Alpha and Omicron SARS-CoV-2 Adaptation in an Upper Respiratory Tract Model

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is currently causing an unprecedented pandemic. Although vaccines and antivirals are limiting the spread, SARS-CoV-2 is still under selective pressure in human and animal populations, as demonstrated by the emergence of variants of concern. To better understand the driving forces leading to new subtypes of SARS-CoV-2, we infected an ex vivo cell model of the human upper respiratory tract with Alpha and Omicron BA.1 variants for one month. Although viral RNA was detected during the entire course of the infection, infectious virus production decreased over time. Sequencing analysis did not show any adaptation in the spike protein, suggesting a key role for the adaptive immune response or adaptation to other anatomical sites for the evolution of SARS-CoV-2.

Keywords: SARS-CoV-2; persistent infection; virus adaptation.

Figure 1

Evolution of SARS-CoV-2 variants ex vivo and in vitro after 25 days of infection. MucilAir tissues were infected with Alpha (B.1.1.7) or Omicron (BA.1) SARS-CoV-2. For 25 days, tissues were maintained at 33 °C and apical washes were performed to collect released SARS-CoV-2 viruses, quantified by RT-qPCR (A) and plaque assay (B). (C) Tissues were fixed and stained with J2 (dsRNA: green), β-tubulin IV (ciliated cells: red), and DAPI (nuclei: blue) at the end of infection. (D) Viruses were deep-sequenced at the end of infection ex vivo or after 11 passages in Vero E6. Mutations that were not present in the original sample are shown (created with biorender.com). (E) Nucleotide changes and percentage of reads present in the different samples. The results are the mean and SEM of two (B.1.1.7) or three (BA.1) MucilAir. p-value < 0.0001 (****).