Omicron breakthrough infections in vaccinated or previously infected hamsters

Abstract

The ongoing SARS-CoV-2 epidemic was marked by the repeated emergence and replacement of "variants" with genetic and phenotypic distance from the ancestral strains, the most recent examples being viruses of the Omicron lineage. Here, we describe a hamster direct contact exposure challenge model to assess protection against reinfection conferred by either vaccination or prior infection. We found that two doses of self-amplifying RNA vaccine based on the ancestral Spike ameliorated weight loss following Delta infection and decreased viral loads but had minimal effect on Omicron BA.1 infection. Prior vaccination followed by Delta or BA.1 breakthrough infections led to a high degree of cross-reactivity to all tested variants, suggesting that repeated exposure to antigenically distinct Spikes, via infection and/or vaccination drives a cross-reactive immune response. Prior infection with ancestral or Alpha variant was partially protective against BA.1 infection, whereas all animals previously infected with Delta and exposed to BA.1 became reinfected, although they shed less virus than BA.1-infected naive hamsters. Hamsters reinfected with BA.1 after prior Delta infection emitted infectious virus into the air, indicating that they could be responsible for onwards airborne transmission. We further tested whether prior infection with BA.1 protected from reinfection with Delta or later Omicron sublineages BA.2, BA.4, or BA.5. BA.1 was protective against BA.2 but not against Delta, BA.4, or BA.5 reinfection. These findings suggest that cohorts whose only immune experience of COVID-19 is Omicron BA.1 infection may be vulnerable to future circulation of reemerged Delta-like derivatives, as well as emerging Omicron sublineages.

Keywords: SARS-CoV-2; hamster; reinfection; transmission; vaccine.

Fig. 1.

Delta and Omicron BA.1 infection of hamsters vaccinated with a self-amplifying Wuhan-Hu Spike RNA vaccine. (A) Experimental design. Two groups of hamsters were vaccinated with self-amplifying RNA (saRNA) Wuhan Spike or the saRNA-HIV vaccine. The vaccination schedule was a priming dose followed 4 wk later by a boost. Two weeks after the boost, the vaccinated hamsters were cohoused with donor hamsters which had been inoculated intranasally with 100 PFU Delta or BA.1 from 1 day post inoculation (DPI). Each cage housed one donor, one saRNA-Spike vaccinee, and one saRNA-HIV vaccinee hamster. (B) Pseudovirus neutralisation assays were performed using vaccinated hamster sera collected 2 wk after the boost (detection limit = 40, dotted line). Geometric means (blue) and fold changes (black) are shown. (C and D) The infectious virus shedding profile and area under the curve (AUC) in nasal wash samples of vaccinated hamsters exposed to Delta (n = 4 cages) (C) or BA.1 donors (n = 4 cages) (D). Nasal wash samples were collected daily and assessed by plaque assay (detection limit = 10 PFU/mL, dotted line). The symbols represent mean and SD in virus shedding curves, and median in AUC. (E) Pseudovirus neutralisation assays were performed using vaccinated hamster sera collected 2 wk after the exposure. Statistically significant differences were determined using the Mann–Whitney U test (*P < 0.05, **P < 0.01, and ***P < 0.001).

Fig. 2.

Reinfection of hamsters previously infected with earlier variants following direct contact exposure to Omicron BA.1. (A) Experimental design. Four groups of four hamsters each were inoculated intranasally with 100 PFU of either a wild-type isolate with D614G (WT/D614G), an Alpha isolate, a Delta isolate, or PBS. Six weeks later, two previously infected hamsters were cohoused with a donor hamster inoculated with 100 PFU of BA.1 from 1 day post inoculation (DPI). The direct contact transmission experiments were conducted in two cages (n = 2 biological replicates). (B–E) Virus-shedding profiles of donors (lines) and direct contact hamsters (bars) are shown. The hamsters in cage 1 are indicated by the solid line and unpatterned bars; the hamsters in cage 2 are indicated by the dotted line and patterned bars. (B) Naive hamster exposed to BA.1 donor. (C) Hamster previously infected with WT/D614G exposed to BA.1 donor. (D) Hamster previously infected with Alpha exposed to BA.1 donor. (E) Hamster previously infected with Delta exposed to BA.1 donor. Nasal wash samples were collected daily and assessed by plaque assay (detection limit = 10 PFU/mL, dash line). (F) AUC of infectious viral loads in direct contact hamsters. (G) Potential for onwards transmission determined by measuring infectious virus deposited from air at 30 cm, 60 cm, and 90 cm from the naive hamsters and the hamsters previously infected with Delta exposed to BA.1 donor on 3 DPI. Individual data points and median are shown (F and G). Statistically significant differences were determined using the Mann–Whitney U test (*P < 0.05, ns = not significant).

Fig. 3.

Reinfection of hamsters previously infected with Omicron BA.1 following direct contact exposure to BA.2, BA.4, BA.5, or Delta. Four groups of four hamsters each were inoculated intranasally by 100 PFU of BA.1. Six weeks later two previously inoculated hamsters were co-housed with a donor hamster inoculated with 100 PFU of either a BA.2, a BA.4, a BA.5 or a Delta isolate from 1 day post inoculation (DPI). (A–H) Virus-shedding profiles of donors (lines) and direct contact hamsters (bars) are shown. The hamsters in cage 1 are indicated by the solid line and unpatterned bars; the hamsters in cage 2 are indicated by the dotted line and patterned bars. (A–D) Naive hamster exposed to BA.2 donor (A), BA.4 donor (B), BA.5 donor (C), or Delta donor (D; two delta donors were killed on 7 DPI). (E–H) Hamsters previously infected with BA.1 exposed to BA.2 donor (E), BA.4 donor (F), BA.5 donor (G), or Delta donor (H). Nasal wash samples were collected daily and assessed by plaque assay (Detection limit = 10 PFU/mL, dash line). (I–L) AUC of infectious viral loads in the hamsters previously infected with BA.1 exposed to BA.2 donor (I), BA.4 donor (J), BA.5 donor (K), or Delta donor (L). (M) Potential for onwards transmission by measuring infectious virus deposited from air at 30 cm, 60 cm, and 90 cm from the hamsters previously infected with BA.1 exposed to BA.2, BA.4, BA.5, or Delta donor on 3 DPI. Individual data points and median are shown (I–M). Statistically significant differences were determined using the Mann–Whitney test (*P < 0.05, ns = not significant).