This article is devoted to applying bioinformatics and immunoinformatics approaches for the development of a multi-epitope mRNA vaccine against the spike glycoproteins of circulating SARS-CoV-2 variants in selected African countries. The study’s relevance is dictated by the fact that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) began its global threat at the end of 2019 and since then has had a devastating impact on the whole world. Measures to reduce threats from the pandemic include social restrictions, restrictions on international travel, and vaccine development. In most cases, vaccine development depends on the spike glycoprotein, which serves as a medium for its entry into host cells. Although several variants of SARS-CoV-2 have emerged from mutations crossing continental boundaries, about 6000 delta variants have been reported along the coast of more than 20 countries in Africa, with South Africa accounting for the highest percentage. This also applies to the omicron variant of the SARS-CoV-2 virus in South Africa. The authors suggest that bioinformatics and immunoinformatics approaches be used to develop a multi-epitope mRNA vaccine against the spike glycoproteins of circulating SARS-CoV-2 variants in selected African countries. Various immunoinformatics tools have been used to predict T- and B-lymphocyte epitopes. The epitopes were further subjected to multiple evaluations to select epitopes that could elicit a sustained immunological response. The candidate vaccine consisted of seven epitopes, a highly immunogenic adjuvant, an MHC I-targeting domain (MITD), a signal peptide, and linkers. The molecular weight (MW) was predicted to be 223.1 kDa, well above the acceptable threshold of 110 kDa on an excellent vaccine candidate. In addition, the results showed that the candidate vaccine was antigenic, non-allergenic, non-toxic, thermostable, and hydrophilic. The vaccine candidate has good population coverage, with the highest range in East Africa (80.44%) followed by South Africa (77.23%). West Africa and North Africa have 76.65% and 76.13%, respectively, while Central Africa (75.64%) has minimal coverage. Among seven epitopes, no mutations were observed in 100 randomly selected SARS-CoV-2 spike glycoproteins in the study area. Evaluation of the secondary structure of the vaccine constructs revealed a stabilized structure showing 36.44% alpha-helices, 20.45% drawn filaments, and 33.38% random helices. Molecular docking of the TLR4 vaccine showed that the simulated vaccine has a high binding affinity for TLR-4, reflecting its ability to stimulate the innate and adaptive immune response.

At this present stage of COVID-19 re-emergence, designing an effective candidate vaccine for different variants of SARS-CoV-2 is a study worthy of consideration. This research used bioinformatics tools to design an mRNA vaccine that captures all the circulating variants and lineages of the virus in its construct. Sequences of these viruses were retrieved across the six continents and analyzed using different tools to screen for the preferable CD8⁺ T lymphocytes (CTL), CD4⁺ T lymphocytes (HTL), and B-cell epitopes. These epitopes were used to design the vaccine. In addition, several other co-translational residues were added to the construct of an mRNA vaccine whose molecular weight is 285.29686 kDa with an estimated pI of 9.2 and has no cross affinity with the human genome with an estimated over 68% to cover the world population. It is relatively stable, with minimal deformability in its interaction with the human innate immune receptor, which includes TLR 3 and TLR 9. The overall result has proven that the designed candidate vaccine is capable of modulating cell-mediated immune responses by activating the actions of CD4⁺ T cells, natural killer cells, and macrophages, and displayed an increased memory T cell and B cell activities, which may further be validated via in vivo and in vitro techniques.

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Background: Acinetobacter baumannii, a nosocomial pathogen, has emerged as a major clinical threat due to its ability to resist a broad range of antibiotics, contributing to the increased morbidity and mortality in hospital settings. This characteristic of Acinetobacter baumannii as a multiple-drug resistant (MDR) organism poses a critical global health challenge, necessitating an urgent need for alternative therapeutic strategies, such as vaccine development, as a preventive measure. In this study, we employ the method of reverse vaccinology and immunoinformatic tools to design a novel rRNA-based vaccine targeting the 16S and 23S rRNA of Acinetobacter baumannii. Results: 16S and 23S rRNA sequences of Acinetobacter baumannii were retrieved from the National Center for Biotechnology Information database (NCBI). The B and T cells’ epitopes were predicted from these retrieved sequences using bioinformatics tools. The epitopes generated were further analyzed for antigenicity, toxicity, and allergenicity. The epitopes that passed these screenings, including key structural elements, were used in the design of the vaccine. The vaccine constructs were further assessed for their physicochemical properties and dynamics. Structural modeling and molecular docking studies confirmed effective binding to Toll-like receptor 4 (TLR-4), while immune simulations demonstrated the potential to elicit robust and durable immune responses. Conclusions: This study demonstrates the potential of reverse vaccinology and immunoinformatics approaches in designing a novel rRNA-based vaccine targeting the 16S and 23S rRNA of Acinetobacter baumannii. By identifying highly antigenic, non-toxic, and non-allergenic epitopes and incorporating them into a structurally optimized rRNA-based vaccine construct, we present a promising candidate capable of eliciting strong immune responses. However, limitations such as the unavailability of datasets, especially on the 5S rRNA region in the databases, are a roadblock that needs to be addressed.

The coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread globally. Understanding the transmission dynamics of SARS-CoV-2 contamination in the environment is essential for infection control policies. This study aims to provide a phylodynamic analysis and distribution pattern of SARS-CoV-2 from the environment in terms of Source, clades, lineages, and their location. Ninety (90) retrieved whole-genome sequences of environmental sources from GISAID were investigated to determine the evolutionary process of SARS-CoV-2 and mutation in the isolated nucleotide sequences. The analysis was carried out using R, MAFFT, and MEGA X software. Out of the five countries studied, Austria has the highest distribution with sixty-five samples (72.2%), and the highest isolates of 68 (75.6%) were from raw sewage. The highest clade in circulation as obtained from the study is G with lineages B. The phylogeny of SARS-CoV-2 whole-genome sequences from Austria, the United States, China, Brazil, and Liechtenstein indicated that the SARS-CoV-2 viruses were all clustered together, irrespective of sequence geographic location. The study concluded by demonstrating a clear interconnection between the phylogeny of SARS-CoV-2 isolates from various geographic locations, all of which were locked in the same cluster regardless of their environment specimen. Thus, depicting the possibility of their origination from a common ancestor. Highlight Environmental sources of specimen isolated from raw sewage have the highest occurring specimen sequence, while those from breathing air, door handle, and wastewater have the lowest sequence. Environmental surveillance of SARS-CoV-2 is of great importance to control the spread of the virus. Untreated raw sewage should be of more priority for the environmental surveillance of the virus. Eighteen (18) nucleotide sequences from this study’s multiple sequence alignment shared a 90% similarity with the Wuhan-Hu-1 reference genome, indicating a common evolutionary origin.