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. 2021 Nov 3;184(24):5932–5949.e15. doi: 10.1016/j.cell.2021.10.027

Figure 4.

Figure 4

Infection of the respiratory mucosa with B.1.1.7/Alpha versus non-B.1.1.7/non-Alpha

(A) Confocal fluorescence images of sections through the RM of COVID #60, infected with a non-Alpha lineage (top), and of COVID #68, infected with Alpha (bottom). Several ciliated cells harboring FOXJ1 puncta are diffusely filled with nucleocapsid-IR signal, and some contain orf1ab-sense puncta (top) or S-sense puncta (bottom). DAPI served as nuclear stain.

(B and C) BaseScope chromogenic stainings with a mix of two probes designed for wt S and the HV deletion (B), or a mix of two probes designed for wt orf1ab and the SGF deletion (C). The presence of teal and absence of red precipitate is diagnostic for infection with a non-Alpha lineage (B and C, top). Conversely, the presence of red and absence of teal precipitate is consistent with infection with Alpha (B and C, bottom).