Abstract

Detailed knowledge about the dynamics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is important for uncovering the viral and host factors that contribute to coronavirus disease 2019 (COVID-19) pathogenesis. Old-World nonhuman primates recapitulate mild to moderate cases of COVID-19, thereby serving as important pathogenesis models. We 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. Genomic RNA from the animals inoculated with the irradiated virus was found to be highly stable, whereas subgenomic RNA, an indicator of viral replication, was found to degrade quickly. We 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, we were able to determine that replication of the virus in the lungs appeared to occur mainly in pneumocytes, whereas macrophages drove the inflammatory response. 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, our 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.

Highlights

  • A wealth of clinical and laboratory studies have been reported concerning severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19) [1, 2]

  • To study SARS-CoV-2 infection and its consequences, two groups of four African green monkeys were inoculated with a total dose of 2.6x106 50% Tissue Culture Infectious Dose (TCID50) of replication-competent virus, while two control animals were inoculated with virus inactivated by gamma-irradiation

  • Using traditional virological methods as well as scRNA-Seq, we have begun to parse out the infection dynamics which occur as the disease progresses and virus is eventually cleared in the African green monkey model of mild COVID-19

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Summary

Introduction

A wealth of clinical and laboratory studies have been reported concerning severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19) [1, 2]. Sequencing of single cells in BALF [6] and upper respiratory tract swabs [7] collected from patients with COVID-19 has detected markers of severe disease in hospitalized individuals. Others have examined the immune response to infection by utilizing single cell sequencing to profile peripheral blood mononuclear cell samples from patients with COVID-19 [8, 9]. Both approaches have limited power to address the dynamics of

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