SARS-CoV-2 Variant and Vaccines Development

A special issue of Vaccines (ISSN 2076-393X). This special issue belongs to the section "COVID-19 Vaccines and Vaccination".

Deadline for manuscript submissions: closed (31 December 2022) | Viewed by 10493

Special Issue Editors


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Guest Editor
Division of Pathology, ICAR-Indian Veterinary Research Institute, Bareilly 243122, India
Interests: microbiology; immunology; virology; diagnosis, vaccines; immunomodulation; infectious diseases; pathogens; public health; zoonosis; biomedicine

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Guest Editor
Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, West Bengal 700126, India
Interests: microbiology; immunology; virology; biotechnology; public health

Special Issue Information

Dear Colleagues,

Several variants of SARS-CoV-2 have emerged and newer variants and mutants / strains are continuously emerging owing to this rapidly evolving virus and gaining higher mutations facilitating waves of surging COVID-19 cases amid the ongoing COVID-19 pandemic. Various variants of concerns (VOCs) and variants of interests (VOIs) have emerged, and among these Alpha, Beta, Gamma, Delta and Omicron (VOCs) are of major concerns with regards to adverse public health implications. Delta and Omicron variants possess high transmissibility and can overpower vaccine induced immunity and antibodies-based therapeutics resulting into breakthrough infections in vaccinated people and recovered patients as well reinfection cases are on rise. More recently, different lineages of Omicoron (BA.1/BA.1.1, BA.2 or BA.3) have been recognized as well as recombinant variants of SARS-CoV-2 with Omicron and Delta combinations have been reported (XD, XE, XF), which reflects the continuous evolution of the pandemic virus and its variants. Several repurposed and antiviral drugs have been used for emergency purposes, however any optimal drug of choice to treat COVID-19 patients is still awaited. Booster doses of vaccines are being recommended to increase the protective immunity levels in vaccinated individuals for safeguarding from emerging variants, especially VOCs.  

For tackling COVID-19 pandemic, researchers across the globe made very high efforts which lead to development of vaccines within one year, and different vaccines were subsequently rolled out across several countries with the availability of Moderna, Pfizer/BioNTech, AstraZeneca and other vaccines, utilizing different vaccine platforms. However, recent reports have show that variants such as Delta and Omicron show immune evasion and antibody escape mechanisms for mostly all the kinds of vaccines, resulting in rise in COVID-19 cases and breakthrough infections. Besides, probable risks are always there for emergence of any newer variants that might gain both higher transmission ability and more lethality. Such adverse scenario of lesser protection being rendered by existing COVID-19 vaccines have forced researchers and health agencies to rethink for updating and modifying the current vaccines as well as design newer vaccines to combat SARS-CoV-2 and emerging variants. 

Development of advanced vaccines that could provide a broad range of protection against all the emerging variants or the upcoming variants of SARS-CoV-2 is the need of the present times to put a halt on the pandemic. Advances in developing newer vaccines / new generation vaccines need to focus on designing variant-specific vaccines, multivariant (multiple antigen-based) vaccines, mutation-proof vaccines, pancoronavirus and universal vaccines, and multitopevaccines that would be highly efficacious to tackle multiple emerging SARS-CoV-2 variants and variants of future by counteracting the immune escape properties and render adequate protection against COVID-19. Exploring various advanced techniques and platforms, the development of CRISPR-based vaccines, artificial intelligence-based vaccines, immunoinformatics- and immunomics-based vaccines, nanotechnolology based vaccines / nanovaccines, nucleic acid-based and protein subunit-based vaccines, and cytotoxic T-cell-based vaccine should be given due emphasis. Several COVID-19 intranasal vaccines are also being developed, which could elicit both systematic immunity and strong mucosal immunity that aid in inhibiting the virus at mucosal levels (nasal cavity, lungs), prevent viral replication, reduce virus shedding, thus preventing its further transmission and spread. 

To achieve a more extensive understanding of recent scientific knowledge, current trends and advances being made in vaccine development against SARS-CoV-2 and its emerging variants, this Special issue is focused on the recent scientific and technical progresses made in this field along with future prospects. Based on your extensive knowledge and experience, we invite you to contribute with an original report, original observation or review, on recent advances and futuristic vision in developing better vaccines to tackle SARS-CoV-2 and emerging variants.

Dr. Kuldeep Dhama
Dr. Chiranjib Chakraborty
Guest Editors

Manuscript Submission Information

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Published Papers (4 papers)

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Research

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30 pages, 2248 KiB  
Article
A Synthetic Biology Approach for Vaccine Candidate Design against Delta Strain of SARS-CoV-2 Revealed Disruption of Favored Codon Pair as a Better Strategy over Using Rare Codons
by Pankaj Gurjar, Noushad Karuvantevida, Igor Vladimirovich Rzhepakovsky, Azmat Ali Khan and Rekha Khandia
Vaccines 2023, 11(2), 487; https://doi.org/10.3390/vaccines11020487 - 20 Feb 2023
Cited by 5 | Viewed by 1965
Abstract
The SARS-CoV-2 delta variant (B.1.617.2) appeared for the first time in December 2020 and later spread worldwide. Currently available vaccines are not so efficacious in curbing the viral pathogenesis of the delta strain of COVID; therefore, the development of a safe and effective [...] Read more.
The SARS-CoV-2 delta variant (B.1.617.2) appeared for the first time in December 2020 and later spread worldwide. Currently available vaccines are not so efficacious in curbing the viral pathogenesis of the delta strain of COVID; therefore, the development of a safe and effective vaccine is required. In the present study, we envisaged molecular patterns in the structural genes’ spike, nucleoprotein, membrane, and envelope of the SARS-CoV-2 delta variant. The study was based on determining compositional features, dinucleotide odds ratio, synonymous codon usage, positive and negative codon contexts, rare codons, and insight into relatedness between the human host isoacceptor tRNA and preferred codons from the structural genes. We found specific patterns, including a significant abundance of T nucleotide over all other three nucleotides. The underrepresentation of GpA, GpG, CpC, and CpG dinucleotides and the overrepresentation of TpT, ApA, CpT, and TpG were observed. A preference towards ACT- (Thr), AAT- (Asn), TTT- (Phe), and TTG- (Leu) initiated codons and aversion towards CGG (Arg), CCG (Pro), and CAC (His) was present in the structural genes of the delta strain. The interaction between the host tRNA pool and preferred codons of the envisaged structural genes revealed that the virus preferred the codons for those suboptimal numbers of isoacceptor tRNA were present. We see this as a strategy adapted by the virus to keep the translation rate low to facilitate the correct folding of viral proteins. The information generated in the study helps design the attenuated vaccine candidate against the SARS-CoV-2 delta variant using a synthetic biology approach. Three strategies were tested: changing TpT to TpA, introducing rare codons, and disrupting favored codons. It found that disrupting favored codons is a better approach to reducing virus fitness and attenuating SARS-CoV-2 delta strain using structural genes. Full article
(This article belongs to the Special Issue SARS-CoV-2 Variant and Vaccines Development)
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36 pages, 38597 KiB  
Article
Integrative Bioinformatics Approaches Indicate a Particular Pattern of Some SARS-CoV-2 and Non-SARS-CoV-2 Proteins
by Chiranjib Chakraborty, Manojit Bhattacharya, Srijan Chatterjee, Ashish Ranjan Sharma, Rudra P. Saha, Kuldeep Dhama and Govindasamy Agoramoorthy
Vaccines 2023, 11(1), 38; https://doi.org/10.3390/vaccines11010038 - 23 Dec 2022
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Abstract
Pattern recognition plays a critical role in integrative bioinformatics to determine the structural patterns of proteins of viruses such as SARS-CoV-2. This study identifies the pattern of SARS-CoV-2 proteins to depict the structure–function relationships of the protein alphabets of SARS-CoV-2 and COVID-19. The [...] Read more.
Pattern recognition plays a critical role in integrative bioinformatics to determine the structural patterns of proteins of viruses such as SARS-CoV-2. This study identifies the pattern of SARS-CoV-2 proteins to depict the structure–function relationships of the protein alphabets of SARS-CoV-2 and COVID-19. The assembly enumeration algorithm, Anisotropic Network Model, Gaussian Network Model, Markovian Stochastic Model, and image comparison protein-like alphabets were used. The distance score was the lowest with 22 for “I” and highest with 40 for “9”. For post-processing and decision, two protein alphabets “C” (PDB ID: 6XC3) and “S” (PDB ID: 7OYG) were evaluated to understand the structural, functional, and evolutionary relationships, and we found uniqueness in the functionality of proteins. Here, models were constructed using “SARS-CoV-2 proteins” (12 numbers) and “non-SARS-CoV-2 proteins” (14 numbers) to create two words, “SARS-CoV-2” and “COVID-19”. Similarly, we developed two slogans: “Vaccinate the world against COVID-19” and “Say no to SARS-CoV-2”, which were made with the proteins structure. It might generate vaccine-related interest to broad reader categories. Finally, the evolutionary process appears to enhance the protein structure smoothly to provide suitable functionality shaped by natural selection. Full article
(This article belongs to the Special Issue SARS-CoV-2 Variant and Vaccines Development)
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10 pages, 246 KiB  
Article
Short-Term Adverse Effects Immediately after the Start of COVID-19 Booster Vaccination in Vietnam
by Duy Cuong Nguyen, Thi Loi Dao, Thi Minh Dieu Truong, Thu Huong Nguyen, Thu Nga Phan, Ha My Nguyen, Thi Dung Pham, Xuan Bai Nguyen, Thanh Binh Nguyen and Van Thuan Hoang
Vaccines 2022, 10(8), 1325; https://doi.org/10.3390/vaccines10081325 - 16 Aug 2022
Cited by 11 | Viewed by 1900
Abstract
Background: Risk communication is necessary to improve the booster vaccination rate, but Vietnam does not have a system to collect and disclose such information. Therefore, the purpose of this study was to clarify adverse reactions and their frequency in the early period after [...] Read more.
Background: Risk communication is necessary to improve the booster vaccination rate, but Vietnam does not have a system to collect and disclose such information. Therefore, the purpose of this study was to clarify adverse reactions and their frequency in the early period after booster vaccination, and to obtain primary data for improving the booster vaccination rate. Methods: A cross-sectional survey was conducted among adults aged ≥18 years. Clinical data were collected 14 days after booster vaccination by using a standard questionnaire. Results: A total of 1322 participants were included with median age = 23 and sex ratio (Male/Female) = 0.53. AstraZeneca was the most commonly used vaccine for the first and second doses, while Pfizer was the most commonly used vaccine for booster shots. Injection site pain, fatigue, and myalgia were the most common side effect reported (71.9%, 28.1%, and 21.8%, respectively). Compared to previous COVID-19 vaccine injections, 81.9% of participants reported that their symptoms were similar or milder after receiving the booster dose. They were more likely to present injection site pain (OR = 1.43, p < 0.0001) and lymphadenopathy (OR = 4.76, p < 0.0001) after receiving the booster shot. Fever (OR = 0.33, p < 0.0001) and fatigue (OR = 0.77, p = 0.002) were less often reported after booster shots compared to the first and second injections. The severity of symptoms occurring after booster dose versus first and second doses increased significantly with each additional year of age and among participants receiving the Pfizer and Moderna vaccines. Conclusion: Adverse reactions to booster vaccination are minor and their incidence is the same as for the first or the second vaccination. Multicenter studies with larger sample sizes on the side effects and safety of COVID-19 vaccine booster shots need to be conducted to make the population less worried, in order to increase the vaccination rate, to protect individuals’ and communities’ health. Full article
(This article belongs to the Special Issue SARS-CoV-2 Variant and Vaccines Development)

Review

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19 pages, 2348 KiB  
Review
SARS-CoV-2 Vaccines, Vaccine Development Technologies, and Significant Efforts in Vaccine Development during the Pandemic: The Lessons Learned Might Help to Fight against the Next Pandemic
by Chiranjib Chakraborty, Manojit Bhattacharya and Kuldeep Dhama
Vaccines 2023, 11(3), 682; https://doi.org/10.3390/vaccines11030682 - 17 Mar 2023
Cited by 12 | Viewed by 4113
Abstract
We are currently approaching three years since the beginning of the coronavirus disease 2019 (COVID-19) pandemic. SARS-CoV-2 has caused extensive disruptions in everyday life, public health, and the global economy. Thus far, the vaccine has worked better than expected against the virus. During [...] Read more.
We are currently approaching three years since the beginning of the coronavirus disease 2019 (COVID-19) pandemic. SARS-CoV-2 has caused extensive disruptions in everyday life, public health, and the global economy. Thus far, the vaccine has worked better than expected against the virus. During the pandemic, we experienced several things, such as the virus and its pathogenesis, clinical manifestations, and treatments; emerging variants; different vaccines; and the vaccine development processes. This review describes how each vaccine has been developed and approved with the help of modern technology. We also discuss critical milestones during the vaccine development process. Several lessons were learned from different countries during the two years of vaccine research, development, clinical trials, and vaccination. The lessons learned during the vaccine development process will help to fight the next pandemic. Full article
(This article belongs to the Special Issue SARS-CoV-2 Variant and Vaccines Development)
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