Project Team

Pr Michaela Müller-Trutwin, PhD, Professor at Institut Pasteur and the head of the “HIV, Inflammation and Persistence” Unit, Insitut Pasteur France

Dr Nicolas Huot, PhD,  Postdoctoral researcher with a background in molecular and structural virology, including research on mechanism of HSV-1 and HIV latency, Insitut Pasteur France

Project investigator Dr. Nicholas Huot

Project Summary:

A project in a non-human primate model to determine how macrophage and natural killer cell dynamics impact SARS-CoV-2 persistence. The project is probing several key questions about persistence mechanisms, including:

  1. To what degree are extended tissue types such as lymph nodes, lung, intestine, and bone marrow SARS-CoV-2 reservoir sites?
  2. Are alveolar macrophage the only long term immune cell viral reservoir in the lung or are there other types of cells where SARS-CoV-2 can persist for many months or years in the lung? Can macrophage in other tissues, such as the gut, also be long-term reservoirs for SARS-CoV-2?
  3. Are there factors that can favor or inhibit the induction of more efficient anti-SARS-CoV-2 natural killer cells?
  4. Are there biomarkers in the blood that can indicate the presence/lack of adaptive and efficient natural killer cells in the lung, and be associated with the level of viral persistence in the lung?

Project Background:

An image by the project team showing tunneling nanotubes forming between SARS-CoV-2 infected cells

A growing number of studies show that SARS-CoV-2 can persist for months, or even years, in a wide range of tissues. This persistence is increasingly connected to long COVID and related chronic disease development. However specific mechanisms underlying viral persistence remain to be fully understood. These include better defining the immune cells inside which SARS-CoV-2 can persist, and better delineating how problems with the immune response – including problems with natural killer cell activity – can facilitate persistence.

The project team recently published an important paper shedding light on these questions in the journal Nature. In a non-human primate model they show that SARS-CoV-2 can persist in alveolar macrophages of the lung for at least 6 – 18 months after the onset of infection, even when the virus was undetectable in tracheal and nasal swab samples. They provide evidence that SARS-CoV-2 replicates in these alveolar macrophage and that it disseminates from cell-to-cell. They further demonstrated that the cytokine IFN-γ strongly inhibits SARS-CoV-2 replication in alveolar macrophage in the lab, and that IFN-γ production was impaired in alveolar macrophage and natural killer cells isolated from the lung fluids of SARS-CoV-2 convalescent monkeys. IFN-γ, however, acted as a double-edge sword as it also increased MHC-E expression on alveolar macrophage.

Specifically they showed that a peptide derived from the N-terminal part of the Spike protein binds to MHC-E and this inhibited natural killer cells from non-infected animals. When analyzing the natural killer cells from the convalescent animals, they observed that in about half of the animals, natural killer cells escaped this MHC-E mediated inhibition. These natural killer cells had thus adapted to the infection. The animals possessing such adaptive natural killer cells were those with the lowest levels or no detectable persisting virus. Thus, there appear to be a key role for natural killer cells in the regulation of long-term viral persistence in the lung.

In the current project the team will follow these leads to further explore SARS-CoV-2 persistence mechanisms and immune control via many experiments. They will search for SARS-CoV-2 in the tissues of non-human primates seven months after infection, including the presence of infectious virus in distinct tissues (lung, intestine, lymph nodes, bone marrow, cerebrospinal fluid), and different types of cells (macrophages, epithelial cells), using imaging, cell biology and molecular state-of-the art methods. This allows for an in-depth comparative quantitative analysis of viral persistence between distinct tissues and cell types. It also allows for analysis of viral reservoirs with regard to other factors such as viral load and inflammatory profiles in acute infection.

The team will also use single cell genome-wide transcriptome analysis of adaptive natural killer cells isolated from BALF of convalescent animals to identify biomarkers in blood that can potentially indicate the presence/lack of adaptive and efficient natural killer cells associated with viral persistence cells in the lung. Overall, the analysis will reveal the molecular profile of the MHC-E restricted natural killer cells in animals with no or less persisting virus, representing an important step in knowledge that can be used for the future development of immunotherapies targeting SARS-CoV-2 reservoirs.