SARS-CoV-2 infection starts in nasal ciliated cells

Journal of
Clinical Investigation

The discovery that multiciliated cells in the
nasal epithelium are the first cells to be targeted in early COVID-19 infection
might provide the rationale for treatment using suitable antiviral nasal sprays.

Led by Director KOH Gou Young, scientists from the Center for Vascular
Research within the Institute for Basic Science, South Korea, have recently
uncovered the processes involved in the earliest stages of COVID-19 infection.
The group accomplished this by combining immunofluorescence staining (IFS) and
single-cell RNA-sequencing (scRNA-seq) of the molecules that are involved in
the viral entry process. Through this, Koh and his colleagues identified the
exact target of the coronavirus at the cellular level by comparing the results
of the subjects infected with COVID-19 with those of healthy controls.

The researchers first looked for the presence of ACE2, TMPRSS2, and
FURIN, which are the predominant SARS-CoV-2 entry-related molecules, on the
surfaces of various types of cells in the nasal epithelium. It was found that
these proteins were present in high quantities on ciliated cells. Moreover, the
apical (upper) sides of these cells showed higher levels of these molecules in
comparison to the basal (bottom) side. The levels of these proteins were
highest in fully differentiated multiciliated cells. On the other hand, viral
entry proteins were not found in the undifferentiated epithelial cells or
secretory cells such as the goblet cells.

Next, the researchers further studied these nasal epithelial cells using
scRNA-seq and visualized the cells into different clusters using UMAP. Samples
were collected from 4 patients on the first day of their COVID-19 diagnosis,
which were compared against 2 samples from healthy donors. It was found that
the fraction of multicilial cells was greatly reduced in the samples from
infected patients, while there was an increase in the secretory cells and
differentiating cells. This hinted that multicilial cells were the first to be
attacked and killed off by the virus, which are then replaced by the latter
types of cells.

The study also measured the level of SARS-CoV-2 mRNA transcripts within
the various types of cells. Among all the epithelial cells in COVID-19 infected
patients, 38% of the cells were labeled as SARS-CoV-2hi cells. Up to 75% of the
detected genes in these cells were of viral origin, compared to less than 1%
for other clusters of cells. This means that these cells serve as the main
factories for the mass production of SARS-CoV-2 viruses. While it was not
possible to directly identify these cells through RNA seq due to the fact that
they primarily produce viral mRNA, the researchers employed
pseudo-time-trajectory analysis to predict their differentiation paths. The
differentiation trajectory showed that SARS-CoV-2hi cells likely originated
from ciliated cells. Further IFS analysis on the infected patients’ samples
conclusively determined that up to 85% of SARS-CoV-2 factories were in fact
multiciliated cells.

This study was able to determine that multiciliated cells in the nasal
epithelium are the first cells that are targeted in the early COVID-19
infection. This implies that targeting these cells using specific treatments,
such as through nasal sprays, can be an ideal strategy to curb COVID-19
infection in the early stages.

Reference:

Ji Hoon Ahn, JungMo
Kim, Seon Pyo Hong, Sung Yong Choi, Myung Jin Yang, Young Seok Ju, Young Tae
Kim, Ho Min Kim, MD Tazikur Rahman, Man Ki Chung, Sang Duk Hong, Hosung Bae,
Chang-Seop Lee, Gou Young Koh. Nasal ciliated cells are primary targets
for SARS-CoV-2 replication in the early stage of COVID-19. Journal
of Clinical Investigation, 2021; 131 (13) DOI: 10.1172/JCI148517