SARS-CoV-2 Under the Microscopes

When the COVID-19 epidemic began to gather momentum in France back in March 2020, the scientists from the Interferon and Antiviral Restriction team at the Infectious Disease Research Institute of Montpellier did not hesitate for long before tackling the study of its causative virus, SARS-CoV-2. Six months later, how are they getting on? Join us for a visit of this busy laboratory which has resumed its usual research alongside new projects focused on SARS-CoV-2.

The Infectious Disease Research Institute of Montpellier (IRIM) hosts 13 teams, including the Interferon and Antiviral Restriction team that was set up five years ago thanks to funding from ATIP-Avenir. Each year this program enables young researchers to establish their own teams. Led by Caroline Goujon (front, center), the team has nine members working on the viruses of influenza, AIDS, and now SARS-CoV-2. © Inserm/François Guénet

"Although we were not specialists in coronaviruses, we are virologists and very few teams were researching coronaviruses in France back then, explains Caroline Goujon, who leads the Interferon and Antiviral Restriction team at the Infectious Disease Research Institute of Montpellier (IRIM). We could not just stand on the sidelines and do nothing! It went without saying that we too had to participate in the global research effort." While lockdown meant putting all other projects on hold, part of the team has continued to come into the laboratory to study SARS-CoV-2 on a full-time basis. The laboratory has an advantage: Olivier Moncorgé, the researcher having helped to found it alongside Caroline Goujon in 2015, specializes in influenza. And the influenza viruses have at least one thing in common with SARS-CoV-2: they attack the cells of the respiratory system and some of the study techniques are similar. Another strong point is that one of their colleagues had already reached out to Institut Pasteur to request a sample of the novel coronavirus. The Research Center for Infectious Diseases and Anti-infectious Pharmacology (Cemipai), a platform located in the IRIM building used to study class 3 pathogens, such as SARS-CoV-2, also quickly reorganized itself to devote one of its modules to the novel virus. By mid-March, everything was ready. Although only four of the team’s researchers are allowed on the premises, they have worked out a system: while some are combing through the literature, the others are developing molecular tools or cell models. Six months later, how are they getting on?

Study of SARS-CoV-2, Interferon and Antiviral Restriction team at the Infectious Disease Research Institute of Montpellier (IRIM). © Inserm/François Guénet

Some of the team's researchers are now almost entirely devoted to SARS-CoV-2. Since March they have been testing the effects of the virus on over 70 candidate molecules and almost 300 natural extracts derived from fungi in order to pinpoint new therapeutic avenues. They are also studying the impact of interferons: these proteins, which have been the core focus of the laboratory’s research since it was founded, are naturally produced by the cells when they are infected, giving them and their neighboring cells an "antiviral" state aimed at preventing the virus from replicating.

Olivier Moncorgé is getting ready to enter the Cemipai module dedicated to the novel coronavirus. © Inserm/François Guénet

The researchers are studying SARS-CoV-2 at Cemipai. This laboratory, which reports to the CNRS and Université de Montpellier, enables them to conduct research under even stricter microbiological safety conditions than those of their usual laboratory – and is referred to as a P3+ (class 3 pathogen) laboratory. The further into the laboratory you go, the more the pressure decreases so that no flow of potentially contaminated air can escape. A coverall finished off with a gown, mob cap, hood, three pairs of gloves, shoe covers, an FFP3 mask, and protective goggles: this personal protective equipment is essential but not so comfortable when the researchers are spending long hours working in a hermetic environment.

Olivier Moncorgé is observing human cells infected with SARS-CoV-2 that has been genetically modified to express the mNeonGreen fluorescent protein. On the right, the green stains correspond to the cells infected with the virus.© Inserm/François Guénet

To study the mechanisms of the spread of SARS-CoV-2, Olivier Moncorgé is observing primary human cells – which have the advantage of being actual targets of the virus, and also immortalized cell lines – which are easier to manipulate and can proliferate indefinitely in vitro. These have been infected with SARS-CoV-2 that has been genetically modified to express the mNeonGreen fluorescent protein. The fluorescence enables live monitoring of its replication: the virus infects a cell, whose mechanisms it hijacks in order to produce virions, particles containing the viral genome and which can infect new cells. The more the screen fills up with green, the more the virus has infected cells.

On the left, the round and lighter-colored forms observed on the screen are the cells whose membrane has been destroyed by the virus, which are referred to as "lysed cells". In the case of the influenza virus or SARS-CoV-2, these stains can be visible to the naked eye and are referred to as lysis plaques. In order to determine the levels of infectious virus within a sample, the researchers must then perform virus titration, which is determined by counting these lysis plaques.
In the right-hand plate, the wells contain cells that have been placed in contact with different compounds to test their potential antiviral activity. Once infected, the cells will be lysed by the virus unless a compound protects them from infection. Should any cells remain at the end of infection, they will be colored purple, whereas a well that contains dead cells will be translucent. This test is a quick and simple way of identifying antiviral activity against SARS-CoV-2. © Inserm/François Guénet
Joe McKellar © Inserm/François Guénet

PhD student Joe McKellar is studying the action mechanisms of the antiviral protein MX1. This enzyme plays a major role in inhibiting viral replication. The proteins of the MX family (MX1 and MX2) are capable of inhibiting many viruses, such as those of influenza A or acquired immunodeficiency, responsible for AIDS. The blue areas are the nuclei of the cells, which here are of human origin. The green areas signify the presence of MX1 proteins. In humans, this protein is excluded from the nucleus (on the left) whereas in mice, the MX1 protein is located in the nucleus (on the right). Yet these differently-located proteins are both capable of blocking the influenza virus. Studying the location of these proteins helps us to better understand the mechanisms set in motion when the cell defends itself against a virus.