2024-04-16| COVID-19R&D

Breakthrough Screening Platform to Assess SARS-CoV-2 Mutations and Potential Treatments

by Richard Chau
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An interdisciplinary research team from the University of Hong Kong Li Ka Shing Faculty of Medicine (HKUMed) and the Faculty of Engineering has made significant strides in understanding the impact of SARS-CoV-2 mutations on disease severity. Their innovative screening platform, detailed in a paper published in Nature Biomedical Engineering, offers a speed improvement of up to 39 times compared to traditional methods, marking a major leap forward in the quest to identify emerging viral variants that could pose substantial risks to public health.

Related article: Iron Dysregulation Linked to Long COVID Outcomes 

Understanding the Role of Spike Protein Mutations in COVID Severity

SARS-CoV-2 virus, the culprit behind the global COVID-19 pandemic, has been evolving since its emergence. From the Alpha and Gamma variants in the early days, to Delta and Omicron that caused massive global outbreaks, and thousands of other known mutations that have not posed a significant threat, viral mutations continue to occur to this very day, while mutations in the spike protein, which are crucial for viral infection by binding to human ACE2 receptors, can lead to varying levels of infectivity and lethality.

During the course of viral infection, the spike protein of the SARS-CoV-2 virus binds to human angiotensin-converting enzyme 2 (ACE2 receptor). Upon such binding, the coronavirus can enter the infected cells and merge with neighboring uninfected cells to form syncytia, large multinucleated cells produced by two or more uninuclear cells fusing together. The syncytium formation facilitates the transfer of viral genomes to the neighboring cells, promoting virus transmission and increasing the likelihood of severe disease. Prior studies have found that severe COVID-19 cases often exhibit syncytium cells in patients’ lungs, further providing evidence of the connection between spike-driven cell fusion and infection severity. 

An Interdisciplinary Endeavor to Revolutionize Screening Methods

Conventional methods for assessing cell-cell fusion are laborious and time-consuming. Yet, the HKU team revolutionized this process by employing advanced genetic techniques coupled with innovative screening approaches. By utilizing a split green fluorescent protein (GFP) system combined with microfluidics technology, they developed a high-throughput rapid screening platform capable of analyzing numerous spike protein variants and their fusion capabilities at an unprecedented speed, up to 39 times faster than older methods. This innovation allowed for the identification of specific genetic and cellular factors promoting syncytium formation, a crucial step towards developing interventions to impede virus spread.

Their findings highlighted that certain variants, such as the Delta strain, form larger syncytia, potentially indicating higher infectivity and severity. Notably, they identified a single mutation, K854H, capable of transforming the Omicron variant into a strain with increased fusion rates. Apart from mapping mutations, the HKU team conducted a whole-genome CRISPR screening, which identified two cellular proteins, AP2M1 and FCHO2, as the key factors affecting SARS-CoV-2 spike-induced cell fusion, in addition to the ACE2 receptor. This discovery paved the way for testing FDA-approved drugs chlorpromazine (an antipsychotic medication) and fluvoxamine (an antidepressant) as potential inhibitors of syncytium formation. In fact, experiments using hamster lung tissues have already demonstrated promising results. 

Implications for Future Research and Public Health

This study is notable for its interdisciplinary approach, combining CRISPR screening, droplet microfluidics, large-scale mutagenesis, and virology, providing insights into the physiological and pathological consequences of cell-cell fusion. More broadly, by using paired-cell profiling systems, it is possible to study other virus that are capable of inducing syncytium formation other than SARS-CoV-2, such as human immunodeficiency virus (HIV), respiratory syncytial virus (RSV), herpesviruses, as well as other coronaviruses, indicating wider applications beyond COVID-19.

Dr. Alan Wong Siu-lun, corresponding author of the study and Associate Professor in the School of Biomedical Sciences, HKUMed, emphasized the versatility of their innovative systems and the significance of their findings “These innovative systems enable us to rapidly track SARS-CoV-2 mutations on a larger scale and identify treatment options; they can also be broadly applied in the study of various pathological and physiological cell fusion conditions relevant to biomedical research, including cancer immunotherapy.” 

Looking ahead, Prof. Wong also expressed his optimism that the insights gleaned from this study are poised to contribute significantly to public health efforts and the development of new therapeutic strategies for COVID-19 and other diseases involving cell fusion.

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