derived CO₂ adsorbent from the life-cycle perspective.
• “Applied Machine Learning for Prediction of CO₂ Adsorption on Biomass Waste-Derived Porous Carbons” – Published in ES&T (2021, DOI: 10.1021/acs.est.1c01849) and featured with a Supplementary Journal Cover, this manuscript explores the application of machine learning techniques for predicting CO₂ adsorption on biomass waste-derived porous carbons, offering insights into efficient carbon capture technologies.
• “The COVID-19 pandemic necessitates a shift to a plastic circular economy” – Featured in Nature Reviews Earth & Environment (2021, DOI: 10.1038/s43017-021-00223-2), this publication underscores the urgency of transitioning to a plastic circular economy in response to the challenges posed by the COVID-19 pandemic.
• “Dual closed-loop chemical recycling support sustainable mitigation of plastic pollution” – Presented in Matter (2021, DOI: 10.1016/j.matt.2021.03.014), this research outlines a dual closed-loop chemical recycling approach to supporting sustainable mitigation of plastic pollution, highlighting the importance of circular economy principles.

Prof. Ok, along with collaborators, including Prof. Xiangzhou Yuan from Southeast University, has been instrumental in driving these initiatives forward. Their collective efforts have not only advanced scientific knowledge but also paved the way for practical solutions to some of the most pressing environmental challenges of our time.

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Reference

DOI: https://doi.org/10.1021/acs.est.3c10922

About APRU Sustainable Waste Management Program

As a network of leading universities linking the Americas, Asia, and Australasia, APRU (the Association of Pacific Rim Universities) brings together thought leaders, researchers, and policy-makers to exchange ideas and collaborate toward practical solutions to combat the challenges of the 21st century. The APRU Sustainable Waste Management Program focuses on adopting environmentally friendly practices to manage waste effectively while minimizing its negative impacts on the environment and human health. It involves various strategies and approaches to reduce, reuse, recycle, and properly dispose of waste materials together with ESG concepts. Prof. Yong Sik Ok at Korea University serves as the Chair and Program Director of the program, co-directed by Prof. William Mitch at Stanford University. For more information, visit APRU Sustainable Waste Management Program’s website.

About Professor Yong Sik Ok

Professor Yong Sik Ok is a KU HCR Professor. He is the Chair and Program Director of the Sustainable Waste Management Program for the Association of Pacific Rim Universities (APRU) and the President of the International ESG Association and the International Society of Trace Element Biogeochemistry. He maintains a worldwide professional network by serving as the Editor-in-Chief of CleanMat (Wiley Open Access) and the Co-Editor-in-Chief of Critical Reviews in Environmental Science and Technology (CREST, five-year IF:13.6) at Taylor and Francis. Moreover, Prof. Ok has hosted many conferences and forums focusing on Sustainability, UN SDGs, and ESG. The recently concluded 6th Global Conference on ESG Management & Sustainability marked another milestone in Prof. Ok’s ongoing journey toward achieving sustainability and ESG goals together with Prof. Jay Hyuk Rhee (President, KU ESG Research Institute & President, International ESG Association) at Korea University Business School. Importantly, Prof. Ok will chair the 4th Australian Circular Economy Conference, scheduled to take place in Sydney, Australia, in October 2024, together with Prof. Ali Abbas, Director, Waste Transformation Research Hub and the Associate Dean Research, Faculty of Engineering, The University of Sydney.