key: cord-1036650-aissjp8a
authors: Halfmann, Peter J.; Kuroda, Makoto; Maemura, Tadashi; Chiba, Shiho; Armbrust, Tammy; Wright, Ryan; Balaram, Ariane; Florek, Kelsey R.; Bateman, Allen C.; Kawaoka, Yoshihiro
title: Efficacy of vaccination and previous infection against the Omicron BA.1 variant in Syrian hamsters
date: 2022-03-28
journal: Cell Rep
DOI: 10.1016/j.celrep.2022.110688
sha: 814010ab148a661fdcddf819a3b735642ba5bb63
doc_id: 1036650
cord_uid: aissjp8a

The emergence of the SARS-CoV-2 Omicron (B.1.1.529) variant with a surprising number of spike mutations raises concerns about reduced sensitivity of this virus to antibody neutralization and subsequent vaccine breakthrough infections. Here, we infect Moderna mRNA-vaccinated or previously infected hamsters with the Omicron BA.1 variant. While the Moderna mRNA vaccine reduces viral loads in the respiratory tissues upon challenge with an early S-614G isolate, the vaccine efficacy is not as pronounced after infection with the Omicron variant. Previous infection with the early SARS-CoV-2 isolate prevents replication after re-challenge with either virus in the lungs of previously infected hamsters, but the Omicron variant replicates efficiently in nasal turbinate tissue. These results experimentally demonstrate in an animal model that the antigenic changes in the Omicron variant are responsible for vaccine breakthrough and re-infection.

On November 26, 2021, the World Health Organization classified B.1.1.529 (Omicron) as a variant of concern. First detected in South Africa, the Omicron BA.1 variant has quickly become the dominant variant, replacing the former dominant Delta variant (B.1.617.2) in many parts of the world. Staggeringly, the Omicron variant contains over 30 amino acid substitutions in the spike protein including 15 amino acid substitutions in the receptor-binding domain. These extensive amino acid changes in the spike protein are associated with in vitro escape of neutralization to most therapeutic monoclonal antibodies (Cameroni et al., 2021; VanBlargan et al., 2021) and with reduced vaccine-induced neutralizing antibody reactivity with the Omicron variant (Ai et al., 2021; Dejnirattisai et al., 2021) leading to vaccine breakthrough infections (Helmsdal et al., 2021; Zhou et al., 2021) .

Because the Omicron variant is antigenically substantially different from the previously circulating viruses (Tada et al., 2021) and the level of immunity differs among those previously infected and those vaccinated, due to the infecting strains or vaccine types and vaccination dates, it is difficult to determine whether Omicron infections in humans are due to immunity waning or antigenic changes in the infecting virus or both. Here, in the hamster model, we addressed these issues under controlled conditions using the Omicron variant and isolates that are no longer circulating in nature (i.e., a Wuhan-like isolate and an isolate with only a D614G spike mutation).

A significant decrease in the reactivity of vaccine-induced antibodies against the Omicron variant has been reported (Ai et al., 2021; Dejnirattisai et al., 2021) , which may explain vaccine breakthrough infections in the human population (Helmsdal et al., 2021; Zhou et al., 2021) . To experimentally investigate these findings in an animal model, we vaccinated groups of eight J o u r n a l P r e -p r o o f female Syrian golden hamsters once or twice at a 4-week interval with the Moderna mRNA vaccine (35 µg of vaccine per dose). Seven months after vaccination, serum samples were collected to evaluate binding IgG antibody titers as measured by an ELISA. All animals had measurable IgG antibody titers against the spike (S-614G) with approximately 2.6-fold higher antibody titers after two vaccinations [geometric mean titer (GMT) = 8,611 compared to one vaccination; GMT = 3,620]. Antibody titers against the Omicron spike were similar with GMTs of 6,640 and 3,320 after two vaccinations and one vaccination, respectively ( Figure 1E ).

To examine the protective efficacy of the Moderna mRNA vaccine seven months after vaccination, hamsters (8-month-old; vaccinated once or twice) were infected with 1,000 plaqueforming units (pfu) of SARS-CoV-2, specifically a S-614G isolate (n=4 in each vaccine group) or the Omicron variant (n=4 in each vaccine group). Age-matched, unvaccinated hamsters served as controls (n=4 for each virus).

In the unvaccinated, naïve hamsters, the S-614G isolate replicated better than the Omicron variant in the lungs with about a 2-log difference between the isolates [ Figure 1A and 1B (Naive bars), Figure 1E ]. However, the virus titers in the nasal turbinates were similar between the two virus isolates [ Figure 1C and 1D (Naive bars), Figure 1E ]. Two vaccinations reduced the virus titers by 6-log units in the lungs of hamsters infected with the S-614G isolate compared to the infected, unvaccinated control animals ( Figure 1A and 1E). In contrast, two vaccinations only reduced the virus titers by 1.5-log units in the lungs of hamsters infected with the Omicron variant compared to the infected, unvaccinated control animals ( Figure 1B and 1E). Virus loads were also significantly reduced in the lungs of hamsters vaccinated only once and infected with the S-614G isolate (2-log unit reduction compared to the naïve group, p=0.008; Figure 1A and 1E), but one vaccination did not significantly reduce Omicron virus titers in the lungs (0.9-log reduction compared to the naïve group, p=0.177; Figure 1B and 1E). Similar reductions in virus titers were J o u r n a l P r e -p r o o f observed in the nasal turbinates with the greatest reduction after two vaccinations in hamsters infected with the S-614G isolate compared to the Omicron isolate ( Figure 1C , 1D and 1E).

Next, we examined the relationship between the antibody levels induced by vaccination and the virus titers in different tissues. We observed a strong correlation between antibody levels and S-614G virus titers in the lungs (p<0.0001) and nasal turbinates (p=0.0005) (Supplementary Figure 1A) . In Omicron infected, vaccinated hamsters, there was a less, but significant correlation between the antibody levels and virus titers in both tissues [lungs (p=0.0071), nasal turbinates (p=0.0058) (Supplementary Figure 1B) ].

Next, we determined whether a previous infection with SARS-CoV-2 would protect hamsters against a rechallenge with the Omicron variant. Animals were first infected with a S-614G isolate (n=6; 7 months prior) or an original Wuhan-like S-614D isolate (n=4; 22 months prior). Prior to rechallenge, serum was analyzed for spike-specific IgG antibody titers. All animals had high IgG antibody titers against the S-614G antigen as measured by an ELISA (7-month GMT = 32,510; 22-month GMT = 34,443) with 1.4-and 3.4-fold decreases in IgG antibody titers against the Omicron spike antigen (7-month GMT = 22,988; 22-month GMT = 10,159) ( Figure 2E ). We next determined whether the immunity generated by previous infection was sufficient to prevent replication of the Omicron variant in hamsters. We re-infected hamsters with 1,000 pfu of the S-614G isolate or the Omicron variant (infected 7 months prior, n=3 for each virus; infected 22 months prior, n=2 for each virus). Naïve, age-matched hamsters (9-month-old, n=3 for each virus and 23-month-old, n=3 for each virus) were also infected with either virus at the same dose.

Three days after re-challenge, we did not detect any replicating virus in the lungs or nasal turbinates in either group of previously infected hamsters re-challenged with the S-614G isolate Figure 2B and 2E) although this isolate replicated efficiently in the same tissues of naïve animals of both age groups (Figure 2A and 2E) . We also found no detectable replicating virus in the lungs J o u r n a l P r e -p r o o f of either group of previously infected hamsters re-challenged with the Omicron variant ( Figure 2D and 2E). The lack of infectious virus (both the S-614G and the Omicron variant) in the lungs of previously infected, re-challenged hamsters was confirmed by RT-qPCR, as indicated by high Ct values (Supplementary Table 1 ). However, the Omicron variant replicated efficiently in the nasal turbinates in both groups of hamsters infected 7 months prior with the S-614G isolate and those infected 22 months prior with the S-614D isolate ( Figure 2D and 2E) . In naïve hamsters, the Omicron variant again grew less efficiently in the lungs, but to similar titers in the nasal turbinates compared to the S-614G isolate in naïve hamsters (Figure 2A, 2C and 2E ). This better immune response to a previous infection compared to vaccination prevented replication of both isolates (S-614G and the Omicron variant) after re-challenge in the lungs of previously infected hamsters, demonstrating that both short-and long-term immunity was J o u r n a l P r e -p r o o f protective in the lower respiratory tract. However, unlike the S-614G isolate, the Omicron variant replicated efficiently in the upper respiratory tract (nasal turbinate tissue) in previously infected hamsters. Whether this replication in the nasal turbinates of previously infected hamsters can lead to transmission to naïve hamsters will be addressed in the next set of experiments.

Although the hamster model of SARS-CoV-2 infection shares many similarities with infection in humans (Imai et al., 2020) , the differences in immunity induced by vaccination and the kinetics of waning immunity between hamsters and humans is not fully understood or appreciated. These potential differences are limitations in these studies of the Omicron variant.

Furthermore, although the Omicron variant replicates less efficient in the lungs of infected hamsters compared to previous variants. Our group (Halfmann et al., 2022) and another group (Abdelnabi et al., 2022) have shown that the Omicron BA.1 variant is attenuated in the hamster model, resulting in minimal antiviral antigen detection and little inflammation in the lung tissue relative to previous variants. Nevertheless, our results in the hamster model do demonstrate that the Omicron variant partially evades vaccine-induced immunity, whereas a robust immune response to a first infection will protect the lower respiratory tract from a subsequent infection.

We thank Susan Watson for scientific editing. This work was supported, in part, by the National in naïve hamsters from one experimental study. Cumulative antibody and virology data on the Moderna mRNA-vaccinated hamsters (E). Black dots on the X-axis represent virus titers below the limit of detection (≤10 pfu/g). *** p<0.0001, ** p<0.001, and ns; not significant.

Virus replication of the S-614G isolate or the Omicron variant in groups of naïve hamsters (A and C, respectively) or groups of hamsters o C for 30 minutes) serum diluted in PBS-T with 1% milk powder. After a 4-h incubation at room temperature, the plates were washed with PBS-T three times and then incubated with a hamster IgG secondary antibody conjugated with horseradish peroxidase (Invitrogen; 1:7,000 dilution in PBS-T with 1% milk powder). After a 1-h incubation with the secondary antibody, the plates were washed three times with PBS-T and then developed with SigmaFast o-phenylenediamine dihydrochloride solution. After a 10-min incubation, the reaction was stopped with the addition of 3 M hydrochloric acid. The absorbance was measured at a wavelength of 490 nm (OD490). The IgG antibody endpoint titer was defined as the highest serum dilution with an OD490 cut-off value of >0.15.

The sample sizes for the hamster studies were determined from previous studies that demonstrated significant differences among groups. The researchers were not blinded to the group allocations during the experiments. Virus titers from animals are expressed as scatter plots with bars and individual datapoints, obtained by using Graphpad Prism 9. Statistical analyses were performed using two-tailed unpaired Student's t-tests. Correlations between antibody levels and virus titers were determined with the Spearman correlation test. Figure S1 . Correlation between antibody levels and virus titers. Table S1 . Ct values from lungs collected from previously infected hamsters.

J o u r n a l P r e -p r o o f

The omicron (B.1.1.529) SARS-CoV-2 variant of concern does not readily infect Syrian hamsters

Omicron variant showed lower neutralizing sensitivity than other SARS-CoV-2 variants to immune sera elicited by vaccines after boost

Broadly neutralizing antibodies overcome SARS-CoV-2 Omicron antigenic shift. bioRxiv

Reduced neutralisation of SARS-CoV-2 omicron B.1.1.529 variant by postimmunisation serum

SARS-CoV-2 Omicron virus causes attenuated disease in mice and hamsters

Omicron outbreak at a private gathering in the Faroe Islands, infecting 21 of 33 triple-vaccinated healthcare workers. medRxiv

Characterization of a new SARS-CoV-2 variant that emerged in Brazil

Syrian hamsters as a small animal model for SARS-CoV-2 infection and countermeasure development

Increased resistance of SARS-CoV-2 Omicron Variant to Neutralization by Vaccine-Elicited and Therapeutic Antibodies. bioRxiv

An infectious SARS-CoV-2 B.1.1.529 Omicron virus escapes neutralization by several therapeutic monoclonal antibodies. bioRxiv

Vaccine-breakthrough infection by the SARS-CoV-2 Omicron variant elicits broadly cross-reactive immune responses. bioRxiv

to an early isolate • BA.1 replicates less efficiently than an early isolate in the lungs of hamsters • Prior infection does not prevent BA.1 replication in the nasal turbinates of hamsters • Prior infection does prevent BA.1 replication in the lungs of hamsters IN BRIEF Halfmann et al. report that while the Moderna mRNA vaccine reduces BA.1 replication in vaccinated hamsters, the vaccine efficacy is not as pronounced as that against an early prototypical SARS-CoV-2 isolate

In-house; upon request Omicron BA

SARS-CoV-2/UT-NCGM02/Human/2020/Tokyo In-house

house; upon request S-614G Biological samples Residual Moderna vaccine In-house; upon request -limited supply; frozen at -80 0 C Chemicals, peptides, and recombinant proteins S-614G