Respiratory immune characteristics associated withCoronavirus Disease 2019 (COVID-19) severity are currently unclear. We characterized bronchoalveolar lavage fluid immune cells from patients with varying severity of COVID-19 and from healthy people by using single-cell RNA sequencing. Proinflammatory monocyte-derived macrophages were abundant in the bronchoalveolar lavage fluid from patients with severe COVID-9. Moderate cases were characterized by the presence of highly clonally expanded CD8 + T cells. This atlas of the bronchoalveolar immune microenvironment suggests potential mechanisms underlying pathogenesis and recovery in COVID-19.

1 BackgroundThe outbreak of novel coronavirus pneumonia (NCP) caused by

The global pandemic of Coronavirus Disease 2019 (COVID-19) is now ongoing. Rapid and accurate detection of the causative virus SARS-CoV-2 is vital for the treatment and control of COVID-19. In this study, the comparative sensitivity of different respiratory specimens were retrospectively analyzed using 3552 clinical samples from 410 Guangdong CDC (Center for Disease Control and Prevention) confirmed COVID-19 patients. Except for BALF, the sputum possessed the highest positive rate (73.4%∼87.5%), followed by nasal swabs (53.1%∼85.3%) for both severe and mild cases during the first 14 days after illness onset (d.a.o). Viral RNA could be detected in all BALF from the severe group collected as early as 4 days after illness onset (d.a.o) and lasted up to 46 d.a.o., while none of BALF samples from mild group. Moreover, although viral RNA was negative in the upper respiratory samples, it was also positive in BALF samples in most cases from severe group during treatment. Despite of typical ground-glass opacity observed via computed tomographic (CT) scans, no viral RNA was detected in the first 3 or all upper respiratory tract specimens from some COVID-19 patients. In conclusion, sputum is most sensitive for routine laboratory diagnosis of COVID-19, followed by nasal swabs. Detection of viral RNAs in BLAF improves diagnostic accuracy in severe COVID-19 patients.