Epitope Identification and Designing a Potent Multi-epitope Vaccine Construct against SARS-CoV-2 Including the Emerging Variants.

Introduction: The emergence of a novel coronavirus in China has turned into a SARS-CoV-2 pandemic with high fatality. As vaccines are developed through various strategies, their immunogenic potential may drastically vary and thus pose several challenges in offering immune responses against the virus. Methods: In this study, we adopted an immunoinformatics-aided approach for developing a new multi-epitope vaccine construct (MEVC). In silico approach was taken for the identification of B-cell and T-cell epitopes in the Spike protein, for MEVC various cytotoxic T-lymphocyte, helper T-lymphocyte, and B-cell epitopes with the highest affinity for the respective HLA alleles were assembled and joined by linkers. Results: The computational data suggest that the MEVC is nontoxic, nonallergenic and thermostable and elicit both humoral and cell-mediated immune responses. Subsequently, the biological activity of MEVC was assessed by bioinformatic tools using the interaction between the vaccine candidate and the innate immune system receptors TLR3 and TLR4. The epitopes of the construct were analyzed with that of the strains belonging to various clades including the emerging variants having multiple unique mutations in S protein. Conclusions: Due to the advantageous features, the MEVC can be tested in vitro for more practical validation and the study offers immense scope for developing a potential vaccine candidate against SARS-CoV-2 in view of the public health emergency associated with COVID-19 disease caused by SARS-CoV-2.

Immunoinformatic Approach for the identification of T Cell and B Cell Epitopes in the Surface Glycoprotein and Designing a Potent Multiepitope Vaccine Construct Against SARS-CoV-2 including the new UK variant (preprint)

The emergence of a novel coronavirus in China in late 2019 has turned into a SARS-CoV-2 pandemic affecting several millions of people worldwide in a short span of time with high fatality. The crisis is further aggravated by the emergence and evolution of new variant SARS-CoV-2 strains in UK during December, 2020 followed by their transmission to other countries. A major concern is that prophylaxis and therapeutics are not available yet to control and prevent the virus which is spreading at an alarming rate, though several vaccine trials are in the final stage. As vaccines are developed through various strategies, their immunogenic potential may drastically vary and thus pose several challenges in offering both arms of immunity such as humoral and cell-mediated immune responses against the virus. In this study, we adopted an immunoinformatics-aided identification of B cell and T cell epitopes in the Spike protein, which is a surface glycoprotein of SARS-CoV-2, for developing a new Multiepitope vaccine construct (MEVC). MEVC has 575 amino acids and comprises adjuvants and various cytotoxic T-lymphocyte (CTL), helper T-lymphocyte (HTL), and B-cell epitopes that possess the highest affinity for the respective HLA alleles, assembled and joined by linkers. The computational data suggest that the MEVC is non-toxic, non-allergenic and thermostable with the capability to elicit both humoral and cell-mediated immune responses. The population coverage of various countries affected by COVID-19 with respect to the selected B and T cell epitopes in MEVC was also investigated. Subsequently, the biological activity of MEVC was assessed by bioinformatic tools using the interaction between the vaccine candidate and the innate immune system receptors TLR3 and TLR4. The epitopes of the construct were analyzed with that of the strains belonging to various clades including the new variant UK strain having multiple unique mutations in S protein. Due to the advantageous features, the MEVC can be tested in vitro for more practical validation and the study offers immense scope for developing a potential vaccine candidate against SARS-CoV-2 in view of the public health emergency associated with COVID-19 disease caused by SARS-CoV-2.

A Distinct Phylogenetic Cluster of Indian Severe Acute Respiratory Syndrome Coronavirus 2 Isolates.

BACKGROUND: From an isolated epidemic, coronavirus disease 2019 has now emerged as a global pandemic. The availability of genomes in the public domain after the epidemic provides a unique opportunity to understand the evolution and spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus across the globe. METHODS: We performed whole-genome sequencing of 303 Indian isolates, and we analyzed them in the context of publicly available data from India. RESULTS: We describe a distinct phylogenetic cluster (Clade I/A3i) of SARS-CoV-2 genomes from India, which encompasses 22% of all genomes deposited in the public domain from India. Globally, approximately 2% of genomes, which to date could not be mapped to any distinct known cluster, fall within this clade. CONCLUSIONS: The cluster is characterized by a core set of 4 genetic variants and has a nucleotide substitution rate of 1.1 × 10-3 variants per site per year, which is lower than the prevalent A2a cluster. Epidemiological assessments suggest that the common ancestor emerged at the end of January 2020 and possibly resulted in an outbreak followed by countrywide spread. To the best of our knowledge, this is the first comprehensive study characterizing this cluster of SARS-CoV-2 in India.

Laboratory preparedness for SARS-CoV-2 testing in India: Harnessing a network of Virus Research & Diagnostic Laboratories.

Background & objectives: An outbreak of respiratory illness of unknown aetiology was reported from Hubei province of Wuhan, People's Republic of China, in December 2019. The outbreak was attributed to a novel coronavirus (CoV), named as severe acute respiratory syndrome (SARS)-CoV-2 and the disease as COVID-19. Within one month, cases were reported from 25 countries. In view of the novel viral strain with reported high morbidity, establishing early countrywide diagnosis to detect imported cases became critical. Here we describe the role of a countrywide network of VRDLs in early diagnosis of COVID-19. Methods: The Indian Council of Medical Research (ICMR)-National Institute of Virology (NIV), Pune, established screening as well as confirmatory assays for SARS-CoV-2. A total of 13 VRDLs were provided with the E gene screening real-time reverse transcription-polymerase chain reaction (rRT-PCR) assay. VRDLs were selected on the basis of their presence near an international airport/seaport and their past performance. The case definition for testing included all individuals with travel history to Wuhan and symptomatic individuals with travel history to other parts of China. This was later expanded to include symptomatic individuals returning from Singapore, Japan, Hong Kong, Thailand and South Korea. Results: Within a week of standardization of the test at NIV, all VRDLs could initiate testing for SARS-CoV-2. Till February 29, 2020, a total of 2,913 samples were tested. This included both 654 individuals quarantined in the two camps and others fitting within the case definition. The quarantined individuals were tested twice - at days 0 and 14. All tested negative on both occasions. Only three individuals belonging to different districts in Kerala were found to be positive. Interpretation & conclusions: Sudden emergence of SARS-CoV-2 and its potential to cause a pandemic posed an unsurmountable challenge to the public health system of India. However, concerted efforts of various arms of the Government of India resulted in a well-coordinated action at each level. India has successfully demonstrated its ability to establish quick diagnosis of SARS-CoV-2 at NIV, Pune, and the testing VRDLs.

Interventional radiology and COVID-19: evidence-based measures to limit transmission.

As we face an explosion of COVID-19 cases and deal with an unprecedented set of circumstances all over the world, healthcare personnel are at the forefront, dealing with this emerging scenario. Certain subspecialties like interventional radiology entails a greater risk of acquiring and transmitting infection due to the close patient contact and invasive patient care the service provides. This makes it imperative to develop and set guidelines in place to limit transmission and utilize resources in an optimal fashion. A multi-tiered approach needs to be devised and monitored at the administrative level, taking into account the various staff and patient contact points. Based on these factors, work site and health force rearrangements need to be in place while enforcing segregation and disinfection parameters. We are putting forth an all-encompassing review of infection control measures that cover the dynamics of patient care and staff protocols that such a situation demands of an interventional department.