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Van Poelvoorde LAE, Dufrasne FE, Van Gucht S, Saelens X, Roosens NHC. Development of Digital Droplet PCR Targeting the Influenza H3N2 Oseltamivir-Resistant E119V Mutation and Its Performance through the Use of Reverse Genetics Mutants. Curr Issues Mol Biol 2023; 45:2521-2532. [PMID: 36975535 PMCID: PMC10047791 DOI: 10.3390/cimb45030165] [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: 02/10/2023] [Revised: 03/10/2023] [Accepted: 03/14/2023] [Indexed: 03/29/2023] Open
Abstract
The monitoring of antiviral-resistant influenza virus strains is important for public health given the availability and use of neuraminidase inhibitors and other antivirals to treat infected patients. Naturally occurring oseltamivir-resistant seasonal H3N2 influenza virus strains often carry a glutamate-to-valine substitution at position 119 in the neuraminidase (E119V-NA). Early detection of resistant influenza viruses is important for patient management and for the rapid containment of antiviral resistance. The neuraminidase inhibition assay allows the phenotypical identification of resistant strains; however, this test often has limited sensitivity with high variability depending on the virus strain, drugs and assays. Once a mutation such as E119V-NA is known, highly sensitive PCR-based genotypic assays can be used to identify the prevalence of such mutant influenza viruses in clinical samples. In this study, based on an existing reverse transcriptase real-time PCR (RT-qPCR) assay, we developed a reverse transcriptase droplet digital PCR assay (RT-ddPCR) to detect and quantify the frequency of the E119V-NA mutation. Furthermore, reverse genetics viruses carrying this mutation were created to test the performance of the RT-ddPCR assay and compare it to the standard phenotypic NA assay. We also discuss the advantage of using an RT-ddPCR instead of qPCR method in the context of viral diagnostics and surveillance.
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Affiliation(s)
- Laura A E Van Poelvoorde
- Transversal Activities in Applied Genomics, Sciensano, Juliette Wytsmanstraat 14, 1050 Brussels, Belgium
- National Influenza Centre, Department of Infectious Diseases in Humans, Laboratory of Viral Diseases, Sciensano, Engelandstraat 642, 1180 Brussels, Belgium
- Department of Biochemistry and Microbiology, Ghent University, 9052 Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium
| | - François E Dufrasne
- National Influenza Centre, Department of Infectious Diseases in Humans, Laboratory of Viral Diseases, Sciensano, Engelandstraat 642, 1180 Brussels, Belgium
| | - Steven Van Gucht
- National Influenza Centre, Department of Infectious Diseases in Humans, Laboratory of Viral Diseases, Sciensano, Engelandstraat 642, 1180 Brussels, Belgium
| | - Xavier Saelens
- Department of Biochemistry and Microbiology, Ghent University, 9052 Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium
| | - Nancy H C Roosens
- Transversal Activities in Applied Genomics, Sciensano, Juliette Wytsmanstraat 14, 1050 Brussels, Belgium
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52
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Al-Jabri M, Rosero C, Saade EA. Vaccine-Preventable Diseases in Older Adults. Infect Dis Clin North Am 2023; 37:103-121. [PMID: 36805008 DOI: 10.1016/j.idc.2022.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Older adults are at an increased risk of vaccine-preventable diseases partly because of physiologic changes in the immune and other body systems related to age and/or accumulating comorbidities that increase the vulnerability to infections and decrease the response to vaccines. Strategies to improve the response to vaccines include using a higher antigenic dose (such as in the high-dose inactivated influenza vaccines) as well as adding adjuvants (such as MF59 in the adjuvanted inactivated influenza vaccine).
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Affiliation(s)
- Maha Al-Jabri
- Division of Infectious Diseases and HIV Medicine, University Hospitals Cleveland Medical Center, 11100 Euclid Avenue - Mailstop Fol. 5083, Cleveland, OH 44106, USA; Case Western Reserve University, Cleveland, OH, USA
| | - Christian Rosero
- Division of Infectious Diseases and HIV Medicine, University Hospitals Cleveland Medical Center, 11100 Euclid Avenue - Mailstop Fol. 5083, Cleveland, OH 44106, USA; Case Western Reserve University, Cleveland, OH, USA
| | - Elie A Saade
- Division of Infectious Diseases and HIV Medicine, University Hospitals Cleveland Medical Center, 11100 Euclid Avenue - Mailstop Fol. 5083, Cleveland, OH 44106, USA.
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53
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Lei R, Hernandez Garcia A, Tan TJC, Teo QW, Wang Y, Zhang X, Luo S, Nair SK, Peng J, Wu NC. Mutational fitness landscape of human influenza H3N2 neuraminidase. Cell Rep 2023; 42:111951. [PMID: 36640354 PMCID: PMC9931530 DOI: 10.1016/j.celrep.2022.111951] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 11/24/2022] [Accepted: 12/16/2022] [Indexed: 01/07/2023] Open
Abstract
Influenza neuraminidase (NA) has received increasing attention as an effective vaccine target. However, its mutational tolerance is not well characterized. Here, the fitness effects of >6,000 mutations in human H3N2 NA are probed using deep mutational scanning. Our result shows that while its antigenic regions have high mutational tolerance, there are solvent-exposed regions with low mutational tolerance. We also find that protein stability is a major determinant of NA mutational fitness. The deep mutational scanning result correlates well with mutational fitness inferred from natural sequences using a protein language model, substantiating the relevance of our findings to the natural evolution of circulating strains. Additional analysis further suggests that human H3N2 NA is far from running out of mutations despite already evolving for >50 years. Overall, this study advances our understanding of the evolutionary potential of NA and the underlying biophysical constraints, which in turn provide insights into NA-based vaccine design.
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Affiliation(s)
- Ruipeng Lei
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Andrea Hernandez Garcia
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Timothy J C Tan
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Qi Wen Teo
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yiquan Wang
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | | | | | - Satish K Nair
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Jian Peng
- HeliXon Limited, Beijing 100084, China; Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Nicholas C Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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Abbadi N, Mousa JJ. Broadly Protective Neuraminidase-Based Influenza Vaccines and Monoclonal Antibodies: Target Epitopes and Mechanisms of Action. Viruses 2023; 15:200. [PMID: 36680239 PMCID: PMC9861061 DOI: 10.3390/v15010200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 12/31/2022] [Accepted: 01/04/2023] [Indexed: 01/13/2023] Open
Abstract
Neuraminidase (NA) is an important surface protein on influenza virions, playing an essential role in the viral life cycle and being a key target of the immune system. Despite the importance of NA-based immunity, current vaccines are focused on the hemagglutinin (HA) protein as the target for protective antibodies, and the amount of NA is not standardized in virion-based vaccines. Antibodies targeting NA are predominantly protective, reducing infection severity and viral shedding. Recently, NA-specific monoclonal antibodies have been characterized, and their target epitopes have been identified. This review summarizes the characteristics of NA, NA-specific antibodies, the mechanism of NA inhibition, and the recent efforts towards developing NA-based and NA-incorporating influenza vaccines.
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Affiliation(s)
- Nada Abbadi
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
| | - Jarrod J. Mousa
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
- Department of Biochemistry and Molecular Biology, Franklin College of Arts and Sciences, University of Georgia, Athens, GA 30602, USA
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55
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Xie R, Zhang H, Zhang H, Li C, Cui D, Li S, Li Z, Liu H, Huang J. Hemagglutinin expressed by yeast reshapes immune microenvironment and gut microbiota to trigger diverse anti-infection response in infected birds. Front Immunol 2023; 14:1125190. [PMID: 37143654 PMCID: PMC10151582 DOI: 10.3389/fimmu.2023.1125190] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 03/22/2023] [Indexed: 05/06/2023] Open
Abstract
Introduction The H5N8 influenza virus is a highly pathogenic pathogen for poultry and human. Vaccination is the most effective method to control the spread of the virus right now. The traditional inactivated vaccine, though well developed and used widely, is laborious during application and more interests are stimulated in developing alternative approaches. Methods In this study, we developed three hemagglutinin (HA) gene-based yeast vaccine. In order to explore the protective efficacy of the vaccines, the gene expression level in the bursa of Fabricius and the structure of intestinal microflora in immunized animals were analyzed by RNA seq and 16SrRNA sequencing, and the regulatory mechanism of yeast vaccine was evaluated. Results All of these vaccines elicited the humoral immunity, inhibited viral load in the chicken tissues, and provided partial protective efficacy due to the high dose of the H5N8 virus. Molecular mechanism studies suggested that, compared to the traditional inactivated vaccine, our engineered yeast vaccine reshaped the immune cell microenvironment in bursa of Fabricius to promote the defense and immune responses. Analysis of gut microbiota further suggested that oral administration of engineered ST1814G/H5HA yeast vaccine increased the diversity of gut microbiota and the increasement of Reuteri and Muciniphila might benefit the recovery from influenza virus infection. These results provide strong evidence for further clinical use of these engineered yeast vaccine in poultry.
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Affiliation(s)
- Ruyu Xie
- School of Life Science, Tianjin University, Tianjin, China
| | - Huixia Zhang
- School of Life Science, Tianjin University, Tianjin, China
| | - Han Zhang
- School of Life Science, Tianjin University, Tianjin, China
| | - Changyan Li
- School of Life Science, Tianjin University, Tianjin, China
| | - Daqing Cui
- School of Life Science, Tianjin University, Tianjin, China
| | - Shujun Li
- School of Life Science, Tianjin University, Tianjin, China
| | - Zexing Li
- School of Life Science, Tianjin University, Tianjin, China
| | - Hualei Liu
- China Animal Health and Epidemiology Center, Qingdao, Shandong, China
- *Correspondence: Hualei Liu, ; Jinhai Huang,
| | - Jinhai Huang
- School of Life Science, Tianjin University, Tianjin, China
- *Correspondence: Hualei Liu, ; Jinhai Huang,
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Casalino L, Seitz C, Lederhofer J, Tsybovsky Y, Wilson IA, Kanekiyo M, Amaro RE. Breathing and Tilting: Mesoscale Simulations Illuminate Influenza Glycoprotein Vulnerabilities. ACS CENTRAL SCIENCE 2022; 8:1646-1663. [PMID: 36589893 PMCID: PMC9801513 DOI: 10.1021/acscentsci.2c00981] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Indexed: 05/28/2023]
Abstract
Influenza virus has resurfaced recently from inactivity during the early stages of the COVID-19 pandemic, raising serious concerns about the nature and magnitude of future epidemics. The main antigenic targets of influenza virus are two surface glycoproteins, hemagglutinin (HA) and neuraminidase (NA). Whereas the structural and dynamical properties of both glycoproteins have been studied previously, the understanding of their plasticity in the whole-virion context is fragmented. Here, we investigate the dynamics of influenza glycoproteins in a crowded protein environment through mesoscale all-atom molecular dynamics simulations of two evolutionary-linked glycosylated influenza A whole-virion models. Our simulations reveal and kinetically characterize three main molecular motions of influenza glycoproteins: NA head tilting, HA ectodomain tilting, and HA head breathing. The flexibility of HA and NA highlights antigenically relevant conformational states, as well as facilitates the characterization of a novel monoclonal antibody, derived from convalescent human donor, that binds to the underside of the NA head. Our work provides previously unappreciated views on the dynamics of HA and NA, advancing the understanding of their interplay and suggesting possible strategies for the design of future vaccines and antivirals against influenza.
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Affiliation(s)
- Lorenzo Casalino
- Department
of Chemistry and Biochemistry, University
of California San Diego, La Jolla, California92093, United States
| | - Christian Seitz
- Department
of Chemistry and Biochemistry, University
of California San Diego, La Jolla, California92093, United States
| | - Julia Lederhofer
- Vaccine
Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland20892, United States
| | - Yaroslav Tsybovsky
- Electron
Microscopy Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research
Sponsored by the National Cancer Institute, Frederick, Maryland21702, United States
| | - Ian A. Wilson
- Department
of Integrative Structural and Computational Biology and the Skaggs
Institute for Chemical Biology, The Scripps
Research Institute, La Jolla, California92037, United States
| | - Masaru Kanekiyo
- Vaccine
Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland20892, United States
| | - Rommie E. Amaro
- Department
of Chemistry and Biochemistry, University
of California San Diego, La Jolla, California92093, United States
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Santos ACF, Martel F, Freire CSR, Ferreira BJML. Polymeric Materials as Indispensable Tools to Fight RNA Viruses: SARS-CoV-2 and Influenza A. Bioengineering (Basel) 2022; 9:816. [PMID: 36551022 PMCID: PMC9816944 DOI: 10.3390/bioengineering9120816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/03/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
Towards the end of 2019 in Wuhan, suspicions of a new dangerous virus circulating in the air began to arise. It was the start of the world pandemic coronavirus disease 2019 (COVID-19). Since then, considerable research data and review papers about this virus have been published. Hundreds of researchers have shared their work in order to achieve a better comprehension of this disease, all with the common goal of overcoming this pandemic. The coronavirus is structurally similar to influenza A. Both are RNA viruses and normally associated with comparable infection symptoms. In this review, different case studies targeting polymeric materials were appraised to highlight them as an indispensable tool to fight these RNA viruses. In particular, the main focus was how polymeric materials, and their versatile features could be applied in different stages of viral disease, i.e., in protection, detection and treatment.
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Affiliation(s)
- Ariana C. F. Santos
- CICECO-Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Fátima Martel
- Biochemistry Unit, Biomedicine Department, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
- I3S-Institute of Research and Innovation in Health, University of Porto, 4200-135 Porto, Portugal
| | - Carmen S. R. Freire
- CICECO-Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Bárbara J. M. L. Ferreira
- CICECO-Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
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Huang X, Yin G, Cai Y, Hu J, Huang J, Liu Q, Feng X. Identification of Unique and Conserved Neutralizing Epitopes of Vestigial Esterase Domain in HA Protein of the H9N2 Subtype of Avian Influenza Virus. Viruses 2022; 14:2739. [PMID: 36560743 PMCID: PMC9787348 DOI: 10.3390/v14122739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/05/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
The H9N2 subtype of avian influenza virus (AIV) has been reported to infect not only birds, but also humans. The hemagglutinin (HA) protein is the main surface antigen of AIV and plays an important role in the viral infection. For treatment strategies and vaccine development, HA protein has been an important target for the development of broadly neutralizing antibodies against influenza A virus. To investigate the vital target determinant cluster in HA protein in this work, HA gene was cloned and expressed in the prokaryotic expression vector pET28a. The spleen lymphocytes from BALC/c mice immunized with the purified recombinant HA protein were fused with SP2/0 cells. After Hypoxanthine-Aminopterin-Thymidine (HAT) medium screening and indirect ELISA detection, six hybridoma cell lines producing anti-HA monoclonal antibodies were screened. The gradually truncated HA gene expression and western blotting were used to identify their major locations in epitopes specific to these monoclonal antibodies. It was found that the epitopes were located in three areas: 112NVENLEEL119, 117EELRSLFS124, and 170PIQDAQ175. Epitope 112NVENLEEL119 has a partial amino acid crossover with 117EELRSLFS124, which is located in the vestigial esterase domain "110-helix" of HA, and the monoclonal antibody recognizing these epitopes showed the neutralizing activity, suggesting that the region 112NVENLEELRSLFS124 might be a novel neutralizing epitope. The results of the homology analysis showed that these three epitopes were generally conserved in H9N2 subtype AIV, and will provide valuable insights into H9N2 vaccine design and improvement, as well as antibody-based therapies for treatment of H9N2 AIV infection.
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Affiliation(s)
- Xiangyu Huang
- Key Laboratory of Animal Microbiology of China’s Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Guihu Yin
- Key Laboratory of Animal Microbiology of China’s Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Yiqin Cai
- Key Laboratory of Animal Microbiology of China’s Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Jianing Hu
- Key Laboratory of Animal Microbiology of China’s Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Jingwen Huang
- Key Laboratory of Animal Microbiology of China’s Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Qingtao Liu
- Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Xiuli Feng
- Key Laboratory of Animal Microbiology of China’s Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
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Kwon EB, Kim YS, Hwang YH, Kim B, Lee SB, Park SK, Choi MS, Ha H, Choi JG. Antiviral activity of soybean GL 2626/96 (Glycine max) ethanolic extract against influenza A virus in vitro and in vivo. Biomed Pharmacother 2022; 156:113780. [DOI: 10.1016/j.biopha.2022.113780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 09/26/2022] [Accepted: 09/28/2022] [Indexed: 11/02/2022] Open
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Ghalekhani N, Bokaie S, Eybpoosh S, Akbarein H, Sharifi H. Reconstruction of molecular evolution of human influenza A H1N1/2009 virus in Iran and neighboring countries. J Med Virol 2022; 94:5965-5974. [PMID: 36000444 DOI: 10.1002/jmv.28090] [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: 05/02/2022] [Revised: 08/13/2022] [Accepted: 08/22/2022] [Indexed: 01/06/2023]
Abstract
In this study, the time and path of transmission of H1N1 serotype influenza A viruses in Iran and neighboring countries have been investigated by using Bayesian phylogeography analysis on the sequences extracted from the gene bank. We obtained all hemagglutinin (HA) and neuraminidase (NA) nucleotide sequences of influenza H1N1 available up to December 25, 2020, from Iran and its neighboring countries (i.e., Pakistan, Afghanistan, Turkmenistan, Armenia, Azerbaijan, Turkey, and Iraq). We also performed a Bayesian Markov chain Monte Carlo method to infer the evolutionary dynamic and the most recent common ancestor for the HA and NA sequences. Based on the extracted sequences, the age of emergence of H1N1 influenza virus serotype was older in Iran compared to neighboring countries, and with some degree of uncertainty, it seems Tehran had a key role and epicenter of transmission to other cities within Iran. The mean time of the most recent common ancestor of H1N1 viruses was 1989 (95% HPD: 1980-1994) for HA and NA as well. Along with ordinary measures like resource management, diagnostic approaches, and preparedness to fight against viruses that were in place, continuous monitoring, and screening of H1N1 serotype influenza virus in the country, especially by implementation of feasible, effective, and innovative measures at borderline should be initiated and identified gaps and shortage that should be a priority for virus control. It is also important for countries to have a regional monitoring program in addition to internal monitoring programs, as well as to start a virus molecular care program.
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Affiliation(s)
- Nima Ghalekhani
- Divisions of Epidemiology & Zoonoses, Department of Food Hygiene and Quality Control, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran.,HIV/STI Surveillance Research Center, and WHO Collaborating Center for HIV Surveillance, Institute for Futures Studies in Health, Kerman University of Medical Sciences, Kerman, Iran
| | - Saied Bokaie
- Divisions of Epidemiology & Zoonoses, Department of Food Hygiene and Quality Control, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Sana Eybpoosh
- Department of Epidemiology and Biostatistics, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran
| | - Hesameddin Akbarein
- Divisions of Epidemiology & Zoonoses, Department of Food Hygiene and Quality Control, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Hamid Sharifi
- HIV/STI Surveillance Research Center, and WHO Collaborating Center for HIV Surveillance, Institute for Futures Studies in Health, Kerman University of Medical Sciences, Kerman, Iran
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Chavda V, Bezbaruah R, Kalita T, Sarma A, Devi JR, Bania R, Apostolopoulos V. Variant influenza: connecting the missing dots. Expert Rev Anti Infect Ther 2022; 20:1567-1585. [PMID: 36346383 DOI: 10.1080/14787210.2022.2144231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
BACKGROUND In June 2009, the World Health Organization declared a new pandemic, the 2009 swine influenza pandemic (swine flu). The symptoms of the swine flu pandemic causing strain were comparable to most of the symptoms noted by seasonal influenza. AREA COVERED Zoonotic viruses that caused the swine flu pandemic and its preventive measures. EXPERT OPINION As per Centers for Disease Control and Prevention (CDC), the clinical manifestations in humans produced by the 2009 H1N1 'swine flu' virus were equivalent to the manifestations caused by related flu strains. The H1N1 vaccination was the most successful prophylactic measure since it prevented the virus from spreading and reduced the intensity and consequences of the pandemic. Despite the availability of therapeutics, the ongoing evolution and appearance of new strains have made it difficult to develop effective vaccines and therapies. Currently, the CDC recommends yearly flu immunization for those aged 6 months and above. The lessons learned from the A/2009/H1N1 pandemic in 2009 indicated that readiness of mankind toward new illnesses caused by mutant viral subtypes that leap from animals to people must be maintained.
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Affiliation(s)
- Vivek Chavda
- Department of Pharmaceutics and Pharmaceutical Technology, L M College of Pharmacy, Ahmedabad, India
| | - Rajashri Bezbaruah
- Department of Pharmaceutical Sciences, Faculty of Science and Engineering, Dibrugarh University, Dibrugarh, India
| | - Tutumoni Kalita
- Department of Pharmaceutical Chemistry, Regional College of Pharmaceutical Sciences, RIPT Group of Institution, Sonapur, Guwahati, India
| | - Anupam Sarma
- Department of Pharmaceutics, Girijananda Chowdhury Institute of Pharmaceutical Science, Hatkhowapara, Azara, Guwahati, Assam, India
| | - Juti Rani Devi
- NETES Institute of Pharmaceutical Science, Mirza, Guwahati, India
| | - Ratnali Bania
- Pratiksha Institute of Pharmaceutical Sciences, India
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Key amino acid position 272 in neuraminidase determines the replication and virulence of H5N6 avian influenza virus in mammals. iScience 2022; 25:105693. [PMID: 36567717 PMCID: PMC9772848 DOI: 10.1016/j.isci.2022.105693] [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] [Received: 07/29/2022] [Revised: 10/14/2022] [Accepted: 11/24/2022] [Indexed: 12/03/2022] Open
Abstract
Avian influenza H5N6 virus not only wreaks economic havoc in the poultry industry but also threatens human health. Strikingly, as of August 2022, 78 human beings were infected with H5N6, and the spike in the number of human infections with H5N6 occurred during 2021. In the life cycle of influenza virus, neuraminidase (NA) has numerous functions, especially viral budding and replication. Here, we found that NA-D272N mutation became predominant in H5N6 viruses since 2015 and significantly increased the viral replication and virulence in mice. D272N mutation in NA protein increased viral release from erythrocytes, thermostability, early transcription, and accumulation of NA protein. Particularly, the dominant 272 residue switch from N to S has occurred in wild bird-origin H5N6 viruses since late 2016 and N272S mutation induced significantly higher levels of inflammatory cytokines in infected human cells. Therefore, comprehensive surveillance of bird populations needs to be enhanced to monitor mammalian adaptive mutations of H5N6 viruses.
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Casto-Boggess LD, Holland LA, Lawer-Yolar PA, Lucas JA, Guerrette JR. Microscale Quantification of the Inhibition of Neuraminidase Using Capillary Nanogel Electrophoresis. Anal Chem 2022; 94:16151-16159. [PMID: 36343965 PMCID: PMC9686991 DOI: 10.1021/acs.analchem.2c03584] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Neuraminidase inhibitors modulate infections that involve sialic acids, making quantitative analyses of this inhibitory effect important for selecting and designing potential therapeutics. An automated nanogel capillary electrophoresis system is developed that integrates a 5 nL enzyme inhibition reaction in line with a 5 min separation-based assay of the enzymatic product to quantify inhibition as the half maximal inhibitory concentration (IC50) and inhibitor constant (Ki). A neuraminidase enzyme from Clostridium perfringens is non-covalently immobilized in a thermally tunable nanogel positioned in the thermally controlled region of the capillary by increasing the capillary temperature to 37 °C. Aqueous inhibitor solutions are loaded into the capillary during the nanogel patterning step to surround the enzyme zone. The capillary electrophoresis separation provides a means to distinguish the de-sialylated product, enabling the use of sialyllactose which contains the trisaccharide motif observed on serine/threonine-linked (O-linked) glycans. A universal nanogel patterning scheme is developed that does not require pre-mixing of enzymes with inhibitors when an automated capillary electrophoresis instrument is used, thus reducing the consumption of enzymes and enabling adaption of the method to different inhibitors. The universal approach is successfully applied to two classical neuraminidase inhibitors with different electrophoretic mobilities. The IC50 and Ki values obtained for N-acetyl-2,3-dehydro-2-deoxyneuraminic acid (DANA) are 13 ± 3 and 5.0 ± 0.9 μM, respectively, and 28 ± 3 and 11 ± 1 μM, respectively, for Siastatin B. These values agree with literature reports and reflect the weaker inhibition anticipated for Siastatin B in comparison to DANA.
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Affiliation(s)
- Laura D Casto-Boggess
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia26505, United States
| | - Lisa A Holland
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia26505, United States
| | - Paul A Lawer-Yolar
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia26505, United States
| | - John A Lucas
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia26505, United States
| | - Jessica R Guerrette
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia26505, United States
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64
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Liu T, Wang Y, Tan TJC, Wu NC, Brooke CB. The evolutionary potential of influenza A virus hemagglutinin is highly constrained by epistatic interactions with neuraminidase. Cell Host Microbe 2022; 30:1363-1369.e4. [PMID: 36150395 PMCID: PMC9588755 DOI: 10.1016/j.chom.2022.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/27/2022] [Accepted: 09/02/2022] [Indexed: 11/03/2022]
Abstract
Antigenic evolution of the influenza A virus (IAV) hemagglutinin (HA) gene limits efforts to effectively control the spread of the virus in the population. Efforts to understand the mechanisms governing HA antigenic evolution typically examine the HA gene in isolation. This can ignore the importance of balancing HA receptor binding activities with the receptor-destroying activities of the viral neuraminidase (NA) to maintain viral fitness. We hypothesize that the need to maintain functional balance with NA significantly constrains the evolutionary potential of the HA. We use deep mutational scanning and show that variation in NA activity significantly reshapes the HA fitness landscape by modulating the overall mutational robustness of HA. Consistent with this, we observe that different NA backgrounds support the emergence of distinct repertoires of HA escape variants under neutralizing antibody pressure. Our results reveal a critical role for intersegment epistasis in influencing the evolutionary potential of the HA gene.
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Affiliation(s)
- Tongyu Liu
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Yiquan Wang
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Timothy J C Tan
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Nicholas C Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Christopher B Brooke
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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65
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Negi G, Sharma A, Dey M, Dhanawat G, Parveen N. Membrane attachment and fusion of HIV-1, influenza A, and SARS-CoV-2: resolving the mechanisms with biophysical methods. Biophys Rev 2022; 14:1109-1140. [PMID: 36249860 PMCID: PMC9552142 DOI: 10.1007/s12551-022-00999-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 09/16/2022] [Indexed: 10/31/2022] Open
Abstract
Attachment to and fusion with cell membranes are two major steps in the replication cycle of many human viruses. We focus on these steps for three enveloped viruses, i.e., HIV-1, IAVs, and SARS-CoV-2. Viral spike proteins drive the membrane attachment and fusion of these viruses. Dynamic interactions between the spike proteins and membrane receptors trigger their specific attachment to the plasma membrane of host cells. A single virion on cell membranes can engage in binding with multiple receptors of the same or different types. Such dynamic and multivalent binding of these viruses result in an optimal attachment strength which in turn leads to their cellular entry and membrane fusion. The latter process is driven by conformational changes of the spike proteins which are also class I fusion proteins, providing the energetics of membrane tethering, bending, and fusion. These viruses exploit cellular and membrane factors in regulating the conformation changes and membrane processes. Herein, we describe the major structural and functional features of spike proteins of the enveloped viruses including highlights on their structural dynamics. The review delves into some of the case studies in the literature discussing the findings on multivalent binding, membrane hemifusion, and fusion of these viruses. The focus is on applications of biophysical tools with an emphasis on single-particle methods for evaluating mechanisms of these processes at the molecular and cellular levels.
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Affiliation(s)
- Geetanjali Negi
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Anurag Sharma
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Manorama Dey
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Garvita Dhanawat
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Nagma Parveen
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
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66
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Chimeric Virus-like Particles Co-Displaying Hemagglutinin Stem and the C-Terminal Fragment of DnaK Confer Heterologous Influenza Protection in Mice. Viruses 2022; 14:v14102109. [PMID: 36298664 PMCID: PMC9610613 DOI: 10.3390/v14102109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 09/17/2022] [Accepted: 09/20/2022] [Indexed: 11/17/2022] Open
Abstract
Influenza virus hemagglutinin (HA) stem is currently regarded as an extremely promising immunogen for designing universal influenza vaccines. The appropriate antigen-presenting vaccine vector would be conducive to increasing the immunogenicity of the HA stem antigen. In this study, we generated chimeric virus-like particles (cVLPs) co-displaying the truncated C-terminal of DnaK from Escherichia coli and H1 stem or full-length H1 antigen using the baculovirus expression system. Transmission electronic micrography revealed the expression and presentation of H1 stem antigens on the surface of VLPs. Vaccinations of mice with the H1 stem cVLPs induced H1-specific immune responses and provided heterologous immune protection in vivo, which was more effective than vaccinations with VLPs displaying H1 stem alone in protecting mice against weight loss as well as increasing survival rates after lethal influenza viral challenge. The results indicate that the incorporation of the truncated C-terminal of DnaK as an adjuvant protein into the cVLPs significantly enhances the H1-specific immunity and immune protection. We have explicitly identified the VLP platform as an effective way of expressing HA stem antigen and revealed that chimeric VLP is an vaccine vector for developing HA stem-based universal influenza vaccines.
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67
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Influenza A (N1-N9) and Influenza B (B/Victoria and B/Yamagata) Neuraminidase Pseudotypes as Tools for Pandemic Preparedness and Improved Influenza Vaccine Design. Vaccines (Basel) 2022; 10:vaccines10091520. [PMID: 36146598 PMCID: PMC9571397 DOI: 10.3390/vaccines10091520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/05/2022] [Accepted: 09/06/2022] [Indexed: 11/16/2022] Open
Abstract
To better understand how inhibition of the influenza neuraminidase (NA) protein contributes to protection against influenza, we produced lentiviral vectors pseudotyped with an avian H11 hemagglutinin (HA) and the NA of all influenza A (N1–N9) subtypes and influenza B (B/Victoria and B/Yamagata). These NA viral pseudotypes (PV) possess stable NA activity and can be utilized as target antigens in in vitro assays to assess vaccine immunogenicity. Employing these NA PV, we developed an enzyme-linked lectin assay (pELLA) for routine serology to measure neuraminidase inhibition (NI) titers of reference antisera, monoclonal antibodies and post-vaccination sera with various influenza antigens. We also show that the pELLA is more sensitive than the commercially available NA-Fluor™ in detecting NA inhibition in these samples. Our studies may lead to establishing the protective NA titer that contributes to NA-based immunity. This will aid in the design of superior, longer lasting and more broadly protective vaccines that can be employed together with HA-targeted vaccines in a pre-pandemic approach.
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68
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Van Poelvoorde LAE, Delcourt T, Vuylsteke M, De Keersmaecker SCJ, Thomas I, Van Gucht S, Saelens X, Roosens N, Vanneste K. A general approach to identify low-frequency variants within influenza samples collected during routine surveillance. Microb Genom 2022; 8. [PMID: 36169645 DOI: 10.1099/mgen.0.000867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Influenza viruses exhibit considerable diversity between hosts. Additionally, different quasispecies can be found within the same host. High-throughput sequencing technologies can be used to sequence a patient-derived virus population at sufficient depths to identify low-frequency variants (LFV) present in a quasispecies, but many challenges remain for reliable LFV detection because of experimental errors introduced during sample preparation and sequencing. High genomic copy numbers and extensive sequencing depths are required to differentiate false positive from real LFV, especially at low allelic frequencies (AFs). This study proposes a general approach for identifying LFV in patient-derived samples obtained during routine surveillance. Firstly, validated thresholds were determined for LFV detection, whilst balancing both the cost and feasibility of reliable LFV detection in clinical samples. Using a genetically well-defined population of influenza A viruses, thresholds of at least 104 genomes per microlitre and AF of ≥5 % were established as detection limits. Secondly, a subset of 59 retained influenza A (H3N2) samples from the 2016-2017 Belgian influenza season was composed. Thirdly, as a proof of concept for the added value of LFV for routine influenza monitoring, potential associations between patient data and whole genome sequencing data were investigated. A significant association was found between a high prevalence of LFV and disease severity. This study provides a general methodology for influenza LFV detection, which can also be adopted by other national influenza reference centres and for other viruses such as SARS-CoV-2. Additionally, this study suggests that the current relevance of LFV for routine influenza surveillance programmes might be undervalued.
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Affiliation(s)
- Laura A E Van Poelvoorde
- Transversal activities in Applied Genomics, Sciensano, Juliette Wytsmanstraat 14, Brussels, Belgium.,National Influenza Centre, Sciensano, Juliette Wytsmanstraat 14, Brussels, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.,VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
| | - Thomas Delcourt
- Transversal activities in Applied Genomics, Sciensano, Juliette Wytsmanstraat 14, Brussels, Belgium
| | | | | | - Isabelle Thomas
- National Influenza Centre, Sciensano, Juliette Wytsmanstraat 14, Brussels, Belgium
| | - Steven Van Gucht
- National Influenza Centre, Sciensano, Juliette Wytsmanstraat 14, Brussels, Belgium
| | - Xavier Saelens
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.,VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
| | - Nancy Roosens
- Transversal activities in Applied Genomics, Sciensano, Juliette Wytsmanstraat 14, Brussels, Belgium
| | - Kevin Vanneste
- Transversal activities in Applied Genomics, Sciensano, Juliette Wytsmanstraat 14, Brussels, Belgium
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69
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Singh V, Eljaaly K, Md S, Alhakamy NA, Kesharwani P. Triblock copolymeric drug delivery as an emerging nanocarrier for treatment of infectious diseases. J Drug Deliv Sci Technol 2022. [DOI: 10.1016/j.jddst.2022.103691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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70
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Gautam V, Kumar R, Jain VK, Nagpal S. An overview of advancement in aptasensors for influenza detection. Expert Rev Mol Diagn 2022; 22:705-724. [PMID: 35994712 DOI: 10.1080/14737159.2022.2116276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION The platforms for early identification of infectious diseases such as influenza has seen a surge in recent years as delayed diagnosis of such infections can lead to dreadful effects causing large numbers of deaths. The time taken in detection of an infectious disease may vary from a few days to a few weeks depending upon the choice of the techniques. So, there is an urgent need for advanced methodologies for early diagnosis of the influenza. AREAS COVERED The emergence of "Aptasensor" synergistically with biosensors for diagnosis has opened a new era for sensitive, selective and early detection approaches. This review described various conventional as well as advanced methods based on artificial immunogenic nucleotide sequences complementing a part of the virus, i.e., aptamers based aptasensors for influenza diagnosis and the challenges faced in their commercialization. EXPERT OPINION Although numerous traditional methods are available for influenza detection but mostly associated with low sensitivity, specificity, high cost, trained personnel, and animals required for virus culture/ antibody raising as the major drawbacks. Aptamers can be manufactured invitro as 'chemical antibodies' at commercial level, no animal required. Following these advantages, aptamers can pave the way for an efficient diagnostic technique as compared to other existing conventional methods..
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Affiliation(s)
- Varsha Gautam
- Amity Institute for Advanced Research and Studies (Materials & Devices), Amity University, Noida India, India
| | - Ramesh Kumar
- Department of Biotechnology, Indira Gandhi University, Meerpur, India
| | - Vinod Kumar Jain
- Amity Institute for Advanced Research and Studies (Materials & Devices), Amity University, Noida India, India
| | - Suman Nagpal
- Department of Environmental sciences, Indira Gandhi University, Meerpur, India
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71
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Biselli R, Nisini R, Lista F, Autore A, Lastilla M, De Lorenzo G, Peragallo MS, Stroffolini T, D’Amelio R. A Historical Review of Military Medical Strategies for Fighting Infectious Diseases: From Battlefields to Global Health. Biomedicines 2022; 10:2050. [PMID: 36009598 PMCID: PMC9405556 DOI: 10.3390/biomedicines10082050] [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] [Received: 07/27/2022] [Revised: 08/12/2022] [Accepted: 08/13/2022] [Indexed: 11/17/2022] Open
Abstract
The environmental conditions generated by war and characterized by poverty, undernutrition, stress, difficult access to safe water and food as well as lack of environmental and personal hygiene favor the spread of many infectious diseases. Epidemic typhus, plague, malaria, cholera, typhoid fever, hepatitis, tetanus, and smallpox have nearly constantly accompanied wars, frequently deeply conditioning the outcome of battles/wars more than weapons and military strategy. At the end of the nineteenth century, with the birth of bacteriology, military medical researchers in Germany, the United Kingdom, and France were active in discovering the etiological agents of some diseases and in developing preventive vaccines. Emil von Behring, Ronald Ross and Charles Laveran, who were or served as military physicians, won the first, the second, and the seventh Nobel Prize for Physiology or Medicine for discovering passive anti-diphtheria/tetanus immunotherapy and for identifying mosquito Anopheline as a malaria vector and plasmodium as its etiological agent, respectively. Meanwhile, Major Walter Reed in the United States of America discovered the mosquito vector of yellow fever, thus paving the way for its prevention by vector control. In this work, the military relevance of some vaccine-preventable and non-vaccine-preventable infectious diseases, as well as of biological weapons, and the military contributions to their control will be described. Currently, the civil-military medical collaboration is getting closer and becoming interdependent, from research and development for the prevention of infectious diseases to disasters and emergencies management, as recently demonstrated in Ebola and Zika outbreaks and the COVID-19 pandemic, even with the high biocontainment aeromedical evacuation, in a sort of global health diplomacy.
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Affiliation(s)
- Roberto Biselli
- Ispettorato Generale della Sanità Militare, Stato Maggiore della Difesa, Via S. Stefano Rotondo 4, 00184 Roma, Italy
| | - Roberto Nisini
- Dipartimento di Malattie Infettive, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Roma, Italy
| | - Florigio Lista
- Dipartimento Scientifico, Policlinico Militare, Comando Logistico dell’Esercito, Via S. Stefano Rotondo 4, 00184 Roma, Italy
| | - Alberto Autore
- Osservatorio Epidemiologico della Difesa, Ispettorato Generale della Sanità Militare, Stato Maggiore della Difesa, Via S. Stefano Rotondo 4, 00184 Roma, Italy
| | - Marco Lastilla
- Istituto di Medicina Aerospaziale, Comando Logistico dell’Aeronautica Militare, Viale Piero Gobetti 2, 00185 Roma, Italy
| | - Giuseppe De Lorenzo
- Comando Generale dell’Arma dei Carabinieri, Dipartimento per l’Organizzazione Sanitaria e Veterinaria, Viale Romania 45, 00197 Roma, Italy
| | - Mario Stefano Peragallo
- Centro Studi e Ricerche di Sanità e Veterinaria, Comando Logistico dell’Esercito, Via S. Stefano Rotondo 4, 00184 Roma, Italy
| | - Tommaso Stroffolini
- Dipartimento di Malattie Infettive e Tropicali, Policlinico Umberto I, 00161 Roma, Italy
| | - Raffaele D’Amelio
- Dipartimento di Medicina Clinica e Molecolare, Sapienza Università di Roma, Via di Grottarossa 1035-1039, 00189 Roma, Italy
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Casalino L, Seitz C, Lederhofer J, Tsybovsky Y, Wilson IA, Kanekiyo M, Amaro RE. Breathing and tilting: mesoscale simulations illuminate influenza glycoprotein vulnerabilities. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.08.02.502576. [PMID: 35982676 PMCID: PMC9387122 DOI: 10.1101/2022.08.02.502576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Influenza virus has resurfaced recently from inactivity during the early stages of the COVID-19 pandemic, raising serious concerns about the nature and magnitude of future epidemics. The main antigenic targets of influenza virus are two surface glycoproteins, hemagglutinin (HA) and neuraminidase (NA). Whereas the structural and dynamical properties of both glycoproteins have been studied previously, the understanding of their plasticity in the whole-virion context is fragmented. Here, we investigate the dynamics of influenza glycoproteins in a crowded protein environment through mesoscale all-atom molecular dynamics simulations of two evolutionary-linked glycosylated influenza A whole-virion models. Our simulations reveal and kinetically characterize three main molecular motions of influenza glycoproteins: NA head tilting, HA ectodomain tilting, and HA head breathing. The flexibility of HA and NA highlights antigenically relevant conformational states, as well as facilitates the characterization of a novel monoclonal antibody, derived from human convalescent plasma, that binds to the underside of the NA head. Our work provides previously unappreciated views on the dynamics of HA and NA, advancing the understanding of their interplay and suggesting possible strategies for the design of future vaccines and antivirals against influenza.
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Affiliation(s)
- Lorenzo Casalino
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Christian Seitz
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Julia Lederhofer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yaroslav Tsybovsky
- Electron Microscopy Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD 21702, United States
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, United States
| | - Masaru Kanekiyo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Rommie E. Amaro
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
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73
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Application of a ddRT-PCR to quantify seasonal influenza virus for viral isolation. BIOSAFETY AND HEALTH 2022. [DOI: 10.1016/j.bsheal.2022.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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74
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Gass JD, Kellogg HK, Hill NJ, Puryear WB, Nutter FB, Runstadler JA. Epidemiology and Ecology of Influenza A Viruses among Wildlife in the Arctic. Viruses 2022; 14:1531. [PMID: 35891510 PMCID: PMC9315492 DOI: 10.3390/v14071531] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 07/10/2022] [Accepted: 07/10/2022] [Indexed: 02/01/2023] Open
Abstract
Arctic regions are ecologically significant for the environmental persistence and geographic dissemination of influenza A viruses (IAVs) by avian hosts and other wildlife species. Data describing the epidemiology and ecology of IAVs among wildlife in the arctic are less frequently published compared to southern temperate regions, where prevalence and subtype diversity are more routinely documented. Following PRISMA guidelines, this systematic review addresses this gap by describing the prevalence, spatiotemporal distribution, and ecological characteristics of IAVs detected among wildlife and the environment in this understudied region of the globe. The literature search was performed in PubMed and Google Scholar using a set of pre-defined search terms to identify publications reporting on IAVs in Arctic regions between 1978 and February 2022. A total of 2125 articles were initially screened, 267 were assessed for eligibility, and 71 articles met inclusion criteria. IAVs have been detected in multiple wildlife species in all Arctic regions, including seabirds, shorebirds, waterfowl, seals, sea lions, whales, and terrestrial mammals, and in the environment. Isolates from wild birds comprise the majority of documented viruses derived from wildlife; however, among all animals and environmental matrices, 26 unique low and highly pathogenic subtypes have been characterized in the scientific literature from Arctic regions. Pooled prevalence across studies indicates 4.23% for wild birds, 3.42% among tested environmental matrices, and seroprevalences of 9.29% and 1.69% among marine and terrestrial mammals, respectively. Surveillance data are geographically biased, with most data from the Alaskan Arctic and many fewer reports from the Russian, Canadian, North Atlantic, and Western European Arctic. We highlight multiple important aspects of wildlife host, pathogen, and environmental ecology of IAVs in Arctic regions, including the role of avian migration and breeding cycles for the global spread of IAVs, evidence of inter-species and inter-continental reassortment at high latitudes, and how climate change-driven ecosystem shifts, including changes in the seasonal availability and distribution of dietary resources, have the potential to alter host-pathogen-environment dynamics in Arctic regions. We conclude by identifying gaps in knowledge and propose priorities for future research.
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Affiliation(s)
- Jonathon D. Gass
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA 01536, USA; (H.K.K.); (W.B.P.); (F.B.N.); (J.A.R.)
| | - Hunter K. Kellogg
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA 01536, USA; (H.K.K.); (W.B.P.); (F.B.N.); (J.A.R.)
| | - Nichola J. Hill
- Department of Biology, University of Massachusetts, Boston, MA 02125, USA;
| | - Wendy B. Puryear
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA 01536, USA; (H.K.K.); (W.B.P.); (F.B.N.); (J.A.R.)
| | - Felicia B. Nutter
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA 01536, USA; (H.K.K.); (W.B.P.); (F.B.N.); (J.A.R.)
| | - Jonathan A. Runstadler
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA 01536, USA; (H.K.K.); (W.B.P.); (F.B.N.); (J.A.R.)
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75
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Chen TH, Chen CC, Wu SC. Neuraminidase (NA) 370-Loop Mutations of the 2009 Pandemic H1N1 Viruses Affect NA Enzyme Activity, Hemagglutination Titer, Mouse Virulence, and Inactivated-Virus Immunogenicity. Viruses 2022; 14:v14061304. [PMID: 35746775 PMCID: PMC9230709 DOI: 10.3390/v14061304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/07/2022] [Accepted: 06/10/2022] [Indexed: 11/23/2022] Open
Abstract
Hemagglutinin (HA) and neuraminidase (NA) are the two major envelope proteins of influenza viruses. The spatial organization of HA and NA on the virus surface needs to be optimized to promote viral fitness, host specificity, transmissibility, infectivity, and virulence. We previously demonstrated that the recombinant NA protein of the 2009 pandemic H1N1 (pH1N1) with the I365T/S366N mutation in the NA 370-loop elicited higher NA-inhibition antibody titers against the homologous pH1N1 virus and three heterologous H5N1, H3N2, and H7N9 viruses in mice. In this study, we used PR8-based reverse genetics (RG) by replacing the HA and NA genes of A/Texas/05/2009 pH1N1 virus to obtain the wild-type pH1N1 and three NA 370-loop mutant viruses of pH1N1 (I365T/S366N), RG pH1N1 (I365E/S366D), and RG pH1N1 (I365T/S366A). Our results revealed that the viral NA enzyme activity increased for the RG pH1N1(I365T/S366N) and RG pH1N1 (I365E/S366D) viruses but reduced for the RG pH1N1 (I365T/S366A) virus. The increased or decreased NA enzyme activity was found to correlate with the increase or decrease in HA titers of these NA 370-loop mutant viruses. All of these three NA 370-loop mutant RG pH1N1 viruses were less virulent than the wild-type RG pH1N1 virus in mice. Immunizations with the inactivated viruses carrying the three NA 370-loop mutations and the wild-type RG pH1N1 virus were found to elicit approximately the same titers of NA-inhibition antibodies against H1N1 and H5N1 viruses. These results may provide information for developing NA-based influenza virus vaccines.
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Affiliation(s)
- Ting-Hsuan Chen
- Institute of Biotechnology, National Tsing Hua University, Hsinchu 30013, Taiwan;
| | - Chung-Chu Chen
- Department of Internal Medicine, MacKay Memorial Hospital, Hsinchu 30071, Taiwan;
- Teaching Center of Natural Science, Minghsin University of Science and Technology, Hsinchu 30401, Taiwan
| | - Suh-Chin Wu
- Institute of Biotechnology, National Tsing Hua University, Hsinchu 30013, Taiwan;
- Department of Medical Science, National Tsing Hua University, Hsinchu 30013, Taiwan
- Adimmune Corporation, Taichung 42723, Taiwan
- Correspondence:
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Selvaraj C, Shri GR, Vijayakumar R, Alothaim AS, Ramya S, Singh SK. Viral hijacking mechanism in humans through protein-protein interactions. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 131:261-276. [PMID: 35871893 DOI: 10.1016/bs.apcsb.2022.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Numerous viruses have evolved mechanisms to inhibit or alter the host cell's apoptotic response as part of their coevolution with their hosts. The analysis of virus-host protein interactions require an in-depth understanding of both the viral and host protein structures and repertoires, as well as evolutionary mechanisms and pertinent biological facts. Throughout the course of a viral infection, there is constant battle for binding between virus and cellular proteins. Exogenous interfaces facilitating viral-host interactions are well known for constantly targeting and suppressing endogenous interfaces mediating intraspecific interactions, such as viral-viral and host-host connections. In these interactions, the protein-protein interactions (PPIs), are mostly shown as networks (protein interaction networks, PINs), with proteins represented as nodes and their interactions represented as edges. Host proteins with a higher degree of connectivity are more likely to interact with viral proteins. Due to technical advancements, three-dimensional interactions may now be visualized computationally utilizing molecular modeling and cryo-EM approaches. The uniqueness of viral domain repertoires, their evolution, and their activities during viral infection make viruses fascinating models for research. This chapter aims to provide readers a complete picture of the viral hijacking mechanism in protein-protein interactions.
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Affiliation(s)
- Chandrabose Selvaraj
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India.
| | - Gurunathan Rubha Shri
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Rajendran Vijayakumar
- Department of Biology, College of Science in Zulfi, Majmaah University, Majmaah, Saudi Arabia
| | - Abdulaziz S Alothaim
- Department of Biology, College of Science in Zulfi, Majmaah University, Majmaah, Saudi Arabia
| | - Saravanan Ramya
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Sanjeev Kumar Singh
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India.
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The Contribution of Viral Proteins to the Synergy of Influenza and Bacterial Co-Infection. Viruses 2022; 14:v14051064. [PMID: 35632805 PMCID: PMC9143653 DOI: 10.3390/v14051064] [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] [Received: 04/06/2022] [Revised: 05/12/2022] [Accepted: 05/12/2022] [Indexed: 02/04/2023] Open
Abstract
A severe course of acute respiratory disease caused by influenza A virus (IAV) infection is often linked with subsequent bacterial superinfection, which is difficult to cure. Thus, synergistic influenza-bacterial co-infection represents a serious medical problem. The pathogenic changes in the infected host are accelerated as a consequence of IAV infection, reflecting its impact on the host immune response. IAV infection triggers a complex process linked with the blocking of innate and adaptive immune mechanisms required for effective antiviral defense. Such disbalance of the immune system allows for easier initiation of bacterial superinfection. Therefore, many new studies have emerged that aim to explain why viral-bacterial co-infection can lead to severe respiratory disease with possible fatal outcomes. In this review, we discuss the key role of several IAV proteins-namely, PB1-F2, hemagglutinin (HA), neuraminidase (NA), and NS1-known to play a role in modulating the immune defense of the host, which consequently escalates the development of secondary bacterial infection, most often caused by Streptococcus pneumoniae. Understanding the mechanisms leading to pathological disorders caused by bacterial superinfection after the previous viral infection is important for the development of more effective means of prevention; for example, by vaccination or through therapy using antiviral drugs targeted at critical viral proteins.
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78
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Martins de Camargo M, Caetano AR, Ferreira de Miranda Santos IK. Evolutionary pressures rendered by animal husbandry practices for avian influenza viruses to adapt to humans. iScience 2022; 25:104005. [PMID: 35313691 PMCID: PMC8933668 DOI: 10.1016/j.isci.2022.104005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Commercial poultry operations produce and crowd billions of birds every year, which is a source of inexpensive animal protein. Commercial poultry is intensely bred for desirable production traits, and currently presents very low variability at the major histocompatibility complex. This situation dampens the advantages conferred by the MHC’s high genetic variability, and crowding generates immunosuppressive stress. We address the proteins of influenza A viruses directly and indirectly involved in host specificities. We discuss how mutants with increased virulence and/or altered host specificity may arise if few class I alleles are the sole selective pressure on avian viruses circulating in immunocompromised poultry. This hypothesis is testable with peptidomics of MHC ligands. Breeding strategies for commercial poultry can easily and inexpensively include high variability of MHC as a trait of interest, to help save billions of dollars as a disease burden caused by influenza and decrease the risk of selecting highly virulent strains.
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79
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Amirgazin A, Shevtsov A, Karibayev T, Berdikulov M, Kozhakhmetova T, Syzdykova L, Ramankulov Y, Shustov AV. Highly pathogenic avian influenza virus of the A/H5N8 subtype, clade 2.3.4.4b, caused outbreaks in Kazakhstan in 2020. PeerJ 2022; 10:e13038. [PMID: 35256921 PMCID: PMC8898005 DOI: 10.7717/peerj.13038] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 02/09/2022] [Indexed: 01/11/2023] Open
Abstract
Background Large poultry die-offs happened in Kazakhstan during autumn of 2020. The birds' disease appeared to be avian influenza. Northern Kazakhstan was hit first and then the disease propagated across the country affecting eleven provinces. This study reports the results of full-genome sequencing of viruses collected during the outbreaks and investigation of their relationship to avian influenza virus isolates in the contemporary circulation in Eurasia. Methods Samples were collected from diseased birds during the 2020 outbreaks in Kazakhstan. Initial virus detection and subtyping was done using RT-PCR. Ten samples collected during expeditions to Northern and Southern Kazakhstan were used for full-genome sequencing of avian influenza viruses. Phylogenetic analysis was used to compare viruses from Kazakhstan to viral isolates from other world regions. Results Phylogenetic trees for hemagglutinin and neuraminidase show that viruses from Kazakhstan belong to the A/H5N8 subtype and to the hemagglutinin H5 clade 2.3.4.4b. Deduced hemagglutinin amino acid sequences in all Kazakhstan's viruses in this study contain the polybasic cleavage site (KRRKR-G) indicative of the highly pathogenic phenotype. Building phylogenetic trees with the Bayesian phylogenetics results in higher statistical support for clusters than using distance methods. The Kazakhstan's viruses cluster with isolates from Southern Russia, the Russian Caucasus, the Ural region, and southwestern Siberia. Other closely related prototypes are from Eastern Europe. The Central Asia Migratory Flyway passes over Kazakhstan and birds have intermediate stops in Northern Kazakhstan. It is postulated that the A/H5N8 subtype was introduced with migrating birds. Conclusion The findings confirm the introduction of the highly pathogenic avian influenza viruses of the A/Goose/Guangdong/96 (Gs/GD) H5 lineage in Kazakhstan. This virus poses a tangible threat to public health. Considering the results of this study, it looks justifiable to undertake measures in preparation, such as install sentinel surveillance for human cases of avian influenza in the largest pulmonary units, develop a human A/H5N8 vaccine and human diagnostics capable of HPAI discrimination.
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Affiliation(s)
- Asylulan Amirgazin
- National Center for Biotechnology, Nur-Sultan, Akmola Region, Kazakhstan
| | - Alexandr Shevtsov
- National Center for Biotechnology, Nur-Sultan, Akmola Region, Kazakhstan
| | - Talgat Karibayev
- National Reference Veterinary Center, Nur-Sultan, Akmola Region, Kazakhstan
| | - Maxat Berdikulov
- National Reference Veterinary Center, Nur-Sultan, Akmola Region, Kazakhstan
| | | | - Laura Syzdykova
- National Center for Biotechnology, Nur-Sultan, Akmola Region, Kazakhstan
| | - Yerlan Ramankulov
- National Center for Biotechnology, Nur-Sultan, Akmola Region, Kazakhstan,National Laboratory Astana, Nazarbayev University, Nur-Sultan, Akmola Region, Kazakhstan
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80
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Wang H, Zang Y, Zhao Y, Hao D, Kang Y, Zhang J, Zhang Z, Zhang L, Yang Z, Zhang S. Sequence Matching between Hemagglutinin and Neuraminidase through Sequence Analysis Using Machine Learning. Viruses 2022; 14:v14030469. [PMID: 35336876 PMCID: PMC8950662 DOI: 10.3390/v14030469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/15/2022] [Accepted: 02/17/2022] [Indexed: 01/27/2023] Open
Abstract
To date, many experiments have revealed that the functional balance between hemagglutinin (HA) and neuraminidase (NA) plays a crucial role in viral mobility, production, and transmission. However, whether and how HA and NA maintain balance at the sequence level needs further investigation. Here, we applied principal component analysis and hierarchical clustering analysis on thousands of HA and NA sequences of A/H1N1 and A/H3N2. We discovered significant coevolution between HA and NA at the sequence level, which is closely related to the type of host species and virus epidemic years. Furthermore, we propose a sequence-to-sequence transformer model (S2STM), which mainly consists of an encoder and a decoder that adopts a multi-head attention mechanism for establishing the mapping relationship between HA and NA sequences. The training results reveal that the S2STM can effectively realize the “translation” from HA to NA or vice versa, thereby building a relationship network between them. Our work combines unsupervised and supervised machine learning methods to identify the sequence matching between HA and NA, which will advance our understanding of IAVs’ evolution and also provide a novel idea for sequence analysis methods.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Zhiwei Yang
- Correspondence: (Z.Y.); (S.Z.); Tel.: +86-029-8266-8634 (Z.Y.); +86-029-8266-0915 (S.Z.)
| | - Shengli Zhang
- Correspondence: (Z.Y.); (S.Z.); Tel.: +86-029-8266-8634 (Z.Y.); +86-029-8266-0915 (S.Z.)
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81
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An SH, Son SE, Song JH, Hong SM, Lee CY, Lee NH, Jeong YJ, Choi JG, Lee YJ, Kang HM, Choi KS, Kwon HJ. Selection of an Optimal Recombinant Egyptian H9N2 Avian Influenza Vaccine Strain for Poultry with High Antigenicity and Safety. Vaccines (Basel) 2022; 10:vaccines10020162. [PMID: 35214621 PMCID: PMC8876024 DOI: 10.3390/vaccines10020162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 01/17/2022] [Accepted: 01/20/2022] [Indexed: 02/05/2023] Open
Abstract
For the development of an optimized Egyptian H9N2 vaccine candidate virus for poultry, various recombinant Egyptian H9N2 viruses generated by a PR8-based reverse genetics system were compared in terms of their productivity and biosafety since Egyptian H9N2 avian influenza viruses already possess mammalian pathogenicity-related mutations in the hemagglutinin (HA), neuraminidase (NA), and PB2 genes. The Egyptian HA and NA genes were more compatible with PR8 than with H9N2 AIV (01310) internal genes, and the 01310-derived recombinant H9N2 strains acquired the L226Q reverse mutation in HA after passages in eggs. Additionally, the introduction of a strong promoter at the 3′-ends of PB2 and PB1 genes induced an additional mutation of P221S. When recombinant Egyptian H9N2 viruses with intact or reverse mutated HA (L226Q and P221S) and NA (prototypic 2SBS) were compared, the virus with HA and NA mutations had high productivity in ECES but was lower in antigenicity when used as an inactivated vaccine due to its high binding affinity into non-specific inhibitors in eggs. Finally, we substituted the PB2 gene of PR8 with 01310 to remove the replication ability in mammalian hosts and successfully generated the best recombinant vaccine candidate in terms of immunogenicity, antigenicity, and biosafety.
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Affiliation(s)
- Se-Hee An
- Laboratory of Avian Diseases, Department of Farm Animal Medicine, College of Veterinary Medicine and BK21 PLUS for Veterinary Science, Seoul National University, 1, Gwanak-ro, Seoul 88026, Korea; (S.-H.A.); (S.-E.S.); (J.-H.S.); (S.-M.H.)
- Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 88026, Korea
| | - Seung-Eun Son
- Laboratory of Avian Diseases, Department of Farm Animal Medicine, College of Veterinary Medicine and BK21 PLUS for Veterinary Science, Seoul National University, 1, Gwanak-ro, Seoul 88026, Korea; (S.-H.A.); (S.-E.S.); (J.-H.S.); (S.-M.H.)
| | - Jin-Ha Song
- Laboratory of Avian Diseases, Department of Farm Animal Medicine, College of Veterinary Medicine and BK21 PLUS for Veterinary Science, Seoul National University, 1, Gwanak-ro, Seoul 88026, Korea; (S.-H.A.); (S.-E.S.); (J.-H.S.); (S.-M.H.)
| | - Seung-Min Hong
- Laboratory of Avian Diseases, Department of Farm Animal Medicine, College of Veterinary Medicine and BK21 PLUS for Veterinary Science, Seoul National University, 1, Gwanak-ro, Seoul 88026, Korea; (S.-H.A.); (S.-E.S.); (J.-H.S.); (S.-M.H.)
- Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 88026, Korea
| | - Chung-Young Lee
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA;
| | - Nak-Hyung Lee
- KBNP, Inc., 235-9, Chusa-ro, Sinam-myeon, Yesan-gun 32417, Korea; (N.-H.L.); (Y.-J.J.)
| | - Young-Ju Jeong
- KBNP, Inc., 235-9, Chusa-ro, Sinam-myeon, Yesan-gun 32417, Korea; (N.-H.L.); (Y.-J.J.)
| | - Jun-Gu Choi
- Animal and Plant Quarantine Agency, Gimcheon-si 39960, Korea; (J.-G.C.); (Y.-J.L.); (H.-M.K.)
| | - Youn-Jeong Lee
- Animal and Plant Quarantine Agency, Gimcheon-si 39960, Korea; (J.-G.C.); (Y.-J.L.); (H.-M.K.)
| | - Hyun-Mi Kang
- Animal and Plant Quarantine Agency, Gimcheon-si 39960, Korea; (J.-G.C.); (Y.-J.L.); (H.-M.K.)
| | - Kang-Seuk Choi
- Laboratory of Avian Diseases, Department of Farm Animal Medicine, College of Veterinary Medicine and BK21 PLUS for Veterinary Science, Seoul National University, 1, Gwanak-ro, Seoul 88026, Korea; (S.-H.A.); (S.-E.S.); (J.-H.S.); (S.-M.H.)
- Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 88026, Korea
- Correspondence: (K.-S.C.); (H.-J.K.); Tel.: +82-2-880-1266 (K.-S.C. & H.-J.K.); Fax: +82-2-885-6614 (H.-J.K.)
| | - Hyuk-Joon Kwon
- Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 88026, Korea
- Laboratory of Poultry Medicine, Department of Farm Animal Medicine, College of Veterinary Medicine and BK21 PLUS for Veterinary Science, Seoul National University, 1, Gwanak-ro, Seoul 88026, Korea
- Farm Animal Clinical Training and Research Center (FACTRC), GBST, Seoul National University, Seoul 88026, Korea
- Correspondence: (K.-S.C.); (H.-J.K.); Tel.: +82-2-880-1266 (K.-S.C. & H.-J.K.); Fax: +82-2-885-6614 (H.-J.K.)
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Influenza Vaccine: An Engineering Vision from Virological Importance to Production. BIOTECHNOL BIOPROC E 2022; 27:714-738. [PMID: 36313971 PMCID: PMC9589582 DOI: 10.1007/s12257-022-0115-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 06/06/2022] [Accepted: 06/12/2022] [Indexed: 01/26/2023]
Abstract
According to data from the World Health Organization (WHO) every year, millions of people are affected by flu. Flu is a disease caused by influenza viruses. For preventing this, seasonal influenza vaccinations are widely considered the most efficient way to protect against the negative effects of the flu. To date, there is no "one-size-fits-all" vaccine that can be effective all over the world to protect against all seasonal or pandemic influenza virus types. Because influenza virus transforms its genetic structure and it can emerges as immunogenically new (antigenic drift) which causes epidemics or new virus subtype (antigenic shift) which causes pandemics. As a result, annual revaccination or new subtype viral vaccine development is required. Currently, three types of vaccines (inactivated, live attenuated, and recombinant) are approved in different countries. These can be named "conventional influenza vaccines" and their production are based on eggs or cell culture. Although, there is good effort to develop new influenza vaccines for broader and longer period of time protection. In this sense these candidate vaccines are called "universal influenza vaccines". In this article, after we mentioned the short history of flu then virus morphology and infection, we explained the diseases caused by the influenza virus in humans. Afterward, we explained in detail the production methods of available influenza vaccines, types of bioreactors used in cell culture based production, conventional and new vaccine types, and development strategies for better vaccines.
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83
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Jeyaram RA, Radha CA. Investigation on the Binding Properties of N1 Neuraminidase of H5N1 Influenza Virus in Complex with Fluorinated Sialic Acid Analog Compounds—a Study by Molecular Docking and Molecular Dynamics Simulations. BRAZILIAN JOURNAL OF PHYSICS 2022; 52:21. [PMCID: PMC8656140 DOI: 10.1007/s13538-021-01009-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 10/12/2021] [Indexed: 03/19/2024]
Abstract
Worldwide, only two types of antiviral inhibitors (M2 ion channel protein inhibitor and Neuraminidase inhibitors) are approved to treat the influenza viral infection. But the mutation of amino acid sequence in the viral membrane proteins creates the viral resistance to existing antiviral drugs or inhibitors. So the corresponding antiviral drugs have to be reformulated to match these antigenic variations. Fluorination on the carbon–based molecule significantly enriches its biological properties. Hence this study is motivated to design the fluorinated sialic acid (SIA) analog inhibitors for the neuraminidase of H5N1 influenza A virus by substituting fluorine atom at different hydroxyls (O2, O4, O7, O8, and O9) of sialic acid. 100 ns molecular dynamics simulations are carried out for each protein–ligand complex system. NAMD pair interaction energy and MM–PBSA binding free energy calculations predict two possible binding modes for N1–SIA_F2, N1–SIA_F4, and N1–SIA_F7 complexes and single binding mode for N1–SIA_F8 and N1–SIA_F9 complexes. RMSD, RMSF, and hydrogen bonding analyses are used to understand the conformational flexibility and structural stability of each complex system. It has been concluded that the fluorinated sialic acid drug candidates SIA_F2 and SIA_F7 have better inhibiting potency against the N1 neuraminidase of H5N1 influenza virus.
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Affiliation(s)
- R. A. Jeyaram
- Research Laboratory of Molecular Biophysics, Department of Physics, School of Advanced Sciences, Vellore Institute of Technology, Vellore, Tamil Nadu India
| | - C. Anu Radha
- Research Laboratory of Molecular Biophysics, Department of Physics, School of Advanced Sciences, Vellore Institute of Technology, Vellore, Tamil Nadu India
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84
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Chivukula S, Plitnik T, Tibbitts T, Karve S, Dias A, Zhang D, Goldman R, Gopani H, Khanmohammed A, Sarode A, Cooper D, Yoon H, Kim Y, Yan Y, Mundle ST, Groppo R, Beauvais A, Zhang J, Anosova NG, Lai C, Li L, Ulinski G, Piepenhagen P, DiNapoli J, Kalnin KV, Landolfi V, Swearingen R, Fu TM, DeRosa F, Casimiro D. Development of multivalent mRNA vaccine candidates for seasonal or pandemic influenza. NPJ Vaccines 2021; 6:153. [PMID: 34916519 PMCID: PMC8677760 DOI: 10.1038/s41541-021-00420-6] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 11/24/2021] [Indexed: 11/23/2022] Open
Abstract
Recent approval of mRNA vaccines for emergency use against COVID-19 is likely to promote rapid development of mRNA-based vaccines targeting a wide range of infectious diseases. Compared to conventional approaches, this vaccine modality promises comparable potency while substantially accelerating the pace of development and deployment of vaccine doses. Already demonstrated successfully for single antigen vaccines such as for COVID-19, this technology could be optimized for complex multi-antigen vaccines. Herein, utilizing multiple influenza antigens, we demonstrated the suitability of the mRNA therapeutic (MRT) platform for such applications. Seasonal influenza vaccines have three or four hemagglutinin (HA) antigens of different viral subtypes. In addition, influenza neuraminidase (NA), a tetrameric membrane protein, is identified as an antigen that has been linked to protective immunity against severe viral disease. We detail the efforts in optimizing formulations of influenza candidates that use unmodified mRNA encoding full-length HA or full-length NA encapsulated in lipid nanoparticles (LNPs). HA and NA mRNA-LNP formulations, either as monovalent or as multivalent vaccines, induced strong functional antibody and cellular responses in non-human primates and such antigen-specific antibody responses were associated with protective efficacy against viral challenge in mice.
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Affiliation(s)
| | | | | | | | - Anusha Dias
- Translate Bio, a Sanofi Company, Lexington, MA, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Lu Li
- Sanofi Pasteur, Cambridge, MA, USA
| | | | | | | | | | | | | | - Tong-Ming Fu
- Texas Therapeutics Institute, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Frank DeRosa
- Translate Bio, a Sanofi Company, Lexington, MA, USA
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85
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Kumar P, Kumar A. Correlation intensity index (CII) as a benchmark of predictive potential: Construction of quantitative structure activity relationship models for anti-influenza single-stranded DNA aptamers using Monte Carlo optimization. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.131205] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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86
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Creytens S, Pascha MN, Ballegeer M, Saelens X, de Haan CAM. Influenza Neuraminidase Characteristics and Potential as a Vaccine Target. Front Immunol 2021; 12:786617. [PMID: 34868073 PMCID: PMC8635103 DOI: 10.3389/fimmu.2021.786617] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 10/29/2021] [Indexed: 12/28/2022] Open
Abstract
Neuraminidase of influenza A and B viruses plays a critical role in the virus life cycle and is an important target of the host immune system. Here, we highlight the current understanding of influenza neuraminidase structure, function, antigenicity, immunogenicity, and immune protective potential. Neuraminidase inhibiting antibodies have been recognized as correlates of protection against disease caused by natural or experimental influenza A virus infection in humans. In the past years, we have witnessed an increasing interest in the use of influenza neuraminidase to improve the protective potential of currently used influenza vaccines. A number of well-characterized influenza neuraminidase-specific monoclonal antibodies have been described recently, most of which can protect in experimental challenge models by inhibiting the neuraminidase activity or by Fc receptor-dependent mechanisms. The relative instability of the neuraminidase poses a challenge for protein-based antigen design. We critically review the different solutions that have been proposed to solve this problem, ranging from the inclusion of stabilizing heterologous tetramerizing zippers to the introduction of inter-protomer stabilizing mutations. Computationally engineered neuraminidase antigens have been generated that offer broad, within subtype protection in animal challenge models. We also provide an overview of modern vaccine technology platforms that are compatible with the induction of robust neuraminidase-specific immune responses. In the near future, we will likely see the implementation of influenza vaccines that confront the influenza virus with a double punch: targeting both the hemagglutinin and the neuraminidase.
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MESH Headings
- Antibodies, Viral/blood
- Antibodies, Viral/immunology
- Antigenic Drift and Shift
- Antigens, Viral/immunology
- Antigens, Viral/ultrastructure
- Catalytic Domain/genetics
- Catalytic Domain/immunology
- Cross Protection
- Evolution, Molecular
- Humans
- Immunogenicity, Vaccine
- Influenza Vaccines/administration & dosage
- Influenza Vaccines/genetics
- Influenza Vaccines/immunology
- Influenza, Human/immunology
- Influenza, Human/prevention & control
- Influenza, Human/virology
- Alphainfluenzavirus/enzymology
- Alphainfluenzavirus/genetics
- Alphainfluenzavirus/immunology
- Betainfluenzavirus/enzymology
- Betainfluenzavirus/genetics
- Betainfluenzavirus/immunology
- Mutation
- Nanoparticles
- Neuraminidase/administration & dosage
- Neuraminidase/genetics
- Neuraminidase/immunology
- Neuraminidase/ultrastructure
- Vaccines, Synthetic/administration & dosage
- Vaccines, Synthetic/genetics
- Vaccines, Synthetic/immunology
- Vaccines, Synthetic/ultrastructure
- Viral Proteins/administration & dosage
- Viral Proteins/genetics
- Viral Proteins/immunology
- Viral Proteins/ultrastructure
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Affiliation(s)
- Sarah Creytens
- Vlaams Instituut voor Biotechnologie (VIB)-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Mirte N. Pascha
- Section Virology, Division Infectious Diseases & Immunology, Department of Biomolecular Health Sciences, Utrecht University, Utrecht, Netherlands
| | - Marlies Ballegeer
- Vlaams Instituut voor Biotechnologie (VIB)-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Xavier Saelens
- Vlaams Instituut voor Biotechnologie (VIB)-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Cornelis A. M. de Haan
- Section Virology, Division Infectious Diseases & Immunology, Department of Biomolecular Health Sciences, Utrecht University, Utrecht, Netherlands
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87
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Yeo JY, Gan SKE. Peering into Avian Influenza A(H5N8) for a Framework towards Pandemic Preparedness. Viruses 2021; 13:2276. [PMID: 34835082 PMCID: PMC8622263 DOI: 10.3390/v13112276] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/20/2021] [Accepted: 11/12/2021] [Indexed: 12/13/2022] Open
Abstract
2014 marked the first emergence of avian influenza A(H5N8) in Jeonbuk Province, South Korea, which then quickly spread worldwide. In the midst of the 2020-2021 H5N8 outbreak, it spread to domestic poultry and wild waterfowl shorebirds, leading to the first human infection in Astrakhan Oblast, Russia. Despite being clinically asymptomatic and without direct human-to-human transmission, the World Health Organization stressed the need for continued risk assessment given the nature of Influenza to reassort and generate novel strains. Given its promiscuity and easy cross to humans, the urgency to understand the mechanisms of possible species jumping to avert disastrous pandemics is increasing. Addressing the epidemiology of H5N8, its mechanisms of species jumping and its implications, mutational and reassortment libraries can potentially be built, allowing them to be tested on various models complemented with deep-sequencing and automation. With knowledge on mutational patterns, cellular pathways, drug resistance mechanisms and effects of host proteins, we can be better prepared against H5N8 and other influenza A viruses.
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Affiliation(s)
- Joshua Yi Yeo
- Antibody & Product Development Lab, EDDC-BII, Agency for Science, Technology and Research (A*STAR), Singapore 138672, Singapore;
| | - Samuel Ken-En Gan
- Antibody & Product Development Lab, EDDC-BII, Agency for Science, Technology and Research (A*STAR), Singapore 138672, Singapore;
- APD SKEG Pte Ltd., Singapore 439444, Singapore
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88
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Deciphering transmission dynamics and spillover of avian influenza viruses from avian species to swine populations globally. Virus Genes 2021; 57:541-555. [PMID: 34625868 PMCID: PMC8500266 DOI: 10.1007/s11262-021-01873-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 09/26/2021] [Indexed: 12/21/2022]
Abstract
Genome sequences of eleven avian influenza virus (AIV) subtypes have been reported in swine populations from seven countries until August 2020. To unravel the transmission dynamics and spillover events of AIVs from avian reservoirs to swine, full-length hemagglutinin (HA) sequences of AIV subtypes (n = 11) reported from various avian species and swine were retrieved from the ‘Influenza Research Database’. Phylogenetic analysis identified closely related avian and swine AIV sequences suggesting potential spillover events from multiple domestic and wild avian species, including chicken, duck, pigeon, goose, quail, and aquatic birds to swine. Furthermore, N-linked glycosylation analysis of these closely related AIV sequences supported the possibility of multiple spillover events of highly pathogenic H5N1 and low pathogenic H9N2 viruses from various avian species to swine. The principal coordinate analysis further validated these findings for H5N1 and H9N2 viruses; however, spillover events of the other nine AIV subtypes were limited. Interestingly, the presence of potential mammalian adaptation markers, particularly in some of the swine H5N1, H7N9, and H9N2 viruses, suggested that these viruses may have already adapted in swine. The occurrence and circulation of these AIVs in swine, especially the H5N1 and H9N2 viruses with numerous spillover events from the avian reservoirs to swine, pose a significant threat in terms of their reassortment with endemic swine viruses or circulating human influenza viruses within the swine which may facilitate the emergence of a novel influenza virus strain with pandemic potential.
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89
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Targovnik AM, Simonin JA, Mc Callum GJ, Smith I, Cuccovia Warlet FU, Nugnes MV, Miranda MV, Belaich MN. Solutions against emerging infectious and noninfectious human diseases through the application of baculovirus technologies. Appl Microbiol Biotechnol 2021; 105:8195-8226. [PMID: 34618205 PMCID: PMC8495437 DOI: 10.1007/s00253-021-11615-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/20/2021] [Accepted: 09/21/2021] [Indexed: 12/23/2022]
Abstract
Abstract
Baculoviruses are insect pathogens widely used as biotechnological tools in different fields of life sciences and technologies. The particular biology of these entities (biosafety viruses 1; large circular double-stranded DNA genomes, infective per se; generally of narrow host range on insect larvae; many of the latter being pests in agriculture) and the availability of molecular-biology procedures (e.g., genetic engineering to edit their genomes) and cellular resources (availability of cell lines that grow under in vitro culture conditions) have enabled the application of baculoviruses as active ingredients in pest control, as systems for the expression of recombinant proteins (Baculovirus Expression Vector Systems—BEVS) and as viral vectors for gene delivery in mammals or to display antigenic proteins (Baculoviruses applied on mammals—BacMam). Accordingly, BEVS and BacMam technologies have been introduced in academia because of their availability as commercial systems and ease of use and have also reached the human pharmaceutical industry, as incomparable tools in the development of biological products such as diagnostic kits, vaccines, protein therapies, and—though still in the conceptual stage involving animal models—gene therapies. Among all the baculovirus species, the Autographa californica multiple nucleopolyhedrovirus has been the most highly exploited in the above utilities for the human-biotechnology field. This review highlights the main achievements (in their different stages of development) of the use of BEVS and BacMam technologies for the generation of products for infectious and noninfectious human diseases. Key points • Baculoviruses can assist as biotechnological tools in human health problems. • Vaccines and diagnosis reagents produced in the baculovirus platform are described. • The use of recombinant baculovirus for gene therapy–based treatment is reviewed.
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Affiliation(s)
- Alexandra Marisa Targovnik
- Cátedra de Biotecnología, Departamento de Microbiología, Inmunología, Biotecnología y Genética, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, Buenos Aires, 1113, Argentina.
- Instituto de Nanobiotecnología (NANOBIOTEC), Facultad de Farmacia y Bioquímica, CONICET -Universidad de Buenos Aires, Junín 956, Sexto Piso, C1113AAD, 1113, Buenos Aires, Argentina.
| | - Jorge Alejandro Simonin
- Laboratorio de Ingeniería Genética y Biología Celular y Molecular, Área Virosis de Insectos, Instituto de Microbiología Básica y Aplicada, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Buenos Aires, Argentina
| | - Gregorio Juan Mc Callum
- Cátedra de Biotecnología, Departamento de Microbiología, Inmunología, Biotecnología y Genética, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, Buenos Aires, 1113, Argentina
- Instituto de Nanobiotecnología (NANOBIOTEC), Facultad de Farmacia y Bioquímica, CONICET -Universidad de Buenos Aires, Junín 956, Sexto Piso, C1113AAD, 1113, Buenos Aires, Argentina
| | - Ignacio Smith
- Cátedra de Biotecnología, Departamento de Microbiología, Inmunología, Biotecnología y Genética, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, Buenos Aires, 1113, Argentina
- Instituto de Nanobiotecnología (NANOBIOTEC), Facultad de Farmacia y Bioquímica, CONICET -Universidad de Buenos Aires, Junín 956, Sexto Piso, C1113AAD, 1113, Buenos Aires, Argentina
| | - Franco Uriel Cuccovia Warlet
- Laboratorio de Ingeniería Genética y Biología Celular y Molecular, Área Virosis de Insectos, Instituto de Microbiología Básica y Aplicada, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Buenos Aires, Argentina
| | - María Victoria Nugnes
- Laboratorio de Ingeniería Genética y Biología Celular y Molecular, Área Virosis de Insectos, Instituto de Microbiología Básica y Aplicada, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Buenos Aires, Argentina
| | - María Victoria Miranda
- Cátedra de Biotecnología, Departamento de Microbiología, Inmunología, Biotecnología y Genética, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, Buenos Aires, 1113, Argentina
- Instituto de Nanobiotecnología (NANOBIOTEC), Facultad de Farmacia y Bioquímica, CONICET -Universidad de Buenos Aires, Junín 956, Sexto Piso, C1113AAD, 1113, Buenos Aires, Argentina
| | - Mariano Nicolás Belaich
- Laboratorio de Ingeniería Genética y Biología Celular y Molecular, Área Virosis de Insectos, Instituto de Microbiología Básica y Aplicada, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Buenos Aires, Argentina
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90
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Van Poelvoorde LAE, Bogaerts B, Fu Q, De Keersmaecker SCJ, Thomas I, Van Goethem N, Van Gucht S, Winand R, Saelens X, Roosens N, Vanneste K. Whole-genome-based phylogenomic analysis of the Belgian 2016-2017 influenza A(H3N2) outbreak season allows improved surveillance. Microb Genom 2021; 7. [PMID: 34477544 PMCID: PMC8715427 DOI: 10.1099/mgen.0.000643] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Seasonal influenza epidemics are associated with high mortality and morbidity in the human population. Influenza surveillance is critical for providing information to national influenza programmes and for making vaccine composition predictions. Vaccination prevents viral infections, but rapid influenza evolution results in emerging mutants that differ antigenically from vaccine strains. Current influenza surveillance relies on Sanger sequencing of the haemagglutinin (HA) gene. Its classification according to World Health Organization (WHO) and European Centre for Disease Prevention and Control (ECDC) guidelines is based on combining certain genotypic amino acid mutations and phylogenetic analysis. Next-generation sequencing technologies enable a shift to whole-genome sequencing (WGS) for influenza surveillance, but this requires laboratory workflow adaptations and advanced bioinformatics workflows. In this study, 253 influenza A(H3N2) positive clinical specimens from the 2016–2017 Belgian season underwent WGS using the Illumina MiSeq system. HA-based classification according to WHO/ECDC guidelines did not allow classification of all samples. A new approach, considering the whole genome, was investigated based on using powerful phylogenomic tools including beast and Nextstrain, which substantially improved phylogenetic classification. Moreover, Bayesian inference via beast facilitated reassortment detection by both manual inspection and computational methods, detecting intra-subtype reassortants at an estimated rate of 15 %. Real-time analysis (i.e. as an outbreak is ongoing) via Nextstrain allowed positioning of the Belgian isolates into the globally circulating context. Finally, integration of patient data with phylogenetic groups and reassortment status allowed detection of several associations that would have been missed when solely considering HA, such as hospitalized patients being more likely to be infected with A(H3N2) reassortants, and the possibility to link several phylogenetic groups to disease severity indicators could be relevant for epidemiological monitoring. Our study demonstrates that WGS offers multiple advantages for influenza monitoring in (inter)national influenza surveillance, and proposes an improved methodology. This allows leveraging all information contained in influenza genomes, and allows for more accurate genetic characterization and reassortment detection.
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Affiliation(s)
- Laura A E Van Poelvoorde
- Transversal Activities in Applied Genomics, Sciensano, Juliette Wytsmanstraat 14, Brussels, Belgium.,National Influenza Centre, Sciensano, Juliette Wytsmanstraat 14, Brussels, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.,VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
| | - Bert Bogaerts
- Transversal Activities in Applied Genomics, Sciensano, Juliette Wytsmanstraat 14, Brussels, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,Department of Information Technology, IDLab, IMEC, Ghent University, Ghent, Belgium
| | - Qiang Fu
- Transversal Activities in Applied Genomics, Sciensano, Juliette Wytsmanstraat 14, Brussels, Belgium
| | | | - Isabelle Thomas
- National Influenza Centre, Sciensano, Juliette Wytsmanstraat 14, Brussels, Belgium
| | | | - Steven Van Gucht
- National Influenza Centre, Sciensano, Juliette Wytsmanstraat 14, Brussels, Belgium
| | - Raf Winand
- Transversal Activities in Applied Genomics, Sciensano, Juliette Wytsmanstraat 14, Brussels, Belgium
| | - Xavier Saelens
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.,VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
| | - Nancy Roosens
- Transversal Activities in Applied Genomics, Sciensano, Juliette Wytsmanstraat 14, Brussels, Belgium
| | - Kevin Vanneste
- Transversal Activities in Applied Genomics, Sciensano, Juliette Wytsmanstraat 14, Brussels, Belgium
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91
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Van Goethem N, Robert A, Bossuyt N, Van Poelvoorde LAE, Quoilin S, De Keersmaecker SCJ, Devleesschauwer B, Thomas I, Vanneste K, Roosens NHC, Van Oyen H. Evaluation of the added value of viral genomic information for predicting severity of influenza infection. BMC Infect Dis 2021; 21:785. [PMID: 34376182 PMCID: PMC8353062 DOI: 10.1186/s12879-021-06510-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 07/18/2021] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND The severity of an influenza infection is influenced by both host and viral characteristics. This study aims to assess the relevance of viral genomic data for the prediction of severe influenza A(H3N2) infections among patients hospitalized for severe acute respiratory infection (SARI), in view of risk assessment and patient management. METHODS 160 A(H3N2) influenza positive samples from the 2016-2017 season originating from the Belgian SARI surveillance were selected for whole genome sequencing. Predictor variables for severity were selected using a penalized elastic net logistic regression model from a combined host and genomic dataset, including patient information and nucleotide mutations identified in the viral genome. The goodness-of-fit of the model combining host and genomic data was compared using a likelihood-ratio test with the model including host data only. Internal validation of model discrimination was conducted by calculating the optimism-adjusted area under the Receiver Operating Characteristic curve (AUC) for both models. RESULTS The model including viral mutations in addition to the host characteristics had an improved fit ([Formula: see text]=12.03, df = 3, p = 0.007). The optimism-adjusted AUC increased from 0.671 to 0.732. CONCLUSIONS Adding genomic data (selected season-specific mutations in the viral genome) to the model containing host characteristics improved the prediction of severe influenza infection among hospitalized SARI patients, thereby offering the potential for translation into a prospective strategy to perform early season risk assessment or to guide individual patient management.
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Affiliation(s)
- Nina Van Goethem
- Scientific Directorate of Epidemiology and Public Health, Sciensano, J. Wytsmanstraat 14, 1050, Brussels, Belgium.
- Department of Epidemiology and Biostatistics, Institut de Recherche Expérimentale et Clinique, Faculty of Public Health, Université Catholique de Louvain, Clos Chapelle-aux-champs 30, 1200, Woluwe-Saint-Lambert, Belgium.
| | - Annie Robert
- Department of Epidemiology and Biostatistics, Institut de Recherche Expérimentale et Clinique, Faculty of Public Health, Université Catholique de Louvain, Clos Chapelle-aux-champs 30, 1200, Woluwe-Saint-Lambert, Belgium
| | - Nathalie Bossuyt
- Scientific Directorate of Epidemiology and Public Health, Sciensano, J. Wytsmanstraat 14, 1050, Brussels, Belgium
| | - Laura A E Van Poelvoorde
- Transversal Activities in Applied Genomics, Sciensano, J. Wytsmanstraat 14, 1050, Brussels, Belgium
| | - Sophie Quoilin
- Scientific Directorate of Epidemiology and Public Health, Sciensano, J. Wytsmanstraat 14, 1050, Brussels, Belgium
| | | | - Brecht Devleesschauwer
- Scientific Directorate of Epidemiology and Public Health, Sciensano, J. Wytsmanstraat 14, 1050, Brussels, Belgium
- Department of Veterinary Public Health and Food Safety, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Isabelle Thomas
- National Reference Center Influenza, Sciensano, J. Wytsmanstraat 14, 1050, Brussels, Belgium
| | - Kevin Vanneste
- Transversal Activities in Applied Genomics, Sciensano, J. Wytsmanstraat 14, 1050, Brussels, Belgium
| | - Nancy H C Roosens
- Transversal Activities in Applied Genomics, Sciensano, J. Wytsmanstraat 14, 1050, Brussels, Belgium
| | - Herman Van Oyen
- Scientific Directorate of Epidemiology and Public Health, Sciensano, J. Wytsmanstraat 14, 1050, Brussels, Belgium
- Department of Public Health and Primary Care, Ghent University, De Pintelaan 185, 9000, Ghent, Belgium
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92
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Abstract
Most currently used conventional influenza vaccines are based on 1940s technology. Advances in vaccine immunogen design and delivery emerging over the last decade promise new options for improving influenza vaccines. In addition, new technologies for immune profiling provide better-defined immune correlates of protection and precise surrogate biomarkers for vaccine evaluations. Major technological advances include single-cell analysis, high-throughput antibody discovery, next-generation sequencing of antibody gene transcripts, antibody ontogeny, structure-guided immunogen design, nanoparticle display, delivery and formulation options, and better adjuvants. In this review, we provide our prospective outlook for improved influenza vaccines in the foreseeable future.
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Affiliation(s)
- Masaru Kanekiyo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Barney S Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
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93
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Borey M, Blanc F, Lemonnier G, Leplat JJ, Jardet D, Rossignol MN, Ravon L, Billon Y, Bernard M, Estellé J, Rogel-Gaillard C. Links between fecal microbiota and the response to vaccination against influenza A virus in pigs. NPJ Vaccines 2021; 6:92. [PMID: 34294732 PMCID: PMC8298503 DOI: 10.1038/s41541-021-00351-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 06/11/2021] [Indexed: 02/06/2023] Open
Abstract
This study describes the associations between fecal microbiota and vaccine response variability in pigs, using 98 piglets vaccinated against the influenza A virus at 28 days of age (D28) with a booster at D49. Immune response to the vaccine is measured at D49, D56, D63, and D146 by serum levels of IAV-specific IgG and assays of hemagglutination inhibition (HAI). Analysis of the pre-vaccination microbiota characterized by 16S rRNA gene sequencing of fecal DNA reveals a higher vaccine response in piglets with a richer microbiota, and shows that 23 operational taxonomic units (OTUs) are differentially abundant between high and low IAV-specific IgG producers at D63. A stronger immune response is linked with OTUs assigned to the genus Prevotella and family Muribaculaceae, and a weaker response is linked with OTUs assigned to the genera Helicobacter and Escherichia-Shigella. A set of 81 OTUs accurately predicts IAV-specific IgG and HAI titer levels at all time points, highlighting early and late associations between pre-vaccination fecal microbiota composition and immune response to the vaccine.
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Affiliation(s)
- Marion Borey
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France.
| | - Fany Blanc
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Gaëtan Lemonnier
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | | | - Deborah Jardet
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | | | | | | | - Maria Bernard
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Jordi Estellé
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
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94
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Chen J, Wang J, Zhang J, Ly H. Advances in Development and Application of Influenza Vaccines. Front Immunol 2021; 12:711997. [PMID: 34326849 PMCID: PMC8313855 DOI: 10.3389/fimmu.2021.711997] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 06/24/2021] [Indexed: 12/24/2022] Open
Abstract
Influenza A virus is one of the most important zoonotic pathogens that can cause severe symptoms and has the potential to cause high number of deaths and great economic loss. Vaccination is still the best option to prevent influenza virus infection. Different types of influenza vaccines, including live attenuated virus vaccines, inactivated whole virus vaccines, virosome vaccines, split-virion vaccines and subunit vaccines have been developed. However, they have several limitations, such as the relatively high manufacturing cost and long production time, moderate efficacy of some of the vaccines in certain populations, and lack of cross-reactivity. These are some of the problems that need to be solved. Here, we summarized recent advances in the development and application of different types of influenza vaccines, including the recent development of viral vectored influenza vaccines. We also described the construction of other vaccines that are based on recombinant influenza viruses as viral vectors. Information provided in this review article might lead to the development of safe and highly effective novel influenza vaccines.
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Affiliation(s)
- Jidang Chen
- School of Life Science and Engineering, Foshan University, Foshan, China
| | - Jiehuang Wang
- School of Life Science and Engineering, Foshan University, Foshan, China
| | - Jipei Zhang
- School of Life Science and Engineering, Foshan University, Foshan, China
| | - Hinh Ly
- Department of Veterinary & Biomedical Sciences, University of Minnesota, Twin Cities, MN, United States
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95
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Moreira EA, Yamauchi Y, Matthias P. How Influenza Virus Uses Host Cell Pathways during Uncoating. Cells 2021; 10:1722. [PMID: 34359892 PMCID: PMC8305448 DOI: 10.3390/cells10071722] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/25/2021] [Accepted: 07/02/2021] [Indexed: 12/15/2022] Open
Abstract
Influenza is a zoonotic respiratory disease of major public health interest due to its pandemic potential, and a threat to animals and the human population. The influenza A virus genome consists of eight single-stranded RNA segments sequestered within a protein capsid and a lipid bilayer envelope. During host cell entry, cellular cues contribute to viral conformational changes that promote critical events such as fusion with late endosomes, capsid uncoating and viral genome release into the cytosol. In this focused review, we concisely describe the virus infection cycle and highlight the recent findings of host cell pathways and cytosolic proteins that assist influenza uncoating during host cell entry.
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Affiliation(s)
| | - Yohei Yamauchi
- Faculty of Life Sciences, School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, UK;
| | - Patrick Matthias
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland;
- Faculty of Sciences, University of Basel, 4031 Basel, Switzerland
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96
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Aartse A, Eggink D, Claireaux M, van Leeuwen S, Mooij P, Bogers WM, Sanders RW, Koopman G, van Gils MJ. Influenza A Virus Hemagglutinin Trimer, Head and Stem Proteins Identify and Quantify Different Hemagglutinin-Specific B Cell Subsets in Humans. Vaccines (Basel) 2021; 9:717. [PMID: 34358138 PMCID: PMC8310015 DOI: 10.3390/vaccines9070717] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/02/2021] [Accepted: 06/28/2021] [Indexed: 11/16/2022] Open
Abstract
Antibody responses against the influenza A virus hemagglutinin (HA)-protein are studied intensively because they can protect against (re)infection. Previous studies have focused on antibodies targeting the head or stem domains, while other possible specificities are often not taken into account. To study such specificities, we developed a diverse set of HA-domain proteins based on an H1N1pdm2009-like influenza virus strain, including monomeric head and trimeric stem domain, as well as the full HA-trimer. These proteins were used to study the B cell and antibody responses in six healthy human donors. A large proportion of HA-trimer B cells bound exclusively to HA-trimer probe (54-77%), while only 8-18% and 9-23% were able to recognize the stem or head probe, respectively. Monoclonal antibodies (mAbs) were isolated and three of these mAbs, targeting the different domains, were characterized in-depth to confirm the binding profile observed in flow cytometry. The head-directed mAb, targeting an epitope distinct from known head-specific mAbs, showed relatively broad H1N1 neutralization and the stem-directed mAb was able to broadly neutralize diverse H1N1 viruses. Moreover, we identified a trimer-directed mAb that did not compete with known head or stem domain specific mAbs, suggesting that it targets an unknown epitope or conformation of influenza virus' HA. These observations indicate that the described method can characterize the diverse antibody response to HA and might be able to identify HA-specific B cells and antibodies with previously unknown specificities that could be relevant for vaccine design.
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Affiliation(s)
- Aafke Aartse
- Department of Virology, Biomedical Primate Research Centre, 2288 GJ Rijswijk, The Netherlands; (A.A.); (P.M.); (W.M.B.)
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (D.E.); (M.C.); (S.v.L.); (R.W.S.)
| | - Dirk Eggink
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (D.E.); (M.C.); (S.v.L.); (R.W.S.)
| | - Mathieu Claireaux
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (D.E.); (M.C.); (S.v.L.); (R.W.S.)
| | - Sarah van Leeuwen
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (D.E.); (M.C.); (S.v.L.); (R.W.S.)
| | - Petra Mooij
- Department of Virology, Biomedical Primate Research Centre, 2288 GJ Rijswijk, The Netherlands; (A.A.); (P.M.); (W.M.B.)
| | - Willy M. Bogers
- Department of Virology, Biomedical Primate Research Centre, 2288 GJ Rijswijk, The Netherlands; (A.A.); (P.M.); (W.M.B.)
| | - Rogier W. Sanders
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (D.E.); (M.C.); (S.v.L.); (R.W.S.)
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Gerrit Koopman
- Department of Virology, Biomedical Primate Research Centre, 2288 GJ Rijswijk, The Netherlands; (A.A.); (P.M.); (W.M.B.)
| | - Marit J. van Gils
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (D.E.); (M.C.); (S.v.L.); (R.W.S.)
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97
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Barroso SPC, Vicente Dos Santos AC, Souza Dos Santos P, Dos Santos Silva Couceiro JN, Fernandes Ferreira D, Nico D, Morrot A, Lima Silva J, Cheble de Oliveira A. Inactivation of avian influenza viruses by hydrostatic pressure as a potential vaccine development approach. Access Microbiol 2021; 3:000220. [PMID: 34151171 PMCID: PMC8208760 DOI: 10.1099/acmi.0.000220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 03/04/2021] [Indexed: 11/21/2022] Open
Abstract
Vaccines are a recommended strategy for controlling influenza A infections in humans and animals. Here, we describe the effects of hydrostatic pressure on the structure, morphology and functional characteristics of avian influenza A H3N8 virus. The effect of hydrostatic pressure for 3 h on H3N8 virus revealed that the particles were resistant to this condition, and the virus displayed only a discrete conformational change. We found that pressure of 3 kbar applied for 6 h was able to inhibit haemagglutination and infectivity while virus replication was no longer observed, suggesting that full virus inactivation occurred at this point. However, the neuraminidase activity was not affected at this approach suggesting the maintenance of neutralizing antibody epitopes in this key antigen. Our data bring important information for the area of structural virology of enveloped particles and support the idea of applying pressure-induced inactivation as a tool for vaccine production.
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Affiliation(s)
- Shana Priscila Coutinho Barroso
- Laboratório de Termodinâmica de Proteínas e Estruturas Virais Gregorio Weber, Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, 21941-590, Rio de Janeiro, RJ, Brazil.,Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem, Brazil.,Laboratório de Biologia Molecular, Instituto de Pesquisas Biomédicas, Hospital Naval Marcílio Dias, Marinha do Brasil, Brazil
| | - Ana Clara Vicente Dos Santos
- Laboratório de Termodinâmica de Proteínas e Estruturas Virais Gregorio Weber, Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, 21941-590, Rio de Janeiro, RJ, Brazil.,Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem, Brazil
| | - Patrícia Souza Dos Santos
- Laboratório de Termodinâmica de Proteínas e Estruturas Virais Gregorio Weber, Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, 21941-590, Rio de Janeiro, RJ, Brazil.,Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem, Brazil.,Centro Universitário IBMR, Rio de Janeiro, RJ, Brazil
| | | | - Davis Fernandes Ferreira
- Departamento de Virologia, Instituto de Microbiologia Professor Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Dirlei Nico
- Departamento de Virologia, Instituto de Microbiologia Professor Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Alexandre Morrot
- Laboratório de Imunoparasitologia, Instituto Oswaldo Cruz, Rio de Janeiro, RJ, Brazil.,Faculdade de Medicina, Departamento de Clínica Médica, Centro de Pesquisa em Tuberculose,, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Jerson Lima Silva
- Laboratório de Termodinâmica de Proteínas e Estruturas Virais Gregorio Weber, Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, 21941-590, Rio de Janeiro, RJ, Brazil.,Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem, Brazil
| | - Andrea Cheble de Oliveira
- Laboratório de Termodinâmica de Proteínas e Estruturas Virais Gregorio Weber, Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, 21941-590, Rio de Janeiro, RJ, Brazil.,Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem, Brazil
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98
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Nance ML, Labonte JW, Adolf-Bryfogle J, Gray JJ. Development and Evaluation of GlycanDock: A Protein-Glycoligand Docking Refinement Algorithm in Rosetta. J Phys Chem B 2021; 125:10.1021/acs.jpcb.1c00910. [PMID: 34133179 PMCID: PMC8742512 DOI: 10.1021/acs.jpcb.1c00910] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Carbohydrate chains are ubiquitous in the complex molecular processes of life. These highly diverse chains are recognized by a variety of protein receptors, enabling glycans to regulate many biological functions. High-resolution structures of protein-glycoligand complexes reveal the atomic details necessary to understand this level of molecular recognition and inform application-focused scientific and engineering pursuits. When experimental challenges hinder high-throughput determination of quality structures, computational tools can, in principle, fill the gap. In this work, we introduce GlycanDock, a residue-centric protein-glycoligand docking refinement algorithm developed within the Rosetta macromolecular modeling and design software suite. We performed a benchmark docking assessment using a set of 109 experimentally determined protein-glycoligand complexes as well as 62 unbound protein structures. The GlycanDock algorithm can sample and discriminate among protein-glycoligand models of native-like structural accuracy with statistical reliability from starting structures of up to 7 Å root-mean-square deviation in the glycoligand ring atoms. We show that GlycanDock-refined models qualitatively replicated the known binding specificity of a bacterial carbohydrate-binding module. Finally, we present a protein-glycoligand docking pipeline for generating putative protein-glycoligand complexes when only the glycoligand sequence and unbound protein structure are known. In combination with other carbohydrate modeling tools, the GlycanDock docking refinement algorithm will accelerate research in the glycosciences.
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Affiliation(s)
- Morgan L. Nance
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Jason W. Labonte
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Chemistry, Franklin & Marshall College, Lancaster, Pennsylvania 17603, United States
- Department of Chemistry, Gettysburg College, Gettysburg, Pennsylvania 17325, United States
| | - Jared Adolf-Bryfogle
- Protein Design Lab, Institute for Protein Innovation, Boston, Massachusetts 02115, United States
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, Massachusetts 02115, United States
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Jeffrey J. Gray
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
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99
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Xing L, Chen Y, Chen B, Bu L, Liu Y, Zeng Z, Guan W, Chen Q, Lin Y, Qin K, Chen H, Deng X, Wang X, Song W. Antigenic Drift of the Hemagglutinin from an Influenza A (H1N1) pdm09 Clinical Isolate Increases its Pathogenicity In Vitro. Virol Sin 2021; 36:1220-1227. [PMID: 34106413 PMCID: PMC8188537 DOI: 10.1007/s12250-021-00401-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 04/12/2021] [Indexed: 12/30/2022] Open
Abstract
The influenza A (H1N1) pdm09 virus emerged in 2009 and has been continuously circulating in humans for over ten years. Here, we analyzed a clinical influenza A (H1N1) pdm09-infected patient case hospitalized for two months in Guangdong (from December 14, 2019 to February 15, 2020). This isolate, named A/Guangdong/LCF/2019 (LCF/19), was genetically sequenced, rescued by reverse genetics, and phylogenetically analyzed in the context of other relevant pdm09 isolates. Compared with earlier isolates, this pdm09 virus's genetic sequence contains four substitutions, S186P, T188I, D190A, and Q192E, of the hemagglutinin (HA) segment at position 186–192 (H3 numbering) in the epitope Sb, and two of which are located at the 190-helix. Phylogenetic analysis indicated that the epitope Sb started undergoing a rapid antigenic change in 2018. To characterize the pathogenicity of this novel substitution motif, a panel of reassortant viruses containing the LCF/2019 HA segment or the chimeric HA segment with the four substitutions were rescued. Kinetic growth data revealed that the reassortant viruses, including the LCF/2019 with the PTIAAQE substitution, propagated faster than those rescued ones having the STTADQQ motif in the epitope Sb in Madin-Darby Canine Kidney (MDCK) cells. The HI test showed that the binding activity of escape mutant to 2018 pdm09 sera was weaker than GLW/2018, suggesting that old vaccines might not effectively protect people from infection. Due to the difference in the selection of vaccine strains, people vaccinated in the southern hemisphere could still suffer a severe infection if infected with this antigenic drift pdm09 virus.
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Affiliation(s)
- Lei Xing
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510180, China.,Institute of Integration of Traditional and Western Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510180, China
| | - Yunbo Chen
- Artemisinin Research Center, Guangzhou University of Chinese Medicine, Guangzhou, 510405, China
| | - Boqian Chen
- Artemisinin Research Center, Guangzhou University of Chinese Medicine, Guangzhou, 510405, China
| | - Ling Bu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510180, China.,Institute of Integration of Traditional and Western Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510180, China
| | - Ying Liu
- Intensive Care Unit, Guangzhou No.8 People's Hospital of Guangzhou Medical University, Guangzhou, 510060, China
| | - Zhiqi Zeng
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510180, China
| | - Wenda Guan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510180, China
| | - Qigao Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510180, China
| | - Yongping Lin
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510180, China
| | - Kun Qin
- China CDC, National Institute for Viral Disease Control and Prevention, Beijing, 100052, China
| | - Honglin Chen
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, The University of Hong Kong, Hong Kong SAR, China.
| | - Xilong Deng
- Intensive Care Unit, Guangzhou No.8 People's Hospital of Guangzhou Medical University, Guangzhou, 510060, China.
| | - Xinhua Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510180, China. .,Artemisinin Research Center, Guangzhou University of Chinese Medicine, Guangzhou, 510405, China. .,Institute of Integration of Traditional and Western Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510180, China.
| | - Wenjun Song
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510180, China. .,Institute of Integration of Traditional and Western Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510180, China. .,State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, The University of Hong Kong, Hong Kong SAR, China.
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100
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Behbahani M, Moradi M, Mohabatkar H. In silico design of a multi-epitope peptide construct as a potential vaccine candidate for Influenza A based on neuraminidase protein. In Silico Pharmacol 2021; 9:36. [PMID: 33987075 PMCID: PMC8112742 DOI: 10.1007/s40203-021-00095-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 04/30/2021] [Indexed: 01/25/2023] Open
Abstract
Designing an effective vaccine against different subtypes of Influenza A virus is a critical issue in the field of medical biotechnology. At the current study, a novel potential multi-epitope vaccine candidate based on the neuraminidase proteins for seven subtypes of Influenza virus was designed, using the in silico approach. Potential linear B-cell and T-cell binding epitopes from each neuraminidase protein (N1, N2, N3, N4, N6, N7, N8) were predicted by in silico tools of epitope prediction. The selected epitopes were joined by three different linkers, and physicochemical properties, toxicity, and allergenecity were investigated. The final multi-epitope construct was modeled using GalaxyWEB server, and the molecular interactions with immune receptors were investigated and the immune response simulation assay was performed. A multi-epitope construct with GPGPGPG linker with the lowest allergenicity and highest stability was selected. The molecular docking assay indicated the interactions with immune system receptors, including HLA1, HLA2, and TLR-3. Immune response simulation detected both humoral and cellular response, including the elevated count of B-cells, T-cell, and Nk-cells.
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Affiliation(s)
- Mandana Behbahani
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Mohammad Moradi
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Hassan Mohabatkar
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
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