Single-cell RNA sequencing reveals SARS-CoV-2 infection dynamics in the lungs

Detailed knowledge about the dynamics of SARS-CoV-2 infection is important for uncovering the viral and host factors that contribute to COVID-19 pathogenesis. Old-World nonhuman primates recapitulate mild to moderate cases of COVID-19, thereby serving as important pathogenesis models. Researchers from the National Institute of Allergy and Infectious Diseases compared African green monkeys inoculated with infectious SARS-CoV-2 or irradiated, inactivated virus to study the dynamics of virus replication throughout the respiratory tract. Interestingly, genomic RNA from the animals inoculated with the irradiated virus was found to be highly stable, whereas sub-genomic RNA, an indicator of viral replication, was found to degrade quickly. The researchers combined this information with single-cell RNA sequencing of cells isolated from the lung and lung-draining mediastinal lymph nodes and developed new analysis methods for unbiased targeting of important cells in the host response to SARS-CoV-2 infection. Through detection of reads to the viral genome, they were able to determine that replication of the virus in the lungs appeared to occur mainly in pneumocytes, while macrophages drove the inflammatory response. Interestingly, monocyte-derived macrophages recruited to the lungs, rather than tissue resident alveolar macrophages, were most likely to be responsible for phagocytosis of infected cells and cellular debris early in infection, with their roles switching during clearance of infection. Together, this dataset provides a detailed view of the dynamics of virus replication and host responses over the course of mild COVID-19 and serves as a valuable resource to identify therapeutic targets.

Single cell sequencing of mediastinal lymph nodes shows resolution of inflammatory response

(A) The Uniform manifold approximation and projection (UMAP) projection of single cell sequencing data from cells isolated from the mediastinal lymph nodes of all ten animals combined is shown. Each point represents an individual cell and cells are colored based on their cell type. The names of the cell types are placed next to their largest cluster. (B) Single gene expression analysis was used to validate cell type identifications. (C) The percent of total gene counts for each cell is shown for a subset of interferon responsive genes (y-axis). The x-axis denotes cell types and experimental group. (D) The percentage of each cell population (x-axis) that is actively dividing (stage G2M or S) as determined by a profile of gene expression is shown. Each point is an individual animal and bars represent the mean and standard deviation of the samples. (E) The percentage of plasma cells in each sample compared relative to the total cell number is plotted. (F) The percentage of plasmablast cells relative to the number of B cells is plotted. * indicates adjusted p-value < 0.05 as determined by a one-way ANOVA.

Speranza E, Williamson BN, Feldmann F, Sturdevant GL, Pérez LP, Meade-White K, Smith BJ, Lovaglio J, Martens C, Munster VJ, Okumura A, Shaia C, Feldmann H, Best SM, de Wit E. (2021) Single-cell RNA sequencing reveals SARS-CoV-2 infection dynamics in lungs of African green monkeys. Sci Transl Med [Epub ahead of print]. [article]

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