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Pfaar O, Portnoy J, Nolte H, Chaker AM, Luna-Pech JA, Patterson A, Pandya A, Larenas-Linnemann D. Future Directions of Allergen Immunotherapy for Allergic Rhinitis: Experts' Perspective. J Allergy Clin Immunol Pract 2024; 12:32-44. [PMID: 37716529 DOI: 10.1016/j.jaip.2023.08.047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/19/2023] [Accepted: 08/21/2023] [Indexed: 09/18/2023]
Abstract
Allergen immunotherapy (AIT) is broadly used all over the world as the only available disease-modifying treatment option. The aim of this experts' perspective is to address 7 important unmet needs for the further direction of AIT and to provide the readership with the authors' positions on these topics. An international group of experts in the field of AIT have formulated 7 important aspects for the future position of AIT, performed a current literature review, and proposed a consented position on these topics. The aspects discussed and consented by the authors include: (1) alternative routes of allergen application in AIT, (2) potential of recombinant vaccines, (3) the role of allergy diagnosis based on component-resolved diagnosis for AIT composition, (4) the impact of COVID-19 vaccination for further innovations in AIT, (5) potential of combining biologics to AIT, (6) future innovations in high-risk children/adolescents, and (7) the future regulatory position on AIT. Important unmet needs and topics for AIT have been addressed in this expert review. The authors' views and personal position on these 7 aspects have also been elaborated.
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Affiliation(s)
- Oliver Pfaar
- Department of Otorhinolaryngology, Head and Neck Surgery, Section of Rhinology and Allergy, University Hospital Marburg, Philipps-Universität Marburg, Marburg, Germany
| | - Jay Portnoy
- Division of Allergy, Immunology, Pulmonary and Sleep Medicine, Children's Mercy Hospital and University of Missouri-Kansas City, Kansas City, Mo
| | | | - Adam M Chaker
- TUM School of Medicine, Department of Otorhinolaryngology and Center of Allergy and Environment, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Jorge A Luna-Pech
- Departamento de Disciplinas Filosófico, Metodológico e Instrumentales, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | - Amber Patterson
- Department of Pediatrics, University of Toledo College of Medicine, Toledo, Ohio; Auni Allergy, Findlay, Ohio
| | - Aarti Pandya
- Division of Allergy, Immunology, Pulmonary and Sleep Medicine, Children's Mercy Hospital and University of Missouri-Kansas City, Kansas City, Mo
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Cremer J, van Heiningen F, Veldhuijzen I, Benschop K. Characterization of Hepatitis B virus based complete genome analysis improves molecular surveillance and enables identification of a recombinant C/D strain in the Netherlands. Heliyon 2023; 9:e22358. [PMID: 38058647 PMCID: PMC10695994 DOI: 10.1016/j.heliyon.2023.e22358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/23/2023] [Accepted: 11/10/2023] [Indexed: 12/08/2023] Open
Abstract
Hepatitis B Virus (HBV) is classified into 10 HBV genotypes (A-J) based a >7.5 % divergence within the complete genome or a >4 % divergence in the S-gene. In addition, recombinant strains with common breakpoints at the gene boundaries of the preS1/preS2/S- and preC/C-gene are often identified. Analysis of HBV based on the complete genome is essential for public health surveillance as it provides higher genetic resolution to conduct accurate characterization and phylogenetic analysis of circulating strains and identify possible recombinants. Currently two separate assays are used for HBV-surveillance; the S-gene for typing, and due to the higher genetic variation, the C-gene to gain insight in transmission patterns. The aim of the study was to develop a complete genome PCR-assay and evaluate the characterization and circulation of HBV strains through the use of the S-gene, C-gene and complete genome. For this HBV positive samples collected in the period 2017 through 2019 were selected. Analysis of the complete genome showed that complete genome analysis portrays a high genetic resolution that provided accurate characterization and analysis of the different circulating types in the Netherlands and enabled identification and characterization of a recombinant CD strain.
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Affiliation(s)
- Jeroen Cremer
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Francoise van Heiningen
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Irene Veldhuijzen
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Kimberley Benschop
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
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Khan H, Khan A. Genome-wide population structure inferences of human coxsackievirus-A; insights the genotypes diversity and evolution. Infect Genet Evol 2021; 95:105068. [PMID: 34492386 DOI: 10.1016/j.meegid.2021.105068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 08/25/2021] [Accepted: 09/01/2021] [Indexed: 11/24/2022]
Abstract
Coxsackievirus-A (CV-A) is a causative agent of Hand Foot Mouth Disease (HFMD) worldwide. It belongs to the Human Enterovirus genus of the family Picornaviridae. The genomics data availability of CV-A samples, isolated from human host across different continental regions, provide an excellent opportunity to study its genetic composition, diversity, and evolutionary events. The complete genome sequences of 424 CV-A isolates were analyzed through a model-based population genetic approach implemented in the STRUCTURE program. Twelve genetically distinct sub-populations were identified for CV-A isolates with a marked Fst distinction of 0.76991 (P-value = 0.00000). Besides, genetically admixed strains were characterized in the G-Id, G-IIIb clusters constituted by the CV-A12 and CV-A6 enterovirus serotypes. The serotypes depicted inter/intra-genotype recombination and episodic positive selection signatures in the structural and non-structural protein-coding regions. The observed genetic composition of CV-A samples was also deduced by the phylogenetic tree analyses, where a uniform genetic structure was inferred for most of the CV-A genotypes. However, the CV-A6 serotype samples genetically stratified into three sub-populations that may lead to the emergence of new lineages in future. These informations may implicate in planning the effective strategies to combat the coxsackievirus-A-mediated infection.
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Affiliation(s)
- Hizbullah Khan
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan 23200, Khyber Pakhtunkhwa, Pakistan
| | - Asifullah Khan
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan 23200, Khyber Pakhtunkhwa, Pakistan.
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Nadan S, Taylor MB, Page NA. Circulation of classic and recombinant human astroviruses detected in South Africa: 2009 to 2014. J Clin Virol 2020; 135:104719. [PMID: 33388529 DOI: 10.1016/j.jcv.2020.104719] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 11/13/2020] [Accepted: 12/17/2020] [Indexed: 10/22/2022]
Abstract
BACKGROUND Astroviruses (AstVs) are associated with diarrhoeal and extra-intestinal infections in human, animal and avian species. A prevalence of 7% was reported in selected regions in SA while AstVs detected from clinical stool specimens were almost identical phylogenetically to strains identified in environmental and water samples. This study investigated the molecular diversity of astroviruses circulating between 2009 and 2014 in South Africa (SA). METHODS Astroviruses detected in stool specimens collected from hospitalised children were investigated retrospectively. Astroviruses were characterised using type-specific RT-PCR, partial nucleotide sequence analyses in ORF1 and ORF2 and whole genome sequencing. Different genotypes were compared with clinical features to investigate genotype-related associations. The Vesikari severity scale (VSS) was evaluated for scoring astrovirus diarrhoeal infections. RESULTS Of 405 astroviruses detected, 49.9 % (202/405) were characterised into 32 genotypes comprising 66.3 % (134/202) putative-recombinants and 33.7 % (68/202) classic strains. No trends by year of collection, age or site were observed. Whole genome analysis in eight strains revealed that genotypes assigned by partial nucleotide sequence analyses to five astroviruses were incorrect. Bivariate analyses showed there were no significant associations between genotypes and clinical symptoms or severity of infection. A comparison of Vesikari parameters with astrovirus-positive proxy values demonstrated that Vesikari scores for duration of diarrhoea and admission temperatures would result in a milder infection rating in astrovirus-positive cases. CONCLUSIONS Diverse genotypes co-circulated with putative-recombinants predominating. Astrovirus classification was complicated by the lack of a consistent characterisation system and reliable reference database. The VSS should be used cautiously to rate astrovirus diarrhoea. While surveillance in communities and out-patient clinics must be continued, screening for human astroviruses in alternate hosts is needed to determine the reservoir species.
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Affiliation(s)
- Sandrama Nadan
- Centre for Enteric Diseases, National Institute for Communicable Disease, Private Bag X4, Sandringham, 2131, South Africa.
| | - Maureen B Taylor
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Gezina, 0031, South Africa; National Health Laboratory Services, Tshwane Academic Division, Pretoria, South Africa
| | - Nicola A Page
- Centre for Enteric Diseases, National Institute for Communicable Disease, Private Bag X4, Sandringham, 2131, South Africa; Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Gezina, 0031, South Africa
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Su L, Feng Y, Liang S, Zeng Y, Li Y, Yang H, Ye L, Wang Q, Wei D, Yuan D, Lai W, Zhang L. The origin and spread of CRF85_BC, driven by heterosexual transmission among older people in Sichuan, China. BMC Infect Dis 2020; 20:772. [PMID: 33076868 PMCID: PMC7574430 DOI: 10.1186/s12879-020-05488-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 10/08/2020] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND CRF_BC recombinants, including CRF07_BC and CRF08_BC, were considered the predominant subtypes in China. Since the discovery of HIV-1 circulating recombinant form CRF 85_BC in Southwest China in 2016, this BC recombinant forms had been reported in different regions of China. However, the history and magnitude of CRF85_BC transmission were still to be investigated. METHOD We conducted the most recent molecular epidemiology of HIV-1 among newly reported HIV-1 infected patients in Sichuan in 2019 by sequencing and phylogenetic analysis of 1291 pol sequences. Then, we used maximum likelihood approach and the Bayesian Markov chain Monte Carlo (MCMC) sampling of pol sequences to reconstruct the phylogeographic and demographic dynamics of the CRF85_BC. RESULTS HIV-1 CRF85_BC (68/1291, 5.27%) became the fourth most prevalent strain revealing a significant increase in local population. CRF85_BC were only found in heterosexually infected individuals and the majority of CRF85_BC (95.45%) were circulating among the people living with HIV aged 50 years and over (PLHIV50+), suggesting a unique prevalent pattern. The founder lineages of CRF85_BC were likely to have first emerged in Yunnan, a province of Southwest China bordering Sichuan, in the early 2000s. It then spread exponentially to various places (including Guangxi, Sichuan, et al) and became endemic around 2008.6 (2006.7-2010.2) in Sichuan. CONCLUSION Taken together, our findings on HIV-1 subtype CRF85_BC infections provided new insights into the spread of this virus and extended the understanding of the HIV epidemic in China.
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Affiliation(s)
- Ling Su
- Sichuan Provincial Center for Disease Control and Prevention, Center for AIDS/STD Control and Prevention, Chengdu, 610041, Sichuan, China
| | - Yi Feng
- Division of Virology and Immunology, National Center for AIDS/STD Control and Prevention (NCAIDS), China CDC, Beijing, China
| | - Shu Liang
- Sichuan Provincial Center for Disease Control and Prevention, Center for AIDS/STD Control and Prevention, Chengdu, 610041, Sichuan, China
| | - Yali Zeng
- Sichuan Provincial Center for Disease Control and Prevention, Center for AIDS/STD Control and Prevention, Chengdu, 610041, Sichuan, China
| | - Yiping Li
- Sichuan Provincial Center for Disease Control and Prevention, Center for AIDS/STD Control and Prevention, Chengdu, 610041, Sichuan, China
| | - Hong Yang
- Sichuan Provincial Center for Disease Control and Prevention, Center for AIDS/STD Control and Prevention, Chengdu, 610041, Sichuan, China
| | - Li Ye
- Sichuan Provincial Center for Disease Control and Prevention, Center for AIDS/STD Control and Prevention, Chengdu, 610041, Sichuan, China
| | - Qiushi Wang
- Sichuan Provincial Center for Disease Control and Prevention, Center for AIDS/STD Control and Prevention, Chengdu, 610041, Sichuan, China
| | - Dongbin Wei
- Sichuan Provincial Center for Disease Control and Prevention, Center for AIDS/STD Control and Prevention, Chengdu, 610041, Sichuan, China
| | - Dan Yuan
- Sichuan Provincial Center for Disease Control and Prevention, Center for AIDS/STD Control and Prevention, Chengdu, 610041, Sichuan, China
| | - Wenhong Lai
- Sichuan Provincial Center for Disease Control and Prevention, Center for AIDS/STD Control and Prevention, Chengdu, 610041, Sichuan, China
| | - Linglin Zhang
- Sichuan Provincial Center for Disease Control and Prevention, Center for AIDS/STD Control and Prevention, Chengdu, 610041, Sichuan, China.
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Xu J, Wang Y, Ding M, Song G, Wu M, Kang Z, Wang J. Sequence-structure characterization of recombinant polypeptides derived from silk fibroin heavy chain. Mater Sci Eng C Mater Biol Appl 2020; 111:110831. [PMID: 32279784 DOI: 10.1016/j.msec.2020.110831] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 01/09/2020] [Accepted: 03/09/2020] [Indexed: 10/24/2022]
Abstract
The molecular conformation of a biomedical material plays a major role in the stability, bioactivity and controlled release of drugs. In order to identify the impact of fragments derived from Bombyx mori silk fibroin on their structures and to develop a new strategy for controlling drug release, we designed several hydrophobic-hydrophilic recombinants (GS16F1, GS16F4, and GS16F8), and investigated their molecular conformations and conformational changes induced by different storage temperatures and pH values. The results showed that the α-helix characteristic peaks were prominent in the fresh freeze-dried powder with increasing F1 repeats. During storage at 4 °C, 37 °C or 60 °C, the β-turns (especially in GS16F8) and α-helixes turned into β-sheets. The β-sheet content in the polypeptides increased with increasing temperature and F1 repeats. Following induction by different pH values, their molecular conformations changed significantly, but not the same as that of powder storage. The content of β-sheets was GS16F1 > GS16F4 > GS16F8 near the isoelectric point of each polypeptide. With increasing pH value, the β-sheet content of GS16F1 decreased more slowly compared with GS16F4 and GS16F8. These results were satisfactory for structural regulation in the field of drug controlled release research.
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Affiliation(s)
- Jingjing Xu
- National Engineering Laboratory for Modern Silk, College of Textile and Clothing Engineering, Soochow University, No. 199 Ren-ai Road, Suzhou Industrial Park, Suzhou, Jiangsu Province 215123, China
| | - Yining Wang
- Division of Bioscience, University College London, London, WC1E 6BT, UK
| | - Mengyao Ding
- National Engineering Laboratory for Modern Silk, College of Textile and Clothing Engineering, Soochow University, No. 199 Ren-ai Road, Suzhou Industrial Park, Suzhou, Jiangsu Province 215123, China
| | - Guangzhou Song
- National Engineering Laboratory for Modern Silk, College of Textile and Clothing Engineering, Soochow University, No. 199 Ren-ai Road, Suzhou Industrial Park, Suzhou, Jiangsu Province 215123, China
| | - Mingyang Wu
- National Engineering Laboratory for Modern Silk, College of Textile and Clothing Engineering, Soochow University, No. 199 Ren-ai Road, Suzhou Industrial Park, Suzhou, Jiangsu Province 215123, China
| | - Zhao Kang
- National Engineering Laboratory for Modern Silk, College of Textile and Clothing Engineering, Soochow University, No. 199 Ren-ai Road, Suzhou Industrial Park, Suzhou, Jiangsu Province 215123, China
| | - Jiannan Wang
- National Engineering Laboratory for Modern Silk, College of Textile and Clothing Engineering, Soochow University, No. 199 Ren-ai Road, Suzhou Industrial Park, Suzhou, Jiangsu Province 215123, China.
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Bruijnesteijn J, de Groot NG, Otting N, Maccari G, Guethlein LA, Robinson J, Marsh SGE, Walter L, O'Connor DH, Hammond JA, Parham P, Bontrop RE. Nomenclature report for killer-cell immunoglobulin-like receptors (KIR) in macaque species: new genes/alleles, renaming recombinant entities and IPD-NHKIR updates. Immunogenetics 2020; 72:37-47. [PMID: 31781789 DOI: 10.1007/s00251-019-01135-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 10/04/2019] [Indexed: 12/16/2022]
Abstract
The Killer-cell Immunoglobulin-like Receptors (KIR) are encoded by a diverse group of genes, which are characterized by allelic polymorphism, gene duplications, and recombinations, which may generate recombinant entities. The number of reported macaque KIR sequences is steadily increasing, and these data illustrate a gene system that may match or exceed the complexity of the human KIR cluster. This report lists the names of quality controlled and annotated KIR genes/alleles with all the relevant references for two different macaque species: rhesus and cynomolgus macaques. Numerous recombinant KIR genes in these species necessitate a revision of some of the earlier-published nomenclature guidelines. In addition, this report summarizes the latest information on the Immuno Polymorphism Database (IPD)-NHKIR Database, which contains annotated KIR sequences from four non-human primate species.
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Gallardo C, Sánchez EG, Pérez-Núñez D, Nogal M, de León P, Carrascosa ÁL, Nieto R, Soler A, Arias ML, Revilla Y. African swine fever virus (ASFV) protection mediated by NH/P68 and NH/P68 recombinant live-attenuated viruses. Vaccine 2018; 36:2694-2704. [PMID: 29609966 DOI: 10.1016/j.vaccine.2018.03.040] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/08/2018] [Accepted: 03/10/2018] [Indexed: 01/24/2023]
Abstract
The risk of spread of African swine fever virus (ASFV) from Russia and Caucasian areas to several EU countries has recently emerged, making it imperative to improve our knowledge and defensive tools against this important pathogen. The ASFV genome encodes many genes which are not essential for virus replication but are known to control host immune evasion, such as NFκB and the NFAT regulator A238L, the apoptosis inhibitor A224L, the MHC-I antigen presenting modulator EP153R, and the A276R gene, involved in modulating type I IFN. These genes are hypothesized to be involved in virulence of the genotype I parental ASFV NH/P68. We here describe the generation of putative live attenuated vaccines (LAV) prototypes by constructing recombinant NH/P68 viruses lacking these specific genes and containing specific markers.
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Affiliation(s)
- Carmina Gallardo
- European Union Reference Laboratory for ASF, Centro de Investigación en Sanidad Animal (INIA-CISA), Madrid, Spain
| | - Elena G Sánchez
- Virology Department, Centro Biología Molecular Severo Ochoa, CSIC-UAM, Madrid 28049, Spain
| | - Daniel Pérez-Núñez
- Virology Department, Centro Biología Molecular Severo Ochoa, CSIC-UAM, Madrid 28049, Spain
| | - Marisa Nogal
- Virology Department, Centro Biología Molecular Severo Ochoa, CSIC-UAM, Madrid 28049, Spain
| | - Patricia de León
- Virology Department, Centro Biología Molecular Severo Ochoa, CSIC-UAM, Madrid 28049, Spain
| | - Ángel L Carrascosa
- Virology Department, Centro Biología Molecular Severo Ochoa, CSIC-UAM, Madrid 28049, Spain
| | - Raquel Nieto
- European Union Reference Laboratory for ASF, Centro de Investigación en Sanidad Animal (INIA-CISA), Madrid, Spain
| | - Alejandro Soler
- European Union Reference Laboratory for ASF, Centro de Investigación en Sanidad Animal (INIA-CISA), Madrid, Spain
| | - María Luisa Arias
- European Union Reference Laboratory for ASF, Centro de Investigación en Sanidad Animal (INIA-CISA), Madrid, Spain
| | - Yolanda Revilla
- Virology Department, Centro Biología Molecular Severo Ochoa, CSIC-UAM, Madrid 28049, Spain.
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Emeriewen OF, Richter K, Piazza S, Micheletti D, Broggini GAL, Berner T, Keilwagen J, Hanke MV, Malnoy M, Peil A. Towards map-based cloning of FB_Mfu10: identification of a receptor-like kinase candidate gene underlying the Malus fusca fire blight resistance locus on linkage group 10. Mol Breed 2018; 38:106. [PMID: 30174538 PMCID: PMC6096517 DOI: 10.1007/s11032-018-0863-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 07/23/2018] [Indexed: 05/20/2023]
Abstract
Breeding for resistance against the destructive fire blight disease of apples is the most sustainable strategy to control the menace of this disease, and has become increasingly important in European apple breeding programs. Since most cultivars are susceptible, wild accessions have been explored for resistance with quantitative trait loci detected in a few wild species. Fire blight resistance of Malus fusca was described following phenotypic evaluations with a C-type strain of Erwinia amylovora, Ea222_JKI, and the detection of a major QTL on chromosome 10 (Mfu10) of this crabapple. The stability of the resistance of M. fusca and Mfu10 has been evaluated using two other strains, the highly aggressive Canadian S-type strain-Ea3049, and the avrRpt2EA mutant-ZYRKD3-1, both of which overcome the resistance of Malus ×robusta 5, a wild species accession with an already described fire blight resistance gene. To pave the way for positional cloning of the underlying fire blight resistance gene of M. fusca, we have fine mapped the QTL region on linkage group 10 using 1888 individuals and 23 newly developed molecular markers, thus delimiting the interval of interest to 0.33 cM between markers FR39G5T7xT7y/FR24N24RP and FRMf7358424/FR46H22. Tightly linked SSR markers are suitable for marker-assisted selection in breeding programs. Furthermore, a bacterial artificial chromosome (BAC) clone spanning FB_Mfu10 region was isolated and sequenced. One putative fire blight resistance candidate gene of M. fusca was predicted on the sequence of BAC 46H22 within the resistance region that encodes B-lectin and serine/threonine kinase domains.
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Affiliation(s)
- Ofere Francis Emeriewen
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Pillnitzer Platz 3a, 01326 Dresden, Germany
| | - Klaus Richter
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
| | - Stefano Piazza
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via E. Mach 1, 38010 San Michele all ‘Adige, Italy
| | - Diego Micheletti
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via E. Mach 1, 38010 San Michele all ‘Adige, Italy
| | | | - Thomas Berner
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Biosafety in Plant Biotechnology, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
| | - Jens Keilwagen
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Biosafety in Plant Biotechnology, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
| | - Magda-Viola Hanke
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Pillnitzer Platz 3a, 01326 Dresden, Germany
| | - Mickael Malnoy
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via E. Mach 1, 38010 San Michele all ‘Adige, Italy
| | - Andreas Peil
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Pillnitzer Platz 3a, 01326 Dresden, Germany
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Quinteros JA, Lee SW, Markham PF, Noormohammadi AH, Hartley CA, Legione AR, Coppo MJC, Vaz PK, Browning GF. Full genome analysis of Australian infectious bronchitis viruses suggests frequent recombination events between vaccine strains and multiple phylogenetically distant avian coronaviruses of unknown origin. Vet Microbiol 2016; 197:27-38. [PMID: 27938680 DOI: 10.1016/j.vetmic.2016.11.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 11/03/2016] [Accepted: 11/04/2016] [Indexed: 01/30/2023]
Abstract
Vaccines contributed to emergence of recombinant IBV strains. Exotic avian coronaviruses have played a decisive role in recombination events. Recombination breakpoints have been in genes for nsp 2, 3 and 16 and the S protein. Avian coronavirus of unknown origin have been recombining with IBV for 20 years.
Australian strains of infectious bronchitis virus (IBV) have been evolving independently for many years, with control achieved by vaccination with local attenuated strains. Previous studies have documented the emergence of recombinants over the last 20 years, with the most recent one, Ck/Aus/N1/08, detected in 2008. These recombinants did not appear to be controlled by the vaccines currently in use. In this study we sequenced the complete genomes of three emergent Australian strains of IBV (IBV/Ck/Aus/N1/88, IBV/Ck/Aus/N1/03 and IBV/Ck/Aus/N1/08) and a previously incompletely characterised vaccine strain, IBV/Ck/Aus/Armidale, and compared them to the genome of the vaccine strain VicS. We detected multiple recombination events throughout the genome between wild type viruses and the vaccine strains in all three emergent isolates. Moreover, we found that strain N1/88 was not entirely exogenous, as was previously hypothesised. Rather, it originated from a recombination event involving the VicS vaccine strain. The S glycoprotein genes of N1/88 and N1/03 were known to be genetically distinct from previously characterised circulating strains and from each other, and the original donors of these genes remains unknown. The S1 glycoprotein gene of N1/88, a subgroup 2 strain, shares a high nucleotide identity with the sequence of the S1 gene of the recent isolate N1/08. As the subgroup 2 strains have not been isolated for at least 20 years, it appears likely that an unknown avian coronavirus that was the donor of the S1 glycoprotein sequence of N1/88 in the 1980s is still recombining with IBV strains in the field.
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Mauleekoonphairoj J, Vongpunsawad S, Puenpa J, Korkong S, Poovorawan Y. Complete genome sequence analysis of enterovirus 71 isolated from children with hand, foot, and mouth disease in Thailand, 2012-2014. Virus Genes 2015; 51:290-3. [PMID: 26303899 DOI: 10.1007/s11262-015-1239-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 08/17/2015] [Indexed: 10/23/2022]
Abstract
The complete genomic sequences of 14 enterovirus 71 (EV71) strains isolated from children with hand, foot, and mouth disease in Thailand from 2012 to 2014 were determined and compared to enterovirus group A prototypes. Phylogenetic analysis revealed that 13 strains resembled the B5 subgroup, while one strain from a fatal case designated THA_1219 belonged to the C4 subgroup. Similarity plot and bootscan analyses suggested that THA_1219 underwent recombination in the P2 and P3 regions. Full-genome data from this work will contribute to the study of evolution dynamics of EV71.
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Affiliation(s)
- John Mauleekoonphairoj
- Department of Pediatrics, Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Sompong Vongpunsawad
- Department of Pediatrics, Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Jiratchaya Puenpa
- Department of Pediatrics, Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Sumeth Korkong
- Department of Pediatrics, Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Yong Poovorawan
- Department of Pediatrics, Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand.
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Yi X, Gu H, Gao Q, Liu ZL, Bao J. Transcriptome analysis of Zymomonas mobilis ZM4 reveals mechanisms of tolerance and detoxification of phenolic aldehyde inhibitors from lignocellulose pretreatment. Biotechnol Biofuels 2015; 8:153. [PMID: 26396591 PMCID: PMC4578398 DOI: 10.1186/s13068-015-0333-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 09/03/2015] [Indexed: 05/04/2023]
Abstract
BACKGROUND Phenolic aldehydes generated from lignocellulose pretreatment exhibited severe toxic inhibitions on microbial growth and fermentation. Numerous tolerance studies against furfural, 5-hydroxymethyl-2-furaldehyde (HMF), acetate, and ethanol were reported, but studies on inhibition of phenolic aldehyde inhibitors are rare. For ethanologenic strains, Zymomonas mobilis ZM4 is high in ethanol productivity and genetic manipulation feasibility, but sensitive to phenolic aldehyde inhibitors. Molecular mechanisms of tolerance for Z. mobilis toward phenolic aldehydes are not known. RESULTS We took the first insight into genomic response of Z. mobilis ZM4 to the phenolic aldehyde inhibitors derived from lignocellulose pretreatment. The results suggest that the toxicity to cells is caused by the functional group of phenolic aldehyde, similar to furfural and HMF, rather than aromatic groups or phenolic hydroxyl groups. Transcriptome response against 4-hydroxybenzaldehyde, syringaldehyde, and vanillin, representing phenolic groups H, S, and G, respectively, was investigated. The atlas of the important genes responsible for significantly enhanced and repressed genes at the genomic level was illustrated. 272 genes with twofold greater expressions than non-treated controls and 36 gene clusters in response to challenges of these phenolic aldehydes were identified. Several reductases encoded by ZMO1116, ZMO1696, and ZMO1885 were found to play the key roles in reducing phenolic aldehydes into the corresponding phenolic alcohols. Reduction of phenolic aldehydes by overexpression of ZMO1116, ZMO1696, and ZMO1885 in Z. mobilis ZM4 resulted in the increased inhibitor conversion and ethanol productivity, especially for 4-hydroxybenzaldehyde and vanillin. Several transporter genes such as ZMO0282, ZMO0283, ZMO0798, ZMO0799, and ZMO0800 was also displayed significantly increased expressions against the phenolic aldehydes. CONCLUSIONS The genes encoding reductases are with potentials on phenolic aldehydes-tolerant genes contributing to the reduction of phenolic aldehydes into the corresponding phenolic alcohols forms for Z. mobilis ZM4. Overexpression of the key genes improved the conversion ratio and ethanol productivity of 4-hydroxybenzaldehyde and vanillin with high toxicity. New knowledge obtained from this research aids understanding the mechanisms of bacterial tolerance and the development of the next-generation biocatalysts for advanced biofuels production.
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Affiliation(s)
- Xia Yi
- />State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237 China
| | - Hanqi Gu
- />State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237 China
| | - Qiuqiang Gao
- />State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237 China
| | - Z. Lewis Liu
- />US Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, 1815 North University Street, Peoria, IL 61604 USA
| | - Jie Bao
- />State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237 China
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Abstract
Subtyping of HIV has important implications for developing candidate vaccine and understanding the biological behaviour and dynamics of HIV transmission in various populations. The third variable region (V3) in the envelope gene of HIV-1 has been shown to be a major determinant influencing a number of biological characteristics of the virus. HIV-1 evolves by rapid mutation and by recombination, both processes actively contributing to its genetic diversity. Most of the multiple genetic subtypes and intersubtype recombination of HIV-1 that comprise the global pandemic have not been characterized by full genome sequencing. The development of an effective human immunodeficiency virus type-1 (HIV-1) vaccine is likely to depend on knowledge of circulating variants of genes other than the commonly sequenced gag and env genes.
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Affiliation(s)
- A K Sahni
- Reader, Department of Microbiology, Armed Forces Medical College, Pune - 411 040
| | - A Nagendra
- Professor and Head, Department of Microbiology, Armed Forces Medical College, Pune - 411 040
| | - P K Menon
- Reader, Department of Microbiology, Armed Forces Medical College, Pune - 411 040
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