Jeong Seok Lee^1,8,*, June-Young Koh^2,8, Kijong Yi^2,8, Young-Il Kim^3,8, Su-Jin Park^3,4, Eun-Ha Kim³, Se-Mi Kim³, Sung Ho Park⁵, Young Seok Ju^1,2,6, Young Ki Choi^3,7,* & Su-Hyung Park^2,6,*

¹GENOME INSIGHT Inc., Daejeon, Republic of Korea.
²Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.
³College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju, Republic of Korea.
⁴Division of Life Science, Research Institute of Life Science, Gyeongsang National University, Jinju, Korea.
⁵School of Life Sciences, Ulsan National Institute of Science & Technology (UNIST), Ulsan, Republic of Korea.
⁶The Center for Epidemic Preparedness, KAIST Institute, KAIST, Daejeon, Republic of Korea.
⁷Center for Study of Emerging and Re-emerging Viruses, Korea Virus Research Institute, Institute for Basic Science (IBS), Daejeon, Republic of Korea.
⁸These authors contributed equally: Jeong Seok Lee, June-Young Koh, Kijong Yi, Young-Il Kim.

^*Corresponding author.

Few studies have used a longitudinal approach to describe the immune response to SARS-CoV-2 infection. Here, we perform single-cell RNA sequencing of bronchoalveolar lavage fluid cells longitudinally obtained from SARS-CoV-2-infected ferrets. Landscape analysis of the lung immune microenvironment shows distinct changes in cell proportions and characteristics compared to uninfected control, at 2 and 5 days post-infection (dpi). Macrophages are classified into 10 distinct subpopulations with transcriptome changes among monocyte-derived infiltrating macrophages and differentiated M1/M2 macrophages, notably at 2 dpi. Moreover, trajectory analysis reveals gene expression changes from monocyte-derived infiltrating macrophages toward M1 or M2 macrophages and identifies a macrophage subpopulation that has rapidly undergone SARS-CoV-2-mediated activation of inflammatory responses. Finally, we find that M1 or M2 macrophages show distinct patterns of gene modules downregulated by immune-modulatory drugs. Overall, these results elucidate fundamental aspects of the immune response dynamics provoked by SARS-CoV-2 infection.