Updated vaccine protects against SARS-CoV-2 variants including Omicron (B.1.1.529) and prevents transmission in hamsters

SARS-CoV-2 emerged via zoonotic spillover, but continued spread in humans has given rise to variants of concern (VOCs) with mutations in spike that affect transmissibility, virulence, and immune escape. Early in the pandemic, D614G (B.1) became dominant. Subsequently, Alpha, Beta, Gamma, Delta, and Omicron arose with partially convergent spike mutations (e.g., N501Y, E484K/A, K417N/T, L452R, T478K, P681R/N) that enhanced ACE2 affinity and/or reduced neutralization by antibodies elicited by infection or first-generation vaccines. Clinical and in vitro data showed reduced vaccine effectiveness and neutralization against Beta and later Omicron. Most deployed vaccines use ancestral 2019/2020 spike, raising concerns about protection against newer VOCs. The study aims to quantify the loss of efficacy of a YF17D-vectored vaccine expressing prototypic spike in a stringent hamster model versus multiple VOCs, and to test whether an updated, stabilized, variant-informed spike antigen broadens protection, including against Omicron, and reduces transmission.

Prior observations linked specific spike mutations (e.g., N501Y, E484K/A, K417N/T) to increased transmissibility and immune escape. Clinical trials and neutralization studies reported reduced efficacy of several first-generation vaccines (e.g., ChAdOx1 nCoV-19, mRNA vaccines) against Beta, and marked neutralization loss against Omicron. Nonclinical studies in macaques and hamsters indicated partial protection and persistent viral replication when vaccinated with ancestral spike-based vaccines and challenged with Beta. Many therapeutic monoclonal antibodies also lost activity against Omicron. These findings underscore the need to update antigens, similar to seasonal influenza vaccine strain updates, to match the evolving antigenic landscape of SARS-CoV-2.

- Vaccine platform: Yellow fever 17D (YF17D)-based vectors expressing SARS-CoV-2 spike antigens. A prototype construct (YF-S0) used ancestral spike (D614G) stabilized to the prefusion form. An updated construct (YF-S0* or S0*) incorporated 12 amino acid changes from VOCs (primarily Gamma) and three additional proline substitutions (A829P, A942P, V987P) to further stabilize spike, along with mutations ablating the S1/S2 furin cleavage site (RRAR→AAA). - Animals: Female Syrian hamsters (6–8 weeks at start). Housing and procedures followed KU Leuven ethical approvals (P05/2020, P05/2021). Infections and sampling conducted in BSL-3 facilities. - Immunization regimens: Typically two doses on day 0 and day 7 administered intraperitoneally. Some experiments used a single-dose regimen. Doses ranged from 10^4–10^6 PFU depending on experiment/group. - Virus challenges: Intranasal inoculation with SARS-CoV-2 strains representing prototype (Wuhan/D614G), Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), and Omicron (B.1.1.529). Standard challenge doses were generally 10^3–10^6 TCID50; stringent tests used up to 10^7 TCID50 (e.g., high-dose Beta challenge). Omicron challenge performed 7 weeks post-vaccination in some experiments. - Readouts: Viral RNA quantified by RT-qPCR and infectious virus by titration from lungs and nasal washes at defined days post-infection (typically day 4; some cohorts followed to day 12). Lung pathology assessed by H&E histology and scoring. - Serology: Neutralizing antibodies (nAbs) quantified using VSV pseudotyped viruses bearing spike variants (prototype, Beta, Gamma, Delta, Omicron). SNT50 titers determined by four-parameter nonlinear curve fitting. Antigenic cartography performed to visualize antigen-serum relationships across variants. - Correlates of protection: Logistic regression used to relate pre-challenge nAb titers to probability of protection, defining 50% and 90% protection thresholds where possible. - Transmission study: Delta variant transmission assessed by co-housing infected index hamsters (vaccinated or sham) with naïve sentinel hamsters for 2 days, followed by virological and pathological assessment in both index and sentinel animals. - Statistics: Nonparametric Kruskal–Wallis tests; significance at p<0.05. Data presented as medians or geometric means with IQR/95% CI as indicated.

- Prototypic antigen performance: The YF-S0 (ancestral spike) vaccine induced high nAb titers against prototype virus and provided strong protection against prototype SARS-CoV-2 and Alpha in hamsters, with viral loads in lungs reduced to undetectable in most animals. However, efficacy was markedly reduced against Beta; vaccinated animals showed only partial reductions (approximately order-of-magnitude) in viral loads versus sham and breakthrough infections occurred. - Correlates of protection: Similar nAb thresholds predicted protection for prototype and Alpha. For Beta, substantially higher nAb levels were required for 50% protection, and a 90% protective threshold could not be defined under the high-dose challenge conditions, indicating reduced robustness of protection with prototypic antigen. - Updated antigen immunogenicity: The updated YF-S0* vaccine elicited broadly higher nAb titers across VOCs, notably improving responses to Beta and Gamma while maintaining potency against prototype and Delta. - Protection across VOCs: YF-S0* conferred protection against Alpha, Beta, Gamma, and Delta, with elimination of detectable infectious virus from lungs at day 4 post-challenge and markedly improved lung pathology scores compared with sham. - High-dose Beta challenge: Under stringent conditions (10^7 TCID50 Beta), 23/24 YF-S0*-vaccinated hamsters were protected, including all with detectable pre-challenge nAbs. Viral RNA and infectious titers in lungs and nasal washes were dramatically reduced versus sham. - Omicron: YF-S0* induced a pronounced increase in Omicron-specific nAbs (approximately 15-fold; p<0.0001) compared to the prototype construct. Upon Omicron challenge, vaccinated animals had minimal to undetectable infectious virus in lungs and reduced viral RNA in lungs and nasal washes; differences between vaccines may be partly masked by generally poor Omicron replication in hamsters. - Transmission: Vaccination with the updated spike (YF-S′/S0*) prevented Delta transmission from infected index animals to naïve sentinels, with sentinels co-housed with vaccinated index hamsters showing no detectable infectious virus and markedly reduced/absent viral RNA and pathology.

These results show that first-generation vaccines based on ancestral spike can lose protective capacity against certain VOCs, most notably Beta, in a stringent hamster model. By redesigning the antigen to incorporate variant-defining mutations and enhanced prefusion stabilization, the YF17D-vectored vaccine regained and broadened protection, achieving sterilizing-like outcomes in lungs across multiple VOCs and reducing upper respiratory tract viral loads. The updated construct also markedly boosted Omicron-specific neutralization and curtailed Delta transmission in a co-housing model, indicating potential to limit spread in a population. The correlates analysis underscores the need for higher nAb levels to cover immune-escape variants, rationalizing antigen updating. These findings support the strategy of periodically updating COVID-19 vaccine antigens, akin to influenza, to match the evolving antigenic landscape and sustain effectiveness against infection and transmission.

An updated YF17D-vectored SARS-CoV-2 vaccine expressing a stabilized, variant-informed spike antigen (S0*) elicited broad neutralization and provided robust protection in hamsters against prototype virus and VOCs Alpha, Beta, Gamma, Delta, and Omicron. Vaccination eliminated detectable infectious virus from lungs, improved lung pathology, and prevented Delta transmission to naïve cage mates. The work highlights the vulnerability of ancestral spike-based vaccines to immune-escape variants and provides a proof-of-concept that antigen updates can restore and expand protection. Future research should assess durability of protection, optimal dosing and interval, performance against newly emerging variants, mechanisms of transmission blockade, and translation to human clinical efficacy and safety.

- Species/model: Findings are in Syrian hamsters; translation to human efficacy requires clinical validation. - Variant-specific biology: Omicron replicates poorly in hamsters, potentially obscuring quantitative differences between vaccine constructs in this model. - Follow-up and durability: Long-term durability of humoral and cellular immunity, and protection beyond the study timeframes, were not assessed. - Regimens: The rapid two-dose schedule (day 0/7) was used; other intervals/doses may further optimize responses but were not systematically evaluated. - Challenge conditions: High-dose challenges were used for stringency; their relationship to typical human exposure levels is uncertain. - Transmission study scope: Transmission was assessed only for Delta, over a short co-housing period, and with female animals; generalizability to other variants and conditions remains to be shown. - Assays: Neutralization used VSV pseudotypes; although informative, results may differ from authentic virus neutralization in some contexts.