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Lang J, Ma X, Chen P, Serota MD, Andre NM, Whittaker GR, Yang R. Haloperoxidase-mimicking CeO 2-x nanorods for the deactivation of human coronavirus OC43. NANOSCALE 2022; 14:3731-3737. [PMID: 35191916 PMCID: PMC8941489 DOI: 10.1039/d1nr06966g] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Despite the excellent antibacterial and antifouling effects of haloperoxidase (HPO)-mimicking CeO2-x nanorods, their antiviral efficiency has not been explored. Herein, we designed and synthesized CeO2-x nanorods with varying aspect ratios via the hydrothermal method. CeO2-x nanorods catalysed the oxidative bromination of Br- and H2O2 to HOBr, the kinetics of which were studied systematically using a phenol red assay. The CeO2-x nanorods with the optimized aspect ratio (i.e., 4.5) demonstrated strong antiviral efficacies against the human coronavirus OC43, with no visible toxicity to the HCT-8 host cells.
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Affiliation(s)
- Jiayan Lang
- Robert F. Smith School of Chemical & Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA.
| | - Xiaojing Ma
- Robert F. Smith School of Chemical & Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA.
| | - Pengyu Chen
- Robert F. Smith School of Chemical & Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA.
| | - Max D Serota
- Robert F. Smith School of Chemical & Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA.
| | - Nicole M Andre
- Dept. Microbiology & Immunology and Dept Public & Ecosystem Health, Cornell University, Ithaca, NY 14853, USA
| | - Gary R Whittaker
- Dept. Microbiology & Immunology and Dept Public & Ecosystem Health, Cornell University, Ithaca, NY 14853, USA
| | - Rong Yang
- Robert F. Smith School of Chemical & Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA.
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2
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Hossain MS, Pathan AQMSU, Islam MN, Tonmoy MIQ, Rakib MI, Munim MA, Saha O, Fariha A, Reza HA, Roy M, Bahadur NM, Rahaman MM. Genome-wide identification and prediction of SARS-CoV-2 mutations show an abundance of variants: Integrated study of bioinformatics and deep neural learning. INFORMATICS IN MEDICINE UNLOCKED 2021; 27:100798. [PMID: 34812411 PMCID: PMC8598266 DOI: 10.1016/j.imu.2021.100798] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 11/06/2021] [Accepted: 11/15/2021] [Indexed: 01/31/2023] Open
Abstract
Genomic data analysis is a fundamental system for monitoring pathogen evolution and the outbreak of infectious diseases. Based on bioinformatics and deep learning, this study was designed to identify the genomic variability of SARS-CoV-2 worldwide and predict the impending mutation rate. Analysis of 259044 SARS-CoV-2 isolates identified 3334545 mutations with an average of 14.01 mutations per isolate. Globally, single nucleotide polymorphism (SNP) is the most prevalent mutational event. The prevalence of C > T (52.67%) was noticed as a major alteration across the world followed by the G > T (14.59%) and A > G (11.13%). Strains from India showed the highest number of mutations (48) followed by Scotland, USA, Netherlands, Norway, and France having up to 36 mutations. D416G, F106F, P314L, UTR:C241T, L93L, A222V, A199A, V30L, and A220V mutations were found as the most frequent mutations. D1118H, S194L, R262H, M809L, P314L, A8D, S220G, A890D, G1433C, T1456I, R233C, F263S, L111K, A54T, A74V, L183A, A316T, V212F, L46C, V48G, Q57H, W131R, G172V, Q185H, and Y206S missense mutations were found to largely decrease the structural stability of the corresponding proteins. Conversely, D3L, L5F, and S97I were found to largely increase the structural stability of the corresponding proteins. Multi-nucleotide mutations GGG > AAC, CC > TT, TG > CA, and AT > TA have come up in our analysis which are in the top 20 mutational cohort. Future mutation rate analysis predicts a 17%, 7%, and 3% increment of C > T, A > G, and A > T, respectively in the future. Conversely, 7%, 7%, and 6% decrement is estimated for T > C, G > A, and G > T mutations, respectively. T > G\A, C > G\A, and A > T\C are not anticipated in the future. Since SARS-CoV-2 is mutating continuously, our findings will facilitate the tracking of mutations and help to map the progression of the COVID-19 intensity worldwide.
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Affiliation(s)
- Md Shahadat Hossain
- Department of Biotechnology & Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - A Q M Sala Uddin Pathan
- Department of Computer Science and Telecommunication Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Md Nur Islam
- Department of Biotechnology & Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | | | - Mahmudul Islam Rakib
- Department of Computer Science and Telecommunication Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Md Adnan Munim
- Department of Biotechnology & Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Otun Saha
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
| | - Atqiya Fariha
- Department of Biotechnology & Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Hasan Al Reza
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | - Maitreyee Roy
- School of Optometry and Vision Science, Faculty of Medicine and Health, University of New South Wales, Bangladesh
| | - Newaz Mohammed Bahadur
- Department of Applied Chemistry and Chemical Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
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3
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Cardona-Ospina JA, Rojas-Gallardo DM, Garzón-Castaño SC, Jiménez-Posada EV, Rodríguez-Morales AJ. Phylodynamic analysis in the understanding of the current COVID-19 pandemic and its utility in vaccine and antiviral design and assessment. Hum Vaccin Immunother 2021; 17:2437-2444. [PMID: 33606594 PMCID: PMC7898299 DOI: 10.1080/21645515.2021.1880254] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 01/20/2021] [Indexed: 12/14/2022] Open
Abstract
Over the last decades, the use of phylogenetic methods in the study of emerging infectious diseases has gained considerable traction in public health. Particularly, the integration of phylogenetic analyses with the understanding of the pathogen dynamics at the population level has provided powerful tools for epidemiological surveillance systems. In the same way, the development of statistical methods and theory, as well as improvement of computational efficiency for evolutionary analysis, has expanded the use of these tools for vaccine and antiviral development. Today with the Coronavirus Disease 2019 (COVID-19), this seems to be critical. In this article, we discuss how the application of phylodynamic analysis can improve the understanding of current pandemic dynamics as well as the design, selection, and evaluation of vaccine candidates and antivirals.
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Affiliation(s)
- Jaime A. Cardona-Ospina
- Grupo de Investigación Biomedicina, Facultad de Medicina, Fundación Universitaria Autónoma de Las Américas, Pereira, Colombia
- Public Health and Infection Research Group, Faculty of Health Sciences, Universidad Tecnológica de Pereira, Pereira, Colombia
- Emerging Infectious Diseases and Tropical Medicine Research Group. Instituto Para La Investigación en Ciencias Biomédicas - Sci-Help, Pereira, Colombia
| | - Diana M. Rojas-Gallardo
- Grupo de Investigación Biomedicina, Facultad de Medicina, Fundación Universitaria Autónoma de Las Américas, Pereira, Colombia
| | - Sandra C. Garzón-Castaño
- Grupo de Investigación Biomedicina, Facultad de Medicina, Fundación Universitaria Autónoma de Las Américas, Pereira, Colombia
| | - Erika V. Jiménez-Posada
- Emerging Infectious Diseases and Tropical Medicine Research Group. Instituto Para La Investigación en Ciencias Biomédicas - Sci-Help, Pereira, Colombia
| | - Alfonso J. Rodríguez-Morales
- Grupo de Investigación Biomedicina, Facultad de Medicina, Fundación Universitaria Autónoma de Las Américas, Pereira, Colombia
- Public Health and Infection Research Group, Faculty of Health Sciences, Universidad Tecnológica de Pereira, Pereira, Colombia
- Emerging Infectious Diseases and Tropical Medicine Research Group. Instituto Para La Investigación en Ciencias Biomédicas - Sci-Help, Pereira, Colombia
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Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. Biomolecules 2021; 11:biom11070919. [PMID: 34206274 PMCID: PMC8301449 DOI: 10.3390/biom11070919] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/18/2021] [Accepted: 05/21/2021] [Indexed: 02/02/2023] Open
Abstract
SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) protein is the target for the antiviral drug Remdesivir (RDV). With RDV clinical trials on COVID-19 patients showing a reduced hospitalisation time. During the spread of the virus, the RdRp has developed several mutations, with the most frequent being A97V and P323L. The current study sought to investigate whether A97V and P323L mutations influence the binding of RDV to the RdRp of SARS-CoV-2 compared to wild-type (WT). The interaction of RDV with WT-, A97V-, and P323L-RdRp were measured using molecular dynamic (MD) simulations, and the free binding energies were extracted. Results showed that RDV that bound to WT- and A97V-RdRp had a similar dynamic motion and internal residue fluctuations, whereas RDV interaction with P323L-RdRp exhibited a tighter molecular conformation, with a high internal motion near the active site. This was further corroborated with RDV showing a higher binding affinity to P323L-RdRp (-24.1 kcal/mol) in comparison to WT-RdRp (-17.3 kcal/mol). This study provides insight into the potential significance of administering RDV to patients carrying the SARS-CoV-2 P323L-RdRp mutation, which may have a more favourable chance of alleviating the SARS-CoV-2 illness in comparison to WT-RdRp carriers, thereby suggesting further scientific consensus for the usage of Remdesivir as clinical candidate against COVID-19.
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5
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Lee CY, Amrun SN, Chee RS, Goh YS, Mak T, Octavia S, Yeo NK, Chang ZW, Tay MZ, Torres‐Ruesta A, Carissimo G, Poh CM, Fong S, Bei W, Lee S, Young BE, Tan S, Leo Y, Lye DC, Lin RTP, Maurer‐Stroh S, Lee B, Wang C, Renia L, Ng LFP. Human neutralising antibodies elicited by SARS-CoV-2 non-D614G variants offer cross-protection against the SARS-CoV-2 D614G variant. Clin Transl Immunology 2021; 10:e1241. [PMID: 33628442 PMCID: PMC7899292 DOI: 10.1002/cti2.1241] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/21/2020] [Accepted: 12/23/2020] [Indexed: 01/06/2023] Open
Abstract
OBJECTIVES The emergence of a SARS-CoV-2 variant with a point mutation in the spike (S) protein, D614G, has taken precedence over the original Wuhan isolate by May 2020. With an increased infection and transmission rate, it is imperative to determine whether antibodies induced against the D614 isolate may cross-neutralise against the G614 variant. METHODS Antibody profiling against the SARS-CoV-2 S protein of the D614 variant by flow cytometry and assessment of neutralising antibody titres using pseudotyped lentiviruses expressing the SARS-CoV-2 S protein of either the D614 or G614 variant tagged with a luciferase reporter were performed on plasma samples from COVID-19 patients with known D614G status (n = 44 infected with D614, n = 6 infected with G614, n = 7 containing all other clades: O, S, L, V, G, GH or GR). RESULTS Profiling of the anti-SARS-CoV-2 humoral immunity reveals similar neutralisation profiles against both S protein variants, albeit waning neutralising antibody capacity at the later phase of infection. Of clinical importance, patients infected with either the D614 or G614 clade elicited a similar degree of neutralisation against both pseudoviruses, suggesting that the D614G mutation does not impact the neutralisation capacity of the elicited antibodies. CONCLUSIONS Cross-reactivity occurs at the functional level of the humoral response on both the S protein variants, which suggests that existing serological assays will be able to detect both D614 and G614 clades of SARS-CoV-2. More importantly, there should be negligible impact towards the efficacy of antibody-based therapies and vaccines that are currently being developed.
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Affiliation(s)
- Cheryl Yi‐Pin Lee
- A*STAR Infectious Diseases LabsAgency for Science, Technology and Research (A*STAR)Singapore
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
| | - Siti Naqiah Amrun
- A*STAR Infectious Diseases LabsAgency for Science, Technology and Research (A*STAR)Singapore
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
| | - Rhonda Sin‐Ling Chee
- A*STAR Infectious Diseases LabsAgency for Science, Technology and Research (A*STAR)Singapore
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
| | - Yun Shan Goh
- A*STAR Infectious Diseases LabsAgency for Science, Technology and Research (A*STAR)Singapore
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
| | - Tze‐Minn Mak
- National Centre for Infectious DiseasesSingapore
- National Public Health LaboratoryNational Centre for Infectious DiseasesSingapore
| | - Sophie Octavia
- National Centre for Infectious DiseasesSingapore
- National Public Health LaboratoryNational Centre for Infectious DiseasesSingapore
| | - Nicholas Kim‐Wah Yeo
- A*STAR Infectious Diseases LabsAgency for Science, Technology and Research (A*STAR)Singapore
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
| | - Zi Wei Chang
- A*STAR Infectious Diseases LabsAgency for Science, Technology and Research (A*STAR)Singapore
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
| | - Matthew Zirui Tay
- A*STAR Infectious Diseases LabsAgency for Science, Technology and Research (A*STAR)Singapore
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
| | - Anthony Torres‐Ruesta
- A*STAR Infectious Diseases LabsAgency for Science, Technology and Research (A*STAR)Singapore
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
- Department of BiochemistryYong Loo Lin School of MedicineNational University of SingaporeSingapore
| | - Guillaume Carissimo
- A*STAR Infectious Diseases LabsAgency for Science, Technology and Research (A*STAR)Singapore
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
| | - Chek Meng Poh
- A*STAR Infectious Diseases LabsAgency for Science, Technology and Research (A*STAR)Singapore
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
| | - Siew‐Wai Fong
- A*STAR Infectious Diseases LabsAgency for Science, Technology and Research (A*STAR)Singapore
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
- Department of Biological SciencesNational University of SingaporeSingapore
| | - Wang Bei
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
| | - Sandy Lee
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
| | - Barnaby Edward Young
- National Centre for Infectious DiseasesSingapore
- Department of Infectious DiseasesTan Tock Seng HospitalSingapore
- Lee Kong Chian School of MedicineNanyang Technological UniversitySingapore
| | - Seow‐Yen Tan
- Department of Infectious DiseasesChangi General HospitalSingapore
| | - Yee‐Sin Leo
- National Centre for Infectious DiseasesSingapore
- Department of Infectious DiseasesTan Tock Seng HospitalSingapore
- Lee Kong Chian School of MedicineNanyang Technological UniversitySingapore
- Yong Loo Lin School of MedicineNational University of Singapore and National University Health SystemSingapore
| | - David C Lye
- National Centre for Infectious DiseasesSingapore
- Department of Infectious DiseasesTan Tock Seng HospitalSingapore
- Lee Kong Chian School of MedicineNanyang Technological UniversitySingapore
- Yong Loo Lin School of MedicineNational University of Singapore and National University Health SystemSingapore
| | - Raymond TP Lin
- National Public Health LaboratoryNational Centre for Infectious DiseasesSingapore
- Department of Microbiology and ImmunologyYong Loo Lin School of MedicineNational University of SingaporeSingapore
| | - Sebastien Maurer‐Stroh
- A*STAR Infectious Diseases LabsAgency for Science, Technology and Research (A*STAR)Singapore
- National Centre for Infectious DiseasesSingapore
- National Public Health LaboratoryNational Centre for Infectious DiseasesSingapore
- Department of Biological SciencesNational University of SingaporeSingapore
- Bioinformatics InstituteAgency for Science Technology and Research (A*STAR)Singapore
| | - Bernett Lee
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
| | - Cheng‐I Wang
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
| | - Laurent Renia
- A*STAR Infectious Diseases LabsAgency for Science, Technology and Research (A*STAR)Singapore
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
| | - Lisa FP Ng
- A*STAR Infectious Diseases LabsAgency for Science, Technology and Research (A*STAR)Singapore
- Singapore Immunology NetworkAgency for Science, Technology and Research (A*STAR)Singapore
- Department of BiochemistryYong Loo Lin School of MedicineNational University of SingaporeSingapore
- National Institute of Health ResearchHealth Protection Research Unit in Emerging and Zoonotic InfectionsUniversity of LiverpoolLiverpoolUK
- Institute of Infection, Veterinary and Ecological SciencesUniversity of LiverpoolLiverpoolUK
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6
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Mohanty E, Mohanty A. Role of artificial intelligence in peptide vaccine design against RNA viruses. INFORMATICS IN MEDICINE UNLOCKED 2021; 26:100768. [PMID: 34722851 PMCID: PMC8536498 DOI: 10.1016/j.imu.2021.100768] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/16/2021] [Accepted: 10/16/2021] [Indexed: 01/18/2023] Open
Abstract
RNA viruses have high rate of replication and mutation that help them adapt and change according to their environmental conditions. Many viral mutants are the cause of various severe and lethal diseases. Vaccines, on the other hand have the capacity to protect us from infectious diseases by eliciting antibody or cell-mediated immune responses that are pathogen-specific. While there are a few reviews pertaining to the use of artificial intelligence (AI) for SARS-COV-2 vaccine development, none focus on peptide vaccination for RNA viruses and the important role played by AI in it. Peptide vaccine which is slowly coming to be recognized as a safe and effective vaccination strategy has the capacity to overcome the mutant escape problem which is also being currently faced by SARS-COV-2 vaccines in circulation.Here we review the present scenario of peptide vaccines which are developed using mathematical and computational statistics methods to prevent the spread of disease caused by RNA viruses. We also focus on the importance and current stage of AI and mathematical evolutionary modeling using machine learning tools in the establishment of these new peptide vaccines for the control of viral disease.
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Affiliation(s)
- Eileena Mohanty
- Trident School of Biotech Sciences, Trident Academy of Creative Technology (TACT), Bhubaneswar, Odisha, 751024, India
| | - Anima Mohanty
- School of Biotechnology (KSBT), KIIT University-2, Bhubaneswar, 751024, India
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Wang R, Hozumi Y, Yin C, Wei GW. Decoding SARS-CoV-2 Transmission and Evolution and Ramifications for COVID-19 Diagnosis, Vaccine, and Medicine. J Chem Inf Model 2020; 60:5853-5865. [PMID: 32530284 PMCID: PMC7318555 DOI: 10.1021/acs.jcim.0c00501] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Indexed: 12/20/2022]
Abstract
Tremendous effort has been given to the development of diagnostic tests, preventive vaccines, and therapeutic medicines for coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Much of this development has been based on the reference genome collected on January 5, 2020. Based on the genotyping of 15 140 genome samples collected up to June 1, 2020, we report that SARS-CoV-2 has undergone 8309 single mutations which can be clustered into six subtypes. We introduce mutation ratio and mutation h-index to characterize the protein conservativeness and unveil that SARS-CoV-2 envelope protein, main protease, and endoribonuclease protein are relatively conservative, while SARS-CoV-2 nucleocapsid protein, spike protein, and papain-like protease are relatively nonconservative. In particular, we have identified mutations on 40% of nucleotides in the nucleocapsid gene in the population level, signaling potential impacts on the ongoing development of COVID-19 diagnosis, vaccines, and antibody and small-molecular drugs.
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Affiliation(s)
- Rui Wang
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuta Hozumi
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Changchuan Yin
- Department
of Mathematics, Statistics, and Computer Science, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Guo-Wei Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
- Department
of Electrical and Computer Engineering, Michigan State University, East
Lansing, Michigan 48824, United States
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8
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Clark JJ, Gilray J, Orton RJ, Baird M, Wilkie G, Filipe ADS, Johnson N, McInnes CJ, Kohl A, Biek R. Population genomics of louping ill virus provide new insights into the evolution of tick-borne flaviviruses. PLoS Negl Trop Dis 2020; 14:e0008133. [PMID: 32925939 PMCID: PMC7515184 DOI: 10.1371/journal.pntd.0008133] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 09/24/2020] [Accepted: 08/07/2020] [Indexed: 12/30/2022] Open
Abstract
The emergence and spread of tick-borne arboviruses pose an increased challenge to human and animal health. In Europe this is demonstrated by the increasingly wide distribution of tick-borne encephalitis virus (TBEV, Flavivirus, Flaviviridae), which has recently been found in the United Kingdom (UK). However, much less is known about other tick-borne flaviviruses (TBFV), such as the closely related louping ill virus (LIV), an animal pathogen which is endemic to the UK and Ireland, but which has been detected in other parts of Europe including Scandinavia and Russia. The emergence and potential spatial overlap of these viruses necessitates improved understanding of LIV genomic diversity, geographic spread and evolutionary history. We sequenced a virus archive composed of 22 LIV isolates which had been sampled throughout the UK over a period of over 80 years. Combining this dataset with published virus sequences, we detected no sign of recombination and found low diversity and limited evidence for positive selection in the LIV genome. Phylogenetic analysis provided evidence of geographic clustering as well as long-distance movement, including movement events that appear recent. However, despite genomic data and an 80-year time span, we found that the data contained insufficient temporal signal to reliably estimate a molecular clock rate for LIV. Additional analyses revealed that this also applied to TBEV, albeit to a lesser extent, pointing to a general problem with phylogenetic dating for TBFV. The 22 LIV genomes generated during this study provide a more reliable LIV phylogeny, improving our knowledge of the evolution of tick-borne flaviviruses. Our inability to estimate a molecular clock rate for both LIV and TBEV suggests that temporal calibration of tick-borne flavivirus evolution should be interpreted with caution and highlight a unique aspect of these viruses which may be explained by their reliance on tick vectors. Tick-borne pathogens represent a major emerging threat to public health and in recent years have been expanding into new areas. LIV is a neglected virus endemic to the UK and Ireland (though it has been detected in Scandinavia and Russia) which is closely related to the major human pathogen TBEV, but predominantly causes disease in sheep and grouse. The recent detection of TBEV in the UK, which has also emerged elsewhere in Europe, requires more detailed understanding of the spread and sequence diversity of LIV. This could be important for diagnosis and vaccination, but also to improve our understanding of the evolution and emergence of these tick-borne viruses. Here we describe the sequencing of 22 LIV isolates which have been sampled from several host species across the past century. We have utilised this dataset to investigate the evolutionary pressures that LIV is subjected to and have explored the evolution of LIV using phylogenetic analysis. Crucially we were unable to estimate a reliable molecular clock rate for LIV and found that this problem also extends to a larger phylogeny of TBEV sequences. This work highlights a previously unknown caveat of tick-borne flavivirus evolutionary analysis which may be important for understanding the evolution of these important pathogens.
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Affiliation(s)
- Jordan J. Clark
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
- Moredun Research Institute, Edinburgh, United Kingdom
- * E-mail: (JC); (RB)
| | - Janice Gilray
- Moredun Research Institute, Edinburgh, United Kingdom
| | - Richard J. Orton
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Margaret Baird
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Gavin Wilkie
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Ana da Silva Filipe
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Nicholas Johnson
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
- Faculty of Health and Medical Science, University of Surrey, Guildford, Surrey, United Kingdom
| | | | - Alain Kohl
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Roman Biek
- Institute of Biodiversity, Animal Health and Comparative Medicine - University of Glasgow, Glasgow, United Kingdom
- * E-mail: (JC); (RB)
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9
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Stepien CA, Niner MD. Evolutionary trajectory of fish Piscine novirhabdovirus (=Viral Hemorrhagic Septicemia Virus) across its Laurentian Great Lakes history: Spatial and temporal diversification. Ecol Evol 2020; 10:9740-9775. [PMID: 33005343 PMCID: PMC7520192 DOI: 10.1002/ece3.6611] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/04/2020] [Accepted: 05/10/2020] [Indexed: 02/05/2023] Open
Abstract
Piscine novirhabdovirus = Viral Hemorrhagic Septicemia Virus (VHSV) first appeared in the Laurentian Great Lakes with large outbreaks from 2005 to 2006, as a new and novel RNA rhabdovirus subgenogroup (IVb) that killed >30 fish species. Interlude periods punctuated smaller more localized outbreaks in 2007, 2010, and 2017, although some fishes tested positive in the intervals. There have not been reports of outbreaks or positives from 2018, 2019, or 2020. Here, we employ a combined population genetics and phylogenetic approach to evaluate spatial and temporal evolutionary trajectory on its G-gene sequence variation, in comparison with whole-genome sequences (11,083 bp) from a subset of 44 individual isolates (including 40 newly sequenced ones). Our results show that IVb (N = 184 individual fish isolates) diversified into 36 G-gene haplotypes from 2003 to 2017, stemming from two originals ("a" and "b"). G-gene haplotypes "a" and "b" differed by just one synonymous single-nucleotide polymorphism (SNP) substitution, remained the most abundant until 2011, then disappeared. Group "a" descendants (14 haplotypes) remained most prevalent in the Upper and Central Great Lakes, with eight (51%) having nonsynonymous substitutions. Group "b" descendants primarily have occurred in the Lower Great Lakes, including 22 haplotypes, of which 15 (68%) contained nonsynonymous changes. Evolutionary patterns of the whole-genome sequences (which had 34 haplotypes among 44 isolates) appear congruent with those from the G-gene. Virus populations significantly diverged among the Upper, Central, and Lower Great Lakes, diversifying over time. Spatial divergence was apparent in the overall patterns of nucleotide substitutions, while amino acid changes increased temporally. VHSV-IVb thus significantly differentiated across its less than two decades in the Great Lakes, accompanied by declining outbreaks and virulence. Continuing diversification likely allowed the virus to persist at low levels in resident fish populations, and may facilitate its potential for further and future spread to new habitats and nonacclimated hosts.
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Affiliation(s)
- Carol A. Stepien
- Genetics and Genomics Group (G3)NOAA Pacific Marine Environmental Laboratory (PMEL)SeattleWAUSA
| | - Megan D. Niner
- Genetics and Genomics Group (G3), Department of Environmental SciencesUniversity of ToledoToledoOHUSA
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10
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Pathan RK, Biswas M, Khandaker MU. Time series prediction of COVID-19 by mutation rate analysis using recurrent neural network-based LSTM model. CHAOS, SOLITONS, AND FRACTALS 2020; 138:110018. [PMID: 32565626 PMCID: PMC7293453 DOI: 10.1016/j.chaos.2020.110018] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 06/12/2020] [Indexed: 05/20/2023]
Abstract
SARS-CoV-2, a novel coronavirus mostly known as COVID-19 has created a global pandemic. The world is now immobilized by this infectious RNA virus. As of June 15, already more than 7.9 million people have been infected and 432k people died. This RNA virus has the ability to do the mutation in the human body. Accurate determination of mutation rates is essential to comprehend the evolution of this virus and to determine the risk of emergent infectious disease. This study explores the mutation rate of the whole genomic sequence gathered from the patient's dataset of different countries. The collected dataset is processed to determine the nucleotide mutation and codon mutation separately. Furthermore, based on the size of the dataset, the determined mutation rate is categorized for four different regions: China, Australia, the United States, and the rest of the World. It has been found that a huge amount of Thymine (T) and Adenine (A) are mutated to other nucleotides for all regions, but codons are not frequently mutating like nucleotides. A recurrent neural network-based Long Short Term Memory (LSTM) model has been applied to predict the future mutation rate of this virus. The LSTM model gives Root Mean Square Error (RMSE) of 0.06 in testing and 0.04 in training, which is an optimized value. Using this train and testing process, the nucleotide mutation rate of 400th patient in future time has been predicted. About 0.1% increment in mutation rate is found for mutating of nucleotides from T to C and G, C to G and G to T. While a decrement of 0.1% is seen for mutating of T to A, and A to C. It is found that this model can be used to predict day basis mutation rates if more patient data is available in updated time.
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Affiliation(s)
- Refat Khan Pathan
- Department of Computer Science and Engineering, BGC Trust University Bangladesh, Chittagong-4381, Bangladesh
| | - Munmun Biswas
- Department of Computer Science and Engineering, BGC Trust University Bangladesh, Chittagong-4381, Bangladesh
| | - Mayeen Uddin Khandaker
- Centre for Biomedical Physics, School of Healthcare and Medical Sciences, Sunway University, 47500 Bandar Sunway, Selangor, Malaysia
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11
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Khan K, Dimtri F, Vargas C, Surani S. COVID-19: A Review of Emerging Preventative Vaccines and Treatment Strategies. Cureus 2020; 12:e8206. [PMID: 32577324 PMCID: PMC7305574 DOI: 10.7759/cureus.8206] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
COVID-19, which was first detected in the Hubei province of China, has become a global phenomenon. The effects and devastation on both health and economy have been global. At present, there is a substantial amount of research being done to discover suitable treatment modalities. Efforts have been made on the development of potential efficacious vaccines. The development of a vaccine can be complex, expensive as well as time-consuming. Currently, various ongoing clinical trials are in progress that are investigating either pharmacologic therapies or vaccines against this virus. We, in this brief review have tried to address the process and current development efforts of vaccine in progress.
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Affiliation(s)
- Kashmala Khan
- Internal Medicine, Corpus Christi Medical Center, Corpus Christi, USA
| | - Francis Dimtri
- Cardiology, Corpus Christi Medical Center, Corpus Christi, USA
| | - Carlos Vargas
- Internal Medicine, Corpus Christi Medical Center, Corpus Christi, USA
| | - Salim Surani
- Internal Medicine, Corpus Christi Medical Center, Corpus Christi, USA.,Internal Medicine, University of North Texas, Dallas, USA
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12
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Ciccozzi M, Lai A, Zehender G, Borsetti A, Cella E, Ciotti M, Sagnelli E, Sagnelli C, Angeletti S. The phylogenetic approach for viral infectious disease evolution and epidemiology: An updating review. J Med Virol 2019; 91:1707-1724. [PMID: 31243773 DOI: 10.1002/jmv.25526] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 06/24/2019] [Indexed: 12/16/2022]
Abstract
In the last decade, the phylogenetic approach is recurrent in molecular evolutionary analysis. On 12 May, 2019, about 2 296 213 papers are found, but typing "phylogeny" or "epidemiology AND phylogeny" only 199 804 and 20 133 are retrieved, respectively. Molecular epidemiology in infectious diseases is widely used to define the source of infection as so as the ancestral relationships of individuals sampled from a population. Coalescent theory and phylogeographic analysis have had scientific application in several, recent pandemic events, and nosocomial outbreaks. Hepatitis viruses and immunodeficiency virus (human immunodeficiency virus) have been largely studied. Phylogenetic analysis has been recently applied on Polyomaviruses so as in the more recent outbreaks due to different arboviruses type as Zika and chikungunya viruses discovering the source of infection and the geographic spread. Data on sequences isolated by the microorganism are essential to apply the phylogenetic tools and research in the field of infectious disease phylodinamics is growing up. There is the need to apply molecular phylogenetic and evolutionary methods in areas out of infectious diseases, as translational genomics and personalized medicine. Lastly, the application of these tools in vaccine strategy so as in antibiotic and antiviral researchers are encouraged.
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Affiliation(s)
- Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Rome, Italy
| | - Alessia Lai
- Department of Biomedical and Clinical Sciences 'L. Sacco', University of Milan, Milan, Italy
| | - Gianguglielmo Zehender
- Department of Biomedical and Clinical Sciences 'L. Sacco', University of Milan, Milan, Italy
| | - Alessandra Borsetti
- National HIV/AIDS Research Center, Istituto Superiore di Sanità, Roma, Italy
| | - Eleonora Cella
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Rome, Italy
| | - Marco Ciotti
- Laboratory of Molecular Virology, Polyclinic Tor Vergata Foundation, Rome, Italy
| | - Evangelista Sagnelli
- Department of Mental Health and Public Medicine, Section of Infectious Diseases, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Caterina Sagnelli
- Department of Mental Health and Public Medicine, Section of Infectious Diseases, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Silvia Angeletti
- Unit of Clinical Laboratory Science, University Campus Bio-Medico of Rome, Rome, Italy
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13
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Abstract
The influenza virus mutates faster than we previously thought.
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Affiliation(s)
- Bartram L Smith
- Department of Integrative Biology, The University of Texas at Austin, Austin, United States
| | - Claus O Wilke
- Department of Integrative Biology, The University of Texas at Austin, Austin, United States
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14
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Halczok TK, Fischer K, Gierke R, Zeus V, Meier F, Treß C, Balkema-Buschmann A, Puechmaille SJ, Kerth G. Evidence for genetic variation in Natterer's bats (Myotis nattereri) across three regions in Germany but no evidence for co-variation with their associated astroviruses. BMC Evol Biol 2017; 17:5. [PMID: 28056776 PMCID: PMC5217449 DOI: 10.1186/s12862-016-0856-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Accepted: 12/17/2016] [Indexed: 11/18/2022] Open
Abstract
Background As bats have recently been described to harbor many different viruses, several studies have investigated the genetic co-variation between viruses and different bat species. However, little is known about the genetic co-variation of viruses and different populations of the same bat species, although such information is needed for an understanding of virus transmission dynamics within a given host species. We hypothesized that if virus transmission between host populations depends on events linked to gene flow in the bats, genetic co-variation should exist between host populations and astroviruses. Results We used 19 nuclear and one mitochondrial microsatellite loci to analyze the genetic population structure of the Natterer’s bat (Myotis nattereri) within and among populations at different geographical scales in Germany. Further, we correlated the observed bat population structure to that of partial astrovirus sequences (323–394 nt fragments of the RNA-dependent RNA polymerase gene) obtained from the same bat populations. Our analyses revealed that the studied bat colonies can be grouped into three distinct genetic clusters, corresponding to the three geographic regions sampled. Furthermore, we observed an overall isolation-by-distance pattern, while no significant pattern was observed within a geographic region. Moreover, we found no correlation between the genetic distances among the bat populations and the astrovirus sequences they harbored. Even though high genetic similarity of some of the astrovirus haplotypes found in several different regions was detected, identical astrovirus haplotypes were not shared between different sampled regions. Conclusions The genetic population structure of the bat host suggests that mating sites where several local breeding colonies meet act as stepping-stones for gene flow. Identical astrovirus haplotypes were not shared between different sampled regions suggesting that astroviruses are mostly transmitted among host colonies at the local scale. Nevertheless, high genetic similarity of some of the astrovirus haplotypes found in several different regions implies that occasional transmission across regions with subsequent mutations of the virus haplotypes does occur. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0856-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tanja K Halczok
- Ernst-Moritz-Arndt Universität Greifswald, Zoological Institute and Museum, Soldmannstr. 14, 17489, Greifswald, Germany.
| | - Kerstin Fischer
- Friedrich-Loeffler-Institut, Institute of Novel and Emerging Infectious Diseases, Suedufer 10, 17493, Greifswald, Insel Riems, Germany
| | - Robert Gierke
- Ernst-Moritz-Arndt Universität Greifswald, Zoological Institute and Museum, Soldmannstr. 14, 17489, Greifswald, Germany
| | - Veronika Zeus
- Ernst-Moritz-Arndt Universität Greifswald, Zoological Institute and Museum, Soldmannstr. 14, 17489, Greifswald, Germany
| | - Frauke Meier
- Echolot GbR, Eulerstr. 12, 48155, Münster, Germany
| | - Christoph Treß
- Fledermausforschungsprojekt Wooster Teerofen e.V., Gartenstraße 4, 98617, Meiningen, Germany
| | - Anne Balkema-Buschmann
- Friedrich-Loeffler-Institut, Institute of Novel and Emerging Infectious Diseases, Suedufer 10, 17493, Greifswald, Insel Riems, Germany
| | - Sébastien J Puechmaille
- Ernst-Moritz-Arndt Universität Greifswald, Zoological Institute and Museum, Soldmannstr. 14, 17489, Greifswald, Germany
| | - Gerald Kerth
- Ernst-Moritz-Arndt Universität Greifswald, Zoological Institute and Museum, Soldmannstr. 14, 17489, Greifswald, Germany
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15
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Abstract
Over the last three decades, transcriptomic studies of venom gland cells have continuously evolved, opening up new possibilities for exploring the molecular diversity of animal venoms, a prerequisite for the discovery of new drug candidates and molecular phylogenetics. The molecular complexity of animal venoms is much greater than initially thought. In this review, we describe the different technologies available for transcriptomic studies of venom, from the original individual cloning approaches to the more recent global Next Generation Sequencing strategies. Our understanding of animal venoms is evolving, with the discovery of complex and diverse bio-optimized cocktails of compounds, including mostly peptides and proteins, which are now beginning to be studied by academic and industrial researchers.
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16
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Abstract
Immunoinformatics focuses on modeling immune responses for better understanding of the immune system and in many cases for proposing agents able to modify the immune system. The most classical of these agents are vaccines derived from living organisms such as smallpox or polio. More modern vaccines comprise recombinant proteins, protein domains, and in some cases peptides. Generating a vaccine from peptides however requires technologies and concepts very different from classical vaccinology. Immunoinformatics therefore provides the computational tools to propose peptides suitable for formulation into vaccines. This chapter introduces the essential biological concepts affecting design and efficacy of peptide vaccines and discusses current methods and workflows applied to design successful peptide vaccines using computers.
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Affiliation(s)
- Johannes Söllner
- Emergentec Biodevelopment GmbH, Gersthofer Straße 29-31, 1180, Vienna, Austria,
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17
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Luciani F, Bull RA, Lloyd AR. Next generation deep sequencing and vaccine design: today and tomorrow. Trends Biotechnol 2012; 30:443-52. [PMID: 22721705 PMCID: PMC7127335 DOI: 10.1016/j.tibtech.2012.05.005] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Revised: 05/21/2012] [Accepted: 05/21/2012] [Indexed: 12/20/2022]
Abstract
Next generation sequencing (NGS) technologies have redefined the modus operandi in both human and microbial genetics research, allowing the unprecedented generation of very large sequencing datasets on a short time scale and at affordable costs. Vaccine development research is rapidly taking full advantage of the advent of NGS. This review provides a concise summary of the current applications of NGS in relation to research seeking to develop vaccines for human infectious diseases, incorporating studies of both the pathogen and the host. We focus on rapidly mutating viral pathogens, which are major targets in current vaccine research. NGS is unraveling the complex dynamics of viral evolution and host responses against these viruses, thus contributing substantially to the likelihood of successful vaccine development.
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Affiliation(s)
- Fabio Luciani
- Inflammation and Infection Research Centre, School of Medical Sciences, University of New South Wales, Sydney, Australia.
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