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Zhao F, Xu F, Liu X, Hu Y, Wei L, Fan Z, Wang L, Huang Y, Mei S, Guo L, Yang L, Cen S, Wang J, Liang C, Guo F. SERINC5 restricts influenza virus infectivity. PLoS Pathog 2022; 18:e1010907. [PMID: 36223419 PMCID: PMC9591065 DOI: 10.1371/journal.ppat.1010907] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 10/24/2022] [Accepted: 09/30/2022] [Indexed: 11/16/2022] Open
Abstract
SERINC5 is a multi-span transmembrane protein that is incorporated into HIV-1 particles in producing cells and inhibits HIV-1 entry. Multiple retroviruses like HIV-1, equine infectious anemia virus and murine leukemia virus are subject to SERINC5 inhibition, while HIV-1 pseudotyped with envelope glycoproteins of vesicular stomatitis virus and Ebola virus are resistant to SERINC5. The antiviral spectrum and the underlying mechanisms of SERINC5 restriction are not completely understood. Here we show that SERINC5 inhibits influenza A virus infection by targeting virus-cell membrane fusion at an early step of infection. Further results show that different influenza hemagglutinin (HA) subtypes exhibit diverse sensitivities to SERINC5 restriction. Analysis of the amino acid sequences of influenza HA1 strains indicates that HA glycosylation sites correlate with the sensitivity of influenza HA to SERINC5, and the inhibitory effect of SERINC5 was lost when certain HA glycosylation sites were mutated. Our study not only expands the antiviral spectrum of SERINC5, but also reveals the role of viral envelope glycosylation in resisting SERINC5 restriction.
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Affiliation(s)
- Fei Zhao
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Fengwen Xu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Xiaoman Liu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Yamei Hu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Liang Wei
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Zhangling Fan
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Liming Wang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Yu Huang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Shan Mei
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Li Guo
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Long Yang
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Shan Cen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Jianwei Wang
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
- * E-mail: (JW); (CL); (FG)
| | - Chen Liang
- McGill University AIDS Centre, Lady Davis Institute, Jewish General Hospital, Montreal, Quebec, Canada
- * E-mail: (JW); (CL); (FG)
| | - Fei Guo
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
- * E-mail: (JW); (CL); (FG)
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Nabakooza G, Galiwango R, Frost SDW, Kateete DP, Kitayimbwa JM. Molecular Epidemiology and Evolutionary Dynamics of Human Influenza Type-A Viruses in Africa: A Systematic Review. Microorganisms 2022; 10:900. [PMID: 35630344 PMCID: PMC9145646 DOI: 10.3390/microorganisms10050900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 02/01/2023] Open
Abstract
Genomic characterization of circulating influenza type-A viruses (IAVs) directs the selection of appropriate vaccine formulations and early detection of potentially pandemic virus strains. However, longitudinal data on the genomic evolution and transmission of IAVs in Africa are scarce, limiting Africa's benefits from potential influenza control strategies. We searched seven databases: African Journals Online, Embase, Global Health, Google Scholar, PubMed, Scopus, and Web of Science according to the PRISMA guidelines for studies that sequenced and/or genomically characterized Africa IAVs. Our review highlights the emergence and diversification of IAVs in Africa since 1993. Circulating strains continuously acquired new amino acid substitutions at the major antigenic and potential N-linked glycosylation sites in their hemagglutinin proteins, which dramatically affected vaccine protectiveness. Africa IAVs phylogenetically mixed with global strains forming strong temporal and geographical evolution structures. Phylogeographic analyses confirmed that viral migration into Africa from abroad, especially South Asia, Europe, and North America, and extensive local viral mixing sustained the genomic diversity, antigenic drift, and persistence of IAVs in Africa. However, the role of reassortment and zoonosis remains unknown. Interestingly, we observed substitutions and clades and persistent viral lineages unique to Africa. Therefore, Africa's contribution to the global influenza ecology may be understated. Our results were geographically biased, with data from 63% (34/54) of African countries. Thus, there is a need to expand influenza surveillance across Africa and prioritize routine whole-genome sequencing and genomic analysis to detect new strains early for effective viral control.
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Affiliation(s)
- Grace Nabakooza
- Department of Immunology and Molecular Biology, Makerere University, Old Mulago Hill Road, P.O. Box 7072, Kampala 256, Uganda;
- UVRI Centre of Excellence in Infection and Immunity Research and Training (MUII-Plus), Makerere University, Plot No: 51-59 Nakiwogo Road, P.O. Box 49, Entebbe 256, Uganda; (R.G.); (J.M.K.)
| | - Ronald Galiwango
- UVRI Centre of Excellence in Infection and Immunity Research and Training (MUII-Plus), Makerere University, Plot No: 51-59 Nakiwogo Road, P.O. Box 49, Entebbe 256, Uganda; (R.G.); (J.M.K.)
- Centre for Computational Biology, Uganda Christian University, Plot 67-173, Bishop Tucker Road, P.O. Box 4, Mukono 256, Uganda
- African Center of Excellence in Bioinformatics and Data Intensive Sciences, Infectious Diseases Institute, Makerere University, Kampala 256, Uganda
| | - Simon D. W. Frost
- Microsoft Research, Redmond, 14820 NE 36th Street, Washington, DC 98052, USA;
- London School of Hygiene & Tropical Medicine (LSHTM), University of London, Keppel Street, Bloomsbury, London WC1E7HT, UK
| | - David P. Kateete
- Department of Immunology and Molecular Biology, Makerere University, Old Mulago Hill Road, P.O. Box 7072, Kampala 256, Uganda;
- UVRI Centre of Excellence in Infection and Immunity Research and Training (MUII-Plus), Makerere University, Plot No: 51-59 Nakiwogo Road, P.O. Box 49, Entebbe 256, Uganda; (R.G.); (J.M.K.)
| | - John M. Kitayimbwa
- UVRI Centre of Excellence in Infection and Immunity Research and Training (MUII-Plus), Makerere University, Plot No: 51-59 Nakiwogo Road, P.O. Box 49, Entebbe 256, Uganda; (R.G.); (J.M.K.)
- Centre for Computational Biology, Uganda Christian University, Plot 67-173, Bishop Tucker Road, P.O. Box 4, Mukono 256, Uganda
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Ivan FX, Zhou X, Lau SH, Rashid S, Teo JSM, Lee HK, Koay ES, Chan KP, Leo YS, Chen MIC, Kwoh CK, Chow VT. Molecular insights into evolution, mutations and receptor-binding specificity of influenza A and B viruses from outpatients and hospitalized patients in Singapore. Int J Infect Dis 2020; 90:84-96. [PMID: 31669593 DOI: 10.1016/j.ijid.2019.10.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 10/16/2019] [Accepted: 10/18/2019] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND This study compared the genomes of influenza viruses that caused mild infections among outpatients and severe infections among hospitalized patients in Singapore, and characterized their molecular evolution and receptor-binding specificity. METHODS The complete genomes of influenza A/H1N1, A/H3N2 and B viruses that caused mild infections among outpatients and severe infections among inpatients in Singapore during 2012-2015 were sequenced and characterized. Using various bioinformatics approaches, we elucidated their evolutionary, mutational and structural patterns against the background of global and vaccine strains. RESULTS The phylogenetic trees of the 8 gene segments revealed that the outpatient and inpatient strains overlapped with representative global and vaccine strains. We observed a cluster of inpatients with A/H3N2 strains that were closely related to vaccine strain A/Texas/50/2012(H3N2). Several protein sites could accurately discriminate between outpatient versus inpatient strains, with site 221 in neuraminidase (NA) achieving the highest accuracy for A/H3N2. Interestingly, amino acid residues of inpatient but not outpatient isolates at those sites generally matched the corresponding residues in vaccine strains, except at site 145 of hemagglutinin (HA). This would be especially relevant for future surveillance of A/H3N2 strains in relation to their antigenicity and virulence. Furthermore, we observed a trend in which the HA proteins of influenza A/H3N2 and A/H1N1 exhibited enhanced ability to bind both avian and human host cell receptors. In contrast, the binding ability to each receptor was relatively stable for the HA of influenza B. CONCLUSIONS Overall, our findings extend our understanding of the molecular and structural evolution of influenza virus strains in Singapore within the global context of these dynamic viruses.
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Affiliation(s)
- Fransiskus X Ivan
- School of Computer Science and Engineering, Nanyang Technological University, Singapore
| | - Xinrui Zhou
- School of Computer Science and Engineering, Nanyang Technological University, Singapore
| | - Suk Hiang Lau
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Shamima Rashid
- School of Computer Science and Engineering, Nanyang Technological University, Singapore
| | - Jasmine S M Teo
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Hong Kai Lee
- Molecular Diagnosis Centre, National University Hospital, Singapore; Singapore Immunology Network, Agency for Science, Technology and Research, Singapore
| | - Evelyn S Koay
- Molecular Diagnosis Centre, National University Hospital, Singapore; Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Kwai Peng Chan
- Department of Pathology, Singapore General Hospital, Singapore
| | - Yee Sin Leo
- National Centre for Infectious Diseases, Singapore
| | - Mark I C Chen
- National Centre for Infectious Diseases, Singapore; Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Chee Keong Kwoh
- School of Computer Science and Engineering, Nanyang Technological University, Singapore.
| | - Vincent T Chow
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
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Ushirogawa H, Naito T, Tokunaga H, Tanaka T, Nakano T, Terada K, Ohuchi M, Saito M. Re-emergence of H3N2 strains carrying potential neutralizing mutations at the N-linked glycosylation site at the hemagglutinin head, post the 2009 H1N1 pandemic. BMC Infect Dis 2016; 16:380. [PMID: 27503338 PMCID: PMC4977674 DOI: 10.1186/s12879-016-1738-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 07/28/2016] [Indexed: 12/19/2022] Open
Abstract
Background Seasonally prevalent H1N1 and H3N2 influenza A viruses have evolved by antigenic drift; this evolution has resulted in the acquisition of asparagine (N)-linked glycosylation sites (NGSs) in the globular head of hemagglutinin (HA), thereby affecting the antigenic and receptor-binding properties, as well as virulence. An epidemiological survey indicated that although the traditional seasonal H1N1 strain had disappeared, H3N2 became predominant again in the seasons (2010–11 and 2011–12) immediately following the H1N1 pandemic of 2009. Interestingly, although the 2009 pandemic H1N1 strain (H1N1pdm09) lacks additional NGSs, clinically isolated H3N2 strains obtained during these seasons gained N (Asn) residues at positions 45 and 144 of HA that forms additional NGSs. Methods To investigate whether these NGSs are associated with re-emergence of H3N2 within the subtype, we tested the effect of amino acid substitutions on neutralizing activity by using the antisera raised against H3N2 strains with or without additional NGSs. Furthermore, because the N residue at position 144 of HA was identified as the site of mismatch between the vaccine and epidemic strains of 2011–2012, we generated mutant viruses by reverse genetics and tested the functional importance of this particular NGS for antibody-mediated neutralization by intranasal inoculation of mice. Results The results indicated that amino acid substitution at residue 144 significantly affected neutralization activity, acting as an escape mutation. Conclusions Our data suggest that the newly acquired NGSs in the HA globular head may play an important role in the re-emergence of endemic seasonal H3N2 strain by aiding the escape from humoral immunity.
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Affiliation(s)
- Hiroshi Ushirogawa
- Department of Microbiology, Kawasaki Medical School, 577 Matsushima, Kurashiki, Okayama, 701-0192, Japan
| | - Tadasuke Naito
- Department of Microbiology, Kawasaki Medical School, 577 Matsushima, Kurashiki, Okayama, 701-0192, Japan
| | - Hirotoshi Tokunaga
- Department of Hematology, Kawasaki Medical School, 577 Matsushima, Kurashiki, Okayama, 701-0192, Japan
| | - Toshihiro Tanaka
- Department of Pediatrics, Shizuoka Kosei Hospital, 23 Kitaban-cho, Aoi-ku, Shizuoka, 420-8623, Japan
| | - Takashi Nakano
- Department of Pediatrics, Kawasaki Medical School, 577 Matsushima, Kurashiki, Okayama, 701-0192, Japan
| | - Kihei Terada
- Department of Pediatrics, Kawasaki Medical School, 577 Matsushima, Kurashiki, Okayama, 701-0192, Japan
| | - Masanobu Ohuchi
- Department of Microbiology, Kawasaki Medical School, 577 Matsushima, Kurashiki, Okayama, 701-0192, Japan
| | - Mineki Saito
- Department of Microbiology, Kawasaki Medical School, 577 Matsushima, Kurashiki, Okayama, 701-0192, Japan.
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Hrincius ER, Liedmann S, Finkelstein D, Vogel P, Gansebom S, Samarasinghe AE, You D, Cormier SA, McCullers JA. Acute Lung Injury Results from Innate Sensing of Viruses by an ER Stress Pathway. Cell Rep 2015; 11:1591-603. [PMID: 26051937 PMCID: PMC4682876 DOI: 10.1016/j.celrep.2015.05.012] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 01/25/2015] [Accepted: 05/07/2015] [Indexed: 01/22/2023] Open
Abstract
Incursions of new pathogenic viruses into humans from animal reservoirs are occurring with alarming frequency. The molecular underpinnings of immune recognition, host responses, and pathogenesis in this setting are poorly understood. We studied pandemic influenza viruses to determine the mechanism by which increasing glycosylation during evolution of surface proteins facilitates diminished pathogenicity in adapted viruses. ER stress during infection with poorly glycosylated pandemic strains activated the unfolded protein response, leading to inflammation, acute lung injury, and mortality. Seasonal strains or viruses engineered to mimic adapted viruses displaying excess glycans on the hemagglutinin did not cause ER stress, allowing preservation of the lungs and survival. We propose that ER stress resulting from recognition of non-adapted viruses is utilized to discriminate “non-self” at the level of protein processing and to activate immune responses, with unintended consequences on pathogenesis. Understanding this mechanism should improve strategies for treating acute lung injury from zoonotic viral infections. ER stress pathways can mediate immune recognition of zoonotic viruses Glycosylation status of viral proteins regulates activation of ER stress Acute lung injury from pandemic influenza viruses is dependent on this activation Adaptation through glycan addition mediates immune escape of seasonal IAV
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Affiliation(s)
- Eike R Hrincius
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Swantje Liedmann
- Institute of Molecular Virology (IMV), University of Muenster, Muenster 48149, Germany
| | - David Finkelstein
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Peter Vogel
- Department of Veterinary Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Shane Gansebom
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Amali E Samarasinghe
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN 38163, USA; Children's Foundation Research Institute, Le Bonheur Children's Hospital, Memphis, TN 38103, USA
| | - Dahui You
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN 38163, USA; Children's Foundation Research Institute, Le Bonheur Children's Hospital, Memphis, TN 38103, USA
| | - Stephania A Cormier
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN 38163, USA; Children's Foundation Research Institute, Le Bonheur Children's Hospital, Memphis, TN 38103, USA
| | - Jonathan A McCullers
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN 38163, USA; Children's Foundation Research Institute, Le Bonheur Children's Hospital, Memphis, TN 38103, USA.
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Sedzik J, Jastrzebski JP, Grandis M. Glycans of myelin proteins. J Neurosci Res 2014; 93:1-18. [PMID: 25213400 DOI: 10.1002/jnr.23462] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2014] [Revised: 06/19/2014] [Accepted: 07/07/2014] [Indexed: 01/04/2023]
Abstract
Human P0 is the main myelin glycoprotein of the peripheral nervous system. It can bind six different glycans, all linked to Asn(93) , the unique glycosylation site. Other myelin glycoproteins, also with a single glycosylation site (PMP22 at Asn(36) , MOG at Asn(31) ), bind only one glycan. The MAG has 10 glycosylation sites; the glycoprotein OMgp has 11 glycosylation sites. Aside from P0, no comprehensive data are available on other myelin glycoproteins. Here we review and analyze all published data on the physicochemical structure of the glycans linked to P0, PMP22, MOG, and MAG. Most data concern bovine P0, whose glycan moieties have an MW ranging from 1,294.56 Da (GP3) to 2,279.94 Da (GP5). The pI of glycosylated P0 protein varies from pH 9.32 to 9.46. The most charged glycan is MS2 containing three sulfate groups and one glucuronic acid; whereas the least charged one is the BA2 residue. All glycans contain one fucose and one galactose. The most mannose rich are the glycans MS2 and GP4, each of them has four mannoses; OPPE1 contains five N-acetylglucosamines and one sulfated glucuronic acid; GP4 contains one sialic acid. Furthermore, human P0 variants causing both gain and loss of glycosylation have been described and cause peripheral neuropathies with variable clinical severity. In particular, the substitution T(95) →M is a very common in Europe and is associated with a late-onset axonal neuropathy. Although peripheral myelin is made up largely of glycoproteins, mutations altering glycosylation have been described only in P0. This attractive avenue of research requires further study.
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Affiliation(s)
- Jan Sedzik
- Royal Institute of Technology, Department of Chemical Engineering, Protein Crystallization Facility, Stockholm, Sweden; National Institute of Physiological Sciences, Department of Neuroscience and Bioinformatics, Okazaki, Japan
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