Distinct phenotype of SARS-CoV-2 Omicron BA.1 in human primary cells but no increased host range in cell lines of putative mammalian reservoir species

Abstract

SARS-CoV-2's genetic plasticity has led to several variants of concern (VOCs). Here we studied replicative capacity for seven SARS-CoV-2 isolates (B.1, Alpha, Beta, Gamma, Delta, Zeta, and Omicron BA.1) in primary reconstituted airway epithelia (HAE) and lung-derived cell lines. Furthermore, to investigate the host range of Delta and Omicron compared to ancestral SARS-CoV-2, we assessed replication in 17 cell lines from 11 non-primate mammalian species, including bats, rodents, insectivores and carnivores. Only Omicron's phenotype differed in vitro, with rapid but short replication and efficient production of infectious virus in nasal HAEs, in contrast to other VOCs, but not in lung cell lines. No increased infection efficiency for other species was observed, but Delta and Omicron infection efficiency was increased in A549 cells. Notably replication in A549 and Calu3 cells was lower than in nasal HAE. Our results suggest better adaptation of VOCs towards humans, without an extended host range, and may be relevant to the search for the putative intermediate host and reservoirs prior to the pandemic.

Keywords: COVID19; Omicron; Primary airway epithelial cells; Reservoir host; SARS-CoV-2; Variants of concern.

Fig. 1

Replication of SARS-CoV-2 variants 3D in vitro reconstituted from epithelial cells. HAE were infected with SARS-CoV-2 lineages including the ancestral (B1) lineage and the variants Alpha, Beta, Gamma, Zeta, Delta and Omicron. Infections were performed at 37 °C (A) and 33 °C (B) N = 2–4. Viral replication was assessed by the quantification of viral RNA (left panels) and confirmed by infectious particle titration (right panels).

Fig. 2

Replication of SARS-CoV-2 variants in human lung adenocarcinoma cell line. Calu3 cells in 2D cultures were infected with SARS-CoV-2 lineages including the ancestral (B1) lineage and the variants Alpha, Beta, Gamma, Zeta, Delta and Omicron. Infections were performed at 33 °C (A) and 33 °C (B). N = 2–4. Viral replication was assessed by the quantification of viral RNA (left panels) and confirmed by infectious particle titration (right panels).

Fig. 3

Susceptibility of animal cells to SARS-CoV-2 lineages. Mammalian cell lines were tested for infections (at 37 °C and MOI 0.1) using clinical isolates of SARS-CoV-2, including the ancestral B1 lineage (A), Delta (B) and Omicron (C) variants. Viral replication was assessed by the quantification of viral RNA (left panels), comparing the baseline level at 1Hpi (hatched bar) to 96Hpi (open bar). Statistical significance increase was calculated using 2-way ANOVA for fold change. *P < 0.05 and ****P < 0.0001 (N = 3–4). Virus replication in cell lines where a significant increase has been observed was then confirmed by infectious particle titration (right panels). VeroE6 and A549 cells were used as positive and negative controls respectively.