Genome Sequences of 40 SARS-CoV-2 Omicron XBB and XBB.1 sub-lineages in Bangladesh
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PROVIDER: PRJEB58412 | ENA |
REPOSITORIES: ENA
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Project description:Mucosal immunity plays a pivotal role in providing comprehensive protection against upper-airway infections and effectively limiting the shedding and transmission of SARS-CoV-2. Despite its critical importance, there remains a notable absence of nasal spray vaccines endorsed for global use by the World Health Organization. This could be due to the inability of current intranasal vaccines to induce strong mucosal and systemic responses in humans, thus urgently entailing a next-generation of intranasal COVID-19 vaccines with novel and safe technologies. In this study, we prepared a two-component intranasal vaccine that combines adenovirus vectors with a self-assembled subunit protein. Specifically, the adenovirus vector expresses the spike protein of XBB.1.5 variant (Ad5XBB.1.5), and were mixed with the recombinant protein that developed derived from the receptor binding domain (RBD) of XBB.1.5 (RBDXBB.1.5-HR). Combination of Ad5XBB.1.5 and RBDXBB.1.5-HR elicited superior humoral and cellular immunity against XBB.1.5-included variants compared with the individual components. Importantly, the STING signaling pathway was found to be crucial for the adjuvant effect of the adenovirus vector. In addition, to increase the broad-spectrum neutralizing capacities, a trimeric protein derived from the BA.5 variant (RBDBA.5-HR) was incorporated to formulate a three-component vaccine (Ad5XBB.1.5+RBDXBB.1.5-HR+RBDBA.5-HR), indicating the utilization of a combination of an adenovirus-vectored and subunit protein vaccines has the potential to serve as a next-generation intranasal vaccine platform. Of note, intranasally delivery of two-component vaccine provided protective immunity against live Omicron XBB.1.16 virus challenge in mice. Furthermore, the combination of adenovirus and subunit protein vaccine demonstrates excellent tolerability and safety in human subjects, and is able to induce enhanced mucosal immunity as well as high levels of sera neutralizing antibody in all participants. These findings underscore its suitability for clinical application in the prevention of SARS-CoV-2 variants encompassing XBB lineages.
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Project description:Although mRNA-based COVID-19 vaccines have demonstrated high efficacy, their widespread global use remains constrained by high production costs and cold-chain requirements. Modified vaccinia virus Ankara (MVA) is a highly attenuated and thermostable viral vector with low production costs, potent immunogenicity and strong potential for global distribution. Here, we compared head-to-head the long-term immunogenicity and protective efficacy of an MVA-based vaccine candidate with an approved mRNA vaccine in K18-hACE2 mice, both expressing the SARS-CoV-2 Omicron XBB.1.5 spike (S) protein. Mice received by intramuscular route homologous (mRNA/mRNA and MVA/MVA), heterologous (mRNA/MVA), or single-dose MVA regimens. SARS-CoV-2-specific humoral and cellular responses were evaluated at 10 days and 9 months post-boost, as well as antibody levels at intermediate time points, and protection was assessed following intranasal SARS-CoV-2 XBB.1.5 challenge at 9 months post-vaccination. Binding IgG antibodies against the XBB.1.5 S protein remained high throughout the 9-month period in all vaccinated groups, whereas neutralizing antibody titers peaked early after boosting and progressively declined, converging across regimens over time. S-specific CD8⁺ T-cell responses were strongest in mRNA-containing regimens at day 10 post-boost and, although contracted over time, remain detectable at 9 months post-boost in all two-doses groups, with a trend toward enhanced persistence in the heterologous mRNA/MVA regimen. In contrast, S-specific CD4⁺ T-cell responses remained low across all groups. All two-dose regimens conferred robust protection against SARS-CoV-2 XBB.1.5 challenge, significantly reducing viral RNA levels and infectious titers in both the upper and lower respiratory tract. Transcriptomic analysis of lung tissue after virus challenge revealed that vaccinated animals exhibited reduced expression of genes associated with inflammatory myeloid responses, interferon signalling, and cellular stress compared with infected controls, consistent with attenuated pulmonary inflammation. Notably, mRNA and MVA platforms induced distinct yet convergent protective transcriptional signatures, characterized by a shared reduction of interferon‑driven inflammation alongside differential engagement of humoral versus innate/cellular effector pathways, characteristic of effective antiviral immunity. Overall, our findings demonstrate that MVA‑based vaccination induce durable and protective immunity comparable to mRNA vaccines and support its use as both an alternative and complementary platform to broaden and diversify vaccine‑induced immune responses against SARS-CoV-2 and other emerging respiratory viruses.
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Project description:The COVID-19 pandemic was marked by successive waves of SARS-CoV-2 variants with distinct properties. The Omicron variant that emerged in late 2021 showed a major antigenic shift and rapidly spread worldwide. Since then, Omicron-derived variants have maintained their global dominance, for reasons that remain incompletely understood. We report that the original Omicron variant BA.1 evolved several traits that converged in facilitating viral spread. First, Omicron displayed an early replicative advantage over previous variants when grown in a reconstructed nasal epithelium model based on primary human cells. The increase in Omicron replication was more marked at the 33°C temperature characteristic of human nasal passages, resulting in a physiologically relevant advantage. Omicron also caused a decrease in epithelial integrity, as measured by transepithelial electrical resistance and caspase-3 activation. Furthermore, Omicron caused a more marked loss of motile cilia at 33°C than other variants, suggesting a capacity to impair mucociliary clearance. RNAseq analysis showed that Omicron induced a broad transcriptional downregulation of ciliary genes but only a limited upregulation of host innate defense genes at 33°C. The lower production of type I and type III interferons in epithelia infected by Omicron compared to those infected by the Delta variant, at 33°C as well as 37°C, confirmed the increased capacity of Omicron to evade the innate antiviral response. Thus, Omicron combined replication speed, motile cilia impairment, and limited induction of innate antiviral responses when propagated in reconstructed nasal epithelia at physiological temperature. Omicron has the capacity to propagate efficiently but stealthily in the upper respiratory tract, which likely contributed to the evolutionary success of this SARS-CoV-2 variant.
2025-12-13 | GSE295759 | GEO
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