Characterization of two linear epitopes SARS CoV-2 spike protein formulated in tandem repeat

Immunological assessment of NSFu1: A novel fusion molecule constructed from structural proteins of SARS-CoV-2 for improving COVID-19 antibody detection

The SARS-CoV-2 outbreak has claimed millions of lives and caused significant clinical challenges. The availability of a rapid, cost-effective, and sensitive test to detect antibodies at different stages of COVID-19 is crucial for effective clinical management, epidemiological studies, and public health surveillance. Four novel peptides (SF1, SF2, SF4, SF6) and two multi-epitope fusion proteins (SFu1 and NSFu1) from less variable regions of the spike and nucleocapsid proteins were developed. After detailed in silico structural validation, all the proteins were expressed in E. coli (BL21), purified by Ni2+ affinity chromatography, and CD spectroscopy was also executed for secondary structural analysis. The serological potential was assessed by screening 462 plasma samples from symptomatic, asymptomatic, recovered, follow-up COVID-19 cases, and 212 healthy controls. The recombinant antigens SF1, SF2, SF4, SF6, NC, SFu1, and NSFu1 showed ELISA sensitivities of 32.9%, 41.5%, 37.3%, 28.8%, 30.7%, 65.8%, and 82.0%, respectively with specificities ranging from 97 to 99% for symptomatic and asymptomatic COVID-19 cases. The sensitivities for the fusion proteins were nearly equivalent to the combined sensitivities of their constituent antigens. In conclusion, the NSFu1 fusion protein showing 82% sensitivity and 99% specificity could be a potential antigen for developing new molecules to achieve higher sensitivity for COVID-19 antibody detection.

Challenges and strategies in the soluble expression of CTA1-(S14P5)4-DD and CTA1-(S21P2)4-DD fusion proteins as candidates for COVID-19 intranasal vaccines

Developing intranasal vaccines against pandemics and devastating airborne infectious diseases is imperative. The superiority of intranasal vaccines over injectable systemic vaccines is evident, but developing effective intranasal vaccines presents significant challenges. Fusing a protein antigen with the catalytic domain of cholera toxin (CTA1) and the two-domain D of staphylococcal protein A (DD) has significant potential for intranasal vaccines. In this study, we constructed two fusion proteins containing CTA1, tandem repeat linear epitopes of the SARS-CoV-2 spike protein (S14P5 or S21P2), and DD. Structural predictions indicated that each component of the fusion proteins was compatible with its origin. In silico analyses predicted high solubility for both fusion proteins when overexpressed in Escherichia coli. However, contrary to these predictions, the constructs exhibited limited solubility. Lowering the cultivation temperature from 37°C to 18°C did not improve solubility. Inducing expression with IPTG at the early log phase significantly increased soluble CTA1-(S21P2)4-DD but not CTA1-(S14P5)4-DD. Adding non-denaturing detergents (Nonidet P40, Triton X100, or Tween 20) to the extraction buffer significantly enhanced solubility. Despite this, purification experiments yielded low amounts, only 1-2 mg/L of culture, due to substantial losses during the purification stages. These findings highlight the challenges and potential strategies for optimizing soluble expression of CTA1-DD fusion proteins for intranasal vaccines.

Development of a Candidate TMV Epitope Display Vaccine against SARS-CoV-2

Essential in halting the COVID-19 pandemic caused by SARS-CoV-2, it is crucial to have stable, effective, and easy-to-manufacture vaccines. We developed a potential vaccine using a tobacco mosaic virus (TMV) epitope display model presenting peptides derived from the SARS-CoV-2 spike protein. The TMV-epitope fusions in laboratory tests demonstrated binding to the SARS-CoV-2 polyclonal antibodies. The fusion constructs maintained critical epitopes of the SARS-CoV-2 spike protein, and two in particular spanned regions of the receptor-binding domain that have mutated in the more recent SARS-CoV-2 variants. This would allow for the rapid modification of vaccines in response to changes in circulating variants. The TMV-peptide fusion constructs also remained stable for over 28 days when stored at temperatures between -20 and 37 °C, an ideal property when targeting developing countries. Immunogenicity studies conducted on BALB/c mice elicited robust antibody responses against SARS-CoV-2. A strong IFNγ response was also observed in immunized mice. Three of the six TMV-peptide fusion constructs produced virus-neutralizing titers, as measured with a pseudovirus neutralization assay. These TMV-peptide fusion constructs can be combined to make a multivalent vaccine that could be adapted to meet changing virus variants. These findings demonstrate the development of a stable COVID-19 vaccine candidate by combining SARS-CoV-2 spike protein-derived peptides presented on the surface of a TMV nanoparticle.

AlphaFold2 Reveals Structural Patterns of Seasonal Haplotype Diversification in SARS-CoV-2 Spike Protein Variants

The slow experimental acquisition of high-quality atomic structures of the rapidly changing proteins of the COVID-19 virus challenges vaccine and therapeutic drug development efforts. Fortunately, deep learning tools such as AlphaFold2 can quickly generate reliable models of atomic structure at experimental resolution. Current modeling studies have focused solely on definitions of mutant constellations of Variants of Concern (VOCs), leaving out the impact of haplotypes on protein structure. Here, we conduct a thorough comparative structural analysis of S-proteins belonging to major VOCs and corresponding latitude-delimited haplotypes that affect viral seasonal behavior. Our approach identified molecular regions of importance as well as patterns of structural recruitment. The S1 subunit hosted the majority of structural changes, especially those involving the N-terminal domain (NTD) and the receptor-binding domain (RBD). In particular, structural changes in the NTD were much greater than just translations in three-dimensional space, altering the sub-structures to greater extents. We also revealed a notable pattern of structural recruitment with the early VOCs Alpha and Delta behaving antagonistically by suppressing regions of structural change introduced by their corresponding haplotypes, and the current VOC Omicron behaving synergistically by amplifying or collecting structural change. Remarkably, haplotypes altering the galectin-like structure of the NTD were major contributors to seasonal behavior, supporting its putative environmental-sensing role. Our results provide an extensive view of the evolutionary landscape of the S-protein across the COVID-19 pandemic. This view will help predict important regions of structural change in future variants and haplotypes for more efficient vaccine and drug development.