• LOCAL COVID-19 SWAB EXTRACTION KITS TO BE PRODUCED AT SCALE

    11th Aug 2020

    South Africa is on track to manufacture its own Coronavirus disease 2019 (COVID-19) sample purification kits in large quantities within six months, creating a steady local supply that will speed up testing and reduce the country’s reliance on international suppliers amid intense global demand.

    The CSIR’s Dr Previn Naicker says the technology being developed by his team is open source in that it would generate pure samples from nasal and throat swabs that can be tested for the presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral RNA on any platform. The work is being funded by the Department of Science and Innovation, the South African Medical Research Council and the Technology Innovation Agency.

    A reliable local supply of sample purification reagents also addresses the specific problem of patient swabs becoming non-viable for testing because of the lengthy backlogs caused by a lack of reagents. Not only do such long waiting periods compromise test results for individual patients, it compromises the entire disease management process that relies on quarantine along with quick contact tracing and testing.

    “There are testing facilities that are not running at full capacity because there are not enough diagnostic reagents,” Naicker says. “The project will ensure that we close that gap and reduce the turnaround time of testing.”

    The CSIR is working with local partners such as ReSyn Biosciences, a spin-off company of the CSIR that will produce magnetic beads for extracting viral RNA from test samples.

    Magnetic beads offer the advantage that RNA extraction can be automated. “Every step of the diagnostic process that can be automated makes for better testing,” says Naicker.

    As positive cases in South Africa continue to increase at an alarming rate, Naicker says the portion of positive cases in relation to the tests conducted shows that South Africa is under-testing. Experts say the virus will be with us for a long time to come, so Naicker’s team and their local partners plan to optimise the kit within the next two months so that validation (testing on real samples), licencing and regulatory approval by the South African Health Products Regulation Authority (SAHPRA) can take place as soon as possible.

    “If all goes according to plan, we will have a market-ready kit within six months,” says Naicker.

    “Based on the capacity of our local partners, kits for the extraction of a minimum of 5 000 samples can be assembled per day at a certified facility, and we are in discussions with two proposed facilities thus far.” In other words, this technology could support at least an additional 10 000 COVID-19 tests per day.

    “As a scientist working in the health space, to be part of the COVID-19 response is both fulfilling and exciting,” he says. “We all have a desire to make a positive societal impact.”

     

    Story by: Council of Scientific and Industrial Research

     

  • FASTER, LOCAL COVID-19 TEST KITS COULD BE READY BY YEAR-END

    11th Aug 2020

    The CSIR can make enough enzyme for one billion chemical reactions that can be applied in COVID-19 testing, and researchers hope to begin supplying reagents for a faster, one-step test by the end of the year.

    Current polymerase chain reaction (PCR) tests for the presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in nasal and throat swabs involve two steps.

    First, the virus’s genetic material, its RNA, must be converted to DNA using an enzyme called reverse transcriptase, in a reaction called RT-PCR. Second, PCR is then used to make thousands of copies of the DNA, until there are enough of these tiny molecules to detect.

    If the test detects the targeted DNA copies, there must have been viral RNA in the sample, hence the test is positive.

    The CSIR has already established a highly efficient technology to produce the enzyme needed for the second step, says senior researcher Dr Lusisizwe Kwezi. “This enzyme is known as DNA Taq polymerase, and just three grams of the protein, produced in E. coli bacteria in as little as three days, is enough for a billion PCR reactions.”

    This does not equate to COVID-19 tests for a billion people because, among other technical reasons, diagnostic tests must be carefully repeated several times for each patient to ensure accurate results. But it does mean that a huge amount of this important reagent is available locally and affordably.

    Another benefit of the reagent mix is that it contains a special antibody that stops the Taq enzyme from working when it is not needed. This makes it more specific when it has to amplify DNA during the PCR reaction, and more robust for potential future point-of-care testing devices.

    Kwezi says that earlier this month, the CSIR delivered a 3 g batch to local company CapeBio Technologies (Pty) Ltd, which has licenced and commercialised the technology. It will be rolled out to support the national testing effort as soon as CapeBio gets approval from the South African Health Products Regulation Authority (SAHPRA).

    Thanks to funding just awarded through the Strategic Health Innovation Partnership – a partnership between the South African Medical Research Council and the Department of Science and Innovation (DSI) – the CSIR and CapeBio are now working to add the reverse transcriptase enzyme to the mix as well, so that the two-step COVID-19 PCR test can be done in a single step. This will reduce the turn-around time of tests.

    The antibody will be produced in plants rather than in E. coli, and Kwezi says the resulting one-step kit could be ready for national roll-out within six months, pending SAHPRA approval.

    He says local availability of large amounts of such affordable ‘plug-and-play’ reagents, which also allow for faster results delivered to patients, will be critical in managing the pandemic in the long-term, as we know the virus will be with us for a long time.

    Important for all South Africans to note, says Kwezi, is that this key technology in the fight against the worst pandemic the world has seen in a century, began as research years ago to supply the local molecular biology market. ”Back then, little did we know how important this would one day be. This just shows how research and development can translate concepts into technology solutions to emerging challenges whilst producing export products.”

    “It is Archimedes who said, ‘give me a lever long enough and a fulcrum on which to place it, and I shall move the world’,” says Kwezi. “We have the potential in South Africa to respond to this pandemic. We have the know-how, and we are grateful for funding from DSI.”

     

    Story by: Council for Scientific and Industrial Research

  • International research collaborations: how can we shift the power towards Africa?

    28th Jul 2020

    Post-COVID, there’s an opportunity to form lateral research partnerships driven by the needs of African communities.
    GettyImages

    Salome Maswime, University of Cape Town; Kevin Marsh, University of Oxford, and Rifat Atun, Harvard University

    The higher education sector globally has been disrupted by the COVID-19 pandemic. Academics have been discussing various aspects of the disruptions in a series of webinars organised by the University of Cape Town. One area of particular interest is how the pandemic could affect international research collaborations. The Conversation Africa’s Nontobeko Mtshali asked panellists to share their views.

    Could COVID-19 change the power dynamics between African and foreign institutions when it comes to research collaboration?

    Salome Maswime: There have been many successful global research collaborations. But there’s a long history of unequal partnerships and research collaborations between African institutions and research institutions from developed countries. African researchers have often described unequal power dynamics. These have been fuelled by what can be described as a top-down approach, a sense of tokenism. There’s a sense that research agendas are driven by interests of collaborating centres instead of the needs of the communities involved.

    One big change is that, prior to COVID-19, collaborators could travel to conduct research. But implementation is now dependent on the full buy-in of the local institution.

    The pandemic has also compelled us to look for African solutions for Africa, and to ensure that we don’t miss out on the opportunity to be part of important discoveries like vaccines and drug treatments.

    Rifat Atun: COVID-19 will likely affect the power relationship between African and foreign institutions. To date this power relationship has been hugely imbalanced. It’s been in favour of research institutions from high-income countries at the expense of African researchers and institutions.

    The COVID-19 pandemic has clearly revealed that research undertaken in African countries – and subsequent policies related to COVID-19 – are critical not just for Africa but for the world. What’s also apparent is the importance of local contexts in relation to the behaviour of the epidemic and responses to different policies. This has shown how necessary it is to have locally generated research led by researchers who understand local contexts.

    The speed of the epidemic has made it imperative to quickly develop local capacity in Africa to lead and undertake research – and reduce dependence.

    One adverse consequence of the COVID-19 pandemic is the economic crisis that has followed. This is likely to lead to reduced research funding for health. Another adverse effect is the greater national focus on self-sufficiency. It could risk undermining international collaborations.

    Kevin Marsh: It could contribute to a change that long predates the pandemic and which has been gathering pace.

    Historically, we’re all aware of the imbalance in many such relationships. This reflects a structural consequence of colonialism, in terms of where money and scientific expertise and decision making were centred.

    This has in fact begun to change markedly over the last few years. There are now many more researchers on the continent beginning to exercise their autonomy and leadership. The centre of gravity is changing in relation to defining African research priorities and funding.

    Similarly, there are plenty of international collaborators who recognise and support these changes.

    Other factors include the fact that, unlike Ebola, collaboration cannot involve a mass influx of collaborators from “outside”. Another is that there has been real synergy between continental organisations in setting priorities. These include the Africa Centres for Disease Control and Prevention, World Health Organisation Regional Office for Africa and the African Academy of Sciences.

    How could things change?

    Salome Maswime: This could lead to collaborations that are truly lateral with all collaborators involved from the design phase of the project to completion.

    Often organisations with funding have the means to set up research sites and to employ research staff, with little buy-in and minimal engagement from the stakeholders in collaborating institutions. With virtual communication, there’s more transparency and more visibility. And no excuse for lack of representation.

    The African community has also taken a keen interest in science, collaborations, equity and ethics with COVID-19. This could lead to more community engagement with research. It could also see greater effort at improving science communication. Curiosity about the safety of vaccines and drug trials, the risks in Africa and the credibility of the organisations involved are examples of how science has become a priority on the continent.



    Read more:
    Coronavirus: never been a more compelling time for African scientists to work together


    Rifat Atun: The change could be positive. It can empower African research institutions and enable the development of local research capacity that can design, implement and evaluate large research studies in Africa and beyond.

    The new environment gives Africa the opportunity to lead local research and development using local capacity rather than being a “venue” for research for researchers from high-income countries who all too often take the credit for the studies. Africa must develop research and development capacity and transition to greater self-sufficiency in critical supplies of vaccines, medicines and health products.

    Does COVID-19 open possibilities that didn’t exist before?

    Salome Maswime: With the acceleration of virtual communication there’s been wider engagement locally and more South-South partnerships forming. Previously we’d rely on funding for meetings to engage on research projects. But more scientific groups are being formed virtually to respond to COVID-19 and local challenges.

    There are also opportunities to increase research capacity and training through online education. Over the past eight weeks, hundreds of South Africans have attended live webinars run by Professor Mamokgethi Phakeng, the Vice-Chancellor of the University of Cape Town, on postgraduate research methods. This is a great example of an approach to research that inspires and empowers aspiring researchers.

    After the pandemic we have an opportunity to form truly lateral partnerships driven by the needs of African communities.

    Rifat Atun: There’s an opportunity to establish regional and continent-wide research networks to undertake research in Africa. There’s also the opportunity to be part of international and global studies and lead them.

    Kevin Marsh: There is a sudden increase in funding – so in that sense the answer is yes. But more positively and importantly, we’re seeing that the response from the scientific community on the continent in taking leadership has been strong. So in many ways COVID-19 has revealed this rather than caused it.The Conversation

    Salome Maswime, Professor of Global Surgery, University of Cape Town; Kevin Marsh, Professor of Tropical Medicine, University of Oxford, and Rifat Atun, Professor of Global Health Systems, Harvard University

    This article is republished from The Conversation under a Creative Commons license. Read the original article.

  • The Launch of the 2020 Metabolomics Webinar Series

    16th Jul 2020

    The African Centre for Gene Technologies (ACGT) and Metabolomics South Africa (MSA) are always looking for ways to create more Metabolomics platforms for discussions and training. One such initiative was to start up a Metabolomics Webinar Series that will run throughout 2020. The idea is to have a webinar hosted by a local expert once a month or so to discuss a key technique or new data that could be of relevance to the rest of the South African metabolomics community.

    The first webinar of the series was hosted by Dr Shayne Mason on the 9th July 2020 at 14:00. Dr Shayne Mason is from the Laboratory for Infectious Diseases in Human Metabolomics at the North-West University (NWU) Potchefstroom campus. Dr Mason is a research leader at NWU specializing in TB meningitis and biofluid analysis. Dr Mason completed not one, but two BSc degrees; one in Biochemistry and Microbiology and the other in Statistics and Applied Mathematics. He completed his PhD in 2016 as a joint degree between NWU and VU in Amsterdam in the field of nuclear magnetic resonance (NMR) metabolomics. Dr Mason has published over 20 publications in the field and assisted and/or supervised numerous postgraduate students.

    Then idea for this webinar was birthed from a question. One of the issues that stood out at a previous ACGT/MSA workshop was “how does one interpret the NMR spectra to determine the metabolites?” This webinar is aimed at answering that question and more.

    And Answer it did.

    The webinar addressed one of the major challenges in metabolomics which is the identification of metabolites in a highly complex mixture of compounds that produce a forest of peaks in a NMR spectrum. Dr Mason gave a practical stepwise guide description of how to perform 1H-NMR metabolite profiling on multiple complex biological samples. This metabolite identification process, called metabolite profiling, involves fitting the mixture spectrum to a set of individual pure reference spectra obtained from known pure compounds. The fitting process yields not only the identity of the metabolites, but also the accurate concentration of those metabolites. The participants were given a path to successful metabolite profiling that would provide them with a table of metabolite names and their absolute or relative concentrations.

    This webinar was attended by 128 participants from all over South Africa. There was a great Q&A session that followed and this highlighted the need for more of these sorts of meetings. Please look out for future communication about the next webinar and other ACGT events.

    The ACGT is looking forward to your participation in future webinars and events. For more information and suggestions about future events, please contact Mr Molati Nonyane at .

  • CRISPR Gene Editing Prompts Chaos in DNA of Human Embryos

    6th Jul 2020

    The ability of CRISPR gene-editing technology to safely modify human embryos has been cast into doubt after several recent papers described massive disruptions to DNA in embryos subjected to editing.

    Each of the three papers, published this month without peer review on the preprint server bioRxiv, intended to edit only a single gene. But results showed large-scale, unintended DNA deletions and rearrangements in the areas surrounding the targeted sequence. While past research has shown that gene editing can lead to mutations far away from the targeted region, these studies instead draw attention to more localized damage involving larger sequences of DNA that could be overlooked by traditional safety screenings, Nature reports.

    These studies were intended only for research purposes, meaning the embryos were destroyed after the experiment ended. But in response to their findings, many researchers are voicing their objections to further editing. The field itself is still grappling with the fallout from the birth of twin girls as a result of highly controversial CRISPR experiments carried out by He Jiankui at the Southern University of Science and Technology in China in 2018.

    “There’s no sugarcoating this,” Fyodor Urnov, a geneticist and CRISPR researcher at the University of California, Berkeley, who was not involved with the research, tells OneZero. “This is a restraining order for all genome editors to stay the living daylights away from embryo editing.”

    In the first study, published June 5, researchers at the Francis Crick Institute used CRISPR to remove the POU5F1 gene—an important contributor to embryonic development and stem cell pluripotency—in 18 embryos. When they analyzed the effect of the deletion on the genome, they unexpectedly found that eight of these embryos contained additional abnormalities, four of which involved substantial DNA rearrangements and deletions of several thousand base pairs.

    A second group from Columbia University attempted to modify embryos with a blindness-causing mutation in the EYS gene, the most common gene implicated in the onset of a degenerative eye condition called retinitis pigmentosa. But in addition to the expected changes, they reported on June 18 that almost half of the 23 embryos also lost large chunks of the chromosome on which EYS is located. In the most extreme cases, the chromosome disappeared entirely.

    Lastly, a study published June 20 by researchers at Oregon Health & Science University similarly focused on correcting a mutation in the MYBPC3 gene that is known to cause a heart condition. While they were successful in repairing the damage in close to half of the 86 embryos—a complement to their pioneering work in 2017the authors also reported large disruptions in the chromosome containing the gene.

    Taken together, these three studies highlight the contrast between off-target effects, which happen when the CRISPR tools edit someplace unintended, and on-target edits, in which the changes are properly localized but have some unintended consequence. In each case, the on-target effects were unexpected.

    “What that means is that you’re not just changing the gene you want to change, but you’re affecting so much of the DNA around the gene you’re trying to edit that you could be inadvertently affecting other genes and causing problems,” Kiran Musunuru, a cardiologist at the University of Pennsylvania who was not involved in any of the studies, tells OneZero.

    These problems also show just how little is known about the ways in which the body naturally repairs molecular cuts to the genome made by CRISPR technology, Nature reports. Rather than neatly heal the newly cleaved ends of DNA subjected to editing, the mechanism can sometimes be faulty, leading to degraded or broken DNA.

    Speaking to Nature, Urnov says these on-target effects warrant the attention of researchers moving forward. “This is something that all of us in the scientific community will, starting immediately, take more seriously than we already have. This is not a one-time fluke.”

    Story by: Amanda Heidt, for The Scientist

  • Virus protein discovery reveals new plant-animal class of cell division disruptors

    15th Jun 2020

    Viruses are ubiquitous pathogens that can cause severe infectious diseases in both humans and agricultural crops. As most viruses have simple genomes and encode only a few proteins, they must usurp host cell resources for propagation. Understanding what host processes are disrupted and which viral proteins are involved greatly facilitate the design of therapeutic measures for controlling viral diseases in humans and crop plants.

    Recently, researchers from the Institute of Genetics and Developmental Biology (IGDB) of the Chinese Academy of Sciences discovered a plant viral protein named 17K that disrupts host cell division to promote its own propagation in infected tissues. They also linked it structurally to certain animal virus proteins.

    The work was published online in Science Advances on May 13. It is the result of a decade-long collaboration between the IGDB group led by Dr. Wang Daowen and the laboratory of Dr. Zhao Yuqi at the School of Medicine of the University of Maryland.The 17K protein is conserved in a group of cereal-infecting viruses called barley yellow dwarf viruses (BYDVs). Even though BYDVs have been studied for more than 60 years, they frequently cause severe epidemics in global wheat, barley, maize and oat crops, with yellowing and dwarfing as typical results.

    – Please use the following link to access the rest of the article: ScienceX

  • UP Scientists Awarded International Future Leaders African Independent Research Fellowships

    11th Jun 2020

    The African Academy of Sciences and the Royal Society, supported by the UK’s Global Challenges Research Fund, recently announced the second group of recipients of the Future Leaders African Independent Research (FLAIR) fellowship. This is awarded to outstanding early-career African scientists whose research focuses on the needs of the continent.

    The scientists are: Professor Cobus Visagie, Dr Esther Muema and Dr Gudrun Dittrich-Schröder.

    Prof Visagie, Associate Professor at FABI, said that this is the funding he needs “to really expand and establish my research in the agricultural space”. His work is on fungi that produce mycotoxins, one of the biggest threats to African food security.

    Mycotoxin contamination of food and feed pose serious threats to human and animal health in Africa, and often leads to death. According to the Food and Agricultural Organisation, 25% of crops are contaminated with fungi and mycotoxins. This leaves a high percentage of Africans, mostly from the poorest communities, and animals at high risk. Prof Visagie’s project aims to expand, document and disseminate our understanding of the diversity of mycotoxigenic fungi and mycotoxins in food and feed across South Africa.

    Dr Muema is a postdoctoral fellow in the division of Microbiology in the Department of Biochemistry, Genetics and Microbiology at FABI. “As an early-career soil scientist, I see the FLAIR fellowship as a golden opportunity to establish myself, and contribute towards Africa’s food security and sustainable development,” she said. “The enablement to also include master’s students in my project will assist me in growing my career as I contribute to human capital development.”

    Chickpeas not only provide nutrition but also use passenger bacteria, rhizobia, to lock nitrogen into soils, which are weathered and infertile in parts of South Africa. Dr Muema aims to identify local species of rhizobia to better understand their interaction with chickpeas, leading eventually to enhanced crop production and soil fertility. The aim of this project is to identify the diversity of native soil rhizobia that are compatible with chickpeas in different agro-ecological zones in South Africa.

    Dr Gudrun Dittrich-Schröder is a postdoctoral fellow at FABI and the Department of Zoology and Entomology. She will lead investigations into the potential of CRISPR/Cas9 gene editing tools to manage invasive insect pests in agriculture and forestry. This fellowship allows her to work on cutting-edge research that addresses challenges on the continent.

    The agricultural and forestry sectors are critical for future food security, are drivers of the economy and are critically linked to jobs. But pests and diseases are the biggest threats to these sectors. Current control measures cannot keep pace with the increase in pests and diseases –CRISPR/Cas9 gene editing provides a revolutionary method to control pest species. Specific areas in the genome of an insect can be targeted using CRISPR/Cas9 and by using gene drive, may promote the inheritance, and prevalence as a result, of this edited gene in pest populations. Dr Dittrich-Schröder will be using insect species from forestry and agriculture to develop and apply these tools.

    “These are three outstanding young researchers,” said Prof Bernard Slippers, Director of FABI. “We are delighted with the awards and are very proud of them. I have no doubt that the fellowships will provide a significant boost to the next phase of their careers. The fellowships are not only very prestigious, but also generous in terms of the support, networks and training they offer. We are passionate about the mentorship and development of young researchers in FABI and will do everything we can to support them.”

    Story by: Elsabé Brits for the University of Pretoria 

  • Life Scientists receive training in Linux

    Life Scientists receive training in Linux
    8th Jun 2020

    The African Centre for Gene Technologies (ACGT) together with the University of Pretoria’s Centre for Bioinformatics and Computational Biology (CBCB) and the CISCO Networking Academy, have been hosting the annual Linux for Life Scientists Workshops for three straight years now. This year’s course was facilitated fully online; a completely different format from that of previous years due to the current COVID-19 situation.

    Advancements in sequencing platforms and the amount of data generated require specialized skills and programs that generally require some knowledge of command-line. Linux is one such useful alternative operating system for data analysis and visualization. Researchers use open-source Linux to analyse the huge amounts of data they generate on multiple platforms. Linux is an alternative to expensive vendor-specific software that require periodic license renewals.

    The workshop was facilitated by Mr Shaheem Sadien (CISCO Networking Academy) and Professor Fourie Joubert (University of Pretoria). The Linux course facilitated over five webinars spread out over 2 weeks in May 2020. The first webinar served as an introduction to Linux and the rest of the webinars that followed covered navigation, essential commands, resources, clusters and queuing. The workshop participants were representative of all ACGT partner institutions (ARC, CSIR, UJ, UP and Wits), as well as the National Institute for Communicable Diseases (NICD), Tshwane University of Technology (TUT), University of Cape Town (UCT) and University of the Western Cape (UWC).

    The ACGT wishes to thank Mr Molati Nonyane, Ms Itseng Malao, Mr Shaheem Sadien and Prof Fourie Joubert for course content and organization. The ACGT is looking to host another iteration of this course in 2020. Kindly contact our Liaison Scientist, Mr Molati Nonyane () in this regard. The ACGT plans to continue with these kinds capacity building efforts to improve the skills level of South African scientists, especially in the field of bioinformatics and data analysis.

     

     

     

  • COVID-19 Vaccine Researchers Mindful of Immune Enhancement

    29th May 2020

    Most people who contract the dengue virus, a mosquito-borne RNA virus, experience mild symptoms or none at all. In some cases, it can cause a severe illness known as hemorrhagic fever, with bleeding, abnormal blood clotting, and leaky blood vessels that can sometimes lead to a precipitous drop in blood pressure and circulatory collapse. Curiously, in the 1960s, US army scientists in Thailand noticed this life-threatening condition occurred most frequently in two populations: first-time infected babies born to mothers who were immune to dengue, and children who had once experienced a mild or asymptomatic infection, and later contracted the virus a second time. A scary scenario began to crystalize: a second infection was sometimes worse than the first.

    A series of studies in cells, animals, and people eventually gave rise to a possible explanation: antibodies created during a first-time infection could, under very specific circumstances, end up enhancing the disease rather than protecting against subsequent infections. Researchers called this “antibody-dependent enhancement,” or ADE.

    ADE is one form of immune enhancement, a poorly understood group of phenomena occurring when components of our immune system that usually protect against viral infections somehow end up backfiring. It’s a concern in situations when people are continuously re-infected with particular pathogens, and with vaccines that work by injecting snippets of virus to mimic a first infection. Some immunizations, such as those against respiratory syncytial virus (RSV), have been observed in the past to make disease worse when vaccinated individuals contract the virus.

    As far as researchers know, such cases are exceedingly rare across viruses. For SARS-CoV-2, it’s unclear if any forms of immune enhancement could play a role in infections or vaccines under development, but there is no evidence so far.

    “[It’s just] a theoretical risk, but people are being extremely careful to make sure that this risk is not becoming a reality,” notes Paul-Henri Lambert, an immunologist and vaccinologist retired from the University of Geneva who now advises the university’s center of vaccinology and consults for a multinational collaborative project of researchers on safety evaluations of vaccine candidates. “With COVID-19, we have a disease which in eighty percent of people is selectively mild. So what you would not like is to give a vaccine that would not protect well and in a certain percentage of people make the disease worse.”

    No evidence yet for antibody-dependent enhancement in COVID-19

    Dengue remains the best-studied and one of the very few solid examples of ADE. It’s thought to occur in communities where there are multiple viral strains of dengue circulating. While antibodies against one dengue strain will typically reliably protect against that strain, things can go awry when the antibodies encounter a different strain of dengue. Instead of neutralizing the virus—that is, binding to and blocking a protein the pathogen needs to enter host cells—the antibodies only bind to the virus without neutralizing it.

    That can become a problem when immune cells, such as macrophages, dock onto the tail ends of antibodies using specialized receptors known as Fc receptors—which they often do to clear up antibody-virus debris. Because dengue viruses can use Fc receptors to infect cells, if the antibodies aren’t disabling the pathogen, they actually end up helping the virus enter macrophages to infect the cells, Trojan horse–style, explains Dennis Burton, a microbiologist at the Scripps Research Institute in California. This amplifies viral replication, potentially pushing the immune system into over-drive and paving the way for severe disease. “That’s the hallmark of ADE, basically . . . you make infection easier, you infect more cells, you get worse disease.”

    But there are still many questions surrounding ADE and its mechanism. It’s not entirely clear, for instance, if the antibodies are the sole effectors of ADE, or if other parts of the immune system also play a role. Nor is it certain whether it’s strictly the non-neutralizing characteristic of the antibodies that matters most—it could also be that neutralizing antibodies could also allow viruses to infect macrophages if they’re not numerous enough to block all key proteins across a virus’s surface.

    “It might be that any antibody would enhance if you’ve got it at a dose that doesn’t work,” notes James Crowe, an immunologist at Vanderbilt University Medical Center. “This is very hard to study in humans.”

    Solid evidence for ADE in natural viral infections exists only in dengue virus and some of its relatives. There are a handful of other viruses where ADE has been demonstrated in vitro—in experiments that mix macrophages or similar cells with antibodies and virus and see whether the virus is capable of infecting the cells in spite of the presence of antibodies, Crowe explains. Such experiments have found hints of ADE with viruses including Ebola virus, HIV, and coronaviruses such as SARS and MERS. However, it’s still a mystery to what extent this occurs in live organisms in the presence of a functioning immune system. “The immune system typically modulates things to your benefit. I’m not saying that ADE does not occur in the body—I’m just saying it’s difficult to bridge the results in the test tube to what happens in the body,” Crowe says.

    It’s not yet clear if SARS-CoV-2 is capable of infecting macrophages. Although some scientists have reportedly spotted viral protein inside macrophages, whether it actually infects and replicates in macrophages in the body “is something investigators are trying to determine right now,” Crowe says.

    Barney Graham, the deputy director of the National Institute of Allergy and Infectious Diseases’s Vaccine Research Center, which is collaborating with the company Moderna on a coronavirus vaccine, told PNAS last month that he doubts the dengue mechanism of ADE would apply to SARS-CoV-2 because the coronavirus primarily targets ACE2, not Fc, receptors, and has a very different pathogenesis compared to the dengue family. And even for the original SARS that caused an outbreak in 2003, in vitro experiments suggest that it could infect a human cell line using an Fc receptor, but the virus did not reproduce into infectious particles, Graham writes in a perspective article in Science.

    It’s theoretically possible that infections caused by other coronaviruses could generate antibodies in people’s blood and cause ADE upon infection with SARS-CoV-2, but there’s little evidence for this so far, Crowe notes. And in principle, some COVID-19 patients could develop antibodies that don’t neutralize, or produce neutralizing ones at insufficient concentrations, and then develop severe symptoms once they’re infected a second time. But a handful of reported SARS-CoV-2 re-infections have been found to be due to flawed tests. And two preprints appeared last week suggesting that in US patients who received antibody-containing blood plasma transfusions from COVID-19 survivors, the treatment did not make the disease worse, supporting the argument against ADE.

    ADE’s role in vaccine development

    Nevertheless, ADE is a possibility that vaccine scientists are keeping a watchful eye on, in part due to experiences with other vaccines. When researchers in the 1990s tested vaccines against feline infectious peritonitis, a rare and typically fatal coronavirus disease in cats, vaccinated kittens died much sooner than unvaccinated ones after being exposed to the virus.

    Such concerns have pushed some scientists to reconsider vaccine design. One explanation for why some of the early cat coronavirus vaccines caused ADE weren’t using the right vaccine targets, or the targets weren’t specific enough. This could have produced antibodies that target parts of the virus without blocking the specific site on its spike protein which it uses to infect cells—the receptor-binding domain (RBD).

    This is one reason why some investigators, including microbiologist and vaccinologist Maria Bottazzi of the Baylor College of Medicine in Houston, specifically pursue the RBD as a vaccine target–to avoid the possibility of generating non-neutralizing antibodies. “If you’re just giving the immune system the only choice of making an antibody to the receptor binding domain, then you drastically limit the possibility of inducing ADE,” explains her colleague, immunologist David Corry.

    Burton says vaccine tests in animal models will help researchers understand the likelihood of ADE occurring in a COVID-19 vaccine, although that won’t be conclusive proof until clinical tests in humans are conducted. Encouragingly, some recent preliminary vaccine studies found no evidence of ADE. In an April preprint, a team of researchers from the US and China showed that injecting rats with the SARS-CoV-2 RBD protein triggered a burst of neutralizing antibodies, which did not cause ADE when mixed with virus and Fc-expressing cells in vitro. In addition, even a whole inactivated virus vaccine recently tested by Chinese researchers in four macaques protected against exposure to SARS-CoV-2, and the researchers found no evidence of ADE.

    As long as it’s a good vaccine with a specific target that induces a strong neutralizing antibody response, it’s unlikely we’ll see ADE, “certainly not commonly,” Crowe says. “It’s only when you have an ineffective vaccine or antibody that you might see [ADE]. And no one wants to move those [candidates] forward anyway, so that’s why I’m optimistic.”

    Other mechanisms of immune enhancement in vaccines

    Bottazzi says she thinks processes involving other components of the immune system may be more relevant for SARS-CoV-2 vaccine concerns than ADE. Different routes to immune enhancement came to the foreground in the 1960s during clinical trials where young children were immunized with whole-inactivated virus vaccines against respiratory syncytial virus (RSV). When the children contracted RSV naturally a few months after the vaccinations, those who were immunized got a lot sicker than those who weren’t. In fact, in one trial, 80 percent of children in the youngest cohort had to be hospitalized, and two died.

    The syndrome those hospitalized kids developed is called vaccine-associated enhanced respiratory disease (ERD), and is linked with two immunological phenomena, Graham explains in the Science article. The first is a high concentration of binding antibodies that don’t neutralize the virus and result in the formation of antibody-virus complexes that get stuck in the small airways of the lungs, obstructing these spaces and driving inflammation—a mechanism considered different from ADE, Burton explains.

    Researchers also unexpectedly found large numbers of certain white blood cells in the lungs of the children who died, including a proinflammatory kind of cell called an eosinophil, usually associated with allergic reactions. This raised concerns that the vaccine could have somehow primed the immune system to trigger an inappropriate cellular immune response. Normally, vaccines or viral infections trigger a particular group of T helper (Th) cells—known as Th1 cells—to mediate a cascade of reactions involving various infection-fighting immune cells.

    But in several studies in animals that received a similar RSV vaccine, challenge with the RSV virus seemed to trigger certain cytokines that mobilized a very different subpopulation of T helper cells, known as Th2 cells. The lungs of inoculated mice were also packed with inflammatory cells, eosinophils in particular. Researchers hypothesized that the vaccine was inducing a response by Th2 cells, which then attracted eosinophils and somehow induced “a kind of allergic reaction,” Lambert explains.

    A similar phenomenon was seen in animals that received coronavirus vaccines in the past—making researchers such as Bottazzi wary of such forms of immune enhancement. For instance, when researchers administered an inactivated SARS vaccine into mice, and then challenged them with the live virus, they also found eosinophils and other blood cells in the animals’ lungs and livers—a possible sign of Th2-type immune responses. Despite these signs of immune enhancement, that SARS vaccine did a good job in producing neutralizing responses, and vaccinated animals survived.

    Bottazzi cautions against extrapolating from animal studies to humans. It’s possible cellular immune enhancement is an artifact of the animal models or the experimental system.

    Of nearly 140 different COVID-19 vaccine candidates, 15 are already in human trials. “To date, I haven’t seen any clear evidence to support ADE or ERD, but it’s something you want to be aware of for sure,” Burton says. “It may be that the vaccines that are already out there—Moderna, Janssen, and so on—they may turn out to be perfectly great, we just don’t know at this point. I think it’s good to have a plan B, where if there are some problems, you can start working it out quickly what they are, and re-engineering your vaccines based on knowledge about what’s wrong.”

    Story by: Katarina Zimmer for The Scientist 

  • Experts apply microbiome research to agricultural science to increase crop yield

    28th May 2020

    The global demand and consumption of agricultural crops is increasing at a rapid pace. According to the 2019 Global Agricultural Productivity Report, global yield needs to increase at an average annual rate of 1.73 percent to sustainably produce food, feed, fiber and bioenergy for 10 billion people in 2050. In the US, however, agricultural productivity is struggling to keep pace with population growth, highlighting the importance of research into traditional practices as well as new ones.

    In an effort to increase crop yield, scientists at Northern Arizona University’s Pathogen and Microbiome Institute (PMI) are working with Purdue University researchers to study the bacterial and fungal communities in soil to understand how microbiomes are impacting agricultural crops. They believe technological advances in microbiome science will ultimately help farmers around the world grow more food at a lower cost.

    Nicholas Bokulich, a PMI assistant research professor, and Greg Caporaso, an associate professor of biological sciences and director of PMI’s Center for Applied Microbiome Science (CAMS), have been testing a long-held farming belief that phylogenetics—the study of the evolutionary relationship between organisms—should be used to define crop rotation schedules.

    Please use the following link to access the rest of the article: ScienceX

    Story by: Heather Tate