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Kim JH, Bryant H, Fiedler E, Cao T, Rayner JO. Real-time tracking of bioluminescent influenza A virus infection in mice. Sci Rep 2022; 12:3152. [PMID: 35210462 PMCID: PMC8873407 DOI: 10.1038/s41598-022-06667-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 02/04/2022] [Indexed: 01/13/2023] Open
Abstract
Despite the availability of vaccines and antiviral therapies, seasonal influenza infections cause 400,000 human deaths on average per year. Low vaccine coverage and the occurrence of drug-resistant viral strains highlight the need for new and improved countermeasures. While influenza A virus (IAV) engineered to express a reporter gene may serve as a valuable tool for real-time tracking of viral infection, reporter gene insertion into IAV typically attenuates viral pathogenicity, hindering its application to research. Here, we demonstrate that lethal or even sublethal doses of bioluminescent IAV carrying the NanoLuc gene in the C-terminus of PB2 can be tracked in real-time in live mice without compromising pathogenicity. Real-time tracking of this bioluminescent IAV enables spatiotemporal viral replication tracking in animals that will facilitate the development of countermeasures by enhancing the interpretation of clinical signs and prognosis while also allowing less animal usage.
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Affiliation(s)
- Jin H Kim
- Department of Microbiology and Immunology, College of Medicine, University of South Alabama, Mobile, AL, 36688, USA. .,Center for Lung Biology, College of Medicine, University of South Alabama, Mobile, AL, 36688, USA.
| | - Hannah Bryant
- Department of Comparative Medicine, College of Medicine, University of South Alabama, Mobile, AL, 36688, USA
| | - Edward Fiedler
- Department of Microbiology and Immunology, College of Medicine, University of South Alabama, Mobile, AL, 36688, USA
| | - TuAnh Cao
- Department of Microbiology and Immunology, College of Medicine, University of South Alabama, Mobile, AL, 36688, USA
| | - Jonathan O Rayner
- Department of Microbiology and Immunology, College of Medicine, University of South Alabama, Mobile, AL, 36688, USA
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2
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Danilenko AV, Kolosova NP, Shvalov AN, Ilyicheva TN, Svyatchenko SV, Durymanov AG, Bulanovich JA, Goncharova NI, Susloparov IM, Marchenko VY, Tregubchak TV, Gavrilova EV, Maksyutov RA, Ryzhikov AB. Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. PLoS One 2021; 16:e0251019. [PMID: 33914831 PMCID: PMC8084186 DOI: 10.1371/journal.pone.0251019] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 04/19/2021] [Indexed: 02/07/2023] Open
Abstract
Outbreaks of influenza, which is a contagious respiratory disease, occur throughout the world annually, affecting millions of people with many fatal cases. The D222G/N mutations in the hemagglutinin (HA) gene of A(H1N1)pdm09 are associated with severe and fatal human influenza cases. These mutations lead to increased virus replication in the lower respiratory tract (LRT) and may result in life-threatening pneumonia. Targeted NGS analysis revealed the presence of mutations in major and minor variants in 57% of fatal cases, with the proportion of viral variants with mutations varying from 1% to 98% in each individual sample in the epidemic season 2018-2019 in Russia. Co-occurrence of the mutations D222G and D222N was detected in a substantial number of the studied fatal cases (41%). The D222G/N mutations were detected at a low frequency (less than 1%) in the rest of the studied samples from fatal and nonfatal cases of influenza. The presence of HA D222Y/V/A mutations was detected in a few fatal cases. The high rate of occurrence of HA D222G/N mutations in A(H1N1)pdm09 viruses, their increased ability to replicate in the LRT and their association with fatal outcomes points to the importance of monitoring the mutations in circulating A(H1N1)pdm09 viruses for the evaluation of their epidemiological significance and for the consideration of disease prevention and treatment options.
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Affiliation(s)
- Alexey V. Danilenko
- Vector State Research Center of Virology and Biotechnology, Koltsovo, Novosibirsk Region, Russia
| | - Natalia P. Kolosova
- Vector State Research Center of Virology and Biotechnology, Koltsovo, Novosibirsk Region, Russia
| | - Alexander N. Shvalov
- Vector State Research Center of Virology and Biotechnology, Koltsovo, Novosibirsk Region, Russia
| | - Tatyana N. Ilyicheva
- Vector State Research Center of Virology and Biotechnology, Koltsovo, Novosibirsk Region, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Svetlana V. Svyatchenko
- Vector State Research Center of Virology and Biotechnology, Koltsovo, Novosibirsk Region, Russia
| | - Alexander G. Durymanov
- Vector State Research Center of Virology and Biotechnology, Koltsovo, Novosibirsk Region, Russia
| | - Julia A. Bulanovich
- Vector State Research Center of Virology and Biotechnology, Koltsovo, Novosibirsk Region, Russia
| | - Natalia I. Goncharova
- Vector State Research Center of Virology and Biotechnology, Koltsovo, Novosibirsk Region, Russia
| | - Ivan M. Susloparov
- Vector State Research Center of Virology and Biotechnology, Koltsovo, Novosibirsk Region, Russia
| | - Vasiliy Y. Marchenko
- Vector State Research Center of Virology and Biotechnology, Koltsovo, Novosibirsk Region, Russia
| | - Tatyana V. Tregubchak
- Vector State Research Center of Virology and Biotechnology, Koltsovo, Novosibirsk Region, Russia
| | - Elena V. Gavrilova
- Vector State Research Center of Virology and Biotechnology, Koltsovo, Novosibirsk Region, Russia
| | - Rinat A. Maksyutov
- Vector State Research Center of Virology and Biotechnology, Koltsovo, Novosibirsk Region, Russia
| | - Alexander B. Ryzhikov
- Vector State Research Center of Virology and Biotechnology, Koltsovo, Novosibirsk Region, Russia
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3
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Oh KH, Mo JS, Bae YJ, Lee SB, Lai VD, Wang SJ, Mo IP. Amino acid substitutions in low pathogenic avian influenza virus strains isolated from wild birds in Korea. Virus Genes 2018; 54:397-405. [PMID: 29582231 DOI: 10.1007/s11262-018-1550-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Accepted: 03/06/2018] [Indexed: 11/28/2022]
Abstract
Wild birds are natural hosts and reservoirs for influenza A viruses. However, many species, such as many waterfowl, are asymptomatic when infected and so facilitate the generation of viral genetic diversity. Mutations of key genes affect the replicability, pathogenicity, transmissibility, and antiviral resistance of influenza A viruses. In this study, we isolated avian influenza (AI) viruses from wild bird fecal samples and analyzed changes in amino acids over time and geographic region to monitor the biological change of the AI virus. Between 2014 and 2016, we collected 38,921 fresh fecal samples from major wild bird habitats located throughout Korea and isolated 123 AI viruses. We subsequently selected 22 amino acid sites to analyze for changes. These sites included ten sites associated with replication, ten sites associated with pathogenicity, three sites associated with transmission, and seven sites associated with antiviral resistance. We found substitution rates of 71.7% at the C38Y amino acid site within the polymerase basic protein 1 (PB1) gene, 66.7% at the D222G site within the hemagglutinin (HA) 1 gene, and 75.6% at the A184 site within the nucleoprotein (NP) gene. Alterations of the PB1, HA1, and NP genes are closely associated with increased pathogenicity in chickens and mammals. The remaining sites of interest exhibited few modifications. In this study, we confirmed that AI viruses circulating among wild birds in Korea consistently exhibit modifications at amino acid sites linked with replication and pathogenicity.
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Affiliation(s)
- Kwang-Hyun Oh
- Avian Disease Laboratory, College of Veterinary Medicine, Chungbuk National University, Cheongju, 28644, Korea
| | - Jong-Suk Mo
- Avian Disease Laboratory, College of Veterinary Medicine, Chungbuk National University, Cheongju, 28644, Korea
| | - Yeon-Ji Bae
- Avian Disease Laboratory, College of Veterinary Medicine, Chungbuk National University, Cheongju, 28644, Korea
| | - Seung-Baek Lee
- Avian Disease Laboratory, College of Veterinary Medicine, Chungbuk National University, Cheongju, 28644, Korea
| | - Van Dam Lai
- Avian Disease Laboratory, College of Veterinary Medicine, Chungbuk National University, Cheongju, 28644, Korea
| | - Seung-Jun Wang
- Environmental Health Research Division, National Institute of Environmental Research, Incheon, Korea
| | - In-Pil Mo
- Avian Disease Laboratory, College of Veterinary Medicine, Chungbuk National University, Cheongju, 28644, Korea.
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A Y161F Hemagglutinin Substitution Increases Thermostability and Improves Yields of 2009 H1N1 Influenza A Virus in Cells. J Virol 2018; 92:JVI.01621-17. [PMID: 29118117 DOI: 10.1128/jvi.01621-17] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 10/27/2017] [Indexed: 12/20/2022] Open
Abstract
Vaccination is the primary strategy for influenza prevention and control. However, egg-based vaccines, the predominant production platform, have several disadvantages, including the emergence of viral antigenic variants that can be induced during egg passage. These limitations have prompted the development of cell-based vaccines, which themselves are not without issue. Most importantly, vaccine seed viruses often do not grow efficiently in mammalian cell lines. Here we aimed to identify novel high-yield signatures for influenza viruses in continuous Madin-Darby canine kidney (MDCK) and Vero cells. Using influenza A(H1N1)pdm09 virus as the testing platform and an integrating error-prone PCR-based mutagenesis strategy, we identified a Y161F mutation in hemagglutinin (HA) that not only enhanced the infectivity of the resultant virus by more than 300-fold but also increased its thermostability without changing its original antigenic properties. The vaccine produced from the Y161F mutant fully protected mice against lethal challenge with wild-type A(H1N1)pdm09. Compared with A(H1N1)pdm09, the Y161F mutant had significantly higher avidity for avian-like and human-like receptor analogs. Of note, the introduction of the Y161F mutation into HA of seasonal H3N2 influenza A virus (IAV) and canine H3N8 IAV also increased yields and thermostability in MDCK cells and chicken embryotic eggs. Thus, residue F161 plays an important role in determining viral growth and thermostability, which could be harnessed to optimize IAV vaccine seed viruses.IMPORTANCE Although a promising complement to current egg-based influenza vaccines, cell-based vaccines have one large challenge: high-yield vaccine seeds for production. In this study, we identified a molecular signature, Y161F, in hemagglutinin (HA) that resulted in increased virus growth in Madin-Darby canine kidney and Vero cells, two cell lines commonly used for influenza vaccine manufacturing. This Y161F mutation not only increased HA thermostability but also enhanced its binding affinity for α2,6- and α2,3-linked Neu5Ac. These results suggest that a vaccine strain bearing the Y161F mutation in HA could potentially increase vaccine yields in mammalian cell culture systems.
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Host-adaptive mechanism of H5N1 avian influenza virus hemagglutininn. Uirusu 2017; 65:187-198. [PMID: 27760917 DOI: 10.2222/jsv.65.187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The H5N1 subtype is a highly pathogenic avian influenza virus currently circulating in birds in parts of Asia and northeast Africa, which has caused fatal human infections since 1997. Continuous circulation of the virus in endemic areas has allowed genetically diverse viruses to emerge, increasing the risk of H5N1 human infection. Although human infections with H5N1 have to date been limited, experimental evidence of the aerosol transmission of mutated viruses in a mammalian infection model has revealed the pandemic potential of H5N1 virus. One of the most important viral factors for host-adaptation of influenza virus is hemagglutinin (HA), which is the principal antigen on the viral surface and is responsible for viral binding to host receptors as well as endosomal membrane fusion. Our recent reports suggest that a fine balance of the HA properties, including receptor binding specificity and pH stability, is crucial for replication in human respiratory epithelia. This review provides an overview of current knowledge on the host-adaptive mechanism of H5N1 virus HA.
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Ali R, Blackburn RM, Kozlakidis Z. Next-Generation Sequencing and Influenza Virus: A Short Review of the Published Implementation Attempts. HAYATI JOURNAL OF BIOSCIENCES 2016. [DOI: 10.1016/j.hjb.2016.12.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022] Open
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Mei K, Liu G, Chen Z, Gao Z, Zhao L, Jin T, Yu X, Chen Q. Deep sequencing reveals the viral adaptation process of environment-derived H10N8 in mice. INFECTION GENETICS AND EVOLUTION 2015; 37:8-13. [PMID: 26477933 DOI: 10.1016/j.meegid.2015.10.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 09/28/2015] [Accepted: 10/13/2015] [Indexed: 02/05/2023]
Abstract
The H10N8 virus was isolated from the water of Dongting Lake, China. Mice were infected while showing no obvious symptoms and replication was restricted to the lungs. When the wild-type virus was serially passaged in the lungs of mice, the resulting viruses became lethal and capable of replication in many other organs. This offered an applicable model for the exploration of viral genome gradual mutation during adaptation in mice. The different passage viruses from mice lung lavage were named P1, P3, P5, and P7, respectively. We sequenced the four viruses using next-generation sequencing (NGS) to analyze the dynamics of the H10N8 viral genome, polymorphism, and amino acid mutation of related proteins. We aimed to demonstrate how a mutant strain of low pathogenicity could become lethal to mice. Using Illumina high-throughput data, we detected the gradual mutations of F277S, C278Q, F611S and L653P in the polymerase acidic (PA) protein, and of L207V and E627K in the PB2 protein during adaptation. Interestingly, many amino acid sites mutated quickly; the others did so more slowly and remained in a heterozygous state for several generations. The PA amino acids S277 and Q278 have previously been found in clinical wild-type strains, including the human-H10N8 isolate in 2013. This demonstrates that the wild-type H10N8 virus had mutated to adapt to mammalian hosts. These data provide important reference information for influenza virus research.
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Affiliation(s)
- Kun Mei
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Hubei 430071, China; Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Hubei 430062, China; Center for Influenza Research and Early-warning (CASCIRE), Chinese Academy of Sciences, Beijing 100101, China
| | - Guang Liu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Zhenzhen Chen
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Hubei 430071, China; Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Hubei 430062, China
| | - Zhimin Gao
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Hubei 430071, China; Center for Influenza Research and Early-warning (CASCIRE), Chinese Academy of Sciences, Beijing 100101, China
| | - Lihua Zhao
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Hubei 430071, China; Center for Influenza Research and Early-warning (CASCIRE), Chinese Academy of Sciences, Beijing 100101, China
| | - Tao Jin
- BGI-Shenzhen, Shenzhen 518083, China
| | - Xiaolan Yu
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Hubei 430062, China.
| | - Quanjiao Chen
- BGI-Shenzhen, Shenzhen 518083, China; Center for Influenza Research and Early-warning (CASCIRE), Chinese Academy of Sciences, Beijing 100101, China.
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8
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Carbone V, Schneider EK, Rockman S, Baker M, Huang JX, Ong C, Cooper MA, Yuriev E, Li J, Velkov T. Molecular Characterisation of the Haemagglutinin Glycan-Binding Specificity of Egg-Adapted Vaccine Strains of the Pandemic 2009 H1N1 Swine Influenza A Virus. Molecules 2015; 20:10415-34. [PMID: 26056814 PMCID: PMC6272818 DOI: 10.3390/molecules200610415] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 06/01/2015] [Indexed: 12/14/2022] Open
Abstract
The haemagglutinin (HA) glycan binding selectivity of H1N1 influenza viruses is an important determinant for the host range of the virus and egg-adaption during vaccine production. This study integrates glycan binding data with structure-recognition models to examine the impact of the K123N, D225G and Q226R mutations (as seen in the HA of vaccine strains of the pandemic 2009 H1N1 swine influenza A virus). The glycan-binding selectivity of three A/California/07/09 vaccine production strains, and purified recombinant A/California/07/09 HAs harboring these mutations was examined via a solid-phase ELISA assay. Wild-type A/California/07/09 recombinant HA bound specifically to α2,6-linked sialyl-glycans, with no affinity for the α2,3-linked sialyl-glycans in the array. In contrast, the vaccine virus strains and recombinant HA harboring the Q226R HA mutation displayed a comparable pattern of highly specific binding to α2,3-linked sialyl-glycans, with a negligible affinity for α2,6-linked sialyl-glycans. The D225G A/California/07/09 recombinant HA displayed an enhanced binding affinity for both α2,6- and α2,3-linked sialyl-glycans in the array. Notably its α2,6-glycan affinity was generally higher compared to its α2,3-glycan affinity, which may explain why the double mutant was not naturally selected during egg-adaption of the virus. The K123N mutation which introduces a glycosylation site proximal to the receptor binding site, did not impact the α2,3/α2,6 glycan selectivity, however, it lowered the overall glycan binding affinity of the HA; suggesting glycosylation may interfere with receptor binding. Docking models and 'per residues' scoring were employed to provide a structure-recognition rational for the experimental glycan binding data. Collectively, the glycan binding data inform future vaccine design strategies to introduce the D225G or Q226R amino acid substitutions into recombinant H1N1 viruses.
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Affiliation(s)
- Vincenzo Carbone
- AgResearch Limited, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North 4442, New Zealand.
| | - Elena K Schneider
- Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville 3052, Victoria, Australia.
| | - Steve Rockman
- CSL Limited Poplar Road, Parkville 3052, Victoria, Australia.
| | - Mark Baker
- Priority Research Centre in Reproductive Science, School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia.
| | - Johnny X Huang
- Institute for Molecular Bioscience, University of Queensland, 306 Carmody Road St Lucia, QLD 4072, Brisbane, Australia.
| | - Chi Ong
- CSL Limited Poplar Road, Parkville 3052, Victoria, Australia.
| | - Matthew A Cooper
- Institute for Molecular Bioscience, University of Queensland, 306 Carmody Road St Lucia, QLD 4072, Brisbane, Australia.
| | - Elizabeth Yuriev
- Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville 3052, Victoria, Australia.
| | - Jian Li
- Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville 3052, Victoria, Australia.
| | - Tony Velkov
- Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville 3052, Victoria, Australia.
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He L, Jiang K, Wu Q, Duan Z, Xu H, Liu J, Cui Z, Gu M, Wang X, Liu X, Liu X. Two amino acid substitutions in the haemagglutinin of the 2009 pandemic H1N1 virus decrease direct-contact transmission in guinea pigs. J Gen Virol 2014; 95:2612-2617. [PMID: 25135885 DOI: 10.1099/vir.0.067694-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The 2009 pandemic H1N1 influenza A virus spread across the globe and caused the first influenza pandemic of the 21st century. Many of the molecular factors that contributed to the airborne transmission of this pandemic virus have been determined; however, the direct-contact transmission of this virus remains poorly understood. In this study, we report that a combination of two mutations (N159D and Q226R) in the haemagglutinin (HA) protein of the representative 2009 H1N1 influenza virus A/California/04/2009 (CA04) caused a switch in receptor binding preference from the α2,6-sialoglycan to the α2,3-sialoglycan receptor, and decreased the binding intensities for both glycans. In conjunction with a significantly decreased replication efficiency in the nasal epithelium, this limited human receptor binding affinity resulted in inefficient direct-contact transmission of CA04 between guinea pigs. Our findings highlight the role of the HA gene in the transmission of the influenza virus.
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Affiliation(s)
- Liang He
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, PR China
| | - Kaijun Jiang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, PR China
| | - Qiwen Wu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, PR China
| | - Zhiqiang Duan
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, PR China
| | - Haixu Xu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, PR China
| | - Jingjing Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, PR China
| | - Zhu Cui
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, PR China
| | - Min Gu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, PR China
| | - Xiaoquan Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, PR China
| | - Xiaowen Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, PR China
| | - Xiufan Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, PR China
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10
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Resende PC, Motta FC, Oliveira MDLA, Gregianini TS, Fernandes SB, Cury ALF, do Carmo D. Rosa M, Souza TML, Siqueira MM. Polymorphisms at residue 222 of the hemagglutinin of pandemic influenza A(H1N1)pdm09: association of quasi-species to morbidity and mortality in different risk categories. PLoS One 2014; 9:e92789. [PMID: 24667815 PMCID: PMC3965456 DOI: 10.1371/journal.pone.0092789] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 02/25/2014] [Indexed: 02/05/2023] Open
Abstract
The D222G substitution in the hemagglutinin (HA) gene of the pandemic influenza A(H1N1)pdm09 virus has been identified as a potential virulence marker, because this change allows for virus invasion deeper into the respiratory tract. In this study, we analyzed D, G and N polymorphisms at residue 222 by pyrosequencing (PSQ). We initially analyzed 401 samples from Brazilian patients. These were categorized with respect to clinical conditions due to influenza infection (mild, serious or fatal) and sub-stratified by risky factors. The frequency of mixed population of virus, with more than one polymorphism at residue 222, was significantly higher in serious (10.6%) and fatal (46.7%) influenza cases, whereas those who showed mild influenza infections were all infected by D222 wild-type. Mixtures of quasi-species showed a significant association of mortality, especially for those with risk factors, in special pregnant women. These results not only reinforce the association between D222G substitution and influenza A(H1N1)pdm09-associated morbidity and mortality, but also add the perspective that a worse clinical prognosis is most likely correlated with mixtures of quasi-species at this HA residue. Therefore, quasi-species may have a critical and underestimated role in influenza-related clinical outcomes.
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Affiliation(s)
- Paola Cristina Resende
- Laboratório de Vírus Respiratórios e do Sarampo, Instituto Oswaldo Cruz/ FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
- * E-mail:
| | - Fernando C. Motta
- Laboratório de Vírus Respiratórios e do Sarampo, Instituto Oswaldo Cruz/ FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Maria de Lourdes A. Oliveira
- Laboratório de Vírus Respiratórios e do Sarampo, Instituto Oswaldo Cruz/ FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Tatiana S. Gregianini
- Laboratório Central de Saúde Pública do Estado do Rio de Grande do Sul -Fundação estadual de produção e pesquisa em saúde seção de virologia, Porto Alegre, Rio Grande do Sul, Brazil
| | - Sandra B. Fernandes
- Laboratório Central de Saúde Pública do Estado de Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Ana Luisa F. Cury
- Laboratório Central de Saúde Pública do Estado de Minas Gerais/Instituto Octávio Magalhães e Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | | | - Thiago Moreno L. Souza
- Laboratório de Vírus Respiratórios e do Sarampo, Instituto Oswaldo Cruz/ FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marilda M. Siqueira
- Laboratório de Vírus Respiratórios e do Sarampo, Instituto Oswaldo Cruz/ FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
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Corcioli F, Arvia R, Pierucci F, Clausi V, Bonizzoli M, Peris A, Azzi A. HA222 polymorphism in Influenza A(H1N1) 2009 isolates from Intensive Care Units and ambulatory patients during three influenza seasons. Virus Res 2014; 180:39-42. [DOI: 10.1016/j.virusres.2013.12.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Revised: 12/05/2013] [Accepted: 12/11/2013] [Indexed: 10/25/2022]
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12
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Yasugi M, Kubota-Koketsu R, Yamashita A, Kawashita N, Du A, Misaki R, Kuhara M, Boonsathorn N, Fujiyama K, Okuno Y, Nakaya T, Ikuta K. Emerging antigenic variants at the antigenic site Sb in pandemic A(H1N1)2009 influenza virus in Japan detected by a human monoclonal antibody. PLoS One 2013; 8:e77892. [PMID: 24147093 PMCID: PMC3797713 DOI: 10.1371/journal.pone.0077892] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 09/05/2013] [Indexed: 11/18/2022] Open
Abstract
The swine-origin pandemic A(H1N1)2009 virus, A(H1N1)pdm09, is still circulating in parts of the human population. To monitor variants that may escape from vaccination specificity, antigenic characterization of circulating viruses is important. In this study, a hybridoma clone producing human monoclonal antibody against A(H1N1)pdm09, designated 5E4, was prepared using peripheral lymphocytes from a vaccinated volunteer. The 5E4 showed viral neutralization activity and inhibited hemagglutination. 5E4 escape mutants harbored amino acid substitutions (A189T and D190E) in the hemagglutinin (HA) protein, suggesting that 5E4 recognized the antigenic site Sb in the HA protein. To study the diversity of Sb in A(H1N1)pdm09, 58 viral isolates were obtained during the 2009/10 and 2010/11 winter seasons in Osaka, Japan. Hemagglutination-inhibition titers were significantly reduced against 5E4 in the 2010/11 compared with the 2009/10 samples. Viral neutralizing titers were also significantly decreased in the 2010/11 samples. By contrast, isolated samples reacted well to ferret anti-A(H1N1)pdm09 serum from both seasons. Nonsynonymous substitution rates revealed that the variant Sb and Ca2 sequences were being positively selected between 2009/10 and 2010/11. In 7,415 HA protein sequences derived from GenBank, variants in the antigenic sites Sa and Sb increased significantly worldwide from 2009 to 2013. These results indicate that the antigenic variants in Sb are likely to be in global circulation currently.
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Affiliation(s)
- Mayo Yasugi
- Department of Virology, Research Institute for Microbial Diseases (RIMD), Osaka University, Suita, Osaka, Japan
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka, Japan
- The Japan Science and Technology Agency/Japan International Cooperation Agency, Science and Technology Research Partnership for Sustainable Development (JST/JICA, SATREPS), Tokyo, Japan
| | - Ritsuko Kubota-Koketsu
- Department of Virology, Research Institute for Microbial Diseases (RIMD), Osaka University, Suita, Osaka, Japan
- Kanonji Institute, The Research Foundation for Microbial Diseases of Osaka University, Kanonji, Kagawa, Japan
- The Japan Science and Technology Agency/Japan International Cooperation Agency, Science and Technology Research Partnership for Sustainable Development (JST/JICA, SATREPS), Tokyo, Japan
| | - Akifumi Yamashita
- Department of Genome Informatics, RIMD, Osaka University, Suita, Osaka, Japan
| | - Norihito Kawashita
- Department of Environmental Pharmacometrics, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
| | - Anariwa Du
- Department of Virology, Research Institute for Microbial Diseases (RIMD), Osaka University, Suita, Osaka, Japan
- The Japan Science and Technology Agency/Japan International Cooperation Agency, Science and Technology Research Partnership for Sustainable Development (JST/JICA, SATREPS), Tokyo, Japan
| | - Ryo Misaki
- Applied Microbiology Laboratory, International Center of Biotechnology, Osaka University, Suita, Osaka, Japan
- The Japan Science and Technology Agency/Japan International Cooperation Agency, Science and Technology Research Partnership for Sustainable Development (JST/JICA, SATREPS), Tokyo, Japan
| | - Motoki Kuhara
- Ina Laboratory, Medical & Biological Laboratories Corporation, Ltd., Ina, Nagano, Japan
- The Japan Science and Technology Agency/Japan International Cooperation Agency, Science and Technology Research Partnership for Sustainable Development (JST/JICA, SATREPS), Tokyo, Japan
| | - Naphatsawan Boonsathorn
- Department of Medical Sciences, Ministry of Public Health, Muang, Nonthaburi, Thailand
- The Japan Science and Technology Agency/Japan International Cooperation Agency, Science and Technology Research Partnership for Sustainable Development (JST/JICA, SATREPS), Tokyo, Japan
| | - Kazuhito Fujiyama
- Applied Microbiology Laboratory, International Center of Biotechnology, Osaka University, Suita, Osaka, Japan
- The Japan Science and Technology Agency/Japan International Cooperation Agency, Science and Technology Research Partnership for Sustainable Development (JST/JICA, SATREPS), Tokyo, Japan
| | - Yoshinobu Okuno
- Kanonji Institute, The Research Foundation for Microbial Diseases of Osaka University, Kanonji, Kagawa, Japan
| | - Takaaki Nakaya
- International Research Center for Infectious Diseases, RIMD, Osaka University, Suita, Osaka, Japan
- The Japan Science and Technology Agency/Japan International Cooperation Agency, Science and Technology Research Partnership for Sustainable Development (JST/JICA, SATREPS), Tokyo, Japan
| | - Kazuyoshi Ikuta
- Department of Virology, Research Institute for Microbial Diseases (RIMD), Osaka University, Suita, Osaka, Japan
- The Japan Science and Technology Agency/Japan International Cooperation Agency, Science and Technology Research Partnership for Sustainable Development (JST/JICA, SATREPS), Tokyo, Japan
- * E-mail:
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13
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Jiménez-Alberto A, Alvarado-Facundo E, Ribas-Aparicio RM, Castelán-Vega JA. Analysis of adaptation mutants in the hemagglutinin of the influenza A(H1N1)pdm09 virus. PLoS One 2013; 8:e70005. [PMID: 23894575 PMCID: PMC3720954 DOI: 10.1371/journal.pone.0070005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Accepted: 06/17/2013] [Indexed: 12/17/2022] Open
Abstract
Hemagglutinin is the major surface glycoprotein of influenza viruses. It participates in the initial steps of viral infection through receptor binding and membrane fusion events. The influenza pandemic of 2009 provided a unique scenario to study virus evolution. We performed molecular dynamics simulations with four hemagglutinin variants that appeared throughout the 2009 influenza A (H1N1) pandemic. We found that variant 1 (S143G, S185T) likely arose to avoid immune recognition. Variant 2 (A134T), and variant 3 (D222E, P297S) had an increased binding affinity for the receptor. Finally, variant 4 (E374K) altered hemagglutinin stability in the vicinity of the fusion peptide. Variants 1 and 4 have become increasingly predominant, while variants 2 and 3 declined as the pandemic progressed. Our results show some of the different strategies that the influenza virus uses to adapt to the human host and provide an example of how selective pressure drives antigenic drift in viral proteins.
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MESH Headings
- Adaptation, Physiological/genetics
- Hemagglutinin Glycoproteins, Influenza Virus/chemistry
- Hemagglutinin Glycoproteins, Influenza Virus/genetics
- Hemagglutinin Glycoproteins, Influenza Virus/immunology
- Hemagglutinin Glycoproteins, Influenza Virus/metabolism
- Humans
- Influenza A Virus, H1N1 Subtype/genetics
- Influenza A Virus, H1N1 Subtype/immunology
- Influenza A Virus, H1N1 Subtype/metabolism
- Influenza A Virus, H1N1 Subtype/physiology
- Influenza Pandemic, 1918-1919
- Influenza, Human/epidemiology
- Influenza, Human/virology
- Molecular Dynamics Simulation
- Molecular Epidemiology
- Static Electricity
- Surface Properties
- Thermodynamics
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Affiliation(s)
- Alicia Jiménez-Alberto
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Distrito Federal, Mexico City, Mexico
| | - Esmeralda Alvarado-Facundo
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Distrito Federal, Mexico City, Mexico
- Center for Biologics Evaluation and Research, US Food and Drug Administration, Bethesda, Maryland, United States of America
| | - Rosa María Ribas-Aparicio
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Distrito Federal, Mexico City, Mexico
| | - Juan A. Castelán-Vega
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Distrito Federal, Mexico City, Mexico
- * E-mail:
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14
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A (H1N1) pdm09 HA D222 variants associated with severity and mortality in patients during a second wave in Mexico. Virol J 2013; 10:41. [PMID: 23369604 PMCID: PMC3583722 DOI: 10.1186/1743-422x-10-41] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Accepted: 01/28/2013] [Indexed: 12/02/2022] Open
Abstract
Background Pandemic type A (H1N1) influenza arose in early 2009, probably in Mexico and the United States, and reappeared in North America in September for seven more months. An amino acid substitution in the hemagglutinin (HA), D222G, has been reported in a significant proportion of patients with a severe and fatal outcome. We studied the prevalence of HA222 substitutions in patients in Mexico during the second wave and its association with clinical outcome and pathogenicity in a mouse model. Methods The nucleotide sequences of hemagglutinin (HA) from viruses collected from 77 patients were determined including 50 severe and fatal cases and 27 ambulatory cases. Deep sequencing was done on 5 samples from severe or fatal cases in order to determine the quasispecies proportion. Weight loss and mortality due to infection with cultured influenza viruses were analyzed in a mouse model. Results Viruses from 14 out of 50 hospitalized patients (28%) had a non aspartic acid residue at the HA 222 position (nD222), while all 27 ambulatory patients had D222 (p = 0.0014). G222 was detected as sole species or in coexistence with N222 and D222 in 12 patients with severe disease including 8 who died. N222 in coexistence with D222 was detected in 1 patient who died and co-occurrence of A222 and V222, together with D222, was detected in another patient who died. The patients with a nD222 residue had higher mortality (71.4%), compared to the group with only D222 (22.2%, p = 0.0008). Four of the 14 viruses from hospitalized patients were cultured and intranasally infected into mice. Two viruses with G222 were lethal while a third virus, with G222, caused only mild illness in mice similar to the fourth virus that contained D222. Conclusions We confirm the elevated incidence of HA222 (H1N1)pdm09 variants in severe disease and mortality. Both clinical and mouse infection data support the idea that nD222 mutations contribute to increased severity of disease but additional determinants in disease outcome may be present.
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Selleri M, Piralla A, Rozera G, Giombini E, Bartolini B, Abbate I, Campanini G, Rovida F, Dossena L, Capobianchi MR, Baldanti F. Detection of haemagglutinin D222 polymorphisms in influenza A(H1N1)pdm09-infected patients by ultra-deep pyrosequencing. Clin Microbiol Infect 2012; 19:668-73. [PMID: 22862843 DOI: 10.1111/j.1469-0691.2012.03984.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
This study was aimed at establishing the genetic heterogeneity of influenza virus haemagglutinin (HA) gene quasi-species and the polymorphisms at codon 222, by application of ultra-deep pyrosequencing (UDPS) to respiratory samples from patients hospitalized for influenza A(H1N1)pdm09 infection, presenting with severe or moderate-mild disease. HA diversity was significantly higher in samples collected from patients with severe manifestations than in those from patients with moderate-mild manifestations (p 0.02). D222 polymorphism was detected in 40.7% of patients by UDPS, and in only 7.1% by Sanger sequencing. D222E, D222G, D222N and D222A were observed in 37.0%, 11.1%, 7.4% and 3.7% of patients, respectively; 10.7% of samples harboured more than two variants. The relative frequency of each single variant showed a wide range of intrapatient variation. D222G/N/A were detected, as either minor or predominant variants, only in severe cases, whereas D222E was equally represented in severe and moderate-mild infections. Other amino acid variants were observed at different positions within the analysed HA fragment. Consistent with higher heterogeneity, non-D222 variants were more frequently detected in severe cases than in moderate-mild cases. In addition, seven non-D222 mutations carried by minority variants, not previously described, were observed.
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Affiliation(s)
- M Selleri
- Laboratory of Virology, National Institute for Infectious Diseases INMI IRCCS L. Spallanzani, Rome, Italy
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Haemagglutinin D222G mutation found in a fatal case of pandemic (H1N1) flu in Tunisia. Arch Virol 2012; 157:1813-4. [PMID: 22684533 DOI: 10.1007/s00705-012-1349-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Accepted: 04/20/2012] [Indexed: 10/28/2022]
Abstract
Recently, the D222G substitution was observed in the HA of pandemic (H1N1) 2009 viruses isolated from fatal cases in several countries. We made a similar observation in one fatal case in Tunisia showing a D222G substitution in a virus isolate. The man was 47 years old and had no other subjacent pathologies or any known risk factors. He died after three days, suffering from severe respiratory symptoms of flu. The causal link of the D222G substitution in Tunisia with virulence must be verified. Further study is warranted to elucidate the intriguing relationship between the D222G substitution and severe disease. Constant molecular surveillance is important to monitor the pathogenicity of circulating strains and evaluate vaccine efficacy.
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17
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Ramadhany R, Yasugi M, Nakamura S, Daidoji T, Watanabe Y, Takahashi K, Ikuta K, Nakaya T. Tropism of Pandemic 2009 H1N1 Influenza a Virus. Front Microbiol 2012; 3:128. [PMID: 22493594 PMCID: PMC3318191 DOI: 10.3389/fmicb.2012.00128] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Accepted: 03/19/2012] [Indexed: 11/13/2022] Open
Abstract
Substitutions at the receptor-binding site of the pandemic H1N1 2009 influenza A virus (H1N1pdm) hemagglutinin (HA) gene may be critical in determining whether a virus binds to human or avian receptors. Previous reports suggest that HA Gly222 and/or Arg223 allow viruses to bind preferentially to the α2,3-linked sialic acid found in avian species. We also demonstrated that serial passaging of influenza A virus in embryonated chicken eggs increased viral growth 32- to 64-fold, coincident with the increased prevalence of Gly222 or Arg223 in HA protein (Yasugi et al., 2012). In this study, we showed that the minor genotype of α2,3-linkage-tropic viruses in upper airways became dominant after passaging through chicken eggs. Viruses possessing HA containing N125D-Q223R, N125D-D187E-Q223R, K119N-D222G, and K119N-N129S-D222G, were detected in both clinical specimens and egg-passaged samples. These results might suggest that egg-adapted viruses, likely represented by α2,3-linkage-tropic virus, were also present in human upper airways as a minor population and transmitted in humans during the outbreak of H1N1pdm.
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Affiliation(s)
- Ririn Ramadhany
- International Research Center for Infectious Diseases, Research Institute for Microbial Diseases, Osaka University Suita, Osaka, Japan
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