S Trimer Derived from SARS-CoV-2 B.1.351 and B.1.618 Induced Effective Immune Response against Multiple SARS-CoV-2 Variants

SARS-CoV-2 variant survey: Comparison of RT-PCR screening with TGS and variant distribution across two divisions of Bangladesh

BACKGROUND

The widespread increase in multiple variants of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) since 2020 is causing significant health concerns worldwide. While whole-genome sequencing (WGS) has played a leading role in surveillance programs, many local laboratories lack the expertise and resources. Thus, we aimed to investigate the circulating SARS-CoV-2 variants and evaluate the performance of multiplexed real-time reverse transcription-PCR (RT-PCR) for screening and monitoring the emergence of new SARS-CoV-2 variants in Bangladesh.

METHODS

A total of 600 confirmed SARS-CoV-2-positive cases were enrolled either prospectively or retrospectively from two divisions of Bangladesh. The samples were screened by variant RT-PCR targeting five mutations of the spike gene (N501Y, P681R, L452R, E484K, E484Q). A subsample of the study population was also selected for third-generation sequencing (TGS) and the results were compared to the variant RT-PCR screening. An in-depth comparison was made between the two methods in terms of congruence and cost-benefit.

RESULT

Seven variants were detected among samples, with similar distributions of the variants across both divisions. Variant RT-PCR for the targeted mutations lead to a 98.5% call rate; only nine samples failed to be determined. No association was found regarding the demographic features, clinical criteria, or routine RT-PCR Ct values across the variants. The clade diversity of the sequenced subpopulation (n = 99) exhibited similar distributions across the two study sites and other epidemiologic variables. Variant RT-PCR successfully distinguished variants of concern (VOCs) and variants of interest (VOIs); however, 8% discrepancy was observed for the closest lineages. Moreover, the variant RT-PCR represented an ideal balance of cost, time, and accuracy that outweigh their limitations.

CONCLUSION

Based on the strong agreement of variant RT-PCR with TGS, such rapid, easily accessible approaches of rapid strain typing are essential in the context of pandemic responses to guide both treatment decisions and public health measures.

SARS-CoV-2 spike-FLIPr fusion protein plus lipidated FLIPr protects against various SARS-CoV-2 variants in hamsters

Vaccine-induced mucosal immunity and broad protective capacity against various severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants remain inadequate. Formyl peptide receptor-like 1 inhibitory protein (FLIPr), produced by Staphylococcus aureus, can bind to various Fcγ receptor subclasses. Recombinant lipidated FLIPr (rLF) was previously found to be an effective adjuvant. In this study, we developed a vaccine candidate, the recombinant Delta SARS-CoV-2 spike (rDS)-FLIPr fusion protein (rDS-F), which employs the property of FLIPr binding to various Fcγ receptors. Our study shows that rDS-F plus rLF promotes rDS capture by dendritic cells. Intranasal vaccination of mice with rDS-F plus rLF increases persistent systemic and mucosal antibody responses and CD4/CD8 T-cell responses. Importantly, antibodies induced by rDS-F plus rLF vaccination neutralize Delta, Wuhan, Alpha, Beta, and Omicron strains. Additionally, rDS-F plus rLF provides protective effects against various SARS-CoV-2 variants in hamsters by reducing inflammation and viral loads in the lung. Therefore, rDS-F plus rLF is a potential vaccine candidate to induce broad protective responses against various SARS-CoV-2 variants.IMPORTANCEMucosal immunity is vital for combating pathogens, especially in the context of respiratory diseases like COVID-19. Despite this, most approved vaccines are administered via injection, providing systemic but limited mucosal protection. Developing vaccines that stimulate both mucosal and systemic immunity to address future coronavirus mutations is a growing trend. However, eliciting strong mucosal immune responses without adjuvants remains a challenge. In our study, we have demonstrated that using a recombinant severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike-formyl peptide receptor-like 1 inhibitory protein (FLIPr) fusion protein as an antigen, in combination with recombinant lipidated FLIPr as an effective adjuvant, induced simultaneous systemic and mucosal immune responses through intranasal immunization in mice and hamster models. This approach offered protection against various SARS-CoV-2 strains, making it a promising vaccine candidate for broad protection. This finding is pivotal for future broad-spectrum vaccine development.