The status of COVID-19 vaccines in India: A review.

The outbreak of SARS-CoV-2, an etiologic agent of the COVID-19 pandemic disease in late December 2019 has left the whole world aghast with huge health and economic losses. Due to a lack of specific knowledge and understanding at the initial stages, an unprecedented rise in COVID-19 cases has been recorded globally. Various preventive measures and strategies were implemented, however, for the radical control of SARS-CoV-2 infections; it seems that the only effective way to control the ongoing infections is large-scale vaccination. So far, WHO has approved 11 vaccines for emergency use namely Pfizer/BioNTech, Oxford/Astra Zeneca, Johnson and Johnson, Moderna, Covilo, Novavax, Covovax, Spikevax, Can Sino, Comirnaty, and Coronavac while five other needs approval. The worldwide vaccination dataset reveals that 65.7% of the world population has received their first dose of the COVID-19 vaccine. As a consequence of the proactive implementation of India's vaccination program, a historical milestone of administering over 1.9 billion doses of COVID-19 vaccines have been achieved on 19th May 2022. This review summarizes the different types of traditional and modern vaccine designing strategies with an emphasis on COVID-19. Moreover, the review highlights the status of vaccines for COVID-19 approved in India which includes both indigenous and non-indigenous vaccines. The present article also encompasses vaccine designing and developmental strategies, efficacy, safety profile and usage among the population, and the efficacy of modern vaccines over traditional ones.

El brote de SARS-CoV-2, un agente etiológico de la enfermedad pandémica COVID-19, a fines de diciembre de 2019, ha dejado al mundo entero horrorizado con enormes pérdidas económicas y de salud. Debido a la falta de conocimiento y comprensión específicos en las etapas iniciales, se ha registrado un aumento sin precedentes en los casos de COVID-19 a nivel mundial. Sin embargo, se implementaron diversas medidas y estrategias preventivas para el control radical de las infecciones por SARS-CoV-2; parece que la única forma eficaz de controlar las infecciones en curso es la vacunación a gran escala. Hasta el momento, la OMS ha aprobado 11 vacunas para uso de urgencia Pfizer/BioNTech, Oxford/Astra Zeneca, Johnson and Johnson, Moderna, Covilo, Novavax, Covovax, Spikevax, Can Sino, Comirnaty y Coronavac, mientras que otras cinco necesitan aprobación. El conjunto de datos de vacunación mundial revela que el 65,7% de la población mundial ha recibido su primera dosis de la vacuna COVID-19. Como consecuencia de la implementación proactiva del programa de vacunación de la India, el 19 de mayo de 2022 se logró un hito histórico de administrar más de 1900 millones de dosis de vacunas contra el COVID-19. Esta revisión resume los diferentes tipos de estrategias de diseño de vacunas tradicionales y modernas con énfasis sobre COVID-19. Además, la revisión destaca el estado de las vacunas para COVID-19 aprobadas en India, que incluye vacunas tanto indígenas como no indígenas. El presente artículo también abarca estrategias de diseño y desarrollo de vacunas, eficacia, perfil de seguridad y uso entre la población, y la eficacia de las vacunas modernas sobre las tradicionales.

The status of COVID-19 vaccines in India: A Review. El estado de las vacunas COVID-19 en India: Una revisión

The outbreak of SARS-CoV-2, an etiologic agent of the COVID-19 pandemic disease in late December 2019 has left the whole world aghast with huge health and economic losses. Due to a lack of specific knowledge and understanding at the initial stages, an unprecedented rise in COVID-19 cases has been recorded globally. Various preventive measures and strategies were implemented, however, for the radical control of SARS-CoV-2 infections;it seems that the only effective way to control the ongoing infections is large-scale vaccination. So far, WHO has approved 11 vaccines for emergency use Pfizer/BioNTech, Oxford/Astra Zeneca, Johnson and Johnson, Moderna, Covilo, Novavax, Covovax, Spikevax, Can Sino, Comirnaty, and Coronavac while five other needs approval. The worldwide vaccination dataset reveals that 65.7% of the world population has received their first dose of the COVID-19 vaccine. As a consequence of the proactive implementation of India's vaccination program, a historical milestone of administering over 1.9 billion doses of COVID-19 vaccines have been achieved on 19th May 2022. This review summarizes the different types of traditional and modern vaccine designing strategies with an emphasis on COVID-19. Moreover, the review highlights the status of vaccines for COVID-19 approved in India which includes both indigenous and non-indigenous vaccines. The present article also encompasses vaccine designing and developmental strategies, efficacy, safety profile and usage among the population, and the efficacy of modern vaccines over traditional ones.

Genome sequence analysis of nsp15 from SARS-CoV-2

SARS-CoV-2 (Severe Acute Respiratory Syndrome), a causative agent of COVID-19 disease created a pandemic situation worldwide. Nsp15 is a uridine specific endoribonuclease encoded by the genome of SARS-CoV-2. It plays important role in processing viral RNA and, thus evades the host immune system. Therefore, it is of interest to identify mutants of nsp15 amongst Asian SARS-CoV-2 isolates, where a total of 1795 mutations, from 7793 sequences of Asia submitted till 31st January 2022, amongst which A231V, H234Y, K109N, K259R and S261A mutations were found frequent. Hence, we report data on the predicted secondary structure of wild type form followed by hydropathy plot, physiochemical properties, Ramachandran plot, B-cell epitopes prediction and protein modeling of wild type and mutant of nsp15 protein. Data shows that nsp15 of SARS-CoV-2 is a pontential candidate for the development of vaccine to control the infections of SARS-CoV-2.

Rejuvenating impact of COVID-19 lockdown on major environmental parameters: an Indian perspective

The recent coronavirus outbreak caused severe impact on the life of people. Despite of several health and economic losses, COVID-19 pandemic induced lockdown proved to be a boon for the environment. This review highlights the positive impact of COVID-19 induced lockdown on the environment;enumerating its effect on air quality indices, water quality indices, wildlife and noise pollution, therefore, focussing on the brighter side of the effects of lockdown. Notably, in India, rivers like Ganga and Yamuna showed a drastic reduction in water pollutant levels. For the first time in a generation, the Himalayas were visible from various parts of India. The amount of waste generated also showed a decline during the lockdown, and wildlife was seen blooming. During the lockdown period temperature levels were also recorded low as compared to 2019 between March to June. Hence, this review emphasizes the beneficial impacts of lockdown on different pollution parameters as well as wildlife in India.

Genome sequence analysis of nsp15 from SARS-CoV-2.

SARS-CoV-2 (Severe Acute Respiratory Syndrome), a causative agent of COVID-19 disease created a pandemic situation worldwide. Nsp15 is a uridine specific endoribonuclease encoded by the genome of SARS-CoV-2. It plays important role in processing viral RNA and, thus evades the host immune system. Therefore, it is of interest to identify mutants of nsp15 amongst Asian SARS-CoV-2 isolates, where a total of 1795 mutations, from 7793 sequences of Asia submitted till 31st January 2022, amongst which A231V, H234Y, K109N, K259R and S261A mutations were found frequent. Hence, we report data on the predicted secondary structure of wild type form followed by hydropathy plot, physiochemical properties, Ramachandran plot, B-cell epitopes prediction and protein modeling of wild type and mutant of nsp15 protein. Data shows that nsp15 of SARS-CoV-2 is a pontential candidate for the development of vaccine to control the infections of SARS-CoV-2.

Analysis of SARS-CoV-2 mutations in the main viral protease (NSP5) and its implications on the vaccine designing strategies.

SARS-CoV-2 (Severe Acute Respiratory Syndrome), an etiolating agent of novel COVID-19 (coronavirus 2019) pandemic, rapidly spread worldwide, creating an unprecedented public health crisis globally. NSP5, the main viral protease, is a highly conserved protein, encoded by the genome of SARS-CoV-2 and plays an important role in the viral replication cycle. In the present study, we detected a total of 33 mutations from 675 sequences submitted from India in the month of March 2020 to April 2021. Out of 33 mutations, we selected 8 frequent mutations (K236R, N142L, K90R, A7V, L75F, C22N, H246Y and I43V) for further analysis. Subsequently, protein models were constructed, revealing significant alterations in the 3-D structure of NSP5 protein when compared to the wild type protein sequence which also altered the secondary structure of NSP5 protein. Further, we identified 9 B-cell, 10 T-cell and 6 MHC-I promising epitopes using predictive tools of immunoinformatics, out of these epitopes some were non-allergenic as well as highly immunogenic. Results of our study, however, revealed that 10 B-cell epitopes reside in the mutated region of NSP5. Additionally, hydrophobicity, physiochemical properties, toxicity and stability of NSP5 protein were estimated to demonstrate the specificity of the multiepitope candidates. Taken together, variations arising as a consequence of multiple mutations may cause alterations in the structure and function of NSP5 which generate crucial insights to better understand structural aspects of SARS-CoV-2. Our study also revealed, NSP5, a main protease, can be a potentially good target for the design and development of vaccine candidate against SARS-CoV-2.

El SARS-CoV-2 (Síndrome Respiratorio Agudo Severo), un agente etiológico de la nueva pandemia de COVID-19 (coronavirus 2019), se propagó rápidamente por todo el mundo y creó una crisis de salud pública sin precedentes a nivel mundial. El NSP5, la proteasa viral principal, es una proteína altamente conservada, codificada por el genoma del SARS-CoV-2 y juega un papel importante en el ciclo de replicación viral. En el presente estudio se detectaron un total de 33 mutaciones de 675 secuencias presentadas desde la India en el mes de marzo de 2020 a abril de 2021. De 33 mutaciones, se seleccionaron 8 mutaciones frecuentes (K236R, N142L, K90R, A7V, L75F, C22N, H246Y e I43V) para su posterior análisis. Posteriormente, se construyeron modelos proteicos que revelaron alteraciones significativas en la estructura 3D de las proteínas NSP5 en comparación con la secuencia de proteínas de tipo silvestre que también alteraron la estructura secundaria de la proteína NSP5. Además, se identificaron 9 epítopos prometedores de células B, 10 de células T y 6 de MHC-I, utilizando herramientas predictivas de inmunoinformática, algunos no alergénicos y altamente inmunogénicos. Los resultados de nuestro estudio, sin embargo, revelaron que 10 epítopos de células B residen en la región mutada de NSP5. Adicionalmente, se estimó la hidrofobicidad, propiedades fisicoquímicas, toxicidad y estabilidad de la proteína NSP5 para demostrar la especificidad de los candidatos multiepítopos. En conjunto, las variaciones que surgen como consecuencia de múltiples mutaciones pueden causar alteraciones en la estructura y función del NSP5 que generan conocimientos cruciales para entender mejor los aspectos estructurales del SARS-CoV-2. Nuestro estudio también reveló que el NSP5, una proteasa principal, puede ser un blanco potencialmente bueno para el diseño y desarrollo de la vacuna candidata contra el SARS-CoV-2.

Identification of recurrent mutations in exonuclease (nsp14); a potential drug target in SARS-CoV-2.

CONTEXT: The rapid outbreak of SARS-CoV-2 has become a significant global health concern, highlighting the dire need for antiviral therapeutic agents. RNA-dependent RNA polymerase (RdRp) of coronavirus plays crucial roles in RNA synthesis, and hence remains the druggable target for the treatment of this disease. The most potent broad-spectrum inhibitors of viral RdRp are members of nucleoside analogs (NAs). However, SARS-CoV-2 proved to be a challenging one for the novel NA drug designing strategy because coronavirus possesses an exonuclease (ExoN) domain that is capable of excising NAs, thus showing resistance to existing antiviral drugs. AIM: The objective of our study was to compare the SARS-CoV-2 exonuclease (nsp14) protein sequence of Wuhan-type virus with those of Indian SARS-Cov-2 isolates and to study the effect of multiple mutations on the secondary structure alterations of proteins. SUBJECTS AND METHODS: Multiple-sequence alignment of exonuclease amino-acid sequences followed by phylogenetic analysis and prediction of its secondary structure of the protein was performed. RESULTS: Altogether, seven mutations were detected in the nsp14 of Indian SARS-CoV-2 isolates. Subsequently, prediction of their secondary structures revealed that mutations altered the structural stability of exonuclease proteins. CONCLUSIONS: Present findings, therefore, further suggest that evolvability of SARS-CoV-2 is primarily associated with the onset of multiple novel mutations that rapidly spread at several new locations of the viral genome and also provides important insight to develop specific control strategies to fight against COVID-19 infections.

Identification and characterization of mutations in the SARS-CoV-2 RNA-dependent RNA polymerase as a promising antiviral therapeutic target.

The causative agent of COVID-19 is a novel betacoronavirus or severe acute respiratory syndrome coronavirus (SARS-CoV-2), which has emerged as a pandemic of global concern. Considering its rapid transmission, WHO has declared public health emergency on 11th March 2020 worldwide. SARS-CoV-2 is a genetically diverse positive sense RNA virus that typically exhibit high rates of mutation than DNA viruses. Higher rates of mutation bring higher genomic variability which may lead to viral evolution and enabling viruses to evade the pre-existing immunity of host and quickly acquire drug resistance properties. The objective of our study was to compare the SARS-CoV-2 RdRp sequences of Indian SARS-CoV-2 isolates with those of Wuhan type virus. A total of 384 point mutations were detected from 488 sequence of the RdRp protein of Indian SARS-CoV-2 genome, out of which seven were used for subsequent study. Furthermore, prediction of secondary structure, protein modeling and its dynamics were performed which revealed that seven mutations (R118C, T148I, Y149C, E802A, Q822H, V880I and D893Y) significantly altered the stability and flexibility of RdRp protein. Present study was therefore, undertaken to analyze the variations occurring in RdRp due to multiple mutations leading to the alterations in the structure and function of RNA-dependent RNA polymerase which is essential for the replication /transcription of this virus and hence can be utilized as a promising therapeutic target to curb SARS-CoV-2 infections.

Immunoinformatics Identification of B- and T-Cell Epitopes in the RNA-Dependent RNA Polymerase of SARS-CoV-2.

SARS-CoV-2 (Severe acute respiratory syndrome coronavirus-2) is a newly emerged beta coronavirus and etiolating agent of COVID-19. Considering the unprecedented increasing number of COVID-19 cases, the World Health Organization declared a public health emergency internationally on 11th March 2020. However, existing drugs are insufficient in dealing with this contagious virus infection; therefore, a vaccine is exigent to curb this pandemic disease. In the present study, B- and T-cell immune epitopes were identified for RdRp (RNA-dependent RNA polymerase) protein using immunoinformatic techniques, which is proved to be a rapid and efficient method to explore the candidate peptide vaccine. Subsequently, antigenicity and interactions with HLA (human leukocyte antigen) alleles were estimated. Further, physicochemical properties, allergenicity, toxicity, and stability of RdRp protein were evaluated to demonstrate the specificity of the epitope candidates. Interestingly, we identified a total of 36 B-cell and 16 T-cell epitopes using epitopes predictive tools. Among the predicted epitopes, 26 B-cell and 9 T-cell epitopes showed non-allergenic, non-toxic, and highly antigenic properties. Altogether, our study revealed that RdRp of SARS-CoV-2 (an epitope-based peptide fragment) can be a potentially good candidate for the development of a vaccine against SARS-CoV-2.