Replication of SARS-CoV-2 Omicron BA.2 variant in ex vivo cultures of the human upper and lower respiratory tract

Abstract

Background: The Omicron BA.2 sublineage has replaced BA.1 worldwide and has comparable levels of immune evasion to BA.1. These observations suggest that the increased transmissibility of BA.2 cannot be explained by the antibody evasion.

Methods: Here, we characterized the replication competence and respiratory tissue tropism of three Omicron variants (BA.1, BA.1.1, BA.2), and compared these with the wild-type virus and Delta variant, in human nasal, bronchial and lung tissues cultured ex vivo.

Findings: BA.2 replicated more efficiently in nasal and bronchial tissues at 33°C than wild-type, Delta and BA.1. Both BA.2 and BA.1 had higher replication competence than wild-type and Delta viruses in bronchial tissues at 37°C. BA.1, BA.1.1 and BA.2 replicated at a lower level in lung parenchymal tissues compared to wild-type and Delta viruses.

Interpretation: Higher replication competence of Omicron BA.2 in the human upper airway at 33°C than BA.1 may be one of the reasons to explain the current advantage of BA.2 over BA.1. A lower replication level of the tested Omicron variants in human lung tissues is in line with the clinical manifestations of decreased disease severity of patients infected with the Omicron strains compared with other ancestral strains.

Funding: This work was supported by US National Institute of Allergy and Infectious Diseases and the Theme-Based Research Scheme under University Grants Committee of Hong Kong Special Administrative Region, China.

Keywords: Bronchial tissue; Nasal tissue; Omicron BA.2; Pathogenicity; SARS-CoV-2; Transmission.

Figure 1

Viral replication kinetics of SARS-CoV-2 variants in ex vivo cultures of human respiratory tract. Viral replication of SARS-CoV-2 variants in human ex vivo nasal turbinate at 33°C (A and B), bronchus at 33°C (C, E, G) or 37°C (D, F, G) and lung at 37°C (H and I). The horizontal dotted line denotes the limit of detection in the TCID₅₀ assay. Viral titres from A, C, D and H are depicted as area under the curve (AUC) (B, E, F, G and I). Data are presented as geometric mean values. Error bars indicate SD with N = 4 (nasal, individual donors); N = 5 (bronchus, individual donors); N = 6 (lung, individual donors). *P < 0.05; **P < 0.01; ***P < 0.001; ****P < 0.0001, (A, C, D and H, Two-way ANOVA followed by Tukey's test; B, E, F and I, One-way ANOVA followed by Tukey's test; G, two-tailed T test).

Figure 2

Tissue tropism of SARS-CoV-2 variants in ex vivo cultures of human respiratory tract. Immunohistochemical staining of SARS-CoV-2 nucleoprotein in ex vivo cultures of human nasal turbinate at 48 hpi (A), bronchus with infection at 33°C (B), 37°C at 72 hpi (C) and lung tissues at 72 hpi (D) infected with wild-type (WT), Delta and Omicron variants (BA.1, BA.1.1 and BA.2). Positive cells are red-brown. Scale bar, 100 μm. The images are representative of two individual donors.

Figure 3

Thermal inactivation curves at 33°C. Infectious virus titres in cell culture wells at 33˚C (A). The horizontal dotted line denotes the limit of detection in the TCID₅₀ assay. Percentages of infectious viral titre calculated with reference to the titres at 0 h (B). Graphs show the mean values. Error bars indicate SD with N = 3 independent experiments. **P < 0.01; ***P < 0.001; ****P < 0.0001, (Two-way ANOVA followed by Tukey's test).