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Ren M, Abdullah SW, Pei C, Guo H, Sun S. Use of virus-like particles and nanoparticle-based vaccines for combating picornavirus infections. Vet Res 2024; 55:128. [PMID: 39350170 PMCID: PMC11443892 DOI: 10.1186/s13567-024-01383-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 08/15/2024] [Indexed: 10/04/2024] Open
Abstract
Picornaviridae are non-enveloped ssRNA viruses that cause diseases such as poliomyelitis, hand-foot-and-mouth disease (HFMD), hepatitis A, encephalitis, myocarditis, and foot-and-mouth disease (FMD). Virus-like particles (VLPs) vaccines mainly comprise particles formed through the self-assembly of viral capsid proteins (for enveloped viruses, envelope proteins are also an option). They do not contain the viral genome. On the other hand, the nanoparticles vaccine (NPs) is mainly composed of self-assembling biological proteins or nanomaterials, with viral antigens displayed on the surface. The presentation of viral antigens on these particles in a repetitive array can elicit a strong immune response in animals. VLPs and NPs can be powerful platforms for multivalent antigen presentation. This review summarises the development of virus-like particle vaccines (VLPs) and nanoparticle vaccines (NPs) against picornaviruses. By detailing the progress made in the fight against various picornaviruses such as poliovirus (PV), foot-and-mouth disease virus (FMDV), enterovirus (EV), Senecavirus A (SVA), and encephalomyocarditis virus (EMCV), we in turn highlight the significant strides made in vaccine technology. These advancements include diverse construction methods, expression systems, elicited immune responses, and the use of various adjuvants. We see promising prospects for the continued development and optimisation of VLPs and NPs vaccines. Future research should focus on enhancing these vaccines' immunogenicity, stability, and delivery methods. Moreover, expanding our understanding of the interplay between these vaccines and the immune system will be crucial. We hope these insights will inspire and guide fellow researchers in the ongoing quest to combat picornavirus infections more effectively.
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Affiliation(s)
- Mei Ren
- State Key Laboratory for Animal Disease Control and Prevention, CollegeofVeterinaryMedicine, Lanzhou UniversityLanzhou Veterinary Research InstituteChinese Academy of Agricultural Sciences, Lanzhou, 730000, China
- Gembloux Agro-Biotech, University of Liege, Gembloux, Belgium
| | - Sahibzada Waheed Abdullah
- Livestock and dairy development department peshawar, Government of Khyber Pakhtunkhwa, Peshawar, Pakistan
| | - Chenchen Pei
- State Key Laboratory for Animal Disease Control and Prevention, CollegeofVeterinaryMedicine, Lanzhou UniversityLanzhou Veterinary Research InstituteChinese Academy of Agricultural Sciences, Lanzhou, 730000, China
| | - Huichen Guo
- State Key Laboratory for Animal Disease Control and Prevention, CollegeofVeterinaryMedicine, Lanzhou UniversityLanzhou Veterinary Research InstituteChinese Academy of Agricultural Sciences, Lanzhou, 730000, China
| | - Shiqi Sun
- State Key Laboratory for Animal Disease Control and Prevention, CollegeofVeterinaryMedicine, Lanzhou UniversityLanzhou Veterinary Research InstituteChinese Academy of Agricultural Sciences, Lanzhou, 730000, China.
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Ju DU, Park D, Kim IH, Kim S, Yoo HM. Development of Human Rhinovirus RNA Reference Material Using Digital PCR. Genes (Basel) 2023; 14:2210. [PMID: 38137032 PMCID: PMC10742479 DOI: 10.3390/genes14122210] [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: 10/03/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
The human rhinovirus (RV) is a positive-stranded RNA virus that causes respiratory tract diseases affecting both the upper and lower halves of the respiratory system. RV enhances its replication by concentrating RNA synthesis within a modified host membrane in an intracellular compartment. RV infections often occur alongside infections caused by other respiratory viruses, and the RV virus may remain asymptomatic for extended periods. Alongside qualitative detection, it is essential to accurately quantify RV RNA from clinical samples to explore the relationships between RV viral load, infections caused by the virus, and the resulting symptoms observed in patients. A reference material (RM) is required for quality evaluation, the performance evaluation of molecular diagnostic products, and evaluation of antiviral agents in the laboratory. The preparation process for the RM involves creating an RV RNA mixture by combining RV viral RNA with RNA storage solution and matrix. The resulting RV RNA mixture is scaled up to a volume of 25 mL, then dispensed at 100 µL per vial and stored at -80 °C. The process of measuring the stability and homogeneity of RV RMs was conducted by employing reverse transcription droplet digital polymerase chain reaction (RT-ddPCR). Digital PCR is useful for the analysis of standards and can help to improve measurement compatibility: it represents the equivalence of a series of outcomes for reference materials and samples being analyzed when a few measurement procedures are employed, enabling objective comparisons between quantitative findings obtained through various experiments. The number of copies value represents a measured result of approximately 1.6 × 105 copies/μL. The RM has about an 11% bottle-to-bottle homogeneity and shows stable results for 1 week at temperatures of 4 °C and -20 °C and for 12 months at a temperature of -80 °C. The developed RM can enhance the dependability of RV molecular tests by providing a precise reference value for the absolute copy number of a viral target gene. Additionally, it can serve as a reference for diverse studies.
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Affiliation(s)
- Dong U Ju
- Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea
- School of Biomedical Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Dongju Park
- Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea
| | - Il-Hwan Kim
- Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea
| | - Seil Kim
- Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea
- Department of Precision Measurement, University of Science & Technology (UST), Daejeon 34113, Republic of Korea
| | - Hee Min Yoo
- Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea
- Department of Precision Measurement, University of Science & Technology (UST), Daejeon 34113, Republic of Korea
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Zhao P, Shao N, Dong J, Su H, Sui H, Zhang T, Yang F. Genetic diversity and characterization of rhinoviruses from Chinese clinical samples with a global perspective. Microbiol Spectr 2023; 11:e0084023. [PMID: 37733296 PMCID: PMC10715137 DOI: 10.1128/spectrum.00840-23] [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: 02/25/2023] [Accepted: 08/03/2023] [Indexed: 09/22/2023] Open
Abstract
IMPORTANCE Based on clinical samples collected in China, we detected and reported 22 types for the first time in China, as well as three types for the first time in Asia, and reported their genetic characteristics and diversity. We identified a novel type of Rhinovirus (RV), A110, highlighting its unique genetic features. We annotated the genomic structure and serotype of all the existing RV sequences in the database, and four novel RV types were identified and their genetic diversity reported. Combined with the sequence annotation, we constructed a complete VP1 data set of RV and conducted the first large-scale evolutionary dynamics analysis of RV. Based on a high-quality data set, we conducted a comprehensive analysis of the guanine-cytosine (GC) content variations among serotypes of RVs. This study provides crucial theoretical support and valuable data for understanding RV's genetic diversity and developing antiviral strategies.
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Affiliation(s)
- Peng Zhao
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Nan Shao
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jie Dong
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Haoxiang Su
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hongtao Sui
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ting Zhang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Fan Yang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences, Beijing, China
- State Key Laboratory of Respiratory Health and Multimorbidity, Beijing, China
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Fox CR, Kedarinath K, Neal CJ, Sheiber J, Kolanthai E, Kumar U, Drake C, Seal S, Parks GD. Broad-Spectrum, Potent, and Durable Ceria Nanoparticles Inactivate RNA Virus Infectivity by Targeting Virion Surfaces and Disrupting Virus-Receptor Interactions. Molecules 2023; 28:5190. [PMID: 37446852 DOI: 10.3390/molecules28135190] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 06/29/2023] [Accepted: 07/01/2023] [Indexed: 07/15/2023] Open
Abstract
There is intense interest in developing long-lasting, potent, and broad-spectrum antiviral disinfectants. Ceria nanoparticles (CNPs) can undergo surface redox reactions (Ce3+ ↔ Ce4+) to generate ROS without requiring an external driving force. Here, we tested the mechanism behind our prior finding of potent inactivation of enveloped and non-enveloped RNA viruses by silver-modified CNPs, AgCNP1 and AgCNP2. Treatment of human respiratory viruses, coronavirus OC43 and parainfluenza virus type 5 (PIV5) with AgCNP1 and 2, respectively, prevented virus interactions with host cell receptors and resulted in virion aggregation. Rhinovirus 14 (RV14) mutants were selected to be resistant to inactivation by AgCNP2. Sequence analysis of the resistant virus genomes predicted two amino acid changes in surface-located residues D91V and F177L within capsid protein VP1. Consistent with the regenerative properties of CNPs, surface-applied AgCNP1 and 2 inactivated a wide range of structurally diverse viruses, including enveloped (OC43, SARS-CoV-2, and PIV5) and non-enveloped RNA viruses (RV14 and feline calicivirus; FCV). Remarkably, a single application of AgCNP1 and 2 potently inactivated up to four sequential rounds of virus challenge. Our results show broad-spectrum and long-lasting anti-viral activity of AgCNP nanoparticles, due to targeting of viral surface proteins to disrupt interactions with cellular receptors.
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Affiliation(s)
- Candace R Fox
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32827, USA
| | - Kritika Kedarinath
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32827, USA
| | - Craig J Neal
- Advanced Materials Processing and Analysis Center, Department of Materials Science and Engineering, University of Central Florida, Orlando, FL 32816, USA
| | - Jeremy Sheiber
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32827, USA
| | - Elayaraja Kolanthai
- Advanced Materials Processing and Analysis Center, Department of Materials Science and Engineering, University of Central Florida, Orlando, FL 32816, USA
| | - Udit Kumar
- Advanced Materials Processing and Analysis Center, Department of Materials Science and Engineering, University of Central Florida, Orlando, FL 32816, USA
| | | | - Sudipta Seal
- Advanced Materials Processing and Analysis Center, Department of Materials Science and Engineering, University of Central Florida, Orlando, FL 32816, USA
- Nano Science Technology Center, University of Central Florida, Orlando, FL 32816, USA
- Biionix Cluster, College of Medicine, University of Central Florida, Orlando, FL 32816, USA
| | - Griffith D Parks
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32827, USA
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Zhou Z, Zhu R, Yang H, Xu L, Chen H, Wu Y, Yin Z, Huang Q, Zhang D, Liu C, Que Y, Zhang J, Xia N, Cheng T. Development of a rapid neutralization testing system for Rhinovirus C15 based on the enzyme-linked immunospot assay. Front Microbiol 2022; 13:983656. [PMID: 36212859 PMCID: PMC9539532 DOI: 10.3389/fmicb.2022.983656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/25/2022] [Indexed: 11/13/2022] Open
Abstract
Human Rhinoviruses (RVs) are dominant pathogens causing a wide range of respiratory tract diseases, posing a huge threat to public health worldwide. Viruses belonging to the RV-C species are more likely to cause severe illnesses and are strongly associated with asthma onset or exacerbations than RV-A or RV-B. Rapid and sensitive detection of neutralizing antibodies (NAbs) against RV-C can promote the development of vaccines and antiviral drugs and help in the diagnosis of viral infection. In this study, a rapid neutralization testing system for RV-C15, based on an enzyme-linked immunospot assay (Nt-ELISPOT) was developed. A monoclonal antibody (MAb), named 9F9, with high binding efficacy for RV-C15 conjugated to horseradish peroxidase (HRP), was used to detect RV-C15-infected cells at a concentration of 2 μg/ml. The optimal infectious dose of RV-C15 was set at 1 × 104 TCID50/well and the cells were fixed with 0.5% formaldehyde diluted in PBS after incubation for 20 h. Compared with the traditional cytopathic effect (CPE)-based neutralization assay (Nt-CPE), Nt-ELISPOT significantly shortened the detection period and showed good consistency with the detection of neutralizing titers of both sera and NAbs. Using Nt-ELISPOT, three anti-RV-C15 NAbs were obtained with IC50 values of 0.16, 0.27, and 11.8 μg/ml, respectively. Moreover, 64 human serum samples collected from a wide range of age groups were tested for NAb against RV-C15 by Nt-ELISPOT. The total seroprevalence was 48.4% (31/64) and the positive rate was lowest in the group under 6 years old. Thus, the Nt-ELISPOT established in this study can be used as a high-throughput and rapid neutralization assay for the screening of NAbs and for seroepidemiological investigation against RV-C15.
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Neugebauer F, Bergs S, Liebert UG, Hönemann M. Human Rhinoviruses in Pediatric Patients in a Tertiary Care Hospital in Germany: Molecular Epidemiology and Clinical Significance. Viruses 2022; 14:v14081829. [PMID: 36016451 PMCID: PMC9415293 DOI: 10.3390/v14081829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/18/2022] [Accepted: 08/18/2022] [Indexed: 11/22/2022] Open
Abstract
Rhinoviruses (RVs) constitute a substantial public health burden. To evaluate their abundance and genetic diversity in pediatric patients, RV RNA in respiratory samples was assessed using real-time RT-PCR and partial nucleic acid sequencing of viral genomes. Additionally, clinical data were retrieved from patient charts to determine the clinical significance of pediatric RV infections. In total, the respiratory specimens of 776 patients (<18 years), collected from 2013 to 2017, were analyzed. Infections occurred throughout the entire year, with peaks occurring in fall and winter, and showed remarkably high intra- and interseasonal diversity for RV genotypes. RV species were detected in the following frequencies: 49.1% RV-A, 5.9% RV-B, and 43.6% RV-C. RV-C was found to be more frequently associated with asthma (p = 0.04) and bronchiolitis (p < 0.001), while RV-A was more frequently associated with fever (p = 0.001) and pneumonia (p = 0.002). Additionally, 35.3% of the patients had co-infections with other pathogens, which were associated with a longer hospital stay (p < 0.001), need for ventilation (p < 0.001), and pneumonia (p < 0.001). Taken together, this study shows pronounced RV genetic diversity in pediatric patients and indicates differences in RV-associated pathologies, as well as an important role for co-infections.
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Nearly Complete Genome Sequences of 12 Types of Human Rhinoviruses Isolated from Pediatric Inpatients in Fukushima, Japan. Microbiol Resour Announc 2022; 11:e0052922. [PMID: 35862917 PMCID: PMC9387279 DOI: 10.1128/mra.00529-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
We reported nearly complete genomic sequences of 12 serotypes of human rhinoviruses (HRVs) isolated from pediatric inpatients in Fukushima, Japan using an air-liquid interface culture of human bronchial tracheal epithelial cells. We found that various serotypes of HRV circulated locally and simultaneously from 2018 to 2021.
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Huang K, Ying T, Wu Y. Single-Domain Antibodies as Therapeutics for Respiratory RNA Virus Infections. Viruses 2022; 14:1162. [PMID: 35746634 PMCID: PMC9230756 DOI: 10.3390/v14061162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 05/21/2022] [Accepted: 05/25/2022] [Indexed: 11/29/2022] Open
Abstract
Over the years, infectious diseases with high morbidity and mortality disrupted human healthcare systems and devastated economies globally. Respiratory viruses, especially emerging or re-emerging RNA viruses, including influenza and human coronavirus, are the main pathogens of acute respiratory diseases that cause epidemics or even global pandemics. Importantly, due to the rapid mutation of viruses, there are few effective drugs and vaccines for the treatment and prevention of these RNA virus infections. Of note, a class of antibodies derived from camelid and shark, named nanobody or single-domain antibody (sdAb), was characterized by smaller size, lower production costs, more accessible binding epitopes, and inhalable properties, which have advantages in the treatment of respiratory diseases compared to conventional antibodies. Currently, a number of sdAbs have been developed against various respiratory RNA viruses and demonstrated potent therapeutic efficacy in mouse models. Here, we review the current status of the development of antiviral sdAb and discuss their potential as therapeutics for respiratory RNA viral diseases.
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Affiliation(s)
- Keke Huang
- MOE/NHC Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China;
| | - Tianlei Ying
- MOE/NHC Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China;
- Shanghai Engineering Research Center for Synthetic Immunology, Shanghai 200032, China
| | - Yanling Wu
- MOE/NHC Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China;
- Shanghai Engineering Research Center for Synthetic Immunology, Shanghai 200032, China
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Zhang Z, Tan L, Tan M, Zhang X, He W, Li M, He J, Pan Y, Xu B, Bin S, Gan Z, Yan L, Sun Y, Jiang H, Sun Q, Zhang Z. Molecular Characterization of the Viral Structural Genes of Human Rhinovirus A11 from Children Hospitalized with Lower Respiratory Tract Infection in Kunming. Int J Infect Dis 2022; 117:274-283. [PMID: 35121125 DOI: 10.1016/j.ijid.2022.01.066] [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: 11/16/2021] [Revised: 01/27/2022] [Accepted: 01/28/2022] [Indexed: 10/19/2022] Open
Abstract
BACKGROUND Human rhinovirus (HRV) is a picornavirus that can cause a variety of respiratory diseases, including the aggravation of chronic respiratory diseases, such as bronchitis, pneumonia, and asthma. Although an increasing number of lower respiratory tract infection cases have been reported with HRV infection in Europe, few such cases have been reported in China. METHODS The complete genomic sequences of HRV-A11 epidemic strains were amplifed and obtained by segmented PCR and sequence, then phylogenetic, nucleotide mutation, recombinant, and comparative analyses of amino acid mutations were performed. RESULTS Phylogenetic analyses showed that the epidemic strains from three rare cases of pneumonia belong to the HRV-A11 subgenotypes. All strains were highly similar to strains from the USA. No obvious homologous recombination signals were observed in epidemic strains. There were 498 nucleotide and 47 amino acid mutations compared to the HRV-A11 prototype strain. Amino acid mutations were observed at the capsid protein region, P1a, RVA2147-2155, and RVA97-114 epitopes of these clinical strains. CONCLUSIONS We reported the first case of HRV-A11-associated lower respiratory tract infection in China. These mutations in the P1a, HRV A-specific CD8, and CD4 T-cell epitopes might provide a reference for virological surveillance and vaccine development.
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Affiliation(s)
- Zhilei Zhang
- Institute of Pediatrics, The Kunming Children' s Hospital, Kunming Medical University, Kunming, PR China; Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, PR China; Yunnan Key Laboratory of Children's Major Disease Research, Kunming, PR China.
| | - Li Tan
- Institute of Pediatrics, The Kunming Children' s Hospital, Kunming Medical University, Kunming, PR China; Department of Respiratory Medicine, The Kunming Children' s Hospital, Kunming, PR China.
| | - Miao Tan
- Institute of Pediatrics, The Kunming Children' s Hospital, Kunming Medical University, Kunming, PR China; Yunnan Key Laboratory of Children's Major Disease Research, Kunming, PR China.
| | - Xiaolin Zhang
- Institute of Pediatrics, The Kunming Children' s Hospital, Kunming Medical University, Kunming, PR China; Yunnan Key Laboratory of Children's Major Disease Research, Kunming, PR China.
| | - Wenji He
- Institute of Pediatrics, The Kunming Children' s Hospital, Kunming Medical University, Kunming, PR China.
| | - Ming Li
- Institute of Pediatrics, The Kunming Children' s Hospital, Kunming Medical University, Kunming, PR China; Department of Respiratory Medicine, The Kunming Children' s Hospital, Kunming, PR China.
| | - Juan He
- Institute of Pediatrics, The Kunming Children' s Hospital, Kunming Medical University, Kunming, PR China; Department of Respiratory Medicine, The Kunming Children' s Hospital, Kunming, PR China.
| | - Yue Pan
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, PR China; Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Diseases, Kunming, PR China.
| | - Bin Xu
- Institute of Pediatrics, The Kunming Children' s Hospital, Kunming Medical University, Kunming, PR China; Department of Laboratory, The Kunming Children' s Hospital, Kunming, PR China.
| | - Songtao Bin
- Institute of Pediatrics, The Kunming Children' s Hospital, Kunming Medical University, Kunming, PR China; Department of Respiratory Medicine, The Kunming Children' s Hospital, Kunming, PR China.
| | - Zhengyan Gan
- Institute of Pediatrics, The Kunming Children' s Hospital, Kunming Medical University, Kunming, PR China; Department of Respiratory Medicine, The Kunming Children' s Hospital, Kunming, PR China.
| | - Lingmei Yan
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, PR China; Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Diseases, Kunming, PR China.
| | - Yuxing Sun
- Institute of Pediatrics, The Kunming Children' s Hospital, Kunming Medical University, Kunming, PR China; Department of Respiratory Medicine, The Kunming Children' s Hospital, Kunming, PR China.
| | - Hongchao Jiang
- Institute of Pediatrics, The Kunming Children' s Hospital, Kunming Medical University, Kunming, PR China; Yunnan Key Laboratory of Children's Major Disease Research, Kunming, PR China.
| | - Qiangming Sun
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, PR China; Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Diseases, Kunming, PR China.
| | - Zhen Zhang
- Institute of Pediatrics, The Kunming Children' s Hospital, Kunming Medical University, Kunming, PR China; Yunnan Key Laboratory of Children's Major Disease Research, Kunming, PR China.
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Murer L, Petkidis A, Vallet T, Vignuzzi M, Greber UF. Chemical Evolution of Rhinovirus Identifies Capsid-Destabilizing Mutations Driving Low-pH-Independent Genome Uncoating. J Virol 2022; 96:e0106021. [PMID: 34705560 PMCID: PMC8791267 DOI: 10.1128/jvi.01060-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 10/20/2021] [Indexed: 12/24/2022] Open
Abstract
Rhinoviruses (RVs) cause recurrent infections of the nasal and pulmonary tracts, life-threatening conditions in chronic respiratory illness patients, predisposition of children to asthmatic exacerbation, and large economic cost. RVs are difficult to treat. They rapidly evolve resistance and are genetically diverse. Here, we provide insight into RV drug resistance mechanisms against chemical compounds neutralizing low pH in endolysosomes. Serial passaging of RV-A16 in the presence of the vacuolar proton ATPase inhibitor bafilomycin A1 (BafA1) or the endolysosomotropic agent ammonium chloride (NH4Cl) promoted the emergence of resistant virus populations. We found two reproducible point mutations in viral proteins 1 and 3 (VP1 and VP3), A2526G (serine 66 to asparagine [S66N]), and G2274U (cysteine 220 to phenylalanine [C220F]), respectively. Both mutations conferred cross-resistance to BafA1, NH4Cl, and the protonophore niclosamide, as identified by massive parallel sequencing and reverse genetics, but not the double mutation, which we could not rescue. Both VP1-S66 and VP3-C220 locate at the interprotomeric face, and their mutations increase the sensitivity of virions to low pH, elevated temperature, and soluble intercellular adhesion molecule 1 receptor. These results indicate that the ability of RV to uncoat at low endosomal pH confers virion resistance to extracellular stress. The data endorse endosomal acidification inhibitors as a viable strategy against RVs, especially if inhibitors are directly applied to the airways. IMPORTANCE Rhinoviruses (RVs) are the predominant agents causing the common cold. Anti-RV drugs and vaccines are not available, largely due to rapid evolutionary adaptation of RVs giving rise to resistant mutants and an immense diversity of antigens in more than 160 different RV types. In this study, we obtained insight into the cell biology of RVs by harnessing the ability of RVs to evolve resistance against host-targeting small chemical compounds neutralizing endosomal pH, an important cue for uncoating of normal RVs. We show that RVs grown in cells treated with inhibitors of endolysosomal acidification evolved capsid mutations yielding reduced virion stability against elevated temperature, low pH, and incubation with recombinant soluble receptor fragments. This fitness cost makes it unlikely that RV mutants adapted to neutral pH become prevalent in nature. The data support the concept of host-directed drug development against respiratory viruses in general, notably at low risk of gain-of-function mutations.
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Affiliation(s)
- Luca Murer
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Anthony Petkidis
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Thomas Vallet
- Institut Pasteur, Viral Populations and Pathogenesis Unit, Department of Virology, CNRS UMR 3569, Paris, France
| | - Marco Vignuzzi
- Institut Pasteur, Viral Populations and Pathogenesis Unit, Department of Virology, CNRS UMR 3569, Paris, France
| | - Urs F. Greber
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
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