Bioinformatics prediction of B and T cell epitopes within the spike and nucleocapsid proteins of SARS-CoV2

Impacts of host factors on susceptibility to SARS-CoV-2 infection and COVID-19 progression

SARS-CoV-2, identified in Wuhan, China, in December 2019, is the third coronavirus responsible for a global epidemic, following SARS-CoV (2002) and MERS-CoV (2012). Given the recent emergence of COVID-19, comprehensive immunological data are still limited. The susceptibility and severity of SARS-CoV-2 infection are influenced by various host factors, including hormonal changes, genetic variations, inflammatory biomarkers, and behavioral attitudes. Identifying genetic factors contributing to infection severity may accelerate therapeutic development, including drug repurposing, natural extracts, and post-vaccine interventions (Initiative and Covid, 2021). This review discusses the human protein machinery involved in (a) SARS-CoV-2 host receptors, (b) the human immune response, and (c) the impact of demographic and genetic differences on individual risk for COVID-19. This review aims to clarify host factors implicated in SARS-CoV-2 susceptibility and progression, highlighting potential therapeutic targets and supportive treatment strategies.

Genomic surveillance and vaccine response to the dominant SARS-CoV-2 XBB lineage in Rio Grande do Sul

The COVID-19 pandemic has been marked by novel viral variants, posing challenges to global public health. Recombination, a viral evolution mechanism, is implicated in SARS-CoV-2's ongoing evolution. The XBB recombinant lineage, known for evading antibody-mediated immunity, exhibits higher transmissibility without increased disease severity. We investigated the prevalence and genomic features of XBB in SARS-CoV-2-positive cases in Rio Grande do Sul (RS), Brazil. We sequenced 357 samples from epidemiological weeks (EW) 47/2022 to 17/2023, and included 389 publicly available sequences. Clinical and epidemiological data were obtained from DATASUS, e-SUS, and SIVEP GRIPE (data recording systems of the Brazilian Ministry of Health). Of these, 143 were classified as XBB and 586 were other Omicron lineages. In March 2023 (EW 10), XBB became dominant, accounting for 83.3% of cases. 97.7% of XBB-infected patients successfully recovered from the infection, with a low mortality rate (2.3%). Even after receiving three vaccine doses and having been previously infected, 59.5% of the patients experienced reinfection with XBB. However, for 54% of the individuals, the interval between their XBB infection and the last vaccine dose exceeded one year, potentially leading to a decline in antibody levels. In addition, we identified 90 mutations in RS circulating XBB, spread throughout the genome, notably in the Spike protein region associated with immune resistance. This study provides insights into the dynamics and impact of a recombinant variant becoming predominant for the first time in the state. Continued surveillance of SARS-CoV-2 genomic evolution is crucial for effective public health management.

In Silico Analysis of a Candidate Multi-epitope Peptide Vaccine Against Human Brucellosis

Brucellosis is one of the neglected endemic zoonoses in the world. Vaccination appears to be a promising health strategy to prevent it. This study used advanced computational techniques to develop a potent multi-epitope vaccine for human brucellosis. Seven epitopes from four main brucella species that infect humans were selected. They had significant potential to induce cellular and humoral responses. They showed high antigenic ability without the allergenic characteristic. In order to improve its immunogenicity, suitable adjuvants were also added to the structure of the vaccine. The physicochemical and immunological properties of the vaccine were evaluated. Then its two and three-dimensional structure was predicted. The vaccine was docked with toll-like receptor4 to assess its ability to stimulate innate immune responses. For successful expression of the vaccine protein in Escherichia coli, in silico cloning, codon optimization, and mRNA stability were evaluated. The immune simulation was performed to reveal the immune response profile of the vaccine after injection. The designed vaccine showed the high ability to induce immune response, especially cellular responses to human brucellosis. It showed the appropriate physicochemical properties, a high-quality structure, and a high potential for expression in a prokaryotic system.

Bioinformatics analysis of multi-epitope peptide vaccines against Hepatitis C virus: a molecular docking study

BACKGROUND

Hepatitis C Virus (HCV) infection is one of the causal agents of liver disease burden. Six multiple antigenic peptides were synthesized including (P315, P412, and P517) plus (P1771, P2121, and P2941) to induce humoral and cellular responses, respectively against HCV infection.

AIM

This paper aimed to employ computational tools to evaluate the efficacy of each peptide individually and to determine the most effective one for better vaccine development and/or immunotherapy.

METHODS

VaxiJen web and AllerTOP servers were used for antigenicity and allergenicity prediction, respectively. The ToxinPred web server was used to investigate the peptide toxicity. Each peptide was docked with its corresponding receptors.

RESULTS

No peptides were expected to be toxic. P315 and P2941 are predicted to have robust antigenic properties, lowest allergenicity, and minimal sOPEP energies. In turn, P315 (derived from gpE1) formed the highest hydrophobic bonds with the BCR and CD81 receptors that will elicit B cell function. P2941 (derived from NS5B) was shown to strongly bind to both CD4 and CD8 receptors that will elicit T cell function.

CONCLUSION

P315 successfully bound to B cell (BCR and CD81) receptors. Also, P2941 is strongly bound to T cell (CD4 and CD8) receptors.

Identifying featured indels associated with SARS-CoV-2 fitness

As an RNA virus, severe acute respiratory coronavirus 2 (SARS-CoV-2) is known for frequent substitution mutations, and substitutions in important genome regions are often associated with viral fitness. However, whether indel mutations are related to viral fitness is generally ignored. Here we developed a computational methodology to investigate indels linked to fitness occurring in over 9 million SARS-CoV-2 genomes. Remarkably, by analyzing 31,642,404 deletion records and 1,981,308 insertion records, our pipeline identified 26,765 deletion types and 21,054 insertion types and discovered 65 indel types with a significant association with Pango lineages. We proposed the concept of featured indels representing the population of specific Pango lineages and variants as substitution mutations and termed these 65 indels as featured indels. The selective pressure of all indel types is assessed using the Bayesian model to explore the importance of indels. Our results exhibited higher selective pressure of indels like substitution mutations, which are important for assessing viral fitness and consistent with previous studies in vitro. Evaluation of the growth rate of each viral lineage indicated that indels play key roles in SARS-CoV-2 evolution and deserve more attention as substitution mutations. IMPORTANCE The fitness of indels in pathogen genome evolution has rarely been studied. We developed a computational methodology to investigate the severe acute respiratory coronavirus 2 genomes and analyze over 33 million records of indels systematically, ultimately proposing the concept of featured indels that can represent specific Pango lineages and identifying 65 featured indels. Machine learning model based on Bayesian inference and viral lineage growth rate evaluation suggests that these featured indels exhibit selection pressure comparable to replacement mutations. In conclusion, indels are not negligible for evaluating viral fitness.

Genomic landscape of alpha-variant of SARS-CoV-2 circulated in Pakistan

In this study, we investigated the genomic variability of alpha-VOC of SARS-CoV-2 in Pakistan, in context of the global population of this variant. A set of 461 whole-genome sequences of Pakistani samples of alpha-variant, retrieved from GISAID, were aligned in MAFFT and used as an input to the Coronapp web-application. Phylogenetic tree was constructed through maximum-likelihood method by downloading the 100 whole-genome sequences of alpha-variant for each of the 12 countries having the largest number of Pakistani diasporas. We detected 1725 mutations, which were further categorized into 899 missense mutations, 654 silent mutations, 52 mutations in non-coding regions, 25 in-frame deletions, 01 in-frame insertion, 51 frameshift deletions, 21 frameshift insertions, 21 stop-gained variants, and 1 stop-gained deletion. We found NSP3 and Spike as the most variable proteins with 355 and 233 mutations respectively. However, some characteristic mutations like Δ144(S), G204R(N), and T1001I, I2230T, del3675-3677(ORF1ab) were missing in the Pakistani population of alpha-variant. Likewise, R1518K(NSP3), P83L(NSP9), and A52V, H164Y(NSP13) were found for the first time in this study. Interestingly, Y145 deletion(S) had 99% prevalence in Pakistan but globally it was just 4.2% prevalent. Likewise, R68S substitution (ORF3a), F120 frameshift deletion, L120 insertion, L118V substitution (ORF8), and N280Y(NSP2) had 20.4%, 14.3%, 14.8%, 9.1%, 13.9% prevalence locally but globally they were just 0.1%, 0.2%, 0.04%, 1.5%, and 2.4% prevalent respectively. The phylogeny analysis revealed that majority of Pakistani samples were grouped together in the same clusters with Italian, and Spanish samples suggesting the transmission of alpha-variant to Pakistan from these western European countries.

Binding and neutralizing abilities of antibodies towards SARS-CoV-2 S2 domain

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants have been reported to be resistant to several neutralizing antibodies (NAbs) targeting Receptor Binding Domain (RBD) and N Terminal Domain (NTD) of spike (S) protein and thus inducing immune escape. However, fewer studies were carried out to investigate the neutralizing ability of S2-specific antibodies. In this research, 10 monoclonal antibodies (mAbs) targeting SARS-CoV-2 S2 subunit were generated from Coronavirus Disease 2019 (COVID-19) convalescent patients by phage display technology and molecular cloning technology. The binding activity of these S2-mAbs toward SARS-CoV-2 S, SARS-CoV-2 S2, SARS-CoV-2 RBD, SARS-CoV-2 NTD, severe acute respiratory syndrome coronavirus (SARS-CoV) S, SARS-CoV S2 and Middle East Respiratory Syndrome Coronavirus (MERS-CoV) S proteins were evaluated by enzyme-linked immunosorbent assay (ELISA). Their neutralizing potency toward SARS-CoV-2 wild-type (WT), B.1.1.7, B.1.351, P.1, B.1.617.2, B.1.1.1 and B.1.621 variants were determined by pseudo-virus-based neutralization assay. Results showed that S2E7-mAb had cross-activity to S or S2 proteins of SARS-CoV-2, SARS-CoV and MERS-CoV, while with limited neutralizing activity to pseudo-viruses of SARS-CoV-2 WT and variants. It is undeniable that the binding and neutralizing activities of the S2-targeting mAbs are significantly weaker than the previously reported antibodies targeting RBD and NTD, but our study may provide some evidences for understanding immune protection and identifying targets for vaccine design based on the conserved S2 subunit.

Identification of three conserved linear B cell epitopes on the SARS-CoV-2 spike protein

Spike (S) glycoproteins is the most significant structural protein of SARS-CoV-2 and a key target for neutralizing antibodies. In light of the ongoing SARS-CoV-2 pandemic, identification and screening of epitopes of spike glycoproteins will provide vital progress in the development of sensitive and specific diagnostic tools. In the present study, NTD, RBD and S2 gene were inserted to the pcDNA3.1(+) vector and designed with N-terminal 6×His-tag for fusion expression in HEK293F cells by transient transfection. Six monoclonal antibodies (4G, 9E, 4B, 7D, 8F, 3D) were prepared using the expressed proteins by cell fusion technique. The characterization of mAbs were performed by indirect -ELISA, western blot and IFA. We designed 49 overlapping synthetized peptides cover the extracellular region of S protein which 6 amino acid residues were offset between adjacent (S1-S49). Peptides S12, S19 and S49 were identified as the immunodominant epitopes regions by the mAbs. These regions were further truncated and the peptides S12.2 ²⁸⁶TDAVDCALDPLS²⁹⁷, S19.2 ⁴⁶⁴FERDISTEIYQA⁴⁷⁵ and S49.4 ¹²⁰²ELGKYEQYIKWP¹²¹³ were identified as B- cell linear epitopes for the first time. Alanine scans showed that, the ^D467, ^I468, ^E471, ^Q474, ^A475 of the epitope S19.2 and ^K1205, ^Q1208, ^Y1209 of the epitope S49.4 were the core sites involved in the mAbs binding. Multiple sequence alignment analysis showed that these three epitopes were highly conserved among the variants of concern (VOCs) and variants of interest (VOIs). Taken together, the findings provide a potential material for rapid diagnosis methods of COVID-19.

Conserved Pattern and Potential Role of Recurrent Deletions in SARS-CoV-2 Evolution

SARS-CoV-2 continues adapting to human hosts during the current worldwide pandemic since 2019. This virus evolves through multiple means, such as single nucleotide mutations and structural variations, which has brought great difficulty to disease prevention and control of COVID-19. Structural variation, including multiple nucleotide changes like insertions and deletions, has a greater impact relative to single nucleotide mutation on both genome structures and protein functions. In this study, we found that deletion occurred frequently in not only SARS-CoV-2 but also in other SARS-related coronaviruses. These deletions showed obvious location bias and formed 45 recurrent deletion regions in the viral genome. Some of these deletions showed proliferation advantages, including four high-frequency deletions (nsp6 Δ106-109, S Δ69-70, S Δ144, and Δ28271) that were detected in around 50% of SARS-CoV-2 genomes and other 19 median-frequency deletions. In addition, the association between deletions and the WHO reported variants of concern (VOC) and variants of interest (VOI) of SARS-CoV-2 indicated that these variants had a unique combination of deletion patterns. In the spike (S) protein, the deletions in SARS-CoV-2 were mainly in the N-terminal domain. Some deletions, such as S Δ144/145 and S Δ243-244, have been confirmed to block the binding sites of neutralizing antibodies. Overall, this study revealed a conservative regional pattern and the potential effect of some deletions in SARS-CoV-2 over the whole genome, providing important evidence for potential epidemic control and vaccine development. IMPORTANCE Mutations in SARS-CoV-2 were studied extensively, while only the structure variations on the spike protein were discussed well in previous studies. To study the role of structural variations in virus evolution, we described the distribution of structure variations on the whole genome. Conserved patterns were found of deletions among SARS-CoV-2, SARS-CoV-2-like, and SARS-CoV-like viruses. There were 45 recurrent deletion regions (RDRs) in SARS-CoV-2 generated through the integration of deleted positions. In these regions, four high-frequency deletions parallelly appeared in multiple strains. Furthermore, in the spike protein, the deletions in SARS-CoV-2 were mainly in the N-terminal domain, blocking the binding sites of some neutralizing antibodies, while the structural variations in SARS-related coronavirus were mainly in the N-terminal domain and receptor binding domain. The receptor binding domain is highly related to hosting recognition. The deletions in the receptor binding domain may play a role in host adaption.

Novel T cell interferon gamma release assay (IGRA) using spike recombinant protein for COVID19 vaccine response and Nucleocapsid for SARS-Cov2 response

We explored the performance of a whole blood interferon gamma release assay (IGRA) based on the stimulation of SARS-Cov2-specific T cells by purified recombinant proteins. Twenty volunteers vaccinated with BNT162b2 were selected first for T cell response evaluation using an in-house IGRA, a commercial IGRA, and ELISpot showing a S2 > S1 poly-epitopic response. Next, 64 vaccinated and 103 non-vaccinated individuals were tested for humoral and T cell response (IGRA-Spike/-nucleocapsid recombinant proteins). Following the second vaccine injection, humoral (100%) and IGRA-Spike T cell (95.3%) responses took place irrespective of sex, age, and vaccine type. The humoral response declined first, followed by IGRA-Spike T cell response after the second vaccine injection. Altogether, this study confirms the utility of the IGRA-Spike/-nucleocapsid assay to complement serology in COVID19 vaccinated individuals and those who have recovered from SARS-Cov2.

The Impact of COVID-19 on Liver Injury

The current coronavirus disease outbreak of 2019 (COVID-19) has led to a global pandemic. The principal cause of mortality in COVID-19 is represented lung injury with the development of acute respiratory distress syndrome (ARDS). In patients with COVID-19 infection, liver injury or liver dysfunction has been reported. It may be associated with the general severity of the disease and serve as a prognostic factor for ARDS development. In COVID-19, the spectrum of liver damage may range from direct SARS-CoV-2 viral proteins, inflammatory processes, hypoxemia, the antiviral drugs induced hepatic injury and the presence of the preexisting liver disease. We highlight in this review important topics such as the epidemiological features, potential causes of liver injury, and the strategies for management and prevention of hepatic injury in COVID-19 patients.

Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia

Background

The SARS-CoV-2 pandemic stimulated an outstanding global sequencing effort, which allowed to monitor viral circulation and evolution. Nuoro province (Sardinia, Italy), characterized by a relatively isolated geographical location and a low population density, was severely hit and displayed a high incidence of infection.

Methods

Amplicon approach Next Generation Sequencing and subsequent variant calling in 92 respiratory samples from SARS-CoV-2 infected patients involved in infection clusters from March 2020 to May 2021.

Results

Phylogenetic analysis displayed a coherent distribution of sequences in terms of lineage and temporal evolution of pandemic. Circulating lineage/clade characterization highlighted a growing diversity over time, with an increasingly growing number of mutations and variability of spike and nucleocapsid proteins, while viral RdRp appeared to be more conserved. A total of 384 different mutations were detected, of which 196 were missense and 147 synonymous ones. Mapping mutations along the viral genome showed an irregular distribution in key genes. S gene was the most mutated gene with missense and synonymous variants frequencies of 58.8 and 23.5%, respectively. Mutation rates were similar for the S and N genes with one mutation every ∼788 nucleotides and every ∼712 nucleotides, respectively. Nsp12 gene appeared to be more conserved, with one mutation every ∼1,270 nucleotides. The frequency of variant Y144F in the spike protein deviated from global values with higher prevalence of this mutation in the island.

Conclusion

The analysis of the 92 viral genome highlighted evolution over time and identified which mutations are more widespread than others. The high number of sequences also permits the identification of subclusters that are characterized by subtle differences, not only in terms of lineage, which may be used to reconstruct transmission clusters. The disclosure of viral genetic diversity and timely identification of new variants is a useful tool to guide public health intervention measures.

Recent progress on the mutations of SARS-CoV-2 spike protein and suggestions for prevention and controlling of the pandemic

Severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) infection has caused a global pandemic in the past year, which poses continuing threat to human beings. To date, more than 3561 mutations in the viral spike protein were identified, including 2434 mutations that cause amino acid changes with 343 amino acids located in the viral receptor-binding domain (RBD). Among these mutations, the most representative ones are substitution mutations such as D614G, N501Y, Y453F, N439K/R, P681H, K417N/T, and E484K, and deletion mutations of ΔH69/V70 and Δ242-244, which confer the virus with enhanced infectivity, transmissibility, and resistance to neutralization. In this review, we discussed the recent findings of SARS-CoV-2 for highlighting mutations and variants on virus transmissibility and pathogenicity. Moreover, several suggestions for prevention and controlling the pandemic are also proposed.

An Updated Review of SARS-CoV-2 Vaccines and the Importance of Effective Vaccination Programs in Pandemic Times

Since the worldwide COVID-19 pandemic was declared a year ago, the search for vaccines has become the top priority in order to restore normalcy after 2.5 million deaths worldwide, overloaded sanitary systems, and a huge economic burden. Vaccine development has represented a step towards the desired herd immunity in a short period of time, owing to a high level of investment, the focus of researchers, and the urge for the authorization of the faster administration of vaccines. Nevertheless, this objective may only be achieved by pursuing effective strategies and policies in various countries worldwide. In the present review, some aspects involved in accomplishing a successful vaccination program are addressed, in addition to the importance of vaccination in a pandemic in the face of unwillingness, conspiracy theories, or a lack of information among the public. Moreover, we provide some updated points related to the landscape of the clinical development of vaccine candidates, specifically, the top five vaccines that are already being assessed in Phase IV clinical trials (BNT162b2, mRNA-1273, AZD1222, Ad26.COV2.S, and CoronaVac).