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Devi SB, Kumar S. Designing a multi-epitope chimeric protein from different potential targets: A potential vaccine candidate against Plasmodium. Mol Biochem Parasitol 2023; 255:111560. [PMID: 37084957 DOI: 10.1016/j.molbiopara.2023.111560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 03/30/2023] [Accepted: 04/03/2023] [Indexed: 04/23/2023]
Abstract
Malaria is an infectious disease that has been a continuous threat to mankind since the time immemorial. Owing to the complex multi-staged life cycle of the plasmodium parasite, an effective malaria vaccine which is fully protective against the parasite infection is urgently needed to deal with the challenges. In the present study, essential parasite proteins were identified and a chimeric protein with multivalent epitopes was generated. The designed chimeric protein consists of best potential B and T cell epitopes from five different essential parasite proteins. Physiochemical studies of the chimeric protein showed that the modeled vaccine construct was thermo-stable, hydrophilic and antigenic in nature. And the binding of the vaccine construct with Toll-like receptor-4 (TLR-4) as revealed by the molecular docking suggests the possible interaction and role of the vaccine construct in activating the innate immune response. The constructed vaccine being a chimeric protein containing epitopes from different potential candidates could target different stages or pathways of the parasite. Moreover, the approach used in this study is time and cost effective, and can be applied in the discoveries of new potential vaccine targets for other pathogens.
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Affiliation(s)
- Sanasam Bijara Devi
- Department of Life science & Bioinformatics, Assam University, Silchar 788011 India.
| | - Sanjeev Kumar
- Department of Life science & Bioinformatics, Assam University, Silchar 788011 India
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2
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de la Fuente J, Contreras M. Vaccinomics: a future avenue for vaccine development against emerging pathogens. Expert Rev Vaccines 2021; 20:1561-1569. [PMID: 34582295 DOI: 10.1080/14760584.2021.1987222] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
INTRODUCTION Vaccines are a major achievement in medical sciences, but the development of more effective vaccines against infectious diseases is essential for prevention and control of emerging pathogens worldwide. The application of omics technologies has advanced vaccinology through the characterization of host-vector-pathogen molecular interactions and the identification of candidate protective antigens. However, major challenges such as host immunity, pathogen and environmental factors, vaccine efficacy and safety need to be addressed. Vaccinomics provides a platform to address these challenges and improve vaccine efficacy and safety. AREAS COVERED In this review, we summarize current information on vaccinomics and propose quantum vaccinomics approaches to further advance vaccine development through the identification and combination of antigen protective epitopes, the immunological quantum. The COVID-19 pandemic caused by SARS-CoV-2 is an example of emerging infectious diseases with global impact on human health. EXPERT OPINION Vaccines are required for the effective and environmentally sustainable intervention for the control of emerging infectious diseases worldwide. Recent advances in vaccinomics provide a platform to address challenges in improving vaccine efficacy and implementation. As proposed here, quantum vaccinomics will contribute to vaccine development, efficacy, and safety by facilitating antigen combinations to target pathogen infection and transmission in emerging infectious diseases.
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Affiliation(s)
- José de la Fuente
- SaBio, Instituto De Investigación En Recursos Cinegéticos Irec-csic-uclm-jccm, Ciudad Real, Spain.,Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK, USA
| | - Marinela Contreras
- Interdisciplinary Laboratory of Clinical Analysis, Interlab-UMU, Regional Campus of International Excellence Campus Mare Nostrum, University of Murcia, Espinardo, Spain
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3
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Ramanathan N, Ramamurthy J, Natarajan G. Numerical Characterization of DNA Sequences for Alignment-free Sequence Comparison - A Review. Comb Chem High Throughput Screen 2021; 25:365-380. [PMID: 34382516 DOI: 10.2174/1386207324666210811101437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 06/16/2021] [Accepted: 06/24/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Biological macromolecules namely, DNA, RNA, and protein have their building blocks organized in a particular sequence and the sequential arrangement encodes evolutionary history of the organism (species). Hence, biological sequences have been used for studying evolutionary relationships among the species. This is usually carried out by multiple sequence algorithms (MSA). Due to certain limitations of MSA, alignment-free sequence comparison methods were developed. The present review is on alignment-free sequence comparison methods carried out using numerical characterization of DNA sequences. <P> Discussion: The graphical representation of DNA sequences by chaos game representation and other 2-dimesnional and 3-dimensional methods are discussed. The evolution of numerical characterization from the various graphical representations and the application of the DNA invariants thus computed in phylogenetic analysis is presented. The extension of computing molecular descriptors in chemometrics to the calculation of new set of DNA invariants and their use in alignment-free sequence comparison in a N-dimensional space and construction of phylogenetic tress is also reviewed. <P> Conclusion: The phylogenetic tress constructed by the alignment-free sequence comparison methods using DNA invariants were found to be better than those constructed using alignment-based tools such as PHLYIP and ClustalW. One of the graphical representation methods is now extended to study viral sequences of infectious diseases for the identification of conserved regions to design peptide-based vaccine by combining numerical characterization and graphical representation.
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Affiliation(s)
- Natarajan Ramanathan
- Department of Chemistry, Sri Sarada Niketan College for Women, Karur-639005, Tamil Nadu. India
| | - Jayalakshmi Ramamurthy
- Department of Computer Science, Sri Sarada Niketan College for Women, Karur-639005, Tamil Nadu. India
| | - Ganapathy Natarajan
- Department of Mechanical Engineering and Industrial Engineering, University of Wisconsin, Platteville, WI 53818. United States
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4
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Abstract
The design for vaccines using in silico analysis of genomic data of different viruses has taken many different paths, but lack of any precise computational approach has constrained them to alignment methods and some alignment-free techniques. In this work, a precise computational approach has been established wherein two new mathematical parameters have been suggested to identify the highly conserved and surface-exposed regions which are spread over a large region of the surface protein of the virus so that one can determine possible peptide vaccine candidates from those regions. The first parameter, w, is the sum of the normalized values of the measure of surface accessibility and the normalized measure of conservativeness, and the second parameter is the area of a triangle formed by a mathematical model named 2D Polygon Representation. This method has been, therefore, used to determine possible vaccine targets against SARS-CoV-2 by considering its surface-situated spike glycoprotein. The results of this model have been verified by a parallel analysis using the older approach of manually estimating the graphs describing the variation of conservativeness and surface-exposure across the protein sequence. Furthermore, the working of the method has been tested by applying it to find out peptide vaccine candidates for Zika and Hendra viruses respectively. A satisfactory consistency of the model results with pre-established results for both the test cases shows that this in silico alignment-free analysis proposed by the model is suitable not only to determine vaccine targets against SARS-CoV-2 but also ready to extend against other viruses.
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Nour I, Hanif A, Alanazi IO, Al-Ashkar I, Alhetheel A, Eifan S. Novel insights of waterborne human rotavirus A in Riyadh (Saudi Arabia) involving G2 predominance and emergence of a thermotolerant sequence. Sci Rep 2021; 11:12132. [PMID: 34108565 PMCID: PMC8190275 DOI: 10.1038/s41598-021-91607-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 05/28/2021] [Indexed: 02/05/2023] Open
Abstract
The routine evaluation of water environments is necessary to manage enteric virus-mediated fecal contamination and the possible emergence of novel variants. Here, we detected human rotavirus A (HRVA) circulating in two wastewater treatment plants, two lakes, irrigation water and a wastewater landfill located in Riyadh. VP7-derived surface protein sequences were assessed by phylogenetic analyses and inspection of thermotolerance-mediated secondary structure and seasonal variation. HRVA was most prevalent at An-Nazim wastewater landfill (AN-WWLF; 63.89%). Phylogenetic analyzes revealed the predominance of HRVA G2 lineage for the first time in Saudi Arabia. Moreover, a single HRVA sequence (2B64I-ANLF3/2018) was recovered at 45 °C from AN-WWLF; secondary structure prediction indicated that this sequence was thermotolerant with a high hydrophobicity, an absence of Ramachandran outliers, and a higher content of proline patches on the protein surface. Varied relationships were significantly observed between sampling areas influenced by temperature ranges (p < 0.05). HRVA prevalence was influenced by seasonal variations, favoring moderate temperatures in late autumn and early winter in all locations. However, a significant temperature impact was detected in Wadi-Hanifah Lake (p = 0.01). Our study extends the knowledge of currently circulating HRVA genotypes, and indicates the probable emergence of thermotolerant strains and seasonally mediated HRVA prevalence.
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Affiliation(s)
- Islam Nour
- grid.56302.320000 0004 1773 5396Botany and Microbiology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Atif Hanif
- grid.56302.320000 0004 1773 5396Botany and Microbiology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Ibrahim O. Alanazi
- grid.452562.20000 0000 8808 6435National Center for Biotechnology, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Ibrahim Al-Ashkar
- grid.56302.320000 0004 1773 5396Biotechnology Laboratory, Plant Production Department, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia ,grid.411303.40000 0001 2155 6022Agronomy Department, Faculty of Agriculture, Al-Azhar University, Cairo, Egypt
| | - Abdulkarim Alhetheel
- grid.56302.320000 0004 1773 5396Department of Pathology and Laboratory Medicine, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Saleh Eifan
- grid.56302.320000 0004 1773 5396Botany and Microbiology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
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6
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Nandy A. Mapping Biomolecular Sequences: Graphical Representations - their Origins, Applications and Future Prospects. Comb Chem High Throughput Screen 2021; 25:354-364. [PMID: 33970841 DOI: 10.2174/1386207324666210510164743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/25/2021] [Accepted: 02/11/2021] [Indexed: 11/22/2022]
Abstract
The exponential growth in the depositories of biological sequence data have generated an urgent need to store, retrieve and analyse the data efficiently and effectively for which the standard practice of using alignment procedures are not adequate due to high demand on computing resources and time. Graphical representation of sequences has become one of the most popular alignment-free strategies to analyse the biological sequences where each basic unit of the sequences - the bases adenine, cytosine, guanine and thymine for DNA/RNA, and the 20 amino acids for proteins - are plotted on a multi-dimensional grid. The resulting curve in 2D and 3D space and the implied graph in higher dimensions provide a perception of the underlying information of the sequences through visual inspection; numerical analyses, in geometrical or matrix terms, of the plots provide a measure of comparison between sequences and thus enable study of sequence hierarchies. The new approach has also enabled studies of comparisons of DNA sequences over many thousands of bases and provided new insights into the structure of the base compositions of DNA sequences In this article we review in brief the origins and applications of graphical representations and highlight the future perspectives in this field.
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Affiliation(s)
- Ashesh Nandy
- Centre for Interdisciplinary Research and Education, Kolkata 700068, India
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7
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Abstract
With the increasing frequency of viral epidemics, vaccines to augment the human immune response system have been the medium of choice to combat viral infections. The tragic consequences of the Zika virus pandemic in South and Central America a few years ago brought the issues into sharper focus. While traditional vaccine development is time-consuming and expensive, recent advances in information technology, immunoinformatics, genetics, bioinformatics, and related sciences have opened the doors to new paradigms in vaccine design and applications.Peptide vaccines are one group of the new approaches to vaccine formulation. In this chapter, we discuss the various issues involved in the design of peptide vaccines and their advantages and shortcomings, with special reference to the Zika virus for which no drugs or vaccines are as yet available. In the process, we outline our work in this field giving a detailed step-by-step description of the protocol we follow for such vaccine design so that interested researchers can easily follow them and do their own designing. Several flowcharts and figures are included to provide a background of the software to be used and results to be anticipated.
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8
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Chakraborty C, Sharma AR, Sharma G, Bhattacharya M, Lee SS. Insight into Evolution and Conservation Patterns of B1-Subfamily Members of GPCR. Int J Pept Res Ther 2020; 26:2505-2517. [PMID: 32421105 PMCID: PMC7223794 DOI: 10.1007/s10989-020-10043-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/30/2020] [Indexed: 11/25/2022]
Abstract
The diverse, evolutionary architectures of proteins can be regarded as molecular fossils, tracing a historical path that marks important milestones across life. The B1-subfamily of GPCRs (G-protein-coupled receptors) are medically significant proteins that comprise 15 transmembrane receptor proteins in Homo sapiens. These proteins control the intracellular concentration of cyclic AMP as well as various vital processes in the body. However, little is known about the evolutionary correlation and conservational blueprint of this GPCR subfamily. We performed a comprehensive analysis to understand the evolutionary architecture among 13 members of the B1-subfamily. Multiple sequence alignment analysis exhibited six multiple sequence aligned blocks and five highly aligned blocks. Molecular phylogenetics indicated that CRHR1 and CRHR2 share a typical ancestral relationship and are siblings in 100% bootstrap replications with a total of 24 nodes observed in the cladogram. CRHR2 has the maximum number of extremely conserved amino acids followed by ADCYAP1R1. The longest continuous number sequence logos (74) were found between sequence location 349 and 423, and consequently, the maximum and minimum logo height recorded was 3.6 bits and 0.18 bits, respectively. Finally, to understand the model and pattern of evolutionary relatedness, the conservation blueprint, and the diversification among the members of a protein family, GPCR distribution from several species throughout the animal kingdom was analysed. Together, the study provides an evolutionary insight and offers a rapid method to explore the potential of depicting the evolutionary relationship, conservation blueprint, and diversification among the B1-subfamily of GPCRs using bioinformatics, algorithm analysis, and mathematical models.
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Affiliation(s)
- Chiranjib Chakraborty
- Adamas University, North, 24 Parganas, Kolkata, 700126 West Bengal India
- Institute for Skeletal Aging & Orthopedic Surgery, Chuncheon Sacred Heart Hospital, Hallym University, Chuncheon, 24252 Republic of Korea
| | - Ashish Ranjan Sharma
- Institute for Skeletal Aging & Orthopedic Surgery, Chuncheon Sacred Heart Hospital, Hallym University, Chuncheon, 24252 Republic of Korea
| | - Garima Sharma
- Neuropsychopharmacology and Toxicology Program, College of Pharmacy, Kangwon National University, Chuncheon, 24341 Republic of Korea
| | - Manojit Bhattacharya
- Institute for Skeletal Aging & Orthopedic Surgery, Chuncheon Sacred Heart Hospital, Hallym University, Chuncheon, 24252 Republic of Korea
| | - Sang-Soo Lee
- Institute for Skeletal Aging & Orthopedic Surgery, Chuncheon Sacred Heart Hospital, Hallym University, Chuncheon, 24252 Republic of Korea
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9
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Abstract
Because of their replication mode and segmented dsRNA genome, homologous recombination is assumed to be rare in the rotaviruses. We analyzed 23,627 complete rotavirus genome sequences available in the NCBI Virus Variation database, and found 109 instances of homologous recombination, at least eleven of which prevailed across multiple sequenced isolates. In one case, recombination may have generated a novel rotavirus VP1 lineage. We also found strong evidence for intergenotypic recombination in which more than one sequence strongly supported the same event, particularly between different genotypes of segment 9, which encodes the glycoprotein, VP7. The recombined regions of many putative recombinants showed amino acid substitutions differentiating them from their major and minor parents. This finding suggests that these recombination events were not overly deleterious, since presumably these recombinants proliferated long enough to acquire adaptive mutations in their recombined regions. Protein structural predictions indicated that, despite the sometimes substantial amino acid replacements resulting from recombination, the overall protein structures remained relatively unaffected. Notably, recombination junctions appear to occur nonrandomly with hot spots corresponding to secondary RNA structures, a pattern seen consistently across segments. In total, we found strong evidence for recombination in nine of eleven rotavirus A segments. Only segments 7 (NSP3) and 11 (NSP5) did not show strong evidence of recombination. Collectively, the results of our computational analyses suggest that, contrary to the prevailing sentiment, recombination may be a significant driver of rotavirus evolution and may influence circulating strain diversity.
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Affiliation(s)
- Irene Hoxie
- Biology Department, Queens College of The City University of New York, 65-30 Kissena Blvd, Queens, NY 11367, USA.,The Graduate Center of The City University of New York, Biology Program, 365 5th Ave, New York, NY 10016, USA
| | - John J Dennehy
- Biology Department, Queens College of The City University of New York, 65-30 Kissena Blvd, Queens, NY 11367, USA.,The Graduate Center of The City University of New York, Biology Program, 365 5th Ave, New York, NY 10016, USA
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10
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Sanasam BD, Kumar S. In-silico structural modeling and epitope prediction of highly conserved Plasmodium falciparum protein AMR1. Mol Immunol 2019; 116:131-139. [PMID: 31648168 DOI: 10.1016/j.molimm.2019.10.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/29/2019] [Accepted: 10/01/2019] [Indexed: 11/17/2022]
Abstract
Malaria caused by Plasmodium falciparum is the most deadly and a major health issue worldwide. In spite of several control programs, there hasn't been much improvement in keeping the disease under control. The appearance of drug resistant strains of Plasmodium in addition to insecticide resistance of the Anopheles vector has been a hurdle. Therefore, it is highly desirable to identify new potential candidates that can be targeted for therapeutic intervention. The present study identifies AMR1, a highly conserved essential protein of Plasmodium falciparum, as a potential candidate for vaccine development. AMR1 is an exposed surface protein with high antigenic property and conservancy among other species of the parasite. Reverse vaccinology approach (RV) is adopted to determine the best epitopes of AMR1 protein. The protein was further evaluated for several important physiochemical parameters. The study revealed the 3D structure of AMR1, as well as the best B cell and helper T-cell epitopes of the protein. These resulted epitopes might be of great importance in the development of an effective vaccine to combat the deadly disease.
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Affiliation(s)
- Bijara Devi Sanasam
- Department of Life science & Bioinformatics, Assam University, Silchar, 788011, India
| | - Sanjeev Kumar
- Department of Life science & Bioinformatics, Assam University, Silchar, 788011, India.
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11
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Basak SC, Majumdar S, Nandy A, Roy P, Dutta T, Vracko M, Bhattacharjee AK. Computer-Assisted and Data Driven Approaches for Surveillance, Drug Discovery, and Vaccine Design for the Zika Virus. Pharmaceuticals (Basel) 2019; 12:ph12040157. [PMID: 31623241 PMCID: PMC6958466 DOI: 10.3390/ph12040157] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 10/14/2019] [Accepted: 10/15/2019] [Indexed: 12/17/2022] Open
Abstract
Human life has been at the edge of catastrophe for millennia due diseases which emerge and reemerge at random. The recent outbreak of the Zika virus (ZIKV) is one such menace that shook the global public health community abruptly. Modern technologies, including computational tools as well as experimental approaches, need to be harnessed fast and effectively in a coordinated manner in order to properly address such challenges. In this paper, based on our earlier research, we have proposed a four-pronged approach to tackle the emerging pathogens like ZIKV: (a) Epidemiological modelling of spread mechanisms of ZIKV; (b) assessment of the public health risk of newly emerging strains of the pathogens by comparing them with existing strains/pathogens using fast computational sequence comparison methods; (c) implementation of vaccine design methods in order to produce a set of probable peptide vaccine candidates for quick synthesis/production and testing in the laboratory; and (d) designing of novel therapeutic molecules and their laboratory testing as well as validation of new drugs or repurposing of drugs for use against ZIKV. For each of these stages, we provide an extensive review of the technical challenges and current state-of-the-art. Further, we outline the future areas of research and discuss how they can work together to proactively combat ZIKV or future emerging pathogens.
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Affiliation(s)
- Subhash C Basak
- Department of Chemistry and Biochemistry, University of Minnesota, Duluth, MN 55812, USA.
| | | | - Ashesh Nandy
- Centre for Interdisciplinary Research and Education, Kolkata 700068, India.
| | - Proyasha Roy
- Centre for Interdisciplinary Research and Education, Kolkata 700068, India.
| | - Tathagata Dutta
- Centre for Interdisciplinary Research and Education, Kolkata 700068, India.
| | - Marjan Vracko
- National Institute of Chemistry, Hajdrihova 19, Ljubljana 1000, Slovenia.
| | - Apurba K Bhattacharjee
- Biomedical Graduate Research Organization, Department of Microbiology and Immunology School of Medicine, Georgetown University, Washington, DC 20057, USA.
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12
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Nandy A, Dey S, Roy P, Basak SC. Epidemics and Peptide Vaccine Response: A Brief Review. Curr Top Med Chem 2019; 18:2202-2208. [PMID: 30417788 DOI: 10.2174/1568026618666181112144745] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 10/29/2018] [Accepted: 11/03/2018] [Indexed: 02/01/2023]
Abstract
We briefly review the situations arising out of epidemics that erupt rather suddenly, threatening life and livelihoods of humans. Ebola, Zika and the Nipah virus outbreaks are recent examples where the viral epidemics have led to considerably high degree of fatalities or debilitating consequences. The problems are accentuated by a lack of drugs or vaccines effective against the new and emergent viruses, and the inordinate amount of temporal and financial resources that are required to combat the novel pathogens. Progress in computational, biological and informational sciences have made it possible to consider design of synthetic vaccines that can be rapidly developed and deployed to help stem the damages. In this review, we consider the pros and cons of this new paradigm and suggest a new system where the manufacturing process can be decentralized to provide more targeted vaccines to meet the urgent needs of protection in case of a rampaging epidemic.
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Affiliation(s)
- Ashesh Nandy
- Centre for Interdisciplinary Research and Education, 404B Jodhpur Park, Kolkata 700068, India
| | - Sumanta Dey
- Centre for Interdisciplinary Research and Education, 404B Jodhpur Park, Kolkata 700068, India
| | - Proyasha Roy
- Centre for Interdisciplinary Research and Education, 404B Jodhpur Park, Kolkata 700068, India
| | - Subhash C Basak
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, 1802 Stanford Avenue, Duluth, MN 5581, United States
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13
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Ghosh S, Malik YS, Kobayashi N. Therapeutics and Immunoprophylaxis Against Noroviruses and Rotaviruses: The Past, Present, and Future. Curr Drug Metab 2018; 19:170-191. [PMID: 28901254 PMCID: PMC5971199 DOI: 10.2174/1389200218666170912161449] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 09/25/2016] [Accepted: 03/19/2017] [Indexed: 12/20/2022]
Abstract
Background: Noroviruses and rotaviruses are important viral etiologies of severe gastroenteritis. Noroviruses are the primary cause of nonbacterial diarrheal outbreaks in humans, whilst rotaviruses are a major cause of childhood diarrhea. Although both enteric pathogens substantially impact human health and economies, there are no approved drugs against noroviruses and rotaviruses so far. On the other hand, whilst the currently licensed rotavirus vaccines have been successfully implemented in over 100 countries, the most advanced norovirus vaccine has recently completed phase-I and II trials. Methods: We performed a structured search of bibliographic databases for peer-reviewed research litera-ture on advances in the fields of norovirus and rotavirus therapeutics and immunoprophylaxis. Results: Technological advances coupled with a proper understanding of viral morphology and replication over the past decade has facilitated pioneering research on therapeutics and immunoprophylaxis against noroviruses and rotaviruses, with promising outcomes in human clinical trials of some of the drugs and vaccines. This review focuses on the various developments in the fields of norovirus and rotavirus thera-peutics and immunoprophylaxis, such as potential antiviral drug molecules, passive immunotherapies (oral human immunoglobulins, egg yolk and bovine colostral antibodies, llama-derived nanobodies, and anti-bodies expressed in probiotics, plants, rice grains and insect larvae), immune system modulators, probiot-ics, phytochemicals and other biological substances such as bovine milk proteins, therapeutic nanoparti-cles, hydrogels and viscogens, conventional viral vaccines (live and inactivated whole virus vaccines), and genetically engineered viral vaccines (reassortant viral particles, virus-like particles (VLPs) and other sub-unit recombinant vaccines including multi-valent viral vaccines, edible plant vaccines, and encapsulated viral particles). Conclusions: This review provides important insights into the various approaches to therapeutics and im-munoprophylaxis against noroviruses and rotaviruses..
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Affiliation(s)
- Souvik Ghosh
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, St. Kitts and Nevis, West Indies.,Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo, Hokkaido, Japan
| | - Yashpal Singh Malik
- Indian Veterinary Research Institute, Izatnagar 243 122, Uttar Pradesh, India
| | - Nobumichi Kobayashi
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo, Hokkaido, Japan
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14
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Singh S. Alignment-Free Analyses of Nucleic Acid Sequences Using Graphical Representation (with Special Reference to Pandemic Bird Flu and Swine Flu). Synth Biol (Oxf) 2018. [PMCID: PMC7121243 DOI: 10.1007/978-981-10-8693-9_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The exponential growth in database of bio-molecular sequences have spawned many approaches towards storage, retrieval, classification and analyses requirements. Alignment-free techniques such as graphical representations and numerical characterisation (GRANCH) methods have enabled some detailed analyses of large sequences and found a number of different applications in the eukaryotic and prokaryotic domain. In particular, recalling the history of pandemic influenza in brief, we have followed the progress of viral infections such as bird flu of 1997 onwards and determined that the virus can spread conserved over space and time, that influenza virus can undergo fairly conspicuous recombination-like events in segmented genes, that certain segments of the neuraminidase and hemagglutinin surface proteins remain conserved and can be targeted for peptide vaccines. We recount in some detail a few of the representative GRANCH techniques to provide a glimpse of how these methods are used in formulating quantitative sequence descriptors to analyse DNA, RNA and protein sequences to derive meaningful results. Finally, we survey the surveillance techniques with a special reference to how the GRANCH techniques can be used for the purpose and recount the forecasts made of possible metamorphosis of pandemic bird flu to pandemic human infecting agents.
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Affiliation(s)
- Shailza Singh
- Department of Pathogenesis and Cellular Response, National Centre for Cell Science, Computational and Systems Biology Lab, Pune, Maharashtra India
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15
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Sen D, Roy P, Nandy A, Basak SC, Das S. Graphical representation methods: How well do they discriminate between homologous gene sequences? Chem Phys 2018; 513:156-164. [PMID: 32287864 PMCID: PMC7116999 DOI: 10.1016/j.chemphys.2018.07.031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 07/21/2018] [Indexed: 01/05/2023]
Abstract
Graphical representation methods constitute a class of alignment-free techniques for comparative study of biomolecular sequences. In this brief commentary, we study how well some of these methods can discriminate among closely related genes.
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Affiliation(s)
- Dwaipayan Sen
- Centre for Interdisciplinary Research and Education, Jodhpur Park, Kolkata 700068, India
| | - Proyasha Roy
- Centre for Interdisciplinary Research and Education, Jodhpur Park, Kolkata 700068, India
| | - Ashesh Nandy
- Centre for Interdisciplinary Research and Education, Jodhpur Park, Kolkata 700068, India
| | - Subhash C Basak
- Department of Chemistry & Biochemistry, University of Minnesota Duluth, 5013 Miller Trunk Highway, Duluth, MN 55811, USA
| | - Sukhen Das
- Physics Department, Jadavpur University, Jadavpur, Kolkata 700032, India
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Mohanty E, Dehury B, Satapathy AK, Dwibedi B. Design and testing of a highly conserved human rotavirus VP8* immunogenic peptide with potential for vaccine development. J Biotechnol 2018; 281:48-60. [PMID: 29886031 DOI: 10.1016/j.jbiotec.2018.06.306] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 05/25/2018] [Accepted: 06/06/2018] [Indexed: 12/11/2022]
Abstract
Rotavirus infection of young children particularly below five years of age resulting in severe diarhoea, is the cause of a large number of infant deaths all over the world, more so in developing countries like India. Vaccines developed against this infection in the last two decades have shown mixed results with some of them leading to complications. Oral vaccines have not been very effective in India. Significant diversity has been found in circulating virus strains in India. Development of a vaccine against diverse genetic variants of the different strains would go a long way in reducing the incidence of infection in developing countries. Success of such a vaccine would depend to a large extent on the antigenic peptide to be used in antibody production. The non-glycosylated protein VP4 on the surface capsid of the virus is important in rota viral immunogenicity and the major antigenic site(s) responsible for neutralization of the virus via VP4 is in the VP8* subunit of VP4. It is necessary that the peptide should be very specific and a peptide sequence which would stimulate both the T and B immunogenic cells would provide maximum protection against the virus. Advanced computational techniques and existing databases of sequences of the VP4 protein of rotavirus help in identification of such specific sequences. Using an in silico approach we have identified a highly conserved VP8* subunit of the VP4 surface protein of rotavirus which shows both T and B cell processivity and is also non-allergenic. This sub-unit could be used in in vivo models for induction of antibodies.
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Affiliation(s)
- Eileena Mohanty
- All India institute of medical sciences, Bhubaneshwar, 751019, Odisha, India.
| | - Budheswar Dehury
- Biomedical Informatics Centre, Regional Medical Research Centre, Indian Council of Medical Research, Bhubaneswar, 751023, Odisha, India.
| | - Ashok Kumar Satapathy
- Immunology Laboratory, Regional Medical Research Centre, Indian Council of Medical Research, Bhubaneswar, 751023, Odisha, India.
| | - Bhagirathi Dwibedi
- All India institute of medical sciences, Bhubaneshwar, 751019, Odisha, India.
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17
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Zafari E, Soleimanjahi H, Mohammadi A, Teimoori A, Mahravani H. Molecular and biological characterization of the human-bovine rotavirus-based reassortant rotavirus. Microb Pathog 2018; 121:65-69. [PMID: 29753872 DOI: 10.1016/j.micpath.2018.05.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 05/09/2018] [Accepted: 05/09/2018] [Indexed: 11/19/2022]
Abstract
Rotaviruses (RV) are the leading cause of acute infantile gastroenteritis, associated with elevated mortality in low-income countries. Morbidity and mortality, length and rates of hospitalization due to RV gastroenteritis are dropping. Improving the quality of newborns life is an ongoing challenge for health-care providers. In this study, homemade reassortant human-bovine rotavirus was developed and biological activity and molecular characterization of candidate vaccine were evaluated for the vaccine stability. Virus titration and purification of reassortant rotavirus strains were evaluated by plaque assays, electropherotyping. The genetic stability after first, third and sixth passage was by sequencing. Due to WHO recommendation, developingment of national capacity for vaccine production in appropriate quantities and at affordable prices is the cornerstone of developing global vaccination policies. Such studies are critical to producing national vaccines and modeling herd protection.
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Affiliation(s)
- Ehsan Zafari
- Department of Virology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Hoorieh Soleimanjahi
- Department of Virology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran.
| | - Ashraf Mohammadi
- Razi Vaccine and Serum Research Institute (RVSRI) Hessark Karadj, Agricultural Research, Education and Extension Organization (AREEO), Tehran, Iran
| | - Ali Teimoori
- Department of Virology, Ahwaz Joundishpor University of Medical Sciences, Ahvaz, IR Iran
| | - Homayon Mahravani
- Razi Vaccine and Serum Research Institute (RVSRI) Hessark Karadj, Agricultural Research, Education and Extension Organization (AREEO), Tehran, Iran
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18
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Dey S, Nandy A, Basak SC, Nandy P, Das S. A Bioinformatics approach to designing a Zika virus vaccine. Comput Biol Chem 2017; 68:143-152. [PMID: 28342423 DOI: 10.1016/j.compbiolchem.2017.03.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 03/03/2017] [Accepted: 03/05/2017] [Indexed: 12/13/2022]
Abstract
The Zika virus infections have reached epidemic proportions in the Latin American countries causing severe birth defects and neurological disorders. While several organizations have begun research into design of prophylactic vaccines and therapeutic drugs, computer assisted methods with adequate data resources can be expected to assist in these measures to reduce lead times through bioinformatics approaches. Using 60 sequences of the Zika virus envelope protein available in the GenBank database, our analysis with numerical characterization techniques and several web based bioinformatics servers identified four peptide stretches on the Zika virus envelope protein that are well conserved and surface exposed and are predicted to have reasonable epitope binding efficiency. These peptides can be expected to form the basis for a nascent peptide vaccine which, enhanced by incorporation of suitable adjuvants, can elicit immune response against the Zika virus infections.
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Affiliation(s)
- Sumanta Dey
- Centre for Interdisciplinary Research and Education, 404 B Jodhpur Park, Kolkata 700068, India; Department of Physics, Jadavpur University, Jadavpur, Kolkata 700032, India
| | - Ashesh Nandy
- Centre for Interdisciplinary Research and Education, 404 B Jodhpur Park, Kolkata 700068, India.
| | - Subhash C Basak
- University of Minnesota Duluth-Natural Resources Research Institute and Department of Chemistry and Biochemistry, University of Minnesota Duluth,5013 Miller Trunk Highway, Duluth, MN 55811, USA
| | - Papiya Nandy
- Centre for Interdisciplinary Research and Education, 404 B Jodhpur Park, Kolkata 700068, India
| | - Sukhen Das
- Centre for Interdisciplinary Research and Education, 404 B Jodhpur Park, Kolkata 700068, India; Department of Physics, Jadavpur University, Jadavpur, Kolkata 700032, India
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Chakraborty C, Bandyopadhyay S, Agoramoorthy G. India's Computational Biology Growth and Challenges. Interdiscip Sci 2016; 8:263-76. [PMID: 27465042 DOI: 10.1007/s12539-016-0179-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 09/08/2015] [Accepted: 09/08/2015] [Indexed: 11/30/2022]
Abstract
India's computational science is growing swiftly due to the outburst of internet and information technology services. The bioinformatics sector of India has been transforming rapidly by creating a competitive position in global bioinformatics market. Bioinformatics is widely used across India to address a wide range of biological issues. Recently, computational researchers and biologists are collaborating in projects such as database development, sequence analysis, genomic prospects and algorithm generations. In this paper, we have presented the Indian computational biology scenario highlighting bioinformatics-related educational activities, manpower development, internet boom, service industry, research activities, conferences and trainings undertaken by the corporate and government sectors. Nonetheless, this new field of science faces lots of challenges.
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Affiliation(s)
- Chiranjib Chakraborty
- Department of Bio-informatics, School of Computer and Information Sciences, Galgotias University, Greater Noida, India
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20
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Dey S, De A, Nandy A. Rational Design of Peptide Vaccines Against Multiple Types of Human Papillomavirus. Cancer Inform 2016; 15:1-16. [PMID: 27279731 PMCID: PMC4890726 DOI: 10.4137/cin.s39071] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 04/19/2016] [Accepted: 04/24/2016] [Indexed: 12/31/2022] Open
Abstract
Human papillomavirus (HPV) occurs in many types, some of which cause cervical, genital, and other cancers. While vaccination is available against the major cancer-causing HPV types, many others are not covered by these preventive measures. Herein, we present a bioinformatics study for the designing of multivalent peptide vaccines against multiple HPV types as an alternative strategy to the virus-like particle vaccines being used now. Our technique of rational design of peptide vaccines is expected to ensure stability of the vaccine against many cycles of mutational changes, elicit immune response, and negate autoimmune possibilities. Using the L1 capsid protein sequences, we identified several peptides for potential vaccine design for HPV 16, 18, 33, 35, 45, and 11 types. Although there are concerns about the epitope-binding affinities for the peptides identified in this process, the technique indicates possibilities of multivalent, adjuvanted, peptide vaccines against a wider range of HPV types, and tailor-made different combinations of the peptides to address frequency variations of types over different population groups as required for prophylaxis and at lower cost than are in use at the present time.
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Affiliation(s)
- Sumanta Dey
- Centre for Interdisciplinary Research and Education, Kolkata, India
| | - Antara De
- Centre for Interdisciplinary Research and Education, Kolkata, India
| | - Ashesh Nandy
- Centre for Interdisciplinary Research and Education, Kolkata, India
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21
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Nandy A, Basak SC. A Brief Review of Computer-Assisted Approaches to Rational Design of Peptide Vaccines. Int J Mol Sci 2016; 17:E666. [PMID: 27153063 PMCID: PMC4881492 DOI: 10.3390/ijms17050666] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 04/25/2016] [Accepted: 04/27/2016] [Indexed: 11/18/2022] Open
Abstract
The growing incidences of new viral diseases and increasingly frequent viral epidemics have strained therapeutic and preventive measures; the high mutability of viral genes puts additional strains on developmental efforts. Given the high cost and time requirements for new drugs development, vaccines remain as a viable alternative, but there too traditional techniques of live-attenuated or inactivated vaccines have the danger of allergenic reactions and others. Peptide vaccines have, over the last several years, begun to be looked on as more appropriate alternatives, which are economically affordable, require less time for development and hold the promise of multi-valent dosages. The developments in bioinformatics, proteomics, immunogenomics, structural biology and other sciences have spurred the growth of vaccinomics where computer assisted approaches serve to identify suitable peptide targets for eventual development of vaccines. In this mini-review we give a brief overview of some of the recent trends in computer assisted vaccine development with emphasis on the primary selection procedures of probable peptide candidates for vaccine development.
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Affiliation(s)
- Ashesh Nandy
- Centre for Interdisciplinary Research and Education, Jodhpur Park, Kolkata 700068, India.
| | - Subhash C Basak
- Natural Resources Research Institute and Department of Chemistry & Biochemistry, University of Minnesota Duluth, Duluth, MN 55811, USA.
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22
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De A, Sarkar T, Nandy A. Bioinformatics studies of Influenza A hemagglutinin sequence data indicate recombination-like events leading to segment exchanges. BMC Res Notes 2016; 9:222. [PMID: 27083561 PMCID: PMC4832483 DOI: 10.1186/s13104-016-2017-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 03/31/2016] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND The influenza genome is highly variable due primarily to two mechanisms: antigenic drift and antigenic shift. A third mechanism for genetic change, known as copy choice or template switching, can arise during replication when, if two viral strains infect a cell, a part of a gene from the second viral strain can be copied into the growing progeny of a gene of the first viral strain as replacement leading to a new variety of the virus. This template switching between the same genes of the two strains is known as homologous recombination. While genetic drift and shift are well-understood, the presence or absence of intra-segment homologous recombination in influenza genomes is controversial. CONTEXT AND PURPOSE OF STUDY We are interested to study the possibility of subunit-wise homologous recombination. The idea is that where well-defined subunits are separated by consensus sequences, it might be possible for template switching to take place at such junctions. The influenza hemagglutinin gene has basically two subunits, HA1 and HA2, with HA1 being mostly surface exposed and containing the active site for binding to cells, while HA2 secures the hemagglutinin to the viral coat. We undertook a thorough search of the major human infecting influenza hemagglutinin gene sequences, viz., the H1N1, H5N1, H3N2 and H7N9 subtypes, over the period 2010-2014 in Asia to determine if certain sequences could be identified that had HA1 from a previous strain and HA2 from another. RESULTS Our search yielded several instances where sequence identities between segments of various strains could be interpreted as indicating possibilities of segment exchange. In some cases, on closer examination they turn out to differ by a few mutations in each segment, due perhaps to the short time span of our database. CONCLUSIONS AND POTENTIAL IMPLICATIONS The study reported here, and in combination with our earlier observations on the neuraminidase, shows that subunit-wise recombination-like events in the influenza genes may be occurring more often than have been accounted for and merits further detailed studies.
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Affiliation(s)
- Antara De
- Centre for Interdisciplinary Research and Education, 404B Jodhpur Park, Kolkata, 700068, India.
| | - Tapati Sarkar
- Physics Department, Jadavpur University, Jadavpur, Kolkata, 700032, India
| | - Ashesh Nandy
- Centre for Interdisciplinary Research and Education, 404B Jodhpur Park, Kolkata, 700068, India
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Sarkar T, Das S, De A, Nandy P, Chattopadhyay S, Chawla-Sarkar M, Nandy A. H7N9 influenza outbreak in China 2013: In silico analyses of conserved segments of the hemagglutinin as a basis for the selection of peptide vaccine targets. Comput Biol Chem 2015; 59 Pt A:8-15. [PMID: 26364271 DOI: 10.1016/j.compbiolchem.2015.08.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 08/03/2015] [Accepted: 08/04/2015] [Indexed: 12/09/2022]
Abstract
The sudden emergence of a human infecting strain of H7N9 influenza virus in China in 2013 leading to fatalities in about 30% of the cases has caused wide concern that additional mutations in the strain leading to human to human transmission could lead to a deadly pandemic. It may happen in a short time span as the outbreak of H7N9 is more and more recurrent, which implies that H7N9 evolution is speeding up. H7N9 flu strains were not known to infect humans before this attack in China in February 2013 and it was solely an avian strain. While currently available drugs such as oseltamivir have been found to be largely effective against the H7N9, albeit with recent reported cases of development of resistance to the drug, there is a necessity to identify alternatives to combat this disease, especially if it assumes pandemic proportions. In our work, we have tried to investigate for the genetic changes in hemagglutinin (HA) protein sequence that lead to human infection by an avian infecting virus and identify possible peptide targets to design vaccines to control this upcoming risk. We identified three highly conserved regions in all H7 subtypes, of which one particular immunogenic surface exposed region was found to be well conserved in all human infecting H7N9 strains (accessed up to 27th March 2014). Compared to H7N9 avian strains, we identified two mutations in this conserved region at the receptor binding site of all post-February 2013 human-infecting H7N9China hemagglutinin protein sequences. One of the mutations is very close (3.6 Å) to the hemagglutinin sialic acid binding pocket that may lead to better binding to human host's sialic acid due to the changes in hydrophobicity of the microenvironment of the binding site. We found that the peptide region with these mutational changes that are specific for human infecting H7N9 virus possess the possibility of being used as target for a peptide vaccine.
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Affiliation(s)
- Tapati Sarkar
- Physics Department, Jadavpur University, Kolkata 700032, India.
| | - Sukhen Das
- Physics Department, Jadavpur University, Kolkata 700032, India
| | - Antara De
- Centre for Interdisciplinary Research and Education, 404B Jodhpur Park, Kolkata 700068, India
| | - Papiya Nandy
- Centre for Interdisciplinary Research and Education, 404B Jodhpur Park, Kolkata 700068, India
| | - Shiladitya Chattopadhyay
- Division of Virology, National Institute of Cholera and Enteric Diseases, Kolkata, West Bengal, India
| | - Mamta Chawla-Sarkar
- Division of Virology, National Institute of Cholera and Enteric Diseases, Kolkata, West Bengal, India
| | - Ashesh Nandy
- Centre for Interdisciplinary Research and Education, 404B Jodhpur Park, Kolkata 700068, India
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24
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Molecular genotyping and quantitation assay for rotavirus surveillance. J Virol Methods 2014; 213:157-63. [PMID: 25526999 DOI: 10.1016/j.jviromet.2014.12.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Revised: 12/01/2014] [Accepted: 12/02/2014] [Indexed: 11/20/2022]
Abstract
Rotavirus genotyping is useful for surveillance purposes especially in areas where rotavirus vaccination has been or will be implemented. RT-PCR based molecular methods have been applied widely, but quantitative assays targeting a broad spectrum of genotypes have not been developed. Three real time RT-PCR panels were designed to identify G1, G2, G9, G12 (panel GI), G3, G4, G8, G10 (panel GII), and P[4], P[6], P[8], P[10], P[11] (panel P), respectively. An assay targeting NSP3 was included in both G panels as an internal control. The cognate assays were also formulated as one RT-PCR-Luminex panel for simultaneous detection of all the genotypes listed above plus P[9]. The assays were evaluated with various rotavirus isolates and 89 clinical samples from Virginia, Bangladesh and Tanzania, and exhibited 95% (81/85) sensitivity compared with the conventional RT-PCR-Gel-electrophoresis method, and 100% concordance with sequencing. Real time assays identified a significantly higher rate of mixed genotypes in Bangladeshi samples than the conventional gel-electrophoresis-based RT-PCR assay (32.5% versus 12.5%, P<0.05). In these mixed infections, the relative abundance of the rotavirus types could be estimated by Cq values. These typing assays detect and discriminate a broad range of G/P types circulating in different geographic regions with high sensitivity and specificity and can be used for rotavirus surveillance.
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