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Xu Q, Cao J, Rai KR, Zhu B, Liu D, Wan C. Codon usage bias of goose circovirus and its adaptation to host. Poult Sci 2024; 103:103775. [PMID: 38713985 PMCID: PMC11091504 DOI: 10.1016/j.psj.2024.103775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 04/03/2024] [Accepted: 04/13/2024] [Indexed: 05/09/2024] Open
Abstract
Goose circovirus (GoCV), a potential immunosuppressive virus possessing a circular single-stranded DNA genome, is widely distributed in both domesticated and wild geese. This virus infection causes significant economic losses in the waterfowl industry. The codon usage patterns of viruses reflect the evolutionary history and genetic architecture, allowing them to adapt quickly to changes in the external environment, particularly to their hosts. In this study, we retrieved the coding sequences (Rep and Cap) and the genome of GoCV from GenBank, conducting comprehensive research to explore the codon usage patterns in 144 GoCV strains. The overall codon usage of the GoCV strains was relatively similar and exhibited a slight bias. The effective number of codons (ENC) indicated a low overall extent of codon usage bias (CUB) in GoCV. Combined with the base composition and relative synonymous codon usage (RSCU) analysis, the results revealed a bias toward A- and G-ending codons in the overall codon usage. Analysis of the ENC-GC3s plot and neutrality plot suggested that natural selection plays an important role in shaping the codon usage pattern of GoCV, with mutation pressure having a minor influence. Furthermore, the correlations between ENC and relative indices, as well as correspondence analysis (COA), showed that hydrophobicity and geographical distribution also contribute to codon usage variation in GoCV, suggesting the possible involvement of natural selection. In conclusion, GoCV exhibits comparatively slight CUB, with natural selection being the major factor shaping the codon usage pattern of GoCV. Our research contributes to a deeper understanding of GoCV evolution and its host adaptation, providing valuable insights for future basic studies and vaccine design related to GoCV.
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Affiliation(s)
- Quanming Xu
- Scientific Research and Experiment Center, Fujian Police College, Fuzhou 350007, China
| | - Jie Cao
- Scientific Research and Experiment Center, Fujian Police College, Fuzhou 350007, China
| | - Kul Raj Rai
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Binling Zhu
- Department of Forensic Science, Fujian Police College, Fuzhou 350007, China
| | - Dan Liu
- China Institute of Veterinary Drug Control, Beijing, 100081, China
| | - Chunhe Wan
- Institute of Animal Husbandry and Veterinary Medicine/Fujian Key Laboratory for Avian Diseases Control and Prevention/Fujian Animal Diseases Control Technology Development Centre, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China.
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Hoang KL, Read TD, King KC. Incomplete immunity in a natural animal-microbiota interaction selects for higher pathogen virulence. Curr Biol 2024; 34:1357-1363.e3. [PMID: 38430909 PMCID: PMC10962313 DOI: 10.1016/j.cub.2024.02.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 12/18/2023] [Accepted: 02/07/2024] [Indexed: 03/05/2024]
Abstract
Incomplete immunity in recovered hosts is predicted to favor more virulent pathogens upon re-infection in the population.1 The microbiota colonizing animals can generate a similarly long-lasting, partial immune response, allowing for infection but dampened disease severity.2 We tracked the evolutionary trajectories of a widespread pathogen (Pseudomonas aeruginosa), experimentally passaged through populations of nematodes immune-primed by a natural microbiota member (P. berkeleyensis). This bacterium can induce genes regulated by a mitogen-activated protein kinase (MAPK) signaling pathway effective at conferring protection against pathogen-induced death despite infection.3 Across host populations, this incomplete immunity selected for pathogens more than twice as likely to kill as those evolved in non-primed (i.e., naive) or immune-compromised (mutants with a knockout of the MAPK ortholog) control populations. Despite the higher virulence, pathogen molecular evolution in immune-primed hosts was slow and constrained. In comparison, evolving pathogens in immune-compromised hosts were characterized by substantial genomic differentiation and attenuated virulence. These findings directly attribute the incomplete host immunity induced from microbiota as a significant force shaping the virulence and evolutionary dynamics of novel infectious diseases.
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Affiliation(s)
- Kim L Hoang
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK; Division of Infectious Diseases, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA 30322, USA.
| | - Timothy D Read
- Division of Infectious Diseases, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA 30322, USA
| | - Kayla C King
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK; Department of Zoology, University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada; Department of Microbiology & Immunology, University of British Columbia, 1365 - 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada.
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3
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Igyártó BZ, Qin Z. The mRNA-LNP vaccines - the good, the bad and the ugly? Front Immunol 2024; 15:1336906. [PMID: 38390323 PMCID: PMC10883065 DOI: 10.3389/fimmu.2024.1336906] [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: 11/11/2023] [Accepted: 01/23/2024] [Indexed: 02/24/2024] Open
Abstract
The mRNA-LNP vaccine has received much attention during the COVID-19 pandemic since it served as the basis of the most widely used SARS-CoV-2 vaccines in Western countries. Based on early clinical trial data, these vaccines were deemed safe and effective for all demographics. However, the latest data raise serious concerns about the safety and effectiveness of these vaccines. Here, we review some of the safety and efficacy concerns identified to date. We also discuss the potential mechanism of observed adverse events related to the use of these vaccines and whether they can be mitigated by alterations of this vaccine mechanism approach.
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Affiliation(s)
- Botond Z. Igyártó
- Department of Microbiology and Immunology, Thomas Jefferson University, Philadelphia, PA, United States
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4
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Gupta S, Gupta D, Bhatnagar S. Analysis of SARS-CoV-2 genome evolutionary patterns. Microbiol Spectr 2024; 12:e0265423. [PMID: 38197644 PMCID: PMC10846092 DOI: 10.1128/spectrum.02654-23] [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: 06/26/2023] [Accepted: 11/20/2023] [Indexed: 01/11/2024] Open
Abstract
The spread of SARS-CoV-2 virus accompanied by public availability of abundant sequence data provides a window for the determination of viral evolutionary patterns. In this study, SARS-CoV-2 genome sequences were collected from seven countries in the period January 2020-December 2022. The sequences were classified into three phases, namely, pre-vaccination, post-vaccination, and recent period. Comparison was performed between these phases based on parameters like mutation rates, selection pressure (dN/dS ratio), and transition to transversion ratios (Ti/Tv). Similar comparisons were performed among SARS-CoV-2 variants. Statistical significance was tested using Graphpad unpaired t-test. The analysis showed an increase in the percent genomic mutation rates post-vaccination and in recent periods across all countries from the pre-vaccination sequences. Mutation rates were highest in NSP3, S, N, and NSP12b before and increased further after vaccination. NSP4 showed the largest change in mutation rates after vaccination. The dN/dS ratios showed purifying selection that shifted toward neutral selection after vaccination. N, ORF8, ORF3a, and ORF10 were under highest positive selection before vaccination. Shift toward neutral selection was driven by E, NSP3, and ORF7a in the after vaccination set. In recent sequences, the largest dN/dS change was observed in E, NSP1, and NSP13. The Ti/Tv ratios decreased with time. C→U and G→U were the most frequent transitions and transversions. However, U→G was the most frequent transversion in recent period. The Omicron variant had the highest genomic mutation rates, while Delta showed the highest dN/dS ratio. Protein-wise dN/dS ratio was also seen to vary across the different variants.IMPORTANCETo the best of our knowledge, there exists no other large-scale study of the genomic and protein-wise mutation patterns during the time course of evolution in different countries. Analyzing the SARS-CoV-2 evolutionary patterns in view of the varying spatial, temporal, and biological signals is important for diagnostics, therapeutics, and pharmacovigilance of SARS-CoV-2.
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Affiliation(s)
- Shubhangi Gupta
- Department of Biological Sciences and Engineering, Computational and Structural Biology Laboratory, Netaji Subhas University of Technology, Dwarka, New Delhi, India
| | - Deepanshu Gupta
- Division of Biotechnology, Computational and Structural Biology Laboratory, Netaji Subhas Institute of Technology, Dwarka, New Delhi, India
| | - Sonika Bhatnagar
- Department of Biological Sciences and Engineering, Computational and Structural Biology Laboratory, Netaji Subhas University of Technology, Dwarka, New Delhi, India
- Division of Biotechnology, Computational and Structural Biology Laboratory, Netaji Subhas Institute of Technology, Dwarka, New Delhi, India
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Mwape I, Laban NM, Chibesa K, Moono A, Silwamba S, Malisheni MM, Chisenga C, Chauwa A, Simusika P, Phiri M, Simuyandi M, Chilengi R, De Beer C, Ojok D. Characterization of Rotavirus Strains Responsible for Breakthrough Diarrheal Diseases among Zambian Children Using Whole Genome Sequencing. Vaccines (Basel) 2023; 11:1759. [PMID: 38140164 PMCID: PMC10748035 DOI: 10.3390/vaccines11121759] [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: 09/21/2023] [Revised: 11/08/2023] [Accepted: 11/10/2023] [Indexed: 12/24/2023] Open
Abstract
The occurrence of rotavirus (RV) infection among vaccinated children in high-burden settings poses a threat to further disease burden reduction. Genetically altered viruses have the potential to evade both natural infection and vaccine-induced immune responses, leading to diarrheal diseases among vaccinated children. Studies characterizing RV strains responsible for breakthrough infections in resource-limited countries where RV-associated diarrheal diseases are endemic are limited. We aimed to characterize RV strains detected in fully vaccinated children residing in Zambia using next-generation sequencing. We conducted whole genome sequencing on Illumina MiSeq. Whole genome assembly was performed using Geneious Prime 2023.1.2. A total of 76 diarrheal stool specimens were screened for RV, and 4/76 (5.2%) were RV-positive. Whole genome analysis revealed RVA/Human-wt/ZMB/CIDRZ-RV2088/2020/G1P[4]-I2-R2-C2-M2-A2-N2-T2-E2-H2 and RVA/Human-wt/ZMB/CIDRZ-RV2106/2020/G12P[4]-I1-R2-C2-M2-A2-N1-T2-E1-H2 strains were mono and multiple reassortant (exchanged genes in bold) respectively, whilst RVA/Human-wt/ZMB/CIDRZ-RV2150/2020/G12P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1 was a typical Wa-like strain. Comparison of VP7 and VP4 antigenic epitope of breakthrough strains and Rotarix strain revealed several amino acid differences. Variations in amino acids in antigenic epitope suggested they played a role in immune evasion of neutralizing antibodies elicited by vaccination. Findings from this study have the potential to inform national RV vaccination strategies and the design of highly efficacious universal RV vaccines.
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Affiliation(s)
- Innocent Mwape
- Enteric Disease and Vaccine Research Unit, Centre for Infectious Disease Research in Zambia, Lusaka P.O. Box 34681, Zambia; (N.M.L.); (A.C.)
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, P.O. Box 241, Cape Town 8000, South Africa;
| | - Natasha Makabilo Laban
- Enteric Disease and Vaccine Research Unit, Centre for Infectious Disease Research in Zambia, Lusaka P.O. Box 34681, Zambia; (N.M.L.); (A.C.)
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Kennedy Chibesa
- Enteric Disease and Vaccine Research Unit, Centre for Infectious Disease Research in Zambia, Lusaka P.O. Box 34681, Zambia; (N.M.L.); (A.C.)
- Division of Medical Virology, School of Pathology, Faculty of Health Sciences, University of the Free State, Bloemfontein P.O. Box 339, South Africa
| | - Andrew Moono
- Enteric Disease and Vaccine Research Unit, Centre for Infectious Disease Research in Zambia, Lusaka P.O. Box 34681, Zambia; (N.M.L.); (A.C.)
| | - Suwilanji Silwamba
- Enteric Disease and Vaccine Research Unit, Centre for Infectious Disease Research in Zambia, Lusaka P.O. Box 34681, Zambia; (N.M.L.); (A.C.)
| | | | - Caroline Chisenga
- Enteric Disease and Vaccine Research Unit, Centre for Infectious Disease Research in Zambia, Lusaka P.O. Box 34681, Zambia; (N.M.L.); (A.C.)
| | - Adriace Chauwa
- Enteric Disease and Vaccine Research Unit, Centre for Infectious Disease Research in Zambia, Lusaka P.O. Box 34681, Zambia; (N.M.L.); (A.C.)
| | - Paul Simusika
- University Teaching Hospitals, Lusaka 10101, Zambia
- Institute of Basic and Biomedical Sciences, Levy Mwanawasa Medical University, Lusaka 10101, Zambia
| | - Mabvuto Phiri
- Enteric Disease and Vaccine Research Unit, Centre for Infectious Disease Research in Zambia, Lusaka P.O. Box 34681, Zambia; (N.M.L.); (A.C.)
| | - Michelo Simuyandi
- Enteric Disease and Vaccine Research Unit, Centre for Infectious Disease Research in Zambia, Lusaka P.O. Box 34681, Zambia; (N.M.L.); (A.C.)
| | - Roma Chilengi
- Enteric Disease and Vaccine Research Unit, Centre for Infectious Disease Research in Zambia, Lusaka P.O. Box 34681, Zambia; (N.M.L.); (A.C.)
| | - Corena De Beer
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, P.O. Box 241, Cape Town 8000, South Africa;
| | - David Ojok
- Enteric Disease and Vaccine Research Unit, Centre for Infectious Disease Research in Zambia, Lusaka P.O. Box 34681, Zambia; (N.M.L.); (A.C.)
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Sheehan J, Ardizzone CM, Khanna M, Trauth AJ, Hagensee ME, Ramsay AJ. Dynamics of Serum-Neutralizing Antibody Responses in Vaccinees through Multiple Doses of the BNT162b2 Vaccine. Vaccines (Basel) 2023; 11:1720. [PMID: 38006052 PMCID: PMC10675463 DOI: 10.3390/vaccines11111720] [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: 10/11/2023] [Revised: 11/08/2023] [Accepted: 11/11/2023] [Indexed: 11/26/2023] Open
Abstract
SARS-CoV-2 mRNA vaccines are administered as effective prophylactic measures for reducing virus transmission rates and disease severity. To enhance the durability of post-vaccination immunity and combat SARS-CoV-2 variants, boosters have been administered to two-dose vaccinees. However, long-term humoral responses following booster vaccination are not well characterized. A 16-member cohort of healthy SARS-CoV-2 naïve participants were enrolled in this study during a three-dose BNT162b2 vaccine series. Serum samples were collected from vaccinees over 420 days and screened for antigen (Ag)-specific antibody titers, IgG subclass distribution, and neutralizing antibody (nAb) responses. Vaccine boosting restored peak Ag-specific titers with sustained α-RBD IgG and IgA antibody responses when measured at six months post-boost. RBD- and spike-specific IgG4 antibody levels were markedly elevated in three-dose but not two-dose immune sera. Although strong neutralization responses were detected in two- and three-dose vaccine sera, these rapidly decayed to pre-immune levels by four and six months, respectively. While boosters enhanced serum IgG Ab reactivity and nAb responses against variant strains, all variants tested showed resistance to two- and three-dose immune sera. Our data reflect the poor durability of vaccine-induced nAb responses which are a strong predictor of protection from symptomatic SARS-CoV-2 infection. The induction of IgG4-switched humoral responses may permit extended viral persistence via the downregulation of Fc-mediated effector functions.
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Affiliation(s)
- Jared Sheehan
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - Caleb M. Ardizzone
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - Mayank Khanna
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - Amber J. Trauth
- Department of Internal Medicine, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - Michael E. Hagensee
- Department of Internal Medicine, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - Alistair J. Ramsay
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
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7
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da Fonseca GC, Cavalcante LTF, Brustolini OJ, Luz PM, Pires DC, Jalil EM, Peixoto EM, Grinsztejn B, Veloso VG, Nazer S, Costa CAM, Villela DAM, Goedert GT, Santos CVBD, Rodrigues NCP, do Couto Motta F, Siqueira MM, Coelho LE, Struchiner CJ, Vasconcelos ATR. Differential Type-I Interferon Response in Buffy Coat Transcriptome of Individuals Infected with SARS-CoV-2 Gamma and Delta Variants. Int J Mol Sci 2023; 24:13146. [PMID: 37685953 PMCID: PMC10487928 DOI: 10.3390/ijms241713146] [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: 07/07/2023] [Revised: 08/07/2023] [Accepted: 08/20/2023] [Indexed: 09/10/2023] Open
Abstract
The innate immune system is the first line of defense against pathogens such as the acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The type I-interferon (IFN) response activation during the initial steps of infection is essential to prevent viral replication and tissue damage. SARS-CoV and SARS-CoV-2 can inhibit this activation, and individuals with a dysregulated IFN-I response are more likely to develop severe disease. Several mutations in different variants of SARS-CoV-2 have shown the potential to interfere with the immune system. Here, we evaluated the buffy coat transcriptome of individuals infected with Gamma or Delta variants of SARS-CoV-2. The Delta transcriptome presents more genes enriched in the innate immune response and Gamma in the adaptive immune response. Interactome and enriched promoter analysis showed that Delta could activate the INF-I response more effectively than Gamma. Two mutations in the N protein and one in the nsp6 protein found exclusively in Gamma have already been described as inhibitors of the interferon response pathway. This indicates that the Gamma variant evolved to evade the IFN-I response. Accordingly, in this work, we showed one of the mechanisms that variants of SARS-CoV-2 can use to avoid or interfere with the host Immune system.
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Affiliation(s)
- Guilherme C. da Fonseca
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Rio de Janeiro 25651-076, Brazil; (G.C.d.F.); (L.T.F.C.); (O.J.B.)
| | - Liliane T. F. Cavalcante
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Rio de Janeiro 25651-076, Brazil; (G.C.d.F.); (L.T.F.C.); (O.J.B.)
| | - Otávio J. Brustolini
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Rio de Janeiro 25651-076, Brazil; (G.C.d.F.); (L.T.F.C.); (O.J.B.)
| | - Paula M. Luz
- Instituto Nacional de Infectologia Evandro Chagas, FIOCRUZ, Rio de Janeiro 21040-360, Brazil; (P.M.L.); (D.C.P.); (E.M.J.); (E.M.P.); (B.G.); (V.G.V.); (S.N.); (L.E.C.)
| | - Debora C. Pires
- Instituto Nacional de Infectologia Evandro Chagas, FIOCRUZ, Rio de Janeiro 21040-360, Brazil; (P.M.L.); (D.C.P.); (E.M.J.); (E.M.P.); (B.G.); (V.G.V.); (S.N.); (L.E.C.)
| | - Emilia M. Jalil
- Instituto Nacional de Infectologia Evandro Chagas, FIOCRUZ, Rio de Janeiro 21040-360, Brazil; (P.M.L.); (D.C.P.); (E.M.J.); (E.M.P.); (B.G.); (V.G.V.); (S.N.); (L.E.C.)
| | - Eduardo M. Peixoto
- Instituto Nacional de Infectologia Evandro Chagas, FIOCRUZ, Rio de Janeiro 21040-360, Brazil; (P.M.L.); (D.C.P.); (E.M.J.); (E.M.P.); (B.G.); (V.G.V.); (S.N.); (L.E.C.)
| | - Beatriz Grinsztejn
- Instituto Nacional de Infectologia Evandro Chagas, FIOCRUZ, Rio de Janeiro 21040-360, Brazil; (P.M.L.); (D.C.P.); (E.M.J.); (E.M.P.); (B.G.); (V.G.V.); (S.N.); (L.E.C.)
| | - Valdilea G. Veloso
- Instituto Nacional de Infectologia Evandro Chagas, FIOCRUZ, Rio de Janeiro 21040-360, Brazil; (P.M.L.); (D.C.P.); (E.M.J.); (E.M.P.); (B.G.); (V.G.V.); (S.N.); (L.E.C.)
| | - Sandro Nazer
- Instituto Nacional de Infectologia Evandro Chagas, FIOCRUZ, Rio de Janeiro 21040-360, Brazil; (P.M.L.); (D.C.P.); (E.M.J.); (E.M.P.); (B.G.); (V.G.V.); (S.N.); (L.E.C.)
| | - Carlos A. M. Costa
- Escola Nacional de Saúde Pública, FIOCRUZ, Rio de Janeiro 21041-210, Brazil; (C.A.M.C.); (N.C.P.R.)
| | - Daniel A. M. Villela
- Programa de Computação Científica (PROCC), FIOCRUZ, Rio de Janeiro 21040-900, Brazil;
| | - Guilherme T. Goedert
- Escola de Matemática Aplicada (EMAp), Fundação Getúlio Vargas, Rio de Janeiro 22250-900, Brazil;
| | - Cleber V. B. D. Santos
- Instituto de Medicina Social Hesio Cordeiro (IMS), Universidade do Estado do Rio de Janeiro, Rio de Janeiro 20550-013, Brazil;
| | - Nadia C. P. Rodrigues
- Escola Nacional de Saúde Pública, FIOCRUZ, Rio de Janeiro 21041-210, Brazil; (C.A.M.C.); (N.C.P.R.)
- Instituto de Medicina Social Hesio Cordeiro (IMS), Universidade do Estado do Rio de Janeiro, Rio de Janeiro 20550-013, Brazil;
| | | | | | - Lara E. Coelho
- Instituto Nacional de Infectologia Evandro Chagas, FIOCRUZ, Rio de Janeiro 21040-360, Brazil; (P.M.L.); (D.C.P.); (E.M.J.); (E.M.P.); (B.G.); (V.G.V.); (S.N.); (L.E.C.)
| | - Claudio J. Struchiner
- Escola de Matemática Aplicada (EMAp), Fundação Getúlio Vargas, Rio de Janeiro 22250-900, Brazil;
- Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro 21040-360, Brazil; (F.d.C.M.); (M.M.S.)
| | - Ana Tereza R. Vasconcelos
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Rio de Janeiro 25651-076, Brazil; (G.C.d.F.); (L.T.F.C.); (O.J.B.)
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8
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Guo X, Zhang Y, Pan Y, Yang K, Tong X, Wang Y. Phylogenetic Analysis and Codon Usage Bias Reveal the Base of Feline and Canine Chaphamaparvovirus for Cross-Species Transmission. Animals (Basel) 2023; 13:2617. [PMID: 37627409 PMCID: PMC10451695 DOI: 10.3390/ani13162617] [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: 05/26/2023] [Revised: 06/29/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
Chaphamaparvoviruses (ChPVs) are ancient viruses that have been detected in a variety of hosts. In this study, through a phylogenetic analysis and the adaptability of ChPV to multiple hosts, we evaluated the basis for the ability of feline (FeChPV) and canine ChPV (CaChPV) for cross-species transmission. Phylogenetic analysis showed that FeChPV and CaChPV were closely related. Notably, two strains of ChPVs isolated from domestic cats and two from dogs clustered together with CaChPVs and FeChPVs, respectively, suggesting that the stringent boundaries between canine and feline ChPV may be broken. Further analysis revealed that CaChPV and FeChPV were more adapted to dogs than to cats. Mutation analysis identified several shared mutations in cross-species-transmissible strains. Furthermore, the VP structures of FeChPV and CaChPV exhibited a high degree of similarity across both cross-species-transmissible and non-cross-species-transmissible strains. However, it is crucial to note that these results are largely computational, and limitations exist in terms of the number and diversity of samples analyzed; the capacity for cross-species transmission should be approached with caution and elucidated in further studies.
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Affiliation(s)
- Xu Guo
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Yingying Zhang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Yang Pan
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Kankan Yang
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen 518000, China
| | - Xinxin Tong
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Yong Wang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
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9
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Reyes C, Patarroyo MA. Adjuvants approved for human use: What do we know and what do we need to know for designing good adjuvants? Eur J Pharmacol 2023; 945:175632. [PMID: 36863555 DOI: 10.1016/j.ejphar.2023.175632] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 02/21/2023] [Accepted: 02/28/2023] [Indexed: 03/04/2023]
Abstract
Adjuvants represent one of the most significant biotechnological solutions regarding vaccine development, thereby broadening the amount of candidates which can now be used and tested in vaccine formulations targeting various pathogens, as antigens which were previously discarded due to their low or null immunogenicity can now be included. Adjuvant development research has grown side-by-side with an increasing body of knowledge regarding immune systems and their recognition of foreign microorganisms. Alum-derived adjuvants were used in human vaccines for many years, even though complete understanding of their vaccination-related mechanism of action was lacking. The amount of adjuvants approved for human use has increased recently in line with attempts to interact with and stimulate the immune system. This review is aimed at summarising what is known about adjuvants, focusing on those approved for use in humans, their mechanism of action and why they are so necessary for vaccine candidate formulations; it also discusses what the future may hold in this growing research field.
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Affiliation(s)
- César Reyes
- PhD Programme in Biotechnology, Faculty of Sciences, Universidad Nacional de Colombia, Carrera 45#26-85, Bogotá, DC 111321, Colombia; Three-dimensional Structures Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50#26-20, Bogotá, DC 111321, Colombia; Animal Science Faculty, Universidad de Ciencias Aplicadas y Ambientales (U.D.C.A), Calle 222#55-37, Bogotá, DC 111166, Colombia.
| | - Manuel A Patarroyo
- Microbiology Department, Faculty of Medicine, Universidad Nacional de Colombia, Carrera 45#26-85, Bogotá, DC 111321, Colombia; Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50#26-20, Bogotá, DC 111321, Colombia.
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Ala U, Bajardi P, Giacobini M, Bertolotti L. Potential Impact of Environmental Pollution by Human Antivirals on Avian Influenza Virus Evolution. Animals (Basel) 2023; 13:ani13071127. [PMID: 37048383 PMCID: PMC10093092 DOI: 10.3390/ani13071127] [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: 01/31/2023] [Revised: 03/01/2023] [Accepted: 03/19/2023] [Indexed: 04/14/2023] Open
Abstract
Antiviral (AV) drugs are the main line of defense against pandemic influenza. However, different administration policies are applied in countries with different stocks of AV drugs. These policies lead to different occurrences of drug metabolites in the aquatic environment, altering animal behavior with evolutionary consequences on viruses. The aim of this study was to investigate the potential impact of environmental pollution by human antivirals, such as oseltamivir carboxylate (OC), on the evolutionary rate of avian influenza. We used NA, HA, NP, and MP viral segments from two groups of neighboring countries sharing migratory routes of wild birds and characterized by different AV stockpiles. BEAST analyses were performed using the uncorrelated lognormal clock evolutionary model and the Bayesian skyline tree prior model. The ratios between the rate of evolution of the NA gene and the HA, NP, and MP segments were considered. The two groups of countries were compared by analyzing the differences in the ratio distributions. Our analyses highlighted a possible different behavior in the evolution of H5N1 2.3 clade viral strains when OC environmental pollution is present. In conclusion, the widespread consumption of antivirals and their presence in wastewater could influence the selective pressure on viruses.
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Affiliation(s)
- Ugo Ala
- Department of Veterinary Sciences, University of Torino, 10095 Grugliasco, TO, Italy
| | - Paolo Bajardi
- Department of Veterinary Sciences, University of Torino, 10095 Grugliasco, TO, Italy
| | - Mario Giacobini
- Department of Veterinary Sciences, University of Torino, 10095 Grugliasco, TO, Italy
| | - Luigi Bertolotti
- Department of Veterinary Sciences, University of Torino, 10095 Grugliasco, TO, Italy
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