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Caridi F, Cañas-Arranz R, Vázquez-Calvo Á, de León P, Calderón KI, Domingo E, Sobrino F, Martín-Acebes MA. Adaptive value of foot-and-mouth disease virus capsid substitutions with opposite effects on particle acid stability. Sci Rep 2021; 11:23494. [PMID: 34873184 PMCID: PMC8648728 DOI: 10.1038/s41598-021-02757-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 11/15/2021] [Indexed: 11/09/2022] Open
Abstract
Foot-and-mouth disease virus (FMDV) is a picornavirus that exhibits an extremely acid sensitive capsid. This acid lability is directly related to its mechanism of uncoating triggered by acidification inside cellular endosomes. Using a collection of FMDV mutants we have systematically analyzed the relationship between acid stability and the requirement for acidic endosomes using ammonium chloride (NH4Cl), an inhibitor of endosome acidification. A FMDV mutant carrying two substitutions with opposite effects on acid-stability (VP3 A116V that reduces acid stability, and VP1 N17D that increases acid stability) displayed a rapid shift towards acid lability that resulted in increased resistance to NH4Cl as well as to concanamicyn A, a different lysosomotropic agent. This resistance could be explained by a higher ability of the mutant populations to produce NH4Cl-resistant variants, as supported by their tendency to accumulate mutations related to NH4Cl-resistance that was higher than that of the WT populations. Competition experiments also indicated that the combination of both amino acid substitutions promoted an increase of viral fitness that likely contributed to NH4Cl resistance. This study provides novel evidences supporting that the combination of mutations in a viral capsid can result in compensatory effects that lead to fitness gain, and facilitate space to an inhibitor of acid-dependent uncoating. Thus, although drug-resistant variants usually exhibit a reduction in viral fitness, our results indicate that compensatory mutations that restore this reduction in fitness can promote emergence of resistance mutants.
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Affiliation(s)
- Flavia Caridi
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), 28049, Madrid, Spain
| | | | | | - Patricia de León
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), 28049, Madrid, Spain
| | | | - Esteban Domingo
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), 28049, Madrid, Spain
| | - Francisco Sobrino
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), 28049, Madrid, Spain.
| | - Miguel A Martín-Acebes
- Department of Biotechnology, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA, CSIC), 28040, Madrid, Spain
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Fish I, Stenfeldt C, Palinski RM, Pauszek SJ, Arzt J. Into the Deep (Sequence) of the Foot-and-Mouth Disease Virus Gene Pool: Bottlenecks and Adaptation during Infection in Naïve and Vaccinated Cattle. Pathogens 2020; 9:pathogens9030208. [PMID: 32178297 PMCID: PMC7157448 DOI: 10.3390/pathogens9030208] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 03/06/2020] [Accepted: 03/09/2020] [Indexed: 12/11/2022] Open
Abstract
Foot-and-mouth disease virus (FMDV) infects hosts as a population of closely related viruses referred to as a quasispecies. The behavior of this quasispecies has not been described in detail in natural host species. In this study, virus samples collected from vaccinated and non-vaccinated cattle up to 35 days post-experimental infection with FMDV A24-Cruzeiro were analyzed by deep-sequencing. Vaccination induced significant differences compared to viruses from non-vaccinated cattle in substitution rates, entropy, and evidence for adaptation. Genomic variation detected during early infection reflected the diversity inherited from the source virus (inoculum), whereas by 12 days post infection, dominant viruses were defined by newly acquired mutations. Mutations conferring recognized fitness gain occurred and were associated with selective sweeps. Persistent infections always included multiple FMDV subpopulations, suggesting distinct foci of infection within the nasopharyngeal mucosa. Subclinical infection in vaccinated cattle included very early bottlenecks associated with reduced diversity within virus populations. Viruses from both animal cohorts contained putative antigenic escape mutations. However, these mutations occurred during later stages of infection, at which time transmission is less likely to occur. This study improves upon previously published work by analyzing deep sequences of samples, allowing for detailed characterization of FMDV populations over time within multiple hosts.
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Affiliation(s)
- Ian Fish
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Orient, NY 11957, USA; (I.F.); (C.S.); (R.M.P.); (S.J.P.)
- Oak Ridge Institute for Science and Education, PIADC Research Participation Program, Oak Ridge, TN 37830, USA
| | - Carolina Stenfeldt
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Orient, NY 11957, USA; (I.F.); (C.S.); (R.M.P.); (S.J.P.)
- College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA
| | - Rachel M. Palinski
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Orient, NY 11957, USA; (I.F.); (C.S.); (R.M.P.); (S.J.P.)
| | - Steven J. Pauszek
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Orient, NY 11957, USA; (I.F.); (C.S.); (R.M.P.); (S.J.P.)
| | - Jonathan Arzt
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Orient, NY 11957, USA; (I.F.); (C.S.); (R.M.P.); (S.J.P.)
- Correspondence:
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3
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Jo HE, You SH, Choi JH, Ko MK, Shin SH, Song J, Jo H, Lee MJ, Kim SM, Kim B, Park JH. Evaluation of novel inactivated vaccines for the SAT 1, SAT 2 and SAT 3 serotypes of foot-and-mouth disease in pigs. Virol J 2019; 16:156. [PMID: 31842907 PMCID: PMC6916012 DOI: 10.1186/s12985-019-1262-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 11/29/2019] [Indexed: 11/14/2022] Open
Abstract
Background The foot-and-mouth disease (FMD) virus is classified into seven serotypes, of which the South African types have South African Territories (SAT)1, SAT2, and SAT3 that are prevalent in Africa. Especially SAT2 have spread to Arabian Peninsula and the Palestinian Autonomous Territories. Of these viruses, the incidence of SAT2 is the highest. It is important to prepare for the spread of the virus to other continents, even though most FMD viruses are bovine-derived. In particular, due to the high breeding density of pigs in Asia, more attention is usually paid to the immunity and protection of pigs than cattle. For this reason, this study investigated the immunity and protection of pigs against the SAT viruses. Methods Specific vaccines were developed for SAT1, SAT2, and SAT3 serotypes. These vaccine viruses were designed to be distinguished from the wild-type strain. An immunogenicity test was conducted using these vaccines in both cattle (n = 5/group) and pigs (n = 20/group). Results High virus-neutralizing titer of antibodies (> 1:100) was induced in only 2 weeks after the immunization of cattle with the individual vaccine for SAT1, SAT2 or SAT3, and a clear immune response was induced after the second immunization in pigs. When the vaccinated pigs (n = 4–5/group) were challenged by the homologous wild-type virus strain 4 weeks after immunization, all the pigs were protected from the challenge. Conclusions This study confirmed that these vaccines can be used against SAT1, SAT2, and SAT3 viruses in cattle and pigs. The vaccine strains developed in this study are expected to be used as vaccines that can protect against FMD in the event of a future FMD outbreak in pigs in consideration of the situation in Asia.
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Affiliation(s)
- Hye-Eun Jo
- Center for Foot-and-Mouth Disease Vaccine Research, Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon, Gyeongsangbuk-do, Republic of Korea
| | - Su-Hwa You
- Center for Foot-and-Mouth Disease Vaccine Research, Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon, Gyeongsangbuk-do, Republic of Korea
| | - Joo-Hyung Choi
- Center for Foot-and-Mouth Disease Vaccine Research, Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon, Gyeongsangbuk-do, Republic of Korea
| | - Mi-Kyeong Ko
- Center for Foot-and-Mouth Disease Vaccine Research, Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon, Gyeongsangbuk-do, Republic of Korea
| | - Sung Ho Shin
- Center for Foot-and-Mouth Disease Vaccine Research, Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon, Gyeongsangbuk-do, Republic of Korea
| | - Jisoo Song
- Center for Foot-and-Mouth Disease Vaccine Research, Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon, Gyeongsangbuk-do, Republic of Korea
| | - Hyundong Jo
- Center for Foot-and-Mouth Disease Vaccine Research, Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon, Gyeongsangbuk-do, Republic of Korea
| | - Min Ja Lee
- Center for Foot-and-Mouth Disease Vaccine Research, Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon, Gyeongsangbuk-do, Republic of Korea
| | - Su-Mi Kim
- Center for Foot-and-Mouth Disease Vaccine Research, Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon, Gyeongsangbuk-do, Republic of Korea
| | - Byounghan Kim
- Center for Foot-and-Mouth Disease Vaccine Research, Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon, Gyeongsangbuk-do, Republic of Korea
| | - Jong-Hyeon Park
- Center for Foot-and-Mouth Disease Vaccine Research, Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon, Gyeongsangbuk-do, Republic of Korea.
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Singh I, Deb R, Kumar S, Singh R, Andonissamy J, Smita S, Sengar GS, Kumar R, Ojha KK, Sahoo NR, Murali S, Chandran R, Nair RV, Lal SB, Mishra DC, Rai A. Deciphering foot-and-mouth disease (FMD) virus-host tropism. J Biomol Struct Dyn 2019; 37:4779-4789. [PMID: 30654708 DOI: 10.1080/07391102.2019.1567386] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The pattern of interactions between foot and mouth disease (FMD) viral protein 1 (VP1) with susceptible and resistant host integrins were deciphered. The putative effect of site-directed mutation on alteration of interaction is illustrated using predicted and validated 3D structures of VP1, mutated VP1 and integrins of Bos taurus, Gallus and Canis. Strong interactions were observed between FMDV-VP1 protein motifs at conserved tripeptide, Arg-Gly-Asp 143RGD145 and at domain 676SIPLQ680 in alpha-integrin of B. taurus. Notably, in-silico site-directed mutation in FMDV-VP1 protein led to complete loss of interaction between FMD-VP1 protein and B. taurus integrin, which confirmed the active role of arginine-glycine-aspartic acid (RGD) domain. Interestingly, in-vitro analysis demonstrates the persistence of the putative tropism site 'SIPLQ' in different cattle breeds undertaken. Thus, the attempt to decipher the tropism of FMDV at host receptor level interaction might be useful for future FMD control strategies through development of mimetic marker vaccines and/or host receptor manipulations. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Indra Singh
- Centre for Agricultural Bio-Informatics ICAR-Indian Agricultural Statistics Research Institute , New Delhi , India
| | - Rajib Deb
- ICAR-Central Institute for Research on Cattle , Meerut , India
| | - Sanjeev Kumar
- Centre for Agricultural Bio-Informatics ICAR-Indian Agricultural Statistics Research Institute , New Delhi , India
| | - Rani Singh
- ICAR-Central Institute for Research on Cattle , Meerut , India
| | | | - Shuchi Smita
- Centre for Agricultural Bio-Informatics ICAR-Indian Agricultural Statistics Research Institute , New Delhi , India
| | | | - Rajiv Kumar
- ICAR-Central Sheep and Wool Research Institute , Avikanagar , India
| | | | | | - S Murali
- ICAR-India National Bureau of Fish Genetic Resources , Lucknow , India
| | - Rejani Chandran
- ICAR-Central Institute of Fisheries Technology , Cochin , India
| | | | - S B Lal
- Centre for Agricultural Bio-Informatics ICAR-Indian Agricultural Statistics Research Institute , New Delhi , India
| | - Dwijesh Chandra Mishra
- Centre for Agricultural Bio-Informatics ICAR-Indian Agricultural Statistics Research Institute , New Delhi , India
| | - Anil Rai
- Centre for Agricultural Bio-Informatics ICAR-Indian Agricultural Statistics Research Institute , New Delhi , India
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Mansour KA, Naser HH, Hussain MH. Clinical, molecular detection and phylogenetic analysis study of local foot-and-mouth disease virus in Al-Qadisiyah province of Iraq. Vet World 2018; 11:1210-1213. [PMID: 30410223 PMCID: PMC6200567 DOI: 10.14202/vetworld.2018.1210-1213] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Accepted: 07/16/2018] [Indexed: 11/16/2022] Open
Abstract
Aim This study was directed during an outbreak of suspected foot-and-mouth disease (FMD) in cattle in Al-Qadisiyah province, Iraq 2016. The disease has made a huge economic loss in livestock. It was suspected that the vaccination has failed to protect the animals from the infection because of the difference in the strains. Consequently, we designed the study to make the diagnosis and detect the strain of the causative virus. Materials and Methods The extraction of the DNA was done on 73 samples and Reverse Transcriptase Polymerase Chain Reaction (RT-PCR) was used in the detection of FMD virus (FMDV) for primary diagnosis, and serotype-specific diagnosis was done with universal primer sets 1F/1R, A-1C612, and O-ARS4 with the expected band of 329, 865, and 1301 bp, respectively. Results Universal primer pair 1F/1R detected FMD in 55 of 73 (75.3%); of these, 37 (67.3%) were females and 18 (32.7%) were males, with high significance (p<0.01) between males and females in the PCR positivity ratio. The tested samples with positive universal primer were amplified with specific primers A-IC612 with no reaction for serotype O-ARS4. Conclusion The products of RT-PCR were sent for RNA sequencing, and the results were 100% positive to serotype A which means that it is the predominant type in Iraq. It may help in the importing or production of the vaccine to make a preventive plan for the disease. The virus of FMD is contagious and dangerous due to its role in the huge economic loses. The detection of this virus is widely explained in lots of articles, but it is more specific and sensitive in RT-PCR and sequencing. Consequently, the authorities responsible for importing and/or production vaccines have to avoid the importing of other serotypes because it will be losing money and more outbreaks will explode.
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Affiliation(s)
- Khalefa Ali Mansour
- Department of Internal and Preventive Veterinary Medicine, College of Veterinary Medicine, University of Al-Qadisiyah, Iraq
| | - Hassan Hachim Naser
- Department of Internal and Preventive Veterinary Medicine, College of Veterinary Medicine, University of Al-Qadisiyah, Iraq
| | - Muthanna Hadi Hussain
- Department of Internal and Preventive Veterinary Medicine, College of Veterinary Medicine, University of Al-Qadisiyah, Iraq
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Abstract
The deterministic force of natural selection and stochastic influence of drift shape RNA virus evolution. New deep-sequencing and microfluidics technologies allow us to quantify the effect of mutations and trace the evolution of viral populations with single-genome and single-nucleotide resolution. Such experiments can reveal the topography of the genotype-fitness landscapes that shape the path of viral evolution. By combining historical analyses, like phylogenetic approaches, with high-throughput and high-resolution evolutionary experiments, we can observe parallel patterns of evolution that drive important phenotypic transitions. These developments provide a framework for quantifying and anticipating potential evolutionary events. Here, we examine emerging technologies that can map the selective landscapes of viruses, focusing on their application to pathogenic viruses. We identify areas where these technologies can bolster our ability to study the evolution of viruses and to anticipate and possibly intervene in evolutionary events and prevent viral disease.
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Affiliation(s)
- Patrick T Dolan
- Department of Biology, Stanford University, E200 Clark Center, 318 Campus Drive, Stanford, CA 94305, USA; Department of Microbiology and Immunology, University of California, San Francisco, 600 16th Street, GH-S572, UCSF Box 2280, San Francisco, CA 94143-2280, USA
| | - Zachary J Whitfield
- Department of Microbiology and Immunology, University of California, San Francisco, 600 16th Street, GH-S572, UCSF Box 2280, San Francisco, CA 94143-2280, USA
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, 600 16th Street, GH-S572, UCSF Box 2280, San Francisco, CA 94143-2280, USA.
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7
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Codoñer FM, Peña R, Blanch-Lombarte O, Jimenez-Moyano E, Pino M, Vollbrecht T, Clotet B, Martinez-Picado J, Draenert R, Prado JG. Gag-protease coevolution analyses define novel structural surfaces in the HIV-1 matrix and capsid involved in resistance to Protease Inhibitors. Sci Rep 2017. [PMID: 28623276 PMCID: PMC5473930 DOI: 10.1038/s41598-017-03260-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Despite the major role of Gag in establishing resistance of HIV-1 to protease inhibitors (PIs), very limited data are available on the total contribution of Gag residues to resistance to PIs. To identify in detail Gag residues and structural interfaces associated with the development of HIV-1 resistance to PIs, we traced viral evolution under the pressure of PIs using Gag-protease single genome sequencing and coevolution analysis of protein sequences in 4 patients treated with PIs over a 9-year period. We identified a total of 38 Gag residues correlated with the protease, 32 of which were outside Gag cleavage sites. These residues were distributed in 23 Gag-protease groups of coevolution, with the viral matrix and the capsid represented in 87% and 52% of the groups. In addition, we uncovered the distribution of Gag correlated residues in specific protein surfaces of the inner face of the viral matrix and at the Cyclophilin A binding loop of the capsid. In summary, our findings suggest a tight interdependency between Gag structural proteins and the protease during the development of resistance of HIV-1 to PIs.
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Affiliation(s)
- Francisco M Codoñer
- Lifesequencing SL, Paterna, Spain.,Universidad Catolica de Valencia, Valencia, Spain
| | - Ruth Peña
- AIDS Research Institute IrsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Oscar Blanch-Lombarte
- AIDS Research Institute IrsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Esther Jimenez-Moyano
- AIDS Research Institute IrsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Maria Pino
- AIDS Research Institute IrsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Thomas Vollbrecht
- Veterans Affairs San Diego Healthcare System, San Diego, California, USA.,University of California San Diego, La Jolla, California, USA
| | - Bonaventura Clotet
- AIDS Research Institute IrsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain.,Universitat de Vic-Universitat Central de Catalunya, Vic, Spain
| | - Javier Martinez-Picado
- AIDS Research Institute IrsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain.,Universitat de Vic-Universitat Central de Catalunya, Vic, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Rika Draenert
- Medizinische Poliklinik, Klinikum der Ludwig-Maximilians-Universität München, Munich, Germany
| | - Julia G Prado
- AIDS Research Institute IrsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain.
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Dennehy JJ. Evolutionary ecology of virus emergence. Ann N Y Acad Sci 2016; 1389:124-146. [PMID: 28036113 PMCID: PMC7167663 DOI: 10.1111/nyas.13304] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 10/24/2016] [Accepted: 11/09/2016] [Indexed: 12/22/2022]
Abstract
The cross-species transmission of viruses into new host populations, termed virus emergence, is a significant issue in public health, agriculture, wildlife management, and related fields. Virus emergence requires overlap between host populations, alterations in virus genetics to permit infection of new hosts, and adaptation to novel hosts such that between-host transmission is sustainable, all of which are the purview of the fields of ecology and evolution. A firm understanding of the ecology of viruses and how they evolve is required for understanding how and why viruses emerge. In this paper, I address the evolutionary mechanisms of virus emergence and how they relate to virus ecology. I argue that, while virus acquisition of the ability to infect new hosts is not difficult, limited evolutionary trajectories to sustained virus between-host transmission and the combined effects of mutational meltdown, bottlenecking, demographic stochasticity, density dependence, and genetic erosion in ecological sinks limit most emergence events to dead-end spillover infections. Despite the relative rarity of pandemic emerging viruses, the potential of viruses to search evolutionary space and find means to spread epidemically and the consequences of pandemic viruses that do emerge necessitate sustained attention to virus research, surveillance, prophylaxis, and treatment.
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Affiliation(s)
- John J Dennehy
- Biology Department, Queens College of the City University of New York, Queens, New York and The Graduate Center of the City University of New York, New York, New York
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Nsamba P, de Beer T, Chitray M, Scott K, Vosloo W, Maree F. Determination of common genetic variants within the non-structural proteins of foot-and-mouth disease viruses isolated in sub-Saharan Africa. Vet Microbiol 2015; 177:106-22. [DOI: 10.1016/j.vetmic.2015.03.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 03/03/2015] [Accepted: 03/04/2015] [Indexed: 10/23/2022]
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10
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Bari FD, Parida S, Tekleghiorghis T, Dekker A, Sangula A, Reeve R, Haydon DT, Paton DJ, Mahapatra M. Genetic and antigenic characterisation of serotype A FMD viruses from East Africa to select new vaccine strains. Vaccine 2014; 32:5794-800. [PMID: 25171846 PMCID: PMC4194315 DOI: 10.1016/j.vaccine.2014.08.033] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 08/01/2014] [Accepted: 08/15/2014] [Indexed: 11/08/2022]
Abstract
Vaccine strain selection for emerging foot-and-mouth disease virus (FMDV) outbreaks in enzootic countries can be addressed through antigenic and genetic characterisation of recently circulating viruses. A total of 56 serotype A FMDVs isolated between 1998 and 2012, from Central, East and North African countries were characterised antigenically by virus neutralisation test using antisera to three existing and four candidate vaccine strains and, genetically by characterising the full capsid sequence data. A Bayesian analysis of the capsid sequence data revealed the viruses to be of either African or Asian topotypes with subdivision of the African topotype viruses into four genotypes (Genotypes I, II, IV and VII). The existing vaccine strains were found to be least cross-reactive (good matches observed for only 5.4-46.4% of the sampled viruses). Three bovine antisera, raised against A-EA-2007, A-EA-1981 and A-EA-1984 viruses, exhibited broad cross-neutralisation, towards more than 85% of the circulating viruses. Of the three vaccines, A-EA-2007 was the best showing more than 90% in-vitro cross-protection, as well as being the most recent amongst the vaccine strains used in this study. It therefore appears antigenically suitable as a vaccine strain to be used in the region in FMD control programmes.
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Affiliation(s)
- Fufa D Bari
- The Pirbright Institute, Pirbright Laboratory, Ash Road, Woking, Surrey GU24 0NF, UK
| | - Satya Parida
- The Pirbright Institute, Pirbright Laboratory, Ash Road, Woking, Surrey GU24 0NF, UK
| | | | - Aldo Dekker
- Central Veterinary Institute, Part of Wageningen UR, Lelystad, The Netherlands
| | | | - Richard Reeve
- The Pirbright Institute, Pirbright Laboratory, Ash Road, Woking, Surrey GU24 0NF, UK; Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Daniel T Haydon
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - David J Paton
- The Pirbright Institute, Pirbright Laboratory, Ash Road, Woking, Surrey GU24 0NF, UK
| | - Mana Mahapatra
- The Pirbright Institute, Pirbright Laboratory, Ash Road, Woking, Surrey GU24 0NF, UK.
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11
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Chitray M, de Beer TAP, Vosloo W, Maree FF. Genetic heterogeneity in the leader and P1-coding regions of foot-and-mouth disease virus serotypes A and O in Africa. Arch Virol 2013; 159:947-61. [PMID: 24221247 PMCID: PMC4010724 DOI: 10.1007/s00705-013-1838-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 07/22/2013] [Indexed: 02/03/2023]
Abstract
Genetic information regarding the leader (L) and complete capsid-coding (P1) region of FMD serotype A and O viruses prevalent on the African continent is lacking. Here, we present the complete L-P1 sequences for eight serotype A and nine serotype O viruses recovered from FMDV outbreaks in East and West Africa over the last 33 years. Phylogenetic analysis of the P1 and capsid-coding regions revealed that the African isolates grouped according to serotype, and certain clusters were indicative of transboundary as well as intra-regional spread of the virus. However, similar analysis of the L region revealed random groupings of isolates from serotypes O and A. Comparisons between the phylogenetic trees derived from the structural coding regions and the L region pointed to a possibility of genetic recombination. The intertypic nucleotide and amino acid variation of all the isolates in this study supported results from previous studies where the externally located 1D was the most variable whilst the internally located 1A was the most conserved, which likely reflects the selective pressures on these proteins. Amino acids identified previously as important for FMDV structure and functioning were found to be highly conserved. The information gained from this study will contribute to the construction of structurally designed FMDV vaccines in Africa.
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Affiliation(s)
- M Chitray
- Agricultural Research Council, Onderstepoort Veterinary Institute, Transboundary Animal Diseases, Private Bag X05, Onderstepoort, Pretoria, South Africa,
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Alam SMS, Amin R, Rahman MZ, Hossain MA, Sultana M. Antigenic heterogeneity of capsid protein VP1 in foot-and-mouth disease virus (FMDV) serotype Asia 1. Adv Appl Bioinform Chem 2013; 6:37-46. [PMID: 23983476 PMCID: PMC3751384 DOI: 10.2147/aabc.s49587] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Foot and mouth disease virus (FMDV), with its seven serotypes, is a highly contagious virus infecting mainly cloven-hoofed animals. The serotype Asia1 occurs mainly in Asian regions. An in-silico approach was taken to reveal the antigenic heterogeneities within the capsid protein VP1 of Asia1. A total of 47 VP1 sequences of Asia1 isolates from different countries of South Asian regions were selected, retrieved from database, and were aligned. The structure of VP1 protein was modeled using a homology modeling approach. Several antigenic sites were identified and mapped onto the three-dimensional protein structure. Variations at these antigenic sites were analyzed by calculating the protein variability index and finding mutation combinations. The data suggested that vaccine escape mutants have derived from only few mutations at several antigenic sites. Five antigenic peptides have been identified as the least variable epitopes, with just fewer amino acid substitutions. Only a limited number of serotype Asia1 antigenic variants were found to be circulated within the South Asian region. This emphasizes a possibility of formulating synthetic vaccines for controlling foot-and-mouth disease by Asia1 serotypes.
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Affiliation(s)
- S M Sabbir Alam
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
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Jamal SM, Ferrari G, Ahmed S, Normann P, Curry S, Belsham GJ. Evolutionary analysis of serotype A foot-and-mouth disease viruses circulating in Pakistan and Afghanistan during 2002-2009. J Gen Virol 2011; 92:2849-2864. [PMID: 21813704 DOI: 10.1099/vir.0.035626-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Foot-and-mouth disease (FMD) is endemic in Pakistan and Afghanistan. Three different serotypes of the virus, namely O, A and Asia-1, are responsible for the outbreaks of this disease in these countries. In the present study, the nucleotide-coding sequences for the VP1 capsid protein (69 samples) or for all four capsid proteins (P1, seven representative samples) of the serotype A FMD viruses circulating in Pakistan and Afghanistan were determined. Phylogenetic analysis of the foot-and-mouth disease virus (FMDV) VP1-coding sequences from these countries collected between 2002 and 2009 revealed the presence of at least four lineages within two distinct genotypes, all belonging to the Asia topotype, within serotype A. The predominant lineage observed was A-Iran05 but three other lineages (a new one is named here A-Pak09) were also identified. The A-Iran05 lineage is still evolving as revealed by the presence of seven distinct variants, the dominant being the A-Iran05AFG-07 and A-Iran05BAR-08 sublineages. The rate of evolution of the A-Iran05 lineage was found to be about 1.2×10(-2) substitutions per nucleotide per year. This high rate of change is consistent with the rapid appearance of new variants of FMDV serotype A in the region. The A22/Iraq FMDV vaccine is antigenically distinct from the A-Iran05BAR-08 viruses. Mapping of the amino acid changes between the capsid proteins of the A22/Iraq vaccine strain and the A-Iran05BAR-08 viruses onto the A22/Iraq capsid structure identified candidate amino acid substitutions, exposed on the virus surface, which may explain this antigenic difference.
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Affiliation(s)
- Syed M Jamal
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan.,National Veterinary Laboratory, Park Road, 45500 Islamabad, Pakistan.,National Veterinary Institute, Technical University of Denmark, Lindholm, 4771 Kalvehave, Denmark
| | - Giancarlo Ferrari
- Food and Agriculture Organization of the United Nations, Rome, Italy
| | - Safia Ahmed
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Preben Normann
- National Veterinary Institute, Technical University of Denmark, Lindholm, 4771 Kalvehave, Denmark
| | - Stephen Curry
- Biophysics Section, Blackett Laboratory, Division of Cell and Molecular Biology, Imperial College London, London SW7 2AZ, UK
| | - Graham J Belsham
- National Veterinary Institute, Technical University of Denmark, Lindholm, 4771 Kalvehave, Denmark
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Sangula AK, Belsham GJ, Muwanika VB, Heller R, Balinda SN, Masembe C, Siegismund HR. Evolutionary analysis of foot-and-mouth disease virus serotype SAT 1 isolates from east Africa suggests two independent introductions from southern Africa. BMC Evol Biol 2010; 10:371. [PMID: 21118525 PMCID: PMC3004922 DOI: 10.1186/1471-2148-10-371] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2010] [Accepted: 11/30/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In East Africa, foot-and-mouth disease virus serotype SAT 1 is responsible for occasional severe outbreaks in livestock and is known to be maintained within the buffalo populations. Little is known about the evolutionary forces underlying its epidemiology in the region. To enhance our appreciation of the epidemiological status of serotype SAT 1 virus in the region, we inferred its evolutionary and phylogeographic history by means of genealogy-based coalescent methods using 53 VP1 coding sequences covering a sampling period from 1948-2007. RESULTS The VP1 coding sequence of 11 serotype SAT 1 FMD viruses from East Africa has been determined and compared with known sequences derived from other SAT 1 viruses from sub-Saharan Africa. Purifying (negative) selection and low substitution rates characterized the SAT 1 virus isolates in East Africa. Two virus groups with probable independent introductions from southern Africa were identified from a maximum clade credibility tree. One group was exclusive to Uganda while the other was present within Kenya and Tanzania. CONCLUSIONS Our results provide a baseline characterization of the inter-regional spread of SAT 1 in sub-Saharan Africa and highlight the importance of a regional approach to trans-boundary animal disease control in order to monitor circulating strains and apply appropriate vaccines.
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Affiliation(s)
- Abraham K Sangula
- Makerere University, Institute of Environment and Natural Resources, Molecular Biology Laboratory, P, O, Box 7298, Kampala, Uganda.
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Codoñer FM, Alfonso-Loeches S, Fares MA. Mutational dynamics of murine angiogenin duplicates. BMC Evol Biol 2010; 10:310. [PMID: 20950426 PMCID: PMC2964713 DOI: 10.1186/1471-2148-10-310] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2010] [Accepted: 10/15/2010] [Indexed: 12/03/2022] Open
Abstract
Background Angiogenin (Ang) is a protein involved in angiogenesis by inducing the formation of blood vessels. The biomedical importance of this protein has come from findings linking mutations in Ang to cancer progression and neurodegenerative diseases. These findings highlight the evolutionary constrain on Ang amino acid sequence. However, previous studies comparing human Angiogenin with homologs from other phylogenetically related organisms have led to the conclusion that Ang presents a striking variability. Whether this variability has an adaptive value per se remains elusive. Understanding why many functional Ang paralogs have been preserved in mouse and rat and identifying functional divergence mutations at these copies may explain the relationship between mutations and function. In spite of the importance of testing this hypothesis from the evolutionarily and biomedical perspectives, this remains yet unaccomplished. Here we test the main mutational dynamics driving the evolution and function of Ang paralogs in mammals. Results We analysed the phylogenetic asymmetries between the different Ang gene copies in mouse and rat in the context of vertebrate Ang phylogeny. This analysis shows strong evidence in support of accelerated evolution in some Ang murine copies (mAng). This acceleration is not due to non-functionalisation because constraints on amino acid replacements remain strong. We identify many of the amino acid sites involved in signal localization and nucleotide binding by Ang to have evolved under diversifying selection. Compensatory effects of many of the mutations at these paralogs and their key structural location in or nearby important functional regions support a possible functional shift (functional divergence) in many Ang copies. Similarities between 3D-structural models for mAng copies suggest that their divergence is mainly functional. Conclusions We identify the main evolutionary dynamics shaping the variability of Angiogenin in vertebrates and highlight the plasticity of this protein after gene duplication. Our results suggest functional divergence among mAng paralogs. This puts forward mAng as a good system candidate for testing functional plasticity of such an important protein while stresses caution when using mouse as a model to infer the consequences of mutations in the single Ang copy of humans.
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Affiliation(s)
- Francisco M Codoñer
- Evolutionary Genetics and Bioinformatics Laboratory, Department of Genetics, Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin, Ireland
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Xiao L, Kehoe PG. Molecular epidemiology of infectious diseases - expanding horizons for IJMEG. INTERNATIONAL JOURNAL OF MOLECULAR EPIDEMIOLOGY AND GENETICS 2010; 1:245-247. [PMID: 21537396 PMCID: PMC3076772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Subscribe] [Scholar Register] [Received: 07/12/2010] [Accepted: 07/15/2010] [Indexed: 05/30/2023]
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Jiang X, Fares MA. Identifying coevolutionary patterns in human leukocyte antigen (HLA) molecules. Evolution 2009; 64:1429-45. [PMID: 19930454 DOI: 10.1111/j.1558-5646.2009.00903.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The antigenic peptide, major histocompatibility complex molecule (MHC; also called human leukocyte antigen, HLA), coreceptor CD8, or CD4 and T-cell receptor (TCR) function as a complex to initiate effectors' mechanisms of the immune system. The tight functional and physical interaction among these molecules may have involved strong coevolution links among domains within and between proteins. Despite the importance of unraveling such dependencies to understand the arms race of host-pathogen interaction, no previous studies have aimed at achieving such an objective. Here, we perform an exhaustive coevolution analysis and show that indeed such dependencies are strongly shaping the evolution and probably the function of these molecules. We identify intramolecular coevolution in HLA class I and II at domains important for their immune activity. Most of the amino acid sites identified to be coevolving in HLAI have been also detected to undergo positive Darwinian selection highlighting therefore their adaptive value. We also identify coevolution among antigen-binding pockets (P1-P9) and among these and TCR-binding sites. Conversely to HLAI, coevolution is weaker in HLAII. Our results support that such coevolutionary patterns are due to selective pressures of host-pathogen coevolution and cooperative binding of TCRs, antigenic peptides, and CD8/CD4 to HLAI and HLAII.
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Affiliation(s)
- Xiaowei Jiang
- Evolutionary Genetics and Bioinformatics Laboratory, Department of Genetics, Smurfit Institute of Genetics, University of Dublin, Trinity College Dublin, Dublin 2, Ireland.
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Molecular Coevolution and the Three-Dimensionality of Natural Selection. Evol Biol 2009. [DOI: 10.1007/978-3-642-00952-5_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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