CARE’s Young Researchers – Introducing Collins Owino, Post-doctoral researcher, Utrecht University

Read about how Collins’s work in understanding how the coronavirus hijacks human host factors and processes has provided us with opportunities to develop therapies to inhibit viral replication.

CARE (Corona Accelerated R&D in Europe) is the largest European research initiative addressing the challenges of COVID-19. It comprises 38 partners, from both industry and academia, in a set-up of eight multidisciplinary work-packages (WPs). In this series, we highlight the work of some of the young researchers involved in CARE as part of their PhD or postdoctoral work. Here, we learn how this opportunity has benefited Collins (Utrech University), while simultaneously benefiting CARE and its ambition to help society defeat COVID-19 and future pandemics.

What experience did you have working on a Public Private Partnership before joining CARE? 

I had no experience in Public Private Partnership before joining CARE but members of our team have participated in such projects before.

Why did you decide to get involved in CARE?

I decided to get involved because I had just experienced the devastating effects of the SARS-CoV-2 pandemic during my Ph.D. studies. I wanted to contribute to a better understanding of the interaction between the virus and human host factors towards developing novel antiviral drugs and vaccines.

How did your involvement in CARE come about?

I became involved in CARE because of my experience studying virus-human host interactions, which aimed at identifying host factors regulating viral infection. We wanted to apply different CRISPR screening strategies to identify novel host factors regulating SARS-CoV-2 infection that could be drug and vaccine targets.

What is CRISP? New Scientist.

Tell us about the work you have been doing in the CARE consortium

My role in the CARE consortium involves performing loss of function screens using CRISPR interference (CRISPRi) (a novel approach for targeted silencing of transcription in cells/gene knockdown – see https://www.nature.com/articles/nprot.2013.132) to identify novel host factors regulating SARS-CoV-2 infection and other coronaviruses. We further apply different RNA interference approaches to validate the role of the newly identified host factors during the virus infection cycle. In addition, we work with other collaborators within the consortium to identify small molecules that could inhibit these factors for possible host-targeting antivirals. We are currently at the final stage of validating some top hits.

What highlights can you share from your time in the CARE consortium so far?

Some highlights from my time in CARE include learning how to work together within a collaborative environment to meet the general goals of CARE. It has also been fulfilling to be an integral member of our team that has conducted several CRISPR screens and validated the newly identified hits to develop host-targeting therapies against coronaviruses.

Why does this work matter?

This work matters because understanding how the virus hijacks human host factors/processes provides us a better opportunity to develop therapies to disrupt these interactions, thereby inhibiting viral replication.

What are or were the biggest challenges you have experienced (and how did you overcome them?)

During my Ph.D., I studied the biology of the hepatitis B virus. When I joined the RNA virus virology group at Utrecht University, I experienced a significant shift in the techniques and experimental procedures for the CARE project. I overcame these challenges quickly through the support and mentorship of my colleagues at UU.

How have you benefited from your involvement in CARE?

I have benefited immensely by interacting with experienced industry and academia experts who are willing to mentor and guide the upcoming scientists within the consortium. I have been able to sharpen my technical as well as interpersonal skills since I joined the consortium.

What advice would you give to someone getting involved in a Public Private Partnership? 

I would tell them that PPPs require collaboration, trust, and a shared commitment to achieving positive outcomes for public and private interests. They provide a noble opportunity to learn from the members of different teams in an open, transparent, and collaborative environment. It is a great experience.

CARE – Infographic: Work Package 1 Anti-coronavirus drug discovery in phenotypic virus-cell-based assays.

CARE has 8 Work Packages but do you know what each one does? Here, you can learn about the Work Package 1 team, their objectives, their partners, their breakthrough moments and more.

The infographic is also available here

CARE – Infographic: Research objectives and Operating model

Do you whish to know what we do and how we do it? Check out this infographic for key details on CARE Research objectives and Operating model.

The infographic is also available here

Published in Antiviral Res: A new image-based and high-throughput platform to identify broad-spectrum coronavirus antivirals

The CARE member, Johnson & Johnson Innovative Medicine, developed a high-content imaging platform compatible with high-throughput screening, with the aim of identifying compounds with antiviral activity and to deprioritize those that induce undesirable phenotypes in host cells.

The immunofluorescence-based assay to assess the antiviral compounds against coronaviruses was adapted for high-throughput screening by shortening assay run times, miniaturizing well size and volumes, combining permeabilization and staining steps, and by using automated image analysis. The inclusion of cellular dyes and immunostaining in combination with in-depth image analysis enabled identification of compounds that induced undesirable phenotypes in host cells, such as changes in cell morphology or in lysosomal activity.

This platform was easily adapted to different SARS-CoV-2 variants (B1, Omicron BA.5 and Omicron XBB.1.5), SARS-CoV and human coronavirus 229E using different antibodies and cell types. With the platform, ~900K compounds were screened and hits were triaged in just four weeks, thereby allowing the identification of potential anti-coronaviral compounds carrying broad-spectrum activity with limited off-target effects.

This new platform is broadly applicable as it can be adapted to include various cell types, viruses, antibodies, and dyes. By developing and running the antiviral assay against different coronavirus strains, it was demonstrated that the assay can most likely be efficiently adapted to test against new SARS-CoV-2 variants or new coronavirus species as soon as they emerge. Given the high risk for future coronavirus outbreaks or other pandemics from new zoonotic reservoirs, the flexibility and broad applicability of this assay are of particular interest.

To learn more, click here: A flexible, image-based, high-throughput platform encompassing in-depth cell profiling to identify broad-spectrum coronavirus antivirals with limited off-target effects

Introducing Utrecht University – a CARE academic organisation

Established in 1636, Utrecht University has a long history and is rich in tradition. Utrecht University was formed by the provincial government in 1636. Recognized as the leading Dutch university according to the Shanghai Ranking, it offers 45 undergraduate and 167 graduate programs, has some 30,000 students served by 7,500 academic staff. Today the university has seven faculties in Veterinary Medicine, Medicine, Science, Geosciences, Social and Behavioural Sciences, Humanities and Law, Economics and Governance.

The primary contributor to CARE from the university is the Virology section at the Faculty of Veterinary Medicine. The Virology section is studying various viruses (coronavirus, picornavirus, influenza, paramyxovirus) with the aim of developing innovative antiviral drugs, therapeutic antibodies and vaccine approaches.

The Virology section was started in 1971 by Prof. Marian Horzinek, who is considered a “Founding Father” of (veterinary) virology in The Netherlands. He started virology research at the university studying Feline Infectious Peritonitis (FIP), a deadly disease in cats due to infection with a feline coronavirus (FCoV). The section has longstanding and extensive experience in coronavirus research, specifically in

1. Receptor identification and virus-receptor interactions
2. Structure-function studies of the viral Spike protein, which is the protein involved in binding receptor(s) and mediating cellular entry and the main target for humoral immune responses, and as such a key viral protein for development of intervention strategies
3. Determinants of coronavirus inter-species transmissibility
4. Viral genome replication and virus-host interactions
5. Development of intervention strategies (antibodies, vaccines, antiviral drugs) and diagnostics for (emerging) coronaviruses

The Virology section comprises approximately 45 members, including researchers at all seniority levels and support staff, rising to up to 60 researchers when housing students performing their MSc internships.

Why did Utrecht University choose to get involved in CARE?

The Virology Section has 50+ years of experience in coronavirus biology and possesses extensive expertise in both human and animal coronaviruses. They have particular expertise in virus structure, virus-receptor interactions, virus entry mechanisms, genome replication and virus-host interactions. The CARE project enabled them to quickly contribute their knowledge with many other research groups, while also benefitting from enhanced collaboration with the CARE partners.

What has Utrecht University delivered for CARE?

UU’s contributions span across various innovations and findings in Work Packages (WPs) 1, 2, 4 and 5. Overall, their efforts aim to identify potential antiviral drugs, peptides, nanobodies and antibodies, to understand their mechanisms of action, and to explore host factors involved in coronavirus infection, which could inform the development of effective therapies against SARS-CoV-2 and other related coronaviruses.

In WP1, they evaluated a large number of small molecules for antiviral activity against SARS-CoV-2 and other coronaviruses, characterized antiviral effects and performed Mechanism of Action studies to reveal their molecular mechanisms.

In WP2, they developed macrocyclic peptide inhibitors and nanobodies targeting the Spike protein of SARS-CoV-2. The team studied the site in Spike that is targeted by the macrocyclic peptide using cryo-Electron Microscopy (cryo-EM). This revealed that the peptide binds to a conserved region of the SARS-CoV-2 spike protein that has hitherto not been exploited by antibodies or small molecules and has not been mutated in any of the variants of concern.

In WP4, they established assays, reagents and structural biology workflows for the assessment and characterization of human neutralizing antibodies (nAbs) against SARS-CoV-2 and variants. The team generated bispecific antibodies to enhance potency and breadth of nAbs against SARS-CoV-2 and related coronaviruses. They also developed broad-spectrum nAbs against porcine deltacoronavirus (PDCoV), an emerging coronavirus with pandemic potential. Finally, they isolated and characterized human antibodies that target host receptor aminopeptidase N (APN). These antibodies are highly resistant to viral escape and can be employed for coronaviruses that share the same receptor for entry, increasing our pandemic preparedness against newly emerging coronaviruses.

In WP5, they determined changes in the metabolome in coronavirus-infected cells and identifying essential host factors for coronavirus infection via genetic CRISPR-cas9 screens. In follow-up experiments, they are investigating the physiological importance of the virus-induced changes in metabolism and the role of the identified host factors for efficient virus replication and/or evasion of infection-limiting host antiviral responses.

For more information about the different work packages, please click here

Who is working in the CARE team at Utrecht University?

The Utrecht University team is led by two Principal Investigators: Professor Dr Frank van Kuppeveld who studies the interaction between viruses and their host; and Dr Berend Jan Bosch (Associate Professor) who studies virus-receptor interactions and cell entry mechanism of membrane-enveloped viruses, particularly coronaviruses.

During the CARE project, Dr Daniel Hurdiss, a structural virologist, was promoted from a post-doctoral researcher to Assistant Professor. He is a structural virologist who, among others, uses cryo-EM to study the 3D structure of viral proteins and understand their functional implications.

Many of UU’s virologists have been involved in CARE from the beginning, all aiming to translate their knowledge into intervention strategies targeting either viral entry and/or replication: Frank Buitenwerf, Marianthi Chatziandreou, Oliver Debski Antoniak, Tim Donselaar, Wenjuan Du, Preeti Hooda, Ruben Hulswit, Yifei Lang, Joline van der Lee, Rutger Luteijn, Wendy Meijer, Vera Nijman, Lonneke Nouwen, Collins Owino, Judith Oymans, Itziar Serna Martin, Jill Ver Eecke, Marleen Zwaagstra. In the first year of CARE, the group of Alexandre Bonvin (Computational Structural Biology) at the university’s Faculty of Science also contributed to CARE.

What benefits have Utrecht University experienced through being part of CARE?

The Utrecht University Virology team has enjoyed the following benefits:

• Access to a broader range of expertise, technologies, and facilities.
• Opportunities to work alongside industry partners, other academic institutions, and governmental agencies which fosters knowledge exchange, interdisciplinary research, and the pooling of diverse perspectives and skills.
• Academic researchers’ opportunities for networking, professional development, and establishing collaborations with leading experts and institutions in the field.
• Support to conduct cutting-edge research, accelerate progress towards the development of effective therapies, and make meaningful contributions to the global effort to combat infectious diseases.

Want to know more about Utrecht University?

https://www.uu.nl/en/organisation/faculty-of-veterinary-medicine/veterinary-research/one-health/infection-immunity/virology