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Aranha MP, Penfound TA, Salehi S, Botteaux A, Smeesters P, Dale JB, Smith JC. Design of Broadly Cross-Reactive M Protein-Based Group A Streptococcal Vaccines. THE JOURNAL OF IMMUNOLOGY 2021; 207:1138-1149. [PMID: 34341168 DOI: 10.4049/jimmunol.2100286] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 06/13/2021] [Indexed: 11/19/2022]
Abstract
Group A streptococcal infections are a significant cause of global morbidity and mortality. A leading vaccine candidate is the surface M protein, a major virulence determinant and protective Ag. One obstacle to the development of M protein-based vaccines is the >200 different M types defined by the N-terminal sequences that contain protective epitopes. Despite sequence variability, M proteins share coiled-coil structural motifs that bind host proteins required for virulence. In this study, we exploit this potential Achilles heel of conserved structure to predict cross-reactive M peptides that could serve as broadly protective vaccine Ags. Combining sequences with structural predictions, six heterologous M peptides in a sequence-related cluster were predicted to elicit cross-reactive Abs with the remaining five nonvaccine M types in the cluster. The six-valent vaccine elicited Abs in rabbits that reacted with all 11 M peptides in the cluster and functional opsonic Abs against vaccine and nonvaccine M types in the cluster. We next immunized mice with four sequence-unrelated M peptides predicted to contain different coiled-coil propensities and tested the antisera for cross-reactivity against 41 heterologous M peptides. Based on these results, we developed an improved algorithm to select cross-reactive peptide pairs using additional parameters of coiled-coil length and propensity. The revised algorithm accurately predicted cross-reactive Ab binding, improving the Matthews correlation coefficient from 0.42 to 0.74. These results form the basis for selecting the minimum number of N-terminal M peptides to include in potentially broadly efficacious multivalent vaccines that could impact the overall global burden of group A streptococcal diseases.
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Affiliation(s)
- Michelle P Aranha
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN; .,Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN
| | - Thomas A Penfound
- Department of Medicine, Division of Infectious Diseases, University of Tennessee Health Science Center, Memphis, TN
| | - Sanaz Salehi
- Department of Medicine, Division of Infectious Diseases, University of Tennessee Health Science Center, Memphis, TN
| | - Anne Botteaux
- Molecular Bacteriology Laboratory, Free University of Brussels, Brussels, Belgium
| | - Pierre Smeesters
- Molecular Bacteriology Laboratory, Free University of Brussels, Brussels, Belgium.,Academic Children's Hospital Queen Fabiola, Free University of Brussels, Brussels, Belgium; and.,Centre for International Child Health, University of Melbourne, Melbourne, Victoria, Australia
| | - James B Dale
- Department of Medicine, Division of Infectious Diseases, University of Tennessee Health Science Center, Memphis, TN;
| | - Jeremy C Smith
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN; .,Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN
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Lu IN, Muller CP, He FQ. Applying next-generation sequencing to unravel the mutational landscape in viral quasispecies. Virus Res 2020; 283:197963. [PMID: 32278821 PMCID: PMC7144618 DOI: 10.1016/j.virusres.2020.197963] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 04/03/2020] [Accepted: 04/04/2020] [Indexed: 02/07/2023]
Abstract
Next-generation sequencing (NGS) has revolutionized the scale and depth of biomedical sciences. Because of its unique ability for the detection of sub-clonal variants within genetically diverse populations, NGS has been successfully applied to analyze and quantify the exceptionally-high diversity within viral quasispecies, and many low-frequency drug- or vaccine-resistant mutations of therapeutic importance have been discovered. Although many works have intensively discussed the latest NGS approaches and applications in general, none of them has focused on applying NGS in viral quasispecies studies, mostly due to the limited ability of current NGS technologies to accurately detect and quantify rare viral variants. Here, we summarize several error-correction strategies that have been developed to enhance the detection accuracy of minority variants. We also discuss critical considerations for preparing a sequencing library from viral RNAs and for analyzing NGS data to unravel the mutational landscape.
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Affiliation(s)
- I-Na Lu
- DKFZ-Division Translational Neurooncology at the WTZ, DKTK partner site, University Hospital Essen, D-45147 Essen, Germany; Department of Infectious Diseases, Aarhus University Hospital, DK-8200 Aarhus N, Denmark.
| | - Claude P Muller
- Department of Infection and Immunity, Luxembourg Institute of Health, L-4354 Esch-Sur-Alzette, Luxembourg; Laboratoire National de Santé, L-3583 Dudelange, Luxembourg
| | - Feng Q He
- Department of Infection and Immunity, Luxembourg Institute of Health, L-4354 Esch-Sur-Alzette, Luxembourg; Institute of Medical Microbiology, University Hospital Essen, University Duisburg-Essen, Essen, Germany.
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Singanallur NB, Anderson DE, Sessions OM, Kamaraj US, Bowden TR, Horsington J, Cowled C, Wang LF, Vosloo W. Probe capture enrichment next-generation sequencing of complete foot-and-mouth disease virus genomes in clinical samples. J Virol Methods 2019; 272:113703. [PMID: 31336142 DOI: 10.1016/j.jviromet.2019.113703] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 07/04/2019] [Accepted: 07/17/2019] [Indexed: 01/02/2023]
Abstract
Next-generation sequencing (NGS) techniques offer an unprecedented "step-change" increase in the quantity and quality of sequence data rapidly generated from a sample and can be applied to obtain ultra-deep coverage of viral genomes. This is not possible with the routinely used Sanger sequencing method that gives the consensus reads, or by cloning approaches. In this study, a targeted-enrichment methodology for the simultaneous acquisition of complete foot-and-mouth disease virus (FMDV) genomes directly from clinical samples is presented. Biotinylated oligonucleotide probes (120 nt) were used to capture and enrich viral RNA following library preparation. To create a virus capture panel targeting serotype O and A simultaneously, 18 baits targeting the highly conserved regions of the 8.3 kb FMDV genome were synthesised, with 14 common to both serotypes, 2 specific to serotype O and 2 specific to serotype A. These baits were used to capture and enrich FMDV RNA (as cDNA) from samples collected during one pathogenesis and two vaccine efficacy trials, where pigs were infected with serotype O or A viruses. After enrichment, FMDV-specific sequencing reads increased by almost 3000-fold. The sequence data were used in variant call analysis to identify single nucleotide polymorphisms (SNPs). This methodology was robust in its ability to capture diverse sequences, was shown to be highly sensitive, and can be easily scaled for large-scale epidemiological studies.
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Affiliation(s)
| | - Danielle E Anderson
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - October M Sessions
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore; Saw Swee Hock School of Public Health, National University of Singapore, Singapore; Department of Pharmacy, National University of Singapore, Singapore
| | - Uma S Kamaraj
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Timothy R Bowden
- Australian Animal Health Laboratory, CSIRO Health and Biosecurity, Geelong, Australia
| | - Jacquelyn Horsington
- Australian Animal Health Laboratory, CSIRO Health and Biosecurity, Geelong, Australia
| | - Christopher Cowled
- Australian Animal Health Laboratory, CSIRO Health and Biosecurity, Geelong, Australia
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Wilna Vosloo
- Australian Animal Health Laboratory, CSIRO Health and Biosecurity, Geelong, Australia
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Yuan L, Chen WJ, Wang JY, Li Y, Tian D, Wang MX, Yu HT, Xu YC, Li D, Zhuang M, Ling H. Divergent Primary Immune Responses Induced by Human Immunodeficiency Virus-1 gp120 and Hepatitis B Surface Antigen Determine Antibody Recall Responses. Virol Sin 2018; 33:502-514. [PMID: 30569292 PMCID: PMC6335216 DOI: 10.1007/s12250-018-0074-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 11/07/2018] [Indexed: 12/19/2022] Open
Abstract
The development of a vaccine based on human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein (Env) that elicits potent protective antibodies against infection has been challenging. Recently, we compared the antibody production patterns of HIV-1 Env gp120 and hepatitis B virus surface antigen (HBsAg) to provide insights into how we may improve the protective efficacy of Env-based immunogens. Our previous study showed that HIV Env and HBsAg display different mechanisms of antibody elicitation and that T cells facilitate the responses to repeated immunizations. Here, to elucidate the detailed roles of primary immunization in immune memory response formation and antibody production, we immunized C57BL/6 mice with each antigen and evaluated the development of T follicular helper (Tfh) cells, germinal centers, and the memory responses involved in prime and boost immunizations. We found that after prime immunization, compared with HBsAg, gp120 induced higher frequencies of Tfh cells and programmed death (PD)-1+ T cells, greater major histocompatibility complex II expression on B cells, comparable activated B cells, but weaker germinal center (GC) reactions and memory B cell responses in the draining lymph nodes, accompanied by slower antibody recall responses and poor immune memory responses. The above results suggested that more PD-1+ T cells arising in primary immunization may serve as major contributors to the slow antibody recall response elicited by HIV-1 Env.
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Affiliation(s)
- Li Yuan
- Department of Microbiology, Harbin Medical University, Harbin, 150081, China
| | - Wen-Jiang Chen
- Department of Microbiology, Harbin Medical University, Harbin, 150081, China
| | - Jia-Ye Wang
- Department of Microbiology, Harbin Medical University, Harbin, 150081, China.,Heilongjiang Provincial Key Laboratory of Infection and Immunity, Key Laboratory of Pathogen Biology, Harbin, 150081, China.,Wu Lien-Teh Institute, Harbin Medical University, Harbin, 150081, China
| | - Yan Li
- Department of Microbiology, Harbin Medical University, Harbin, 150081, China.,Heilongjiang Provincial Key Laboratory of Infection and Immunity, Key Laboratory of Pathogen Biology, Harbin, 150081, China.,Wu Lien-Teh Institute, Harbin Medical University, Harbin, 150081, China
| | - Dan Tian
- Department of Microbiology, Harbin Medical University, Harbin, 150081, China
| | - Ming-Xia Wang
- Department of Microbiology, Harbin Medical University, Harbin, 150081, China
| | - Hao-Tong Yu
- Department of Microbiology, Harbin Medical University, Harbin, 150081, China
| | - Ying-Chu Xu
- Department of Microbiology, Harbin Medical University, Harbin, 150081, China
| | - Di Li
- Department of Microbiology, Harbin Medical University, Harbin, 150081, China.,Heilongjiang Provincial Key Laboratory of Infection and Immunity, Key Laboratory of Pathogen Biology, Harbin, 150081, China.,Wu Lien-Teh Institute, Harbin Medical University, Harbin, 150081, China
| | - Min Zhuang
- Department of Microbiology, Harbin Medical University, Harbin, 150081, China.,Heilongjiang Provincial Key Laboratory of Infection and Immunity, Key Laboratory of Pathogen Biology, Harbin, 150081, China.,Wu Lien-Teh Institute, Harbin Medical University, Harbin, 150081, China
| | - Hong Ling
- Department of Microbiology, Harbin Medical University, Harbin, 150081, China. .,Heilongjiang Provincial Key Laboratory of Infection and Immunity, Key Laboratory of Pathogen Biology, Harbin, 150081, China. .,Wu Lien-Teh Institute, Harbin Medical University, Harbin, 150081, China. .,Department of Immunology, Harbin Medical University, Harbin, 150081, China.
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