Characterization of the SARS-CoV-2 BA.5.5 and BQ.1.1 Omicron variants in mice and hamsters

Abstract

The continued evolution and emergence of novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants have resulted in challenges to vaccine and antibody efficacy. The emergence of each new variant necessitates the need to re-evaluate and refine animal models used for countermeasure testing. Here, we tested a recently circulating SARS-CoV-2 Omicron lineage variant, BQ.1.1, in multiple rodent models including K18-human ACE2 (hACE2) transgenic, C57BL/6J, and 129S2 mice, and Syrian golden hamsters. In contrast to a previously dominant BA.5.5 Omicron variant, inoculation of K18-hACE2 mice with BQ.1.1 resulted in substantial weight loss, a characteristic seen in pre-Omicron variants. BQ.1.1 also replicated to higher levels in the lungs of K18-hACE2 mice and caused greater lung pathology than the BA.5.5 variant. However, in C57BL/6J mice, 129S2 mice, and Syrian hamsters, BQ.1.1 did not cause increased respiratory tract infection or disease compared to animals administered BA.5.5. Moreover, the rates of direct contact or airborne transmission in hamsters were not significantly different after BQ.1.1 and BA.5.5 infections. Taken together, these data suggest that the BQ.1.1 Omicron variant has increased virulence in rodent species that express hACE2, possibly due to the acquisition of unique spike mutations relative to earlier Omicron variants. IMPORTANCE As severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to evolve, there is a need to rapidly assess the efficacy of vaccines and antiviral therapeutics against newly emergent variants. To do so, the commonly used animal models must also be re-evaluated. Here, we determined the pathogenicity of the BQ.1.1 SARS-CoV-2 variant in multiple SARS-CoV-2 animal models including transgenic mice expressing human ACE2 (hACE2), two strains of conventional laboratory mice, and Syrian hamsters. While BQ.1.1 and BA.5.5 infection resulted in similar levels of viral burden and clinical disease in hamsters and the conventional strains of laboratory mice tested, increases in lung infection were detected in hACE2-expressing transgenic mice, which corresponded with greater levels of pro-inflammatory cytokines and lung pathology. Taken together, our data highlight important differences in two closely related Omicron SARS-CoV-2 variant strains and provide a foundation for evaluating countermeasures.

Keywords: BA.5.5; BQ.1.1; SARS-CoV-2; coronavirus; pathogenesis; variants.

Fig 1

BQ.1.1-infection results in increased infection and weight loss in K18-hACE2 mice. C57BL/6J (A), 129S2 (B), or K18-hACE2 (C) mice were inoculated intranasally with 10⁴ FFU of the indicated SARS-CoV-2 strain. Animals were monitored for weight loss (A–C) daily (differences in area under the curves assessed by Student’s t-test with Welch’s correction; **P < 0.01). At 4 or 6 dpi, the indicated tissues were collected. Viral RNA levels in the lungs, nasal turbinates, and nasal washes were determined by RT-qPCR, and infectious virus in the lungs were quantified by plaque assay (lines indicate median ± SEM, dotted lines indicate limits of detection; n = 9–10 mice per group, two experiments; Mann-Whitney test between BA.5.5- and BQ.1.1-infected groups; *P < 0.05, ****P < 0.0001).

Fig 2

BQ.1.1 infection induces inflammatory cytokines and pathology in the lungs of K18-hACE2 mice. (A) Heat map of cytokine and chemokine protein expression levels in lung homogenates. Data from BQ.1.1-infected mice are presented as log₂-transformed fold-change compared to BA.5.5-infected mice. White, baseline; red, increase. (B) Graphs of cytokine and chemokine protein levels in the lungs of naïve, BA.5.5-, or BQ.1.1-infected lungs from K18-hACE2 mice at 6 dpi (line indicates median, dotted lines indicate limits of detection; n = 2–3 naïve, n = 9–10 for all other groups (two-way ANOVA with Tukey’s post-test with comparisons between all groups: *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001). (C) Hematoxylin and eosin staining of lung sections from K18-hACE2 mice were collected 6 days after intranasal inoculation with 10⁴ PFU of the indicated SARS-CoV-2 strain. Images show 2.5× (left), 5× (middle), and 20× (right) power magnification. Scale bars indicate 500, 500, and 100 µm, left-to-right, respectively. Arrows indicate focal immune cell infiltrates (green), alveolar consolidation (blue), and epithelial cell denudation (black). Two representative images are shown from four mice per group from two experiments. (D) Inflammatory foci from mice in (C) were quantified blindly and plotted (Mann-Whitney test between BA.5.5- and BQ.1.1-infected groups; *P < 0.05).

Fig 3

BA.5.5 and BQ.1.1 infections of Syrian hamsters. Hamsters were inoculated intranasally with 2.5 × 10⁴ PFU of the indicated SARS-CoV-2 strain (A). Naïve and BA.5.5- or BQ.1.1-inoculated animals were monitored for weight change daily for 14 days (B). At 3 or 6 dpi, the nasal washes, nasal turbinates, and lungs were collected from each animal and levels of viral RNA and infectious virus were determined by RT-qPCR (C) or plaque assay (D), respectively (lines indicate median ± SEM, dotted lines indicate limits of detection; n = 9–10 hamsters per group per time point, two experiments; Mann-Whitney test between BA.5.5- and BQ.1.1-infected groups; *P < 0.05, **P < 0.01).

Fig 4

BA.5.5 and BQ.1.1 transmission in Syrian hamsters. For transmission studies, donor hamsters were inoculated intranasally with 2.5 × 10⁴ PFU of the indicated SARS-CoV-2 strain. At 24-h post-inoculation, animals were transferred to cages containing naïve contact animals [direct contact; (A)] or porous canisters [airborne; (B)] upwind of naïve contact animals for a total exposure time of 8 h. After exposure, animals were returned to individual cages. At 4-days post-exposure, the percentage of SARS-CoV-2 positive contact hamsters were quantified (C and D, chi-square analysis; ns = not significant). (E) Nasal washes, nasal turbinates, and lungs were collected from contact animals at 4 dpi, and levels of infectious virus were determined (lines indicate median ± SEM, dotted lines indicate limits of detection; n = 6–12 hamsters per group, three experiments). Positive transmission events were registered when infectious virus was detected above the limit of detection within any tissue for a given animal.

Fig 5

Determination of ACE2-BA.5.5/BQ.1.1 RBD binding affinity by BLI. Recombinant human (A) or mouse (B) ACE2-Fc proteins were loaded onto biolayer interferometry (BLI) protein G pins at a concentration of 10 µg/mL and dipped into the indicated concentrations of BA.5.5 or BQ.1.1 RBDs. Samples were allowed to associate and dissociate for 300 and 600 s, respectively. Dashed black curves show fits to a 1:1 binding model with a drifting baseline. (C) Association rate (ka), dissociation rate (kd), and kinetic dissociation constant (K _D ) values were calculated and reported.