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Using a modern genome-wide deletion approach to identify coronavirus host factors in human cells, researchers at the Rega Institute in Belgium discovered a potential new target that could be exploited to develop drugs against the coronavirus disease pandemic. ongoing (COVID-19), but also future highly pathogenic coronavirus outbreaks. The document is currently available at bioRxiv * prepress server.
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which instigated the COVID-19 pandemic, is responsible for the global economic damage and one million deaths. Until now, the search for an effective drug or vaccine has been elusive.
To date, there are seven known human coronaviruses, all of which probably arose as a zoonosis of bats, mice, or other animals. Four of them are the so-called ‘human common cold coronaviruses’ that only cause mild upper respiratory tract illnesses: alphacoronavirus 229E and NL63, and betacoronavirus OC43 and HKU1.
In contrast, betacoronaviruses SARS-CoV, MERS-CoV, and the newer SARS-CoV-2 are highly pathogenic and responsible for severe and potentially fatal respiratory infections. Since animals harbor a wide diversity of coronavirus types with known interspecies transmission, there is a high probability that a new (potentially pandemic) strain will emerge in the future.
But despite this risk, our options to prevent or treat any coronavirus infection are very limited. Therefore, the development of broad-spectrum antivirals against members of this family of viruses is not only necessary for this pandemic, but also to rapidly address and contain similar zoonotic events in the future.
In an exciting new research effort, scientists at the Rega Institute in Leuven, Belgium, carried out a series of genome-wide CRISPR-based genetic screens in human cells to elucidate host factors that are necessary for the SARS-CoV-2 and HCoV-229E. infection and propose possible therapeutic solutions.
Whole genome deletion screens in human cells identify 105 host factors for SARS-CoV-2 and HCoV-229E infection. A) Overview of the experimental steps performed during a whole genome scan for coronavirus host factors. BD) Genome deletion screens were performed on Huh7 cells, with strong selection (high stringency) using HCoV-229E (B) and SARS-CoV-2 (C) or with mild selection of SARS-CoV-2 (low stringency ) (RE). Each circle represents a gene, the size of which corresponds to the importance of enrichment. The y-axis shows the enrichment of sgRNA after virus selection compared to an uninfected control population (D) or the population on the first screen day before infection (B and C). Genes distributed on the x-axis in alphabetical order.
A genome removal screen
In this study, the genome knockout screening mentioned above was performed in human cells without introducing an exogenous receptor. To that end, researchers have used the human liver carcinoma cell line Huh7, where a clinical isolate of SARS-CoV-2 induced a simple cytopathic effect naturally. Less pathogenic HCoV-229E was used as a control strain.
This allowed the researchers to identify broad-spectrum coronavirus host factors, as well as specific host factors for SARS-CoV-2 and HCoV-229E. Huh7 cells were transduced with Brunello’s whole genome library, which was followed by identification of unique leader RNA (sgRNA) by deep sequencing.
Several pharmacological inhibitors have been used to confirm the role of class III phosphoinositide 3-kinase (PI3K in coronavirus infection, which is known to play a role in many processes, including endocytic trafficking and autophagosome initiation and maturation.
Common and Specific Cell Host Factors
“We identified PI3K type 3 as a common host factor for SARS-CoV-2, HCoV-229E and HCoV-OC43, and we demonstrated that small molecules that target this protein could serve as broadly applicable anti-coronavirus inhibitors,” explain the study authors. recommendations.
Their data shows that PI3K type 3 plays a substantial role in the early steps of the SARS-CoV-2 life cycle, such as endocytosis, fusion, translation, or early initiation of replication. In addition, this kinase supports infection by inducing phagophore nucleation or the formation of the autophagosome precursor membrane.
Researchers have also shown that TMEM41B, the important regulator of autophagy (that is, the way our body removes damaged cells to regenerate new ones), is indispensable for HCoV-229E infection, and they pointed to TMEM106B as a Novel cellular host factor crucial for SARS-CoV-2 infection.
More specifically, TMEM106B can promote vesicle acidification in the endolysosomal pathway, facilitating efficient delivery of the SARS-CoV-2 genome into the cytoplasm of human cells, playing an early role in the viral replication cycle (i.e., in the first six hours after infection).
On the other hand, in their SARS-CoV-2 screens, the researchers did not identify ACE2, which is in stark contrast to previous screens that were made on Vero E6 cells or engineered human cells that overexpress ACE2. Furthermore, heparan sulfate has been shown to be quite important for effective infection.
A viable option for today and for the future
“Our results identify novel coronavirus host factors that can potentially serve as drug targets against SARS-CoV-2 or to rapidly combat future zoonotic coronavirus outbreaks,” the study authors summarize in bioRxiv prepress paper.
The periodic emergence of new pathogenic coronaviruses in fact poses a serious threat to public health beyond the current COVID-19 pandemic, meaning that pan-coronavirus inhibitors (such as the one presented in this document) are much needed in our therapeutic arsenal.
However, this study also addresses the notion that different viral agents, although related, may depend on different factors to exploit similar cellular pathways. Therefore, all possibilities of developing a broad spectrum viral inhibitor (particularly for deadly viruses) must be accepted and further investigated.
*Important news
bioRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be considered conclusive, guide clinical practice / health-related behavior, or be treated as established information.
