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Huang ZZ, Tan J, Huang P, Li BS, Guo Q, Liang LJ. The evolutionary features and roles of single nucleotide variants and charged amino acid mutations in influenza outbreaks during NPI period. Sci Rep 2024; 14:20418. [PMID: 39223292 PMCID: PMC11369173 DOI: 10.1038/s41598-024-71349-8] [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: 12/19/2023] [Accepted: 08/27/2024] [Indexed: 09/04/2024] Open
Abstract
The epidemic and outbreaks of influenza B Victoria lineage (Bv) during 2019-2022 led to an analysis of genetic, epitopes, charged amino acids and Bv outbreaks. Based on the National Influenza Surveillance Network (NISN), the Bv 72 strains isolated during 2019-2022 were selected by spatio-temporal sampling, then were sequenced. Using the Compare Means, Correlate and Cluster, the outbreak data were analyzed, including the single nucleotide variant (SNV), amino acid (AA), epitope, evolutionary rate (ER), Shannon entropy value (SV), charged amino acid and outbreak. With the emergence of COVID-19, the non-pharmaceutical interventions (NPIs) made Less distant transmission and only Bv outbreak. The 2021-2022 strains in the HA genes were located in the same subset, but were distinct from the 2019-2020 strains (P < 0.001). The codon G → A transition in nucleotide was in the highest ratio but the transversion of C → A and T → A made the most significant contribution to the outbreaks, while the increase in amino acid mutations characterized by polar, acidic and basic signatures played a key role in the Bv epidemic in 2021-2022. Both ER and SV were positively correlated in HA genes (R = 0.690) and NA genes (R = 0.711), respectively, however, the number of mutations in the HA genes was 1.59 times higher than that of the NA gene (2.15/1.36) from the beginning of 2020 to 2022. The positively selective sites 174, 199, 214 and 563 in HA genes and the sites 73 and 384 in NA genes were evolutionarily selected in the 2021-2022 influenza outbreaks. Overall, the prevalent factors related to 2021-2022 influenza outbreaks included epidemic timing, Tv, Ts, Tv/Ts, P137 (B → P), P148 (B → P), P199 (P → A), P212 (P → A), P214 (H → P) and P563 (B → P). The preference of amino acid mutations for charge/pH could influence the epidemic/outbreak trends of infectious diseases. Here was a good model of the evolution of infectious disease pathogens. This study, on account of further exploration of virology, genetics, bioinformatics and outbreak information, might facilitate further understanding of their deep interaction mechanisms in the spread of infectious diseases.
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Affiliation(s)
- Zhong-Zhou Huang
- Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
- School of Public Health, Sun Yat-Sen University, Guangzhou, 510080, China
- Workstation for Emerging Infectious Disease Control and Prevention, Guangdong Center for Disease Control and Prevention, Guangzhou, 511430, China
| | - Jing Tan
- Workstation for Emerging Infectious Disease Control and Prevention, Guangdong Center for Disease Control and Prevention, Guangzhou, 511430, China
- School of Public Health, Southern Medical University, Guangzhou, 510515, China
- School of Public Health, Southwest Medical University, Luzhou, 646000, China
| | - Ping Huang
- School of Public Health, Sun Yat-Sen University, Guangzhou, 510080, China.
- Workstation for Emerging Infectious Disease Control and Prevention, Guangdong Center for Disease Control and Prevention, Guangzhou, 511430, China.
- Guangdong Key Laboratory of Pathogen Detection for Emerging Infectious Disease Response, Guangdong Center for Disease Control and Prevention, Guangzhou, 511430, China.
- School of Public Health, Southern Medical University, Guangzhou, 510515, China.
| | - Bai-Sheng Li
- Workstation for Emerging Infectious Disease Control and Prevention, Guangdong Center for Disease Control and Prevention, Guangzhou, 511430, China
- Guangdong Key Laboratory of Pathogen Detection for Emerging Infectious Disease Response, Guangdong Center for Disease Control and Prevention, Guangzhou, 511430, China
- School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Qing Guo
- Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Li-Jun Liang
- Workstation for Emerging Infectious Disease Control and Prevention, Guangdong Center for Disease Control and Prevention, Guangzhou, 511430, China
- Guangdong Key Laboratory of Pathogen Detection for Emerging Infectious Disease Response, Guangdong Center for Disease Control and Prevention, Guangzhou, 511430, China
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Akache B, Read AJ, Dudani R, Harrison BA, Williams D, Deschatelets L, Jia Y, Chandan V, Stark FC, Agbayani G, Makinen SR, Hemraz UD, Lam E, Régnier S, Zou W, Kirkland PD, McCluskie MJ. Sulfated Lactosyl Archaeol Archaeosome-Adjuvanted Vaccine Formulations Targeting Rabbit Hemorrhagic Disease Virus Are Immunogenic and Efficacious. Vaccines (Basel) 2023; 11:1043. [PMID: 37376432 DOI: 10.3390/vaccines11061043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 05/24/2023] [Accepted: 05/27/2023] [Indexed: 06/29/2023] Open
Abstract
Vaccines play an important role in maintaining human and animal health worldwide. There is continued demand for effective and safe adjuvants capable of enhancing antigen-specific responses to a target pathogen. Rabbit hemorrhagic disease virus (RHDV) is a highly contagious calicivirus that often induces high mortality rates in rabbits. Herein, we evaluated the activity of an experimental sulfated lactosyl archaeol (SLA) archaeosome adjuvant when incorporated in subunit vaccine formulations targeting RHDV. The subunit antigens consisted of RHDV-CRM197 peptide conjugates or recombinant RHDV2 VP60. SLA was able to enhance antigen-specific antibody titers and cellular responses in mice and rabbits. Three weeks following immunization, antigen-specific antibody levels in rabbits vaccinated with RHDV2 VP60 + SLA were significantly higher than those immunized with antigen alone, with geomean titers of 7393 vs. 117. In addition, the SLA-adjuvanted VP60-based formulations were highly efficacious in a rabbit RHDV2 challenge model with up to 87.5% animals surviving the viral challenge. These findings demonstrate the potential utility of SLA adjuvants in veterinary applications and highlight its activity in different types of mammalian species.
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Affiliation(s)
- Bassel Akache
- National Research Council Canada, Human Health Therapeutics, Ottawa, ON K1A 0R6, Canada
| | - Andrew J Read
- Virology Laboratory, Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, NSW 2567, Australia
| | - Renu Dudani
- National Research Council Canada, Human Health Therapeutics, Ottawa, ON K1A 0R6, Canada
| | - Blair A Harrison
- National Research Council Canada, Human Health Therapeutics, Ottawa, ON K1A 0R6, Canada
| | - Dean Williams
- National Research Council Canada, Human Health Therapeutics, Ottawa, ON K1A 0R6, Canada
| | - Lise Deschatelets
- National Research Council Canada, Human Health Therapeutics, Ottawa, ON K1A 0R6, Canada
| | - Yimei Jia
- National Research Council Canada, Human Health Therapeutics, Ottawa, ON K1A 0R6, Canada
| | - Vandana Chandan
- National Research Council Canada, Human Health Therapeutics, Ottawa, ON K1A 0R6, Canada
| | - Felicity C Stark
- National Research Council Canada, Human Health Therapeutics, Ottawa, ON K1A 0R6, Canada
| | - Gerard Agbayani
- National Research Council Canada, Human Health Therapeutics, Ottawa, ON K1A 0R6, Canada
| | - Shawn R Makinen
- National Research Council Canada, Human Health Therapeutics, Ottawa, ON K1A 0R6, Canada
| | - Usha D Hemraz
- National Research Council Canada, Aquatic and Crop Resource Development, Montreal, QC H4P 2R2, Canada
| | - Edmond Lam
- National Research Council Canada, Aquatic and Crop Resource Development, Montreal, QC H4P 2R2, Canada
| | - Sophie Régnier
- National Research Council Canada, Aquatic and Crop Resource Development, Montreal, QC H4P 2R2, Canada
| | - Wei Zou
- National Research Council Canada, Human Health Therapeutics, Ottawa, ON K1A 0R6, Canada
| | - Peter D Kirkland
- Virology Laboratory, Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, NSW 2567, Australia
| | - Michael J McCluskie
- National Research Council Canada, Human Health Therapeutics, Ottawa, ON K1A 0R6, Canada
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Park JY, Cho SH. Production of monoclonal antibody of heat-labile toxin A subunit to identify enterotoxigenic Escherichia coli by epitope mapping using synthetic peptides. Front Immunol 2023; 14:1152910. [PMID: 37275900 PMCID: PMC10232981 DOI: 10.3389/fimmu.2023.1152910] [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: 01/28/2023] [Accepted: 05/05/2023] [Indexed: 06/07/2023] Open
Abstract
Background Enterotoxigenic Escherichia coli (ETEC) is a major cause of diarrhea through two enterotoxins, a heat-labile toxin and a heat-stable toxin. These toxins alter the cellular signaling pathways, ultimately triggering an increase in chloride secretion and watery diarrhea. Objective For the development of an ETEC vaccine, we attempted to construct a peptide-specific monoclonal antibody library against heat-labile enterotoxin A subunit (LT-A) by epitope mapping using synthetic peptides. Methods Sera produced by five mice immunized with recombinant LT-A protein were examined for specific recognition with synthetic 15-mer and 34-mer peptides of LT-A proteins using enzyme-linked immunosorbent assay. The analysis revealed that the synthetic peptides number 8, 16, 24, 33, 36, 38, and 39 reacted with an anti-LT-A polyclonal antibody. For the possible prediction of LT-A epitopes, each full-length protein sequence was subjected to BCPreds analysis and three-dimensional protein structure analysis. The data showed that three peptides (synthetic peptide numbers: 33, 36, and 38-39) have identical antigenic specificities with LT-A protein, suggesting the usefulness of these linear peptide epitopes. Results Based on these peptides, we produced monoclonal antibodies to improve the specificity of LT-A detection. Monoclonal antibodies produced from two peptides (numbers 33 and 36) showed affinity for an LT-A recombinant antigen. Moreover, peptide epitope prediction analysis showed that the sites of the three peptides were identical to those exhibiting actual antigenicity. Also, it was confirmed that the amino acid sequence that actually showed antigenicity was included in the peptide predicted only by ETEC-LT-A-33. Also, the specificity of the antibody for ETEC-LT-A-33 was validated using bacterial cells, and the neutralizing effect of the antibody was determined by assessing cytokine release in infected HCT-8 cells. Conclusion The monoclonal antibodies produced in this study are useful toolsfor vaccine production against ETEC and can be used to identify peptide antigencandidates.
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Affiliation(s)
- Jun-Young Park
- Division of Zoonotic and Vector Borne Disease Research, Center for Infectious Disease Research, Korea National Institute of Health, Cheongju, Republic of Korea
- Environmental Diseases Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Seung-Hak Cho
- Division of Zoonotic and Vector Borne Disease Research, Center for Infectious Disease Research, Korea National Institute of Health, Cheongju, Republic of Korea
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2019-2020. MASS SPECTROMETRY REVIEWS 2022:e21806. [PMID: 36468275 DOI: 10.1002/mas.21806] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
This review is the tenth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2020. Also included are papers that describe methods appropriate to analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. The review is basically divided into three sections: (1) general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation, quantification and the use of arrays. (2) Applications to various structural types such as oligo- and polysaccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals, and (3) other areas such as medicine, industrial processes and glycan synthesis where MALDI is extensively used. Much of the material relating to applications is presented in tabular form. The reported work shows increasing use of incorporation of new techniques such as ion mobility and the enormous impact that MALDI imaging is having. MALDI, although invented nearly 40 years ago is still an ideal technique for carbohydrate analysis and advancements in the technique and range of applications show little sign of diminishing.
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Affiliation(s)
- David J Harvey
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
- Department of Chemistry, University of Oxford, Oxford, Oxfordshire, United Kingdom
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Lengfeld J, Zhang H, Stoesz S, Murali R, Pass F, Greene MI, Goel PN, Grover P. Challenges in Detection of Serum Oncoprotein: Relevance to Breast Cancer Diagnostics. BREAST CANCER-TARGETS AND THERAPY 2021; 13:575-593. [PMID: 34703307 PMCID: PMC8524259 DOI: 10.2147/bctt.s331844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 10/02/2021] [Indexed: 11/23/2022]
Abstract
Breast cancer is a highly prevalent malignancy that shows improved outcomes with earlier diagnosis. Current screening and monitoring methods have improved survival rates, but the limitations of these approaches have led to the investigation of biomarker evaluation to improve early diagnosis and treatment monitoring. The enzyme-linked immunosorbent assay (ELISA) is a specific and robust technique ideally suited for the quantification of protein biomarkers from blood or its constituents. The continued clinical relevancy of this assay format will require overcoming specific technical challenges, including the ultra-sensitive detection of trace biomarkers and the circumventing of potential assay interference due to the expanding use of monoclonal antibody (mAb) therapeutics. Approaches to increasing the sensitivity of ELISA have been numerous and include employing more sensitive substrates, combining ELISA with the polymerase chain reaction (PCR), and incorporating nanoparticles as shuttles for detection antibodies and enzymes. These modifications have resulted in substantial boosts in the ability to detect extremely low levels of protein biomarkers, with some systems reliably detecting antigen at sub-femtomolar concentrations. Extensive utilization of mAb therapies in oncology has presented an additional contemporary challenge for ELISA, particularly when both therapeutic and assay antibodies target the same protein antigen. Resolution of issues such as epitope overlap and steric hindrance requires a rational approach to the design of diagnostic antibodies that takes advantage of modern antibody generation pipelines, epitope binning techniques and computational methods to strategically target biomarker epitopes. This review discusses technical strategies in ELISA implemented to date and their feasibility to address current constraints on sensitivity and problems with interference in the clinical setting. The impact of these recent advancements will depend upon their transformation from research laboratory protocols into facile, reliable detection systems that can ideally be replicated in point-of-care devices to maximize utilization and transform both the diagnostic and therapeutic monitoring landscape.
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Affiliation(s)
- Justin Lengfeld
- Martell Diagnostic Laboratories, Inc., Roseville, MN, 55113, USA
| | - Hongtao Zhang
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Steven Stoesz
- Martell Diagnostic Laboratories, Inc., Roseville, MN, 55113, USA
| | - Ramachandran Murali
- Department of Biomedical Sciences, Research Division of Immunology; Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Franklin Pass
- Martell Diagnostic Laboratories, Inc., Roseville, MN, 55113, USA
| | - Mark I Greene
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Peeyush N Goel
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Payal Grover
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
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