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Tian Z, Hu T, Holmes EC, Ji J, Shi W. Analysis of the genetic diversity in RNA-directed RNA polymerase sequences: implications for an automated RNA virus classification system. Virus Evol 2024; 10:veae059. [PMID: 39119135 PMCID: PMC11306317 DOI: 10.1093/ve/veae059] [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: 02/05/2024] [Revised: 06/21/2024] [Accepted: 07/24/2024] [Indexed: 08/10/2024] Open
Abstract
RNA viruses are characterized by a broad host range and high levels of genetic diversity. Despite a recent expansion in the known virosphere following metagenomic sequencing, our knowledge of the species rank genetic diversity of RNA viruses, and how often they are misassigned and misclassified, is limited. We performed a clustering analysis of 7801 RNA-directed RNA polymerase (RdRp) sequences representing 1897 established RNA virus species. From this, we identified substantial genetic divergence within some virus species and inconsistency in RNA virus assignment between the GenBank database and The International Committee on Taxonomy of Viruses (ICTV). In particular, 27.57% virus species comprised multiple virus operational taxonomic units (vOTUs), including Alphainfluenzavirus influenzae, Mammarenavirus lassaense, Apple stem pitting virus, and Rotavirus A, with each having over 100 vOTUs. In addition, the distribution of average amino acid identity between vOTUs within single assigned species showed a relatively low threshold: <90% and sometimes <50%. However, when only exemplar sequences from virus species were analyzed, 1889 of the ICTV-designated RNA virus species (99.58%) were clustered into a single vOTU. Clustering of the RdRp sequences from different virus species also revealed that 17 vOTUs contained two distinct virus species. These potential misassignments were confirmed by phylogenetic analysis. A further analysis of average nucleotide identity (ANI) values ranging from 70% to 97.5% revealed that at an ANI of 82.5%, 1559 (82.18%) of the 1897 virus species could be correctly clustered into one single vOTU. However, at ANI values >82.5%, an increasing number of species were clustered into two or more vOTUs. In sum, we have identified some inconsistency and misassignment of the RNA virus species based on the analysis of RdRp sequences alone, which has important implications for the development of an automated RNA virus classification system.
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Affiliation(s)
- Zhongshuai Tian
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, No. 6699 Qingdao Road, Ji’nan 250117, China
- Shanghai Institute of Virology, Shanghai Jiao Tong University School of Medicine, No. 227 Chongqingnanlu, Shanghai 200025, China
| | - Tao Hu
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, No. 6699 Qingdao Road, Ji’nan 250117, China
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
- Laboratory of Data Discovery for Health Limited, 19 Science Park West Avenue, Hong Kong 999077, China
| | - Jingkai Ji
- School of Life Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, No. 619 Changcheng Road, Taian 271000, China
| | - Weifeng Shi
- Shanghai Institute of Virology, Shanghai Jiao Tong University School of Medicine, No. 227 Chongqingnanlu, Shanghai 200025, China
- Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijinerlu, Shanghai 200025, China
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2
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Kessler S, Burke B, Andrieux G, Schinköthe J, Hamberger L, Kacza J, Zhan S, Reasoner C, Dutt TS, Kaukab Osman M, Henao-Tamayo M, Staniek J, Villena Ossa JF, Frank DT, Ma W, Ulrich R, Cathomen T, Boerries M, Rizzi M, Beer M, Schwemmle M, Reuther P, Schountz T, Ciminski K. Deciphering bat influenza H18N11 infection dynamics in male Jamaican fruit bats on a single-cell level. Nat Commun 2024; 15:4500. [PMID: 38802391 PMCID: PMC11130286 DOI: 10.1038/s41467-024-48934-6] [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: 02/12/2024] [Accepted: 05/17/2024] [Indexed: 05/29/2024] Open
Abstract
Jamaican fruit bats (Artibeus jamaicensis) naturally harbor a wide range of viruses of human relevance. These infections are typically mild in bats, suggesting unique features of their immune system. To better understand the immune response to viral infections in bats, we infected male Jamaican fruit bats with the bat-derived influenza A virus (IAV) H18N11. Using comparative single-cell RNA sequencing, we generated single-cell atlases of the Jamaican fruit bat intestine and mesentery. Gene expression profiling showed that H18N11 infection resulted in a moderate induction of interferon-stimulated genes and transcriptional activation of immune cells. H18N11 infection was predominant in various leukocytes, including macrophages, B cells, and NK/T cells. Confirming these findings, human leukocytes, particularly macrophages, were also susceptible to H18N11, highlighting the zoonotic potential of this bat-derived IAV. Our study provides insight into a natural virus-host relationship and thus serves as a fundamental resource for future in-depth characterization of bat immunology.
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Affiliation(s)
- Susanne Kessler
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Bradly Burke
- Center for Vector-borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Geoffroy Andrieux
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center - University of Freiburg, Freiburg, Germany
| | - Jan Schinköthe
- Institute of Veterinary Pathology, Faculty of Veterinary Medicine, Leipzig University, Leipzig, Germany
| | - Lea Hamberger
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Johannes Kacza
- BioImaging Core Facility, Faculty of Veterinary Medicine, University of Leipzig, Leipzig, Germany
| | - Shijun Zhan
- Center for Vector-borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Clara Reasoner
- Center for Vector-borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Taru S Dutt
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Maria Kaukab Osman
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Marcela Henao-Tamayo
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Julian Staniek
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- Department of Rheumatology and Clinical Immunology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Freiburg, Germany
| | - Jose Francisco Villena Ossa
- Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Freiburg, Germany
- Institute for Transfusion Medicine and Gene Therapy, Medical Center-University of Freiburg, Freiburg, Germany
| | - Dalit T Frank
- Center for Vector-borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Wenjun Ma
- Department of Veterinary Pathobiology and Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, USA
| | - Reiner Ulrich
- Institute of Veterinary Pathology, Faculty of Veterinary Medicine, Leipzig University, Leipzig, Germany
| | - Toni Cathomen
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Freiburg, Germany
- Institute for Transfusion Medicine and Gene Therapy, Medical Center-University of Freiburg, Freiburg, Germany
| | - Melanie Boerries
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center - University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), Partner site Freiburg, a partnership between DKFZ and Medical Center - University of Freiburg, Freiburg, Germany
| | - Marta Rizzi
- Department of Rheumatology and Clinical Immunology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Freiburg, Germany
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
- Division of Clinical and Experimental Immunology, Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald, Insel Riems, Germany
| | - Martin Schwemmle
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Peter Reuther
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Tony Schountz
- Center for Vector-borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA.
| | - Kevin Ciminski
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany.
- Faculty of Medicine, University of Freiburg, Freiburg, Germany.
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3
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El-Shesheny R, Franks J, Kandeil A, Badra R, Turner J, Seiler P, Marathe BM, Jeevan T, Kercher L, Hu M, Sim YE, Hui KPY, Chan MCW, Thompson AJ, McKenzie P, Govorkova EA, Russell CJ, Vogel P, Paulson JC, Peiris JSM, Webster RG, Ali MA, Kayali G, Webby RJ. Cross-species spill-over potential of the H9N2 bat influenza A virus. Nat Commun 2024; 15:3449. [PMID: 38664384 PMCID: PMC11045754 DOI: 10.1038/s41467-024-47635-4] [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: 12/20/2023] [Accepted: 04/04/2024] [Indexed: 04/28/2024] Open
Abstract
In 2017, a novel influenza A virus (IAV) was isolated from an Egyptian fruit bat. In contrast to other bat influenza viruses, the virus was related to avian A(H9N2) viruses and was probably the result of a bird-to-bat transmission event. To determine the cross-species spill-over potential, we biologically characterize features of A/bat/Egypt/381OP/2017(H9N2). The virus has a pH inactivation profile and neuraminidase activity similar to those of human-adapted IAVs. Despite the virus having an avian virus-like preference for α2,3 sialic acid receptors, it is unable to replicate in male mallard ducks; however, it readily infects ex-vivo human respiratory cell cultures and replicates in the lungs of female mice. A/bat/Egypt/381OP/2017 replicates in the upper respiratory tract of experimentally-infected male ferrets featuring direct-contact and airborne transmission. These data suggest that the bat A(H9N2) virus has features associated with increased risk to humans without a shift to a preference for α2,6 sialic acid receptors.
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Affiliation(s)
- Rabeh El-Shesheny
- Center of Scientific Excellence for Influenza Virus, National Research Centre, Giza, Egypt
| | - John Franks
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ahmed Kandeil
- Center of Scientific Excellence for Influenza Virus, National Research Centre, Giza, Egypt
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Jasmine Turner
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Patrick Seiler
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Bindumadhav M Marathe
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Trushar Jeevan
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Lisa Kercher
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Meng Hu
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yul Eum Sim
- Department of Biology, Wanek School of Natural Science, High Point University, High Point, NC, USA
| | - Kenrie P Y Hui
- School of Public Health, The University of Hong Kong, Hong Kong, China
| | - Michael C W Chan
- School of Public Health, The University of Hong Kong, Hong Kong, China
| | - Andrew J Thompson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Pamela McKenzie
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Elena A Govorkova
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Charles J Russell
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Peter Vogel
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - James C Paulson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - J S Malik Peiris
- School of Public Health, The University of Hong Kong, Hong Kong, China
| | - Robert G Webster
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mohamed A Ali
- Center of Scientific Excellence for Influenza Virus, National Research Centre, Giza, Egypt
| | | | - Richard J Webby
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA.
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4
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Feoktistova S, Sayganova M, Trutneva K, Glazova O, Blagodatski AS, Shevkova L, Navoikova A, Anisimov Y, Albert E, Mityaeva O, Volchkov P, Deviatkin A. Abundant Intra-Subtype Reassortment Revealed in H13N8 Influenza Viruses. Viruses 2024; 16:568. [PMID: 38675910 PMCID: PMC11054967 DOI: 10.3390/v16040568] [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: 03/04/2024] [Revised: 03/29/2024] [Accepted: 04/05/2024] [Indexed: 04/28/2024] Open
Abstract
Influenza A viruses (IAVs) pose a serious threat to global health. On the one hand, these viruses cause seasonal flu outbreaks in humans. On the other hand, they are a zoonotic infection that has the potential to cause a pandemic. The most important natural reservoir of IAVs are waterfowl. In this study, we investigated the occurrence of IAV in birds in the Republic of Buryatia (region in Russia). In 2020, a total of 3018 fecal samples were collected from wild migratory birds near Lake Baikal. Of these samples, 11 were found to be positive for the H13N8 subtype and whole-genome sequencing was performed on them. All samples contained the same virus with the designation A/Unknown/Buryatia/Arangatui-1/2020. To our knowledge, virus A/Unknown/Buryatia/Arangatui-1/2020 is the first representative of the H13N8 subtype collected on the territory of Russia, the sequence of which is available in the GenBank database. An analysis of reassortments based on the genome sequences of other known viruses has shown that A/Unknown/Buryatia/Arangatui-1/2020 arose as a result of reassortment. In addition, a reassortment most likely occurred several decades ago between the ancestors of the viruses recently collected in China, the Netherlands, the United States and Chile. The presence of such reassortment emphasizes the ongoing evolution of the H13N8 viruses distributed in Europe, North and East Asia, North and South America and Australia. This study underscores the importance of the continued surveillance and research of less-studied influenza subtypes.
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Affiliation(s)
- Sofia Feoktistova
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia; (M.S.); (K.T.); (O.G.); (L.S.); (A.N.); (E.A.); (O.M.); (P.V.)
| | - Marya Sayganova
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia; (M.S.); (K.T.); (O.G.); (L.S.); (A.N.); (E.A.); (O.M.); (P.V.)
| | - Kseniya Trutneva
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia; (M.S.); (K.T.); (O.G.); (L.S.); (A.N.); (E.A.); (O.M.); (P.V.)
| | - Olga Glazova
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia; (M.S.); (K.T.); (O.G.); (L.S.); (A.N.); (E.A.); (O.M.); (P.V.)
| | - Artem S. Blagodatski
- Federal State Budget Institution of Science Institute of Theoretical and Experimental Biophysics, 142290 Pushchino, Russia;
| | - Liudmila Shevkova
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia; (M.S.); (K.T.); (O.G.); (L.S.); (A.N.); (E.A.); (O.M.); (P.V.)
| | - Anna Navoikova
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia; (M.S.); (K.T.); (O.G.); (L.S.); (A.N.); (E.A.); (O.M.); (P.V.)
| | - Yuriy Anisimov
- Baikalsky State Nature Biosphere Reserve, 671220 Tankhoi, Russia;
| | - Eugene Albert
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia; (M.S.); (K.T.); (O.G.); (L.S.); (A.N.); (E.A.); (O.M.); (P.V.)
| | - Olga Mityaeva
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia; (M.S.); (K.T.); (O.G.); (L.S.); (A.N.); (E.A.); (O.M.); (P.V.)
- Department of Fundamental Medicine, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Pavel Volchkov
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia; (M.S.); (K.T.); (O.G.); (L.S.); (A.N.); (E.A.); (O.M.); (P.V.)
- Department of Fundamental Medicine, Lomonosov Moscow State University, 119992 Moscow, Russia
- The Moscow Clinical Scientific Center (MCSC) Named after A.S. Loginov, 111123 Moscow, Russia
| | - Andrey Deviatkin
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia; (M.S.); (K.T.); (O.G.); (L.S.); (A.N.); (E.A.); (O.M.); (P.V.)
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119992 Moscow, Russia
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5
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Couto RDS, Ramos EDSF, Abreu WU, Rodrigues LRR, Marinho LF, Morais VDS, Villanova F, Pandey RP, Deng X, Delwart E, da Costa AC, Leal E. Metagenomic of Liver Tissue Identified at Least Two Genera of Totivirus-like Viruses in Molossus molossus Bats. Microorganisms 2024; 12:206. [PMID: 38276191 PMCID: PMC10819564 DOI: 10.3390/microorganisms12010206] [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: 12/01/2023] [Revised: 01/15/2024] [Accepted: 01/16/2024] [Indexed: 01/27/2024] Open
Abstract
The Totiviridae family of viruses has a unique genome consisting of double-stranded RNA with two open reading frames that encode the capsid protein (Cap) and the RNA-dependent RNA polymerase (RdRpol). Most virions in this family are isometric in shape, approximately 40 nm in diameter, and lack an envelope. There are five genera within this family, including Totivirus, Victorivirus, Giardiavirus, Leishmaniavirus, and Trichomonasvirus. While Totivirus and Victorivirus primarily infect fungi, Giardiavirus, Leishmaniavirus, and Trichomonasvirus infect diverse hosts, including protists, insects, and vertebrates. Recently, new totivirus-like species have been discovered in fish and plant hosts, and through metagenomic analysis, a novel totivirus-like virus (named Tianjin totivirus) has been isolated from bat guano. Interestingly, Tianjin totivirus causes cytopathic effects in insect cells but cannot grow in mammalian cells, suggesting that it infects insects consumed by insectivorous bats. In this study, we used next-generation sequencing and identified totivirus-like viruses in liver tissue from Molossus molossus bats in the Amazon region of Brazil. Comparative phylogenetic analysis based on the RNA-dependent RNA polymerase region revealed that the viruses identified in Molossus bats belong to two distinct phylogenetic clades, possibly comprising different genera within the Totiviridae family. Notably, the mean similarity between the Tianjin totivirus and the totiviruses identified in Molossus bats is less than 18%. These findings suggest that the diversity of totiviruses in bats is more extensive than previously recognized and highlight the potential for bats to serve as reservoirs for novel toti-like viruses.
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Affiliation(s)
- Roseane da Silva Couto
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, PA, Brazil; (R.d.S.C.); (E.d.S.F.R.); (F.V.)
| | - Endrya do Socorro Foro Ramos
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, PA, Brazil; (R.d.S.C.); (E.d.S.F.R.); (F.V.)
| | - Wandercleyson Uchôa Abreu
- Programa de Pos-Graduação REDE Bionorte, Polo Pará, Universidade Federal do Oeste do Pará, Santarém 68040-255, PA, Brazil;
| | - Luis Reginaldo Ribeiro Rodrigues
- Laboratory of Genetics & Biodiversity, Institute of Educational Sciences, Universidade Federal do Oeste do Pará, Santarém 68040-255, PA, Brazil;
| | | | - Vanessa dos Santos Morais
- Laboratory of Virology (LIM 52), Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (V.d.S.M.); (A.C.d.C.)
| | - Fabiola Villanova
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, PA, Brazil; (R.d.S.C.); (E.d.S.F.R.); (F.V.)
| | - Ramendra Pati Pandey
- School of Health Sciences and Technology (SoHST), UPES, Dehradun 248007, Uttarakhand, India;
| | - Xutao Deng
- Vitalant Research Institute, San Francisco, CA 94143, USA;
| | - Eric Delwart
- Department Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA;
| | - Antonio Charlys da Costa
- Laboratory of Virology (LIM 52), Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (V.d.S.M.); (A.C.d.C.)
| | - Elcio Leal
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, PA, Brazil; (R.d.S.C.); (E.d.S.F.R.); (F.V.)
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6
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Kessler S, García-Sastre A, Schwemmle M, Ciminski K. Reverse Genetics of Bat Influenza A Viruses. Methods Mol Biol 2024; 2733:75-86. [PMID: 38064027 DOI: 10.1007/978-1-0716-3533-9_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
New World fruit bats were recently found to harbor two distinct and previously unknown influenza A viruses (IAVs) of the subtypes H17N10 and H18N11. Although viral genome sequences were detected in the liver, intestine, lung, and kidney of infected bats and the complete genome sequences have been isolated from their rectal swab samples, all attempts to isolate an infectious virus from bats in nature have failed. The lack of an infectious bat IAV isolate was overcome by reverse genetic approaches that led to the generation of an infectious virus in vitro. Using such synthetic bat IAVs enabled the identification of their unconventional cell entry via major histocompatibility complex II (MCH-II) molecules and their ability to replicate in mice, ferrets, and bats. Importantly, we also showed that these synthetic recombinant bat IAVs are not able to reassort with conventional IAVs, preventing the acquisition of enhanced transmission properties in non-bat species by reassortment with conventional IAVs. As authentic viruses are key for understanding the molecular biology of bat IAVs, in this chapter, we describe our recently established reverse genetics protocol for generating H17N10 and H18N11 in vitro. This step-by-step protocol starts with cloning of cDNA copies of the viral RNA segments into reverse genetics plasmids, followed by the generation of a highly concentrated stock and finally a method to determine viral titers.
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Affiliation(s)
- Susanne Kessler
- Institute of Virology, Medical Center - University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Martin Schwemmle
- Institute of Virology, Medical Center - University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Kevin Ciminski
- Institute of Virology, Medical Center - University of Freiburg, Freiburg, Germany.
- Faculty of Medicine, University of Freiburg, Freiburg, Germany.
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7
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Cantoni D, Mayora-Neto M, Derveni M, da Costa K, Del Rosario J, Ameh VO, Sabeta CT, Auld B, Hamlet A, Jones IM, Wright E, Scott SD, Giotis ES, Banyard AC, Temperton N. Serological evidence of virus infection in Eidolon helvum fruit bats: implications for bushmeat consumption in Nigeria. Front Public Health 2023; 11:1283113. [PMID: 38106901 PMCID: PMC10723585 DOI: 10.3389/fpubh.2023.1283113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 11/02/2023] [Indexed: 12/19/2023] Open
Abstract
Introduction The Eidolon helvum fruit bat is one of the most widely distributed fruit bats in Africa and known to be a reservoir for several pathogenic viruses that can cause disease in animals and humans. To assess the risk of zoonotic spillover, we conducted a serological survey of 304 serum samples from E. helvum bats that were captured for human consumption in Makurdi, Nigeria. Methods Using pseudotyped viruses, we screened 304 serum samples for neutralizing antibodies against viruses from the Coronaviridae, Filoviridae, Orthomyxoviridae and Paramyxoviridae families. Results We report the presence of neutralizing antibodies against henipavirus lineage GH-M74a virus (odds ratio 6.23; p < 0.001), Nipah virus (odds ratio 4.04; p = 0.00031), bat influenza H17N10 virus (odds ratio 7.25; p < 0.001) and no significant association with Ebola virus (odds ratio 0.56; p = 0.375) in this bat cohort. Conclusion The data suggest a potential risk of zoonotic spillover including the possible circulation of highly pathogenic viruses in E. helvum populations. These findings highlight the importance of maintaining sero-surveillance of E. helvum, and the necessity for further, more comprehensive investigations to monitor changes in virus prevalence, distribution over time, and across different geographic locations.
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Affiliation(s)
- Diego Cantoni
- Viral Pseudotype Unit, Medway School of Pharmacy, Universities of Kent and Greenwich, Chatham, United Kingdom
| | - Martin Mayora-Neto
- Viral Pseudotype Unit, Medway School of Pharmacy, Universities of Kent and Greenwich, Chatham, United Kingdom
| | - Mariliza Derveni
- Viral Pseudotype Unit, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Kelly da Costa
- Viral Pseudotype Unit, Medway School of Pharmacy, Universities of Kent and Greenwich, Chatham, United Kingdom
| | - Joanne Del Rosario
- Viral Pseudotype Unit, Medway School of Pharmacy, Universities of Kent and Greenwich, Chatham, United Kingdom
| | - Veronica O. Ameh
- Department of Veterinary Public Health and Preventive Medicine, College of Veterinary Medicine, Federal University of Agriculture Makurdi, Makurdi, Nigeria
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa
| | - Claude T. Sabeta
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa
- World Organisation for Animal Health Rabies Reference Laboratory, Agricultural Research Council-Onderstepoort Veterinary Research, Onderstepoort, South Africa
| | - Bethany Auld
- Viral Pseudotype Unit, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Arran Hamlet
- Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, United Kingdom
| | - Ian M. Jones
- School of Biological Sciences, University of Reading, Reading, United Kingdom
| | - Edward Wright
- Viral Pseudotype Unit, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Simon D. Scott
- Viral Pseudotype Unit, Medway School of Pharmacy, Universities of Kent and Greenwich, Chatham, United Kingdom
| | - Efstathios S. Giotis
- Department of Infectious Diseases, Imperial College London, London, United Kingdom
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | | | - Nigel Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, Universities of Kent and Greenwich, Chatham, United Kingdom
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8
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Olajide OM, Osman MK, Robert J, Kessler S, Toews LK, Thamamongood T, Neefjes J, Wrobel AG, Schwemmle M, Ciminski K, Reuther P. Evolutionarily conserved amino acids in MHC-II mediate bat influenza A virus entry into human cells. PLoS Biol 2023; 21:e3002182. [PMID: 37410798 DOI: 10.1371/journal.pbio.3002182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 06/02/2023] [Indexed: 07/08/2023] Open
Abstract
The viral hemagglutinins of conventional influenza A viruses (IAVs) bind to sialylated glycans on host cell surfaces for attachment and subsequent infection. In contrast, hemagglutinins of bat-derived IAVs target major histocompatibility complex class II (MHC-II) for cell entry. MHC-II proteins from various vertebrate species can facilitate infection with the bat IAV H18N11. Yet, it has been difficult to biochemically determine the H18:MHC-II binding. Here, we followed a different approach and generated MHC-II chimeras from the human leukocyte antigen DR (HLA-DR), which supports H18-mediated entry, and the nonclassical MHC-II molecule HLA-DM, which does not. In this context, viral entry was supported only by a chimera containing the HLA-DR α1, α2, and β1 domains. Subsequent modeling of the H18:HLA-DR interaction identified the α2 domain as central for this interaction. Further mutational analyses revealed highly conserved amino acids within loop 4 (N149) and β-sheet 6 (V190) of the α2 domain as critical for virus entry. This suggests that conserved residues in the α1, α2, and β1 domains of MHC-II mediate H18-binding and virus propagation. The conservation of MHC-II amino acids, which are critical for H18N11 binding, may explain the broad species specificity of this virus.
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Affiliation(s)
- Okikiola M Olajide
- Institute of Virology, Medical Center - University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Maria Kaukab Osman
- Institute of Virology, Medical Center - University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Jonathan Robert
- Institute of Virology, Medical Center - University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Susanne Kessler
- Institute of Virology, Medical Center - University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Lina Kathrin Toews
- Institute of Virology, Medical Center - University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Thiprampai Thamamongood
- Virology and Cell Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Khlong Nueng, Khlong Luang District, Pathum Thani, Thailand
| | - Jacques Neefjes
- Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center, Leiden, the Netherlands
| | - Antoni G Wrobel
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Martin Schwemmle
- Institute of Virology, Medical Center - University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Kevin Ciminski
- Institute of Virology, Medical Center - University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Peter Reuther
- Institute of Virology, Medical Center - University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
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9
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Su A, Yan M, Pavasutthipaisit S, Wicke KD, Grassl GA, Beineke A, Felmy F, Schmidt S, Esser KH, Becher P, Herrler G. Infection Studies with Airway Organoids from Carollia perspicillata Indicate That the Respiratory Epithelium Is Not a Barrier for Interspecies Transmission of Influenza Viruses. Microbiol Spectr 2023; 11:e0309822. [PMID: 36916937 PMCID: PMC10100918 DOI: 10.1128/spectrum.03098-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 02/11/2023] [Indexed: 03/16/2023] Open
Abstract
Bats are a natural reservoir for many viruses and are considered to play an important role in the interspecies transmission of viruses. To analyze the susceptibility of bat airway cells to infection by viruses of other mammalian species, we developed an airway organoid culture model derived from airways of Carollia perspicillata. Application of specific antibodies for fluorescent staining indicated that the cell composition of organoids resembled those of bat trachea and lungs as determined by immunohistochemistry. Infection studies indicated that Carollia perspicillata bat airway organoids (AOs) from the trachea or the lung are highly susceptible to infection by two different porcine influenza A viruses. The bat AOs were also used to develop an air-liquid interface (ALI) culture system of filter-grown epithelial cells. Infection of these cells showed the same characteristics, including lower virulence and enhanced replication and release of the H1N1/2006 virus compared to infection with H3N2/2007. These observations agreed with the results obtained by infection of porcine ALI cultures with these two virus strains. Interestingly, lectin staining indicated that bat airway cells only contain a small amount of alpha 2,6-linked sialic acid, the preferred receptor determinant for mammalian influenza A viruses. In contrast, large amounts of alpha 2,3-linked sialic acid, the preferred receptor determinant for avian influenza viruses, are present in bat airway epithelial cells. Therefore, bat airway cells may be susceptible not only to mammalian but also to avian influenza viruses. Our culture models, which can be extended to other parts of the airways and to other species, provide a promising tool to analyze virus infectivity and the transmission of viruses both from bats to other species and from other species to bats. IMPORTANCE We developed an organoid culture system derived from the airways of the bat species Carollia perspicillata. Using this cell system, we showed that the airway epithelium of these bats is highly susceptible to infection by influenza viruses of other mammalian species and thus is not a barrier for interspecies transmission. These organoids provide an almost unlimited supply of airway epithelial cells that can be used to generate well-differentiated epithelial cells and perform infection studies. The establishment of the organoid model required only three animals, and can be extended to other epithelia (nose, intestine) as well as to other species (bat and other animal species). Therefore, organoids promise to be a valuable tool for future zoonosis research on the interspecies transmission of viruses (e.g., bat → intermediate host → human).
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Affiliation(s)
- Ang Su
- Department of Infectious Diseases, Institute of Virology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Miaomiao Yan
- Department of Infectious Diseases, Institute of Virology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Suvarin Pavasutthipaisit
- Department of Pathology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
- Department of Pathology, Faculty of Veterinary Medicine, Mahanakorn University of Technology, Bangkok, Thailand
| | - Kathrin D. Wicke
- Institute of Zoology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Guntram A. Grassl
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School and German Center for Infection Research (DZIF), Hannover, Germany
| | - Andreas Beineke
- Department of Pathology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
- Center for Systems Neuroscience, Hannover, Germany
| | - Felix Felmy
- Institute of Zoology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Sabine Schmidt
- Institute of Zoology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Karl-Heinz Esser
- Institute of Zoology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Paul Becher
- Department of Infectious Diseases, Institute of Virology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Georg Herrler
- Department of Infectious Diseases, Institute of Virology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
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10
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Role of Brazilian bats in the epidemiological cycle of potentially zoonotic pathogens. Microb Pathog 2023; 177:106032. [PMID: 36804526 DOI: 10.1016/j.micpath.2023.106032] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 02/07/2023] [Accepted: 02/12/2023] [Indexed: 02/19/2023]
Abstract
Bats (Chiroptera) are flying mammals of great biodiversity and habits. These characteristics contribute for them being natural reservoirs and part of the epidemiological cycle of several potentially zoonotic pathogens, such as viruses, protozoa, fungi and bacteria. Brazil hosts approximately 15% of the world's bat diversity, with 181 distinct species, 68 genera and 9 families. About 60% of infectious diseases in humans are of zoonotic origin and, in the last decades, the detection of zoonotic pathogens in bats and their environment has been reported, such as Rabies virus (RABV) and Histoplasma capsulatum. Thus, the aim of this work was to review the reports of zoonotic pathogens associated with bats in Brazil in the past ten years. We reviewed the main pathogenic microorganisms described and the species of bats most frequently involved in the epidemiological cycles of these zoonotic agents. The obtained data show an upward trend in the detection of zoonotic pathogens in Brazilian bats, such as RABV, Bartonella sp., Histoplasma capsulatum and Leishmania spp., with emphasis on the bat species Artibeus lituratus, Carollia perspicillata, Desmodus rotundus and Molossus molossus. These findings highlight the importance of monitoring bat-associated microrganisms to early identify pathogens that may threaten bat populations, including potentially zoonotic microrganisms, emphasizing the importance of the One Health approach to prevent and mitigate the risks of the emergence of zoonotic diseases.
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11
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No molecular evidence for influenza A virus and coronavirus in bats belonging to the families Phyllostomidae, Vespertilionidae, and Molossidae in the state of São Paulo, Brazil. Braz J Microbiol 2022; 54:523-529. [PMID: 36422849 PMCID: PMC9685036 DOI: 10.1007/s42770-022-00878-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 11/16/2022] [Indexed: 11/25/2022] Open
Abstract
This study aimed to evaluate, by molecular methods, the presence of influenza A virus (IAV) and coronavirus in non-hematophagous bats collected in the state of São Paulo, Brazil. Samples of lung tissue and small intestine from 105 bats belonging to three families (Phyllostomidae, Vespertilionidae, and Molossidae) were collected in 22 municipalities in the state of São Paulo. Genetic identification of bats species was performed by amplification and sequencing of a fragment of 710 bp of the mitochondrial COI gene. In the detection of IAV, genomes were performed by RT-PCR, aiming at the amplification of a 245-bp fragment of the IAV matrix (M) protein gene. For coronaviruses, two fragments of 602 and 440 bp corresponding to segments along the gene encoding the RNA-dependent RNA polymerase (RdRp) were targeted. The detection limit for each of the PCRs was also determined. All samples analyzed here were negative for both viruses, and the lower limit of detection of the PCRs for the amplification of influenza virus A and coronavirus was estimated at 3.5 × 103 and 4.59 genomic copies per microliter, respectively. Although bats have been shown to harbor a large number of pathogens, the results of the present study support the theory that virus circulation in bats in the wild often occurs at low viral loads and that our understanding of the complex infectious dynamics of these viruses in wild conditions is still limited.
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12
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D2I and F9Y Mutations in the NS1 Protein of Influenza A Virus Affect Viral Replication via Regulating Host Innate Immune Responses. Viruses 2022; 14:v14061206. [PMID: 35746676 PMCID: PMC9228823 DOI: 10.3390/v14061206] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/25/2022] [Accepted: 05/30/2022] [Indexed: 12/04/2022] Open
Abstract
Influenza A viruses (IAV) modulate host antiviral responses to promote viral growth and pathogenicity. The non-structural (NS1) protein of influenza A virus has played an indispensable role in the inhibition of host immune responses, especially in limiting interferon (IFN) production. In this study, random site mutations were introduced into the NS1 gene of A/WSN/1933 (WSN, H1N1) via an error prone PCR to construct a random mutant plasmid library. The NS1 random mutant virus library was generated by reverse genetics. To screen out the unidentified NS1 functional mutants, the library viruses were lung-to-lung passaged in mice and individual plaques were picked from the fourth passage in mice lungs. Sanger sequencing revealed that eight different kinds of mutations in the NS1 gene were obtained from the passaged library virus. We found that the NS1 F9Y mutation significantly enhanced viral growth in vitro (MDCK and A549 cells) and in vivo (BALB/c mice) as well as increased virulence in mice. The NS1 D2I mutation attenuated the viral replication and pathogenicity in both in vitro and in vivo models. Further studies demonstrated that the NS1 F9Y mutant virus exhibited systematic and selective inhibition of cytokine responses as well as inhibited the expression of IFN. In addition, the expression levels of innate immunity-related cytokines were significantly up-regulated after the rNS1 D2I virus infected A549 cells. Collectively, our results revealed that the two mutations in the N-terminal of the NS1 protein could alter the viral properties of IAV and provide additional evidence that the NS1 protein is a critical virulence factor. The two characterized NS1 mutations may serve as potential targets for antiviral drugs as well as attenuated vaccine development.
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13
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Yamaoka S, Weisend CM, Swenson VA, Ebihara H. Development of accelerated high-throughput antiviral screening systems for emerging orthomyxoviruses. Antiviral Res 2022; 200:105291. [PMID: 35296419 PMCID: PMC9259280 DOI: 10.1016/j.antiviral.2022.105291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 03/10/2022] [Accepted: 03/12/2022] [Indexed: 11/19/2022]
Abstract
Bourbon virus (BRBV) is an emerging tick-borne orthomyxovirus that causes severe febrile illness in humans. There are no specific treatments for BRBV disease currently available. Here, we developed a highly accessible and robust, quantitative fluorescence-based BRBV minigenome (MG) system and applied it to high-throughput antiviral drug screening. We demonstrated that human dihydroorotate dehydrogenase (DHODH) inhibitors, hDHODH-IN-4 and brequinar, efficiently reduced BRBV RNA synthesis, and validated these findings using infectious BRBV in vitro. The DHODH inhibitors also exhibited high potency in inhibiting MG activities of other orthomyxoviruses with emerging zoonotic potential, including bat influenza A virus, swine influenza D virus, and Thogoto virus. Our newly developed MG system is a powerful platform for antiviral drug screening across the Orthomyxoviridae family, enabling rapid development and deployment of antivirals against future emerging orthomyxoviruses.
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Affiliation(s)
- Satoko Yamaoka
- Mayo Clinic, Department of Infectious Diseases, Rochester, MN, 55905, USA
| | - Carla M Weisend
- Mayo Clinic, Department of Infectious Diseases, Rochester, MN, 55905, USA; Mayo Clinic, Department of Molecular Medicine, Rochester, MN, 55905, USA
| | - Vaille A Swenson
- Mayo Clinic Graduate School of Biomedical Sciences, Virology and Gene Therapy Graduate Program, Rochester, MN, 55905, USA
| | - Hideki Ebihara
- National Institute of Infectious Diseases, Department of Virology I, Tokyo, 162-8640, Japan.
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14
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Fernandes AP, Águeda-Pinto A, Pinheiro A, Rebelo H, Esteves PJ. Evolution of TRIM5 and TRIM22 in Bats Reveals a Complex Duplication Process. Viruses 2022; 14:v14020345. [PMID: 35215944 PMCID: PMC8879501 DOI: 10.3390/v14020345] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/31/2022] [Accepted: 02/04/2022] [Indexed: 12/29/2022] Open
Abstract
The innate immunological response in mammals involves a diverse and complex network of many proteins. Over the last years, the tripartite motif-containing protein 5 (TRIM5) and 22 (TRIM22) have shown promise as restriction factors of a plethora of viruses that infect primates. Although there have been studies describing the evolution of these proteins in a wide range of mammals, no prior studies of the TRIM6/34/5/22 gene cluster have been performed in the Chiroptera order. Here, we provide a detailed analysis of the evolution of this gene cluster in several bat genomes. Examination of different yangochiroptera and yinpterochiroptera bat species revealed a dynamic history of gene expansion occurring in TRIM5 and TRIM22 genes. Multiple copies of TRIM5 were found in the genomes of several bats, demonstrating a very low degree of conservation in the synteny of this gene among species of the Chiroptera order. Our findings also reveal that TRIM22 is often found duplicated in yangochiroptera bat species, an evolutionary phenomenon not yet observed in any other lineages of mammals. In total, we identified 31 TRIM5 and 19 TRIM22 amino acids to be evolving under positive selection, with most of the residues being placed in the PRYSPRY domain, known to be responsible for binding to the viral capsid during restriction in the primate orthologous TRIM proteins. Altogether, our results help to shed light on the distinctive role of bats in nature as reservoirs of viruses, many of which have become threatening zoonotic diseases through virus spillover in the last decades.
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Affiliation(s)
- Alexandre P. Fernandes
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vila do Conde, Portugal; (A.P.F.); (A.Á.-P.); (A.P.); (H.R.)
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vila do Conde, Portugal
| | - Ana Águeda-Pinto
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vila do Conde, Portugal; (A.P.F.); (A.Á.-P.); (A.P.); (H.R.)
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vila do Conde, Portugal
| | - Ana Pinheiro
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vila do Conde, Portugal; (A.P.F.); (A.Á.-P.); (A.P.); (H.R.)
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vila do Conde, Portugal
| | - Hugo Rebelo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vila do Conde, Portugal; (A.P.F.); (A.Á.-P.); (A.P.); (H.R.)
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vila do Conde, Portugal
- CIBIO/InBIO, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal
| | - Pedro J. Esteves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vila do Conde, Portugal; (A.P.F.); (A.Á.-P.); (A.P.); (H.R.)
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vila do Conde, Portugal
- CITS—Centro de Investigac¸ão em Tecnologias da Saúde, Instituto Politécnico de Saúde do Norte (IPSN), Cooperativa de Ensino Superior Politécnico e Universitário (CESPU), 4585-116 Gandra, Portugal
- Correspondence:
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15
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Different but Not Unique: Deciphering the Immunity of the Jamaican Fruit Bat by Studying Its Viriome. Viruses 2022; 14:v14020238. [PMID: 35215832 PMCID: PMC8879847 DOI: 10.3390/v14020238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/20/2022] [Accepted: 01/23/2022] [Indexed: 02/04/2023] Open
Abstract
A specialized and fine-tuned immune response of bats upon infection with viruses is believed to provide the basis for a “friendly” coexistence with these pathogens, which are often lethal for humans and other mammals. First insights into the immunity of bats suggest that bats have evolved to possess their own strategies to cope with viral infections. Yet, the molecular details for this innocuous coexistence remain poorly described and bat infection models are the key to unveiling these secrets. In Jamaican fruit bats (Artibeus jamaicensis), a New World bat species, infection experiments with its (putative) natural viral pathogens Tacaribe virus (TCRV), rabies virus (RABV), and the bat influenza A virus (IAV) H18N11, have contributed to an accurate, though still incomplete, representation of the bat-imposed immunity. Surprisingly, though many aspects of their innate and adaptive immune responses differ from that of the human immune response, such as a contraction of the IFN locus and reduction in the number of immunoglobulin subclasses, variations could also be observed between Jamaican fruit bats and other bat species.
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Sriwilaijaroen N, Suzuki Y. Roles of Glycans and Non-glycans on the Epithelium and in the Immune System in H1-H18 Influenza A Virus Infections. Methods Mol Biol 2022; 2556:205-242. [PMID: 36175637 DOI: 10.1007/978-1-0716-2635-1_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The large variation of influenza A viruses (IAVs) in various susceptible hosts and their rapid evolution, which allows host/tissue switching, host immune escape, vaccine escape, and drug resistance, are difficult challenges for influenza control in all countries worldwide. Access and binding of the IAV to actual receptors at endocytic sites is critical for the establishment of influenza infection. In this chapter, the progress in identification of and roles of glycans and non-glycans on the epithelium and in the immune system in H1-H18 IAV infections are reviewed. The first part of the review is on current knowledge of H1-H16 IAV receptors on the epithelium including sialyl glycans, other negatively charged glycans, and annexins. The second part of the review focuses on H1-H16 IAV receptors in the immune system including acidic surfactant phospholipids, Sia on surfactant proteins, the carbohydrate recognition domain (CRD) of surfactant proteins, Sia on mucins, Sia and C-type lectins on macrophages and dendritic cells, and Sia on NK cells. The third part of the review is about a possible H17-H18 IAV receptor. Binding of these receptors to IAVs may result in inhibition or enhancement of IAV infection depending on their location, host cell type, and IAV strain. Among these receptors, host sialyl glycans are key determinants of viral hemagglutinin (HA) lectins for H1-H16 infections. HA must acquire mutations to bind to sialyl glycans that are dominant on a new target tissue when switching to a new host for efficient transmission and to bind to long sialyl glycans found in the case of seasonal HAs with multiple glycosylation sites as a consequence of immune evasion. Although sialyl receptors/C-type lectins on immune cells are decoy receptors/pathogen recognition receptors for capturing viral HA lectin/glycans protecting HA antigenic sites, some IAV strains do not escape, such as by release with neuraminidase, but hijack these molecules to gain entry and replication in immune cells. An understanding of the virus-host battle tactics at the receptor level might lead to the establishment of novel strategies for effective control of influenza.
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Affiliation(s)
- Nongluk Sriwilaijaroen
- Department of Preclinical Sciences, Faculty of Medicine, Thammasat University, Pathumthani, Thailand.
- Department of Medical Biochemistry, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan.
| | - Yasuo Suzuki
- Department of Medical Biochemistry, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
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17
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Tan CW, Yang X, Anderson DE, Wang LF. Bat virome research: the past, the present and the future. Curr Opin Virol 2021; 49:68-80. [PMID: 34052731 DOI: 10.1016/j.coviro.2021.04.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 04/30/2021] [Indexed: 02/07/2023]
Abstract
Bats have been increasingly recognised as an exceptional reservoir for emerging zoonotic viruses for the past few decades. Recent studies indicate that the unique bat immune system may be partially responsible for their ability to co-exist with viruses with minimal or no clinical diseases. In this review, we discuss the history and importance of bat virome studies and contrast the vast difference between such studies before and after the introduction of next generation sequencing (NGS) in this area of research. We also discuss the role of discovery serology and high-throughput single cell RNA-seq in future bat virome research.
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Affiliation(s)
- Chee Wah Tan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 169857, Singapore
| | - Xinglou Yang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 169857, Singapore; Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Danielle E Anderson
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 169857, Singapore
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 169857, Singapore; SingHealth Duke-NUS Global Health Institute, 169857, Singapore.
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18
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Dual R108K and G189D Mutations in the NS1 Protein of A/H1N1 Influenza Virus Counteract Host Innate Immune Responses. Viruses 2021; 13:v13050905. [PMID: 34068322 PMCID: PMC8153306 DOI: 10.3390/v13050905] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/04/2021] [Accepted: 05/07/2021] [Indexed: 01/23/2023] Open
Abstract
Influenza A viruses (IAV) modulate host antiviral responses to promote growth and pathogenicity. Here, we examined the multifunctional IAV nonstructural protein 1 (NS1) of influenza A virus to better understand factors that contribute to viral replication efficiency or pathogenicity. In 2009, a pandemic H1N1 IAV (A/California/07/2009 pH1N1) emerged in the human population from swine. Seasonal variants of this virus are still circulating in humans. Here, we compared the sequence of a seasonal variant of this H1N1 influenza virus (A/Urumqi/XJ49/2018(H1N1), first isolated in 2018) with the pandemic strain A/California/07/2009. The 2018 virus harbored amino acid mutations (I123V and N205S) in important functional sites; however, 108R and 189G were highly conserved between A/California/07/2009 and the 2018 variant. To better understand interactions between influenza viruses and the human innate immune system, we generated and rescued seasonal 2009 H1N1 IAV mutants expressing an NS1 protein harboring a dual mutation (R108K/G189D) at these conserved residues and then analyzed its biological characteristics. We found that the mutated NS1 protein exhibited systematic and selective inhibition of cytokine responses via a mechanism that may not involve binding to cleavage and polyadenylation specificity factor 30 (CPSF30). These results highlight the complexity underlying host–influenza NS1 protein interactions.
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19
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Yang W, Schountz T, Ma W. Bat Influenza Viruses: Current Status and Perspective. Viruses 2021; 13:v13040547. [PMID: 33805956 PMCID: PMC8064322 DOI: 10.3390/v13040547] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/20/2021] [Accepted: 03/22/2021] [Indexed: 12/11/2022] Open
Abstract
Bats are natural reservoirs for many viruses, including several that are zoonotic. Two unusual H17N10 and H18N11 influenza viruses have been found in New World bats. Although neither of these viruses have been isolated, infectious clone technology has permitted significant progress to understand their biology, which include unique features compared to all other known influenza A viruses. In addition, an H9N2-like influenza A virus was isolated from Old World bats and it shows similar characteristics of normal influenza A viruses. In this review, current status and perspective on influenza A viruses identified in bats is reviewed and discussed.
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Affiliation(s)
- Wenyu Yang
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA;
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO 65211, USA
| | - Tony Schountz
- Center for Vector-Borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA;
| | - Wenjun Ma
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA;
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO 65211, USA
- Correspondence:
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20
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Abstract
Influenza A viruses (IAVs) originating from aquatic waterfowl recurrently cross interspecies barriers, which is greatly facilitated by utilizing cell surface-exposed monosaccharide sialic acids located on vertebrate cells as a universal host cell receptor. These glycan structures are first bound by the viral hemagglutinin (HA) for cell entry and then cleaved by the viral neuraminidase (NA) for particle release. In contrast, viruses of the recently identified bat-borne IAV subtypes H17N10 and H18N11 encode HA and NA homologs unable to interact with sialic acid residues despite a high degree of structural homology with their conventional counterparts. However, the most recent findings show that bat IAV HAs make use of the major histocompatibility complex class II proteins of different vertebrate species to gain entry into host cells, potentially permitting a broader host tropism. This review recapitulates current progress in the field of bat IAV research including the first assessment of the spillover potential of these bat viruses into other mammals.
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21
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Affiliation(s)
- Marcione B. De Oliveira
- Graduate Program in Zoology, National Museum, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista s/n, São Cristóvão, Rio de Janeiro, RJ, 20940-040, Brazil
| | - Cibele R. Bonvicino
- Graduate Program in Zoology, National Museum, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista s/n, São Cristóvão, Rio de Janeiro, RJ, 20940-040, Brazil
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22
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Giotis ES. Inferring the Urban Transmission Potential of Bat Influenza Viruses. Front Cell Infect Microbiol 2020; 10:264. [PMID: 32582567 PMCID: PMC7283454 DOI: 10.3389/fcimb.2020.00264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 05/04/2020] [Indexed: 12/02/2022] Open
Abstract
Bats are considered natural reservoirs of various, potentially zoonotic viruses, exemplified by the influenza A-like viruses H17N10 and H18N11 in asymptomatic Neotropical bats. These influenza viruses are evolutionarily distinct, are poorly adapted to laboratory mice and ferrets and cannot reassort in vitro with conventional strains to form new influenza subtypes. However, they have attracted renewed attention following reports that their entry in host cells is mediated by the trans-species conserved MHC-II proteins, suggesting that they hold zoonotic potential. Despite the recent studies, the viruses' epidemiology and public health significance remain incompletely understood. Delineating the mechanistic basis of the interactions with their hosts and assessing their global distribution are essential in order to fully assess the zoonotic threat that these strains pose.
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Affiliation(s)
- Efstathios S Giotis
- Section of Molecular Virology, Department of Infectious Diseases, Imperial College London, London, United Kingdom.,School of Life Sciences, University of Essex, Colchester, United Kingdom
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23
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Abstract
Influenza A viruses (IAVs) of the H9 subtype are enzootic in Asia, the Middle East, and parts of North and Central Africa, where they cause significant economic losses to the poultry industry. Of note, some strains of H9N2 viruses have been linked to zoonotic episodes of mild respiratory diseases. Because of the threat posed by H9N2 viruses to poultry and human health, these viruses are considered of pandemic concern by the World Health Organization (WHO). H9N2 IAVs continue to diversify into multiple antigenically and phylogenetically distinct lineages that can further promote the emergence of strains with pandemic potential. Somewhat neglected compared with the H5 and H7 subtypes, there are numerous indicators that H9N2 viruses could be involved directly or indirectly in the emergence of the next influenza pandemic. The goal of this work is to discuss the state of knowledge on H9N2 IAVs and to provide an update on the contemporary global situation.
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Affiliation(s)
- Silvia Carnaccini
- Department of Population Health, Poultry Diagnostic and Research Center, University of Georgia, Athens, Georgia 30602, USA
| | - Daniel R Perez
- Department of Population Health, Poultry Diagnostic and Research Center, University of Georgia, Athens, Georgia 30602, USA
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24
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Banerjee A, Mossman KL, Miller MS. Bat Influenza Viruses: Making a Double Agent of MHC Class II. Trends Microbiol 2020; 28:703-706. [PMID: 32409145 PMCID: PMC7167561 DOI: 10.1016/j.tim.2020.04.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 04/06/2020] [Accepted: 04/10/2020] [Indexed: 01/20/2023]
Abstract
MHC class II (MHCII) has recently been identified as a cellular receptor for bat influenza viruses. Here, we discuss the possible implications of viral exploitation of this critical host defense molecule and highlight the need for more intense study of bat–influenza virus interactions.
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Affiliation(s)
- Arinjay Banerjee
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster Immunology Research Centre, McMaster University, Hamilton, ON L8S 4K1, Canada; Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Karen L Mossman
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster Immunology Research Centre, McMaster University, Hamilton, ON L8S 4K1, Canada; Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Matthew S Miller
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster Immunology Research Centre, McMaster University, Hamilton, ON L8S 4K1, Canada; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada.
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25
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26
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Characterization of Experimental Oro-Nasal Inoculation of Seba's Short-Tailed Bats ( Carollia perspicillata) with Bat Influenza A Virus H18N11. Viruses 2020; 12:v12020232. [PMID: 32093076 PMCID: PMC7077217 DOI: 10.3390/v12020232] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 02/06/2020] [Accepted: 02/17/2020] [Indexed: 11/16/2022] Open
Abstract
In 2012 and 2013, the genomic sequences of two novel influenza A virus (IAV) subtypes, designated H17N10 and H18N11, were identified via next-generation sequencing in the feces of the little yellow-shouldered fruit bat (Sturnira lilium) and the flat-faced fruit-eating bat (Artibeus planirostris), respectively. The pathogenesis caused by these viruses in their respective host species is currently insufficiently understood, which is primarily due to the inability to obtain and keep these bat species under appropriate environmental and biosafety conditions. Seba’s short-tailed bats (Carollia perspicillata), in contrast, are close relatives and a natural H18N11 reservoir species, with the advantage of established animal husbandry conditions in academic research. To study viral pathogenesis in more detail, we here oro-nasally inoculated Seba’s short-tailed bats with the bat IAV H18N11 subtype. Following inoculation, bats appeared clinically healthy, but the histologic examination of tissues revealed a mild necrotizing rhinitis. Consistently, IAV-matrix protein and H18-RNA positive cells were seen in lesioned respiratory and olfactory nasal epithelia, as well as in intestinal tissues. A RT-qPCR analysis confirmed viral replication in the conchae and intestines as well as the presence of viral RNA in the excreted feces, without horizontal transmission to naïve contact animals. Moreover, all inoculated animals seroconverted with low titers of neutralizing antibodies.
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27
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Beena V, Saikumar G. Emerging horizon for bat borne viral zoonoses. Virusdisease 2019; 30:321-328. [PMID: 31803797 PMCID: PMC6864002 DOI: 10.1007/s13337-019-00548-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 07/15/2019] [Indexed: 01/20/2023] Open
Abstract
Bats are the only flying placental mammals that constitute the second largest order of mammals and present all around the world except in Arctic, Antarctica and a few oceanic islands. Sixty percent of emerging infectious diseases originating from animals are zoonotic and more than two-thirds of them originate in wildlife. Bats were evolved as a super-mammal for harboring many of the newly identified deadly diseases without any signs and lesions. Their unique ability to fly, particular diet, roosting behavior, long life span, ability to echolocate and critical susceptibility to pathogens make them suitable host to harbor numerous zoonotic pathogens like virus, bacteria and parasite. Many factors are responsible for the emergence of bat borne zoonoses but the most precipitating factor is human intrusions. Deforestation declined the natural habitat and forced the bats and other wild life to move out of their niche. These stressed bats, having lost foraging and behavioral pattern invade in proximity of human habitation. Either directly or indirectly they transmit the viruses to humans and animals. Development of fast detection modern techniques for viruses from the diseased and environmental samples and the lessons learned in the past helped in preventing the severity during the latest outbreaks.
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Affiliation(s)
- V Beena
- 1Present Address: CSIR-Indian Institute of Toxicology Research, Lucknow, UP 226001 India.,2ICAR-Indian Veterinary Research Institute, Bareilly, UP 243122 India
| | - G Saikumar
- 2ICAR-Indian Veterinary Research Institute, Bareilly, UP 243122 India
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28
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Ciminski K, Ran W, Gorka M, Lee J, Malmlov A, Schinköthe J, Eckley M, Murrieta RA, Aboellail TA, Campbell CL, Ebel GD, Ma J, Pohlmann A, Franzke K, Ulrich R, Hoffmann D, García-Sastre A, Ma W, Schountz T, Beer M, Schwemmle M. Bat influenza viruses transmit among bats but are poorly adapted to non-bat species. Nat Microbiol 2019; 4:2298-2309. [PMID: 31527796 DOI: 10.1038/s41564-019-0556-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 08/07/2019] [Indexed: 11/09/2022]
Abstract
Major histocompatibility complex class II (MHC-II) molecules of multiple species function as cell-entry receptors for the haemagglutinin-like H18 protein of the bat H18N11 influenza A virus, enabling tropism of the viruses in a potentially broad range of vertebrates. However, the function of the neuraminidase-like N11 protein is unknown because it is dispensable for viral infection or the release of H18-pseudotyped viruses. Here, we show that infection of mammalian cells with wild-type H18N11 leads to the emergence of mutant viruses that lack the N11 ectodomain and acquired mutations in H18. An infectious clone of one such mutant virus, designated rP11, appeared to be genetically stable in mice and replicated to higher titres in mice and cell culture compared with wild-type H18N11. In ferrets, rP11 antigen and RNA were detected at low levels in various tissues, including the tonsils, whereas the wild-type virus was not. In Neotropical Jamaican fruit bats, wild-type H18N11 was found in intestinal Peyer's patches and was shed to high concentrations in rectal samples, resulting in viral transmission to naive contact bats. Notably, rP11 also replicated efficiently in bats; however, only restored full-length N11 viruses were transmissible. Our findings suggest that wild-type H18N11 replicates poorly in mice and ferrets and that N11 is a determinant for viral transmission in bats.
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Affiliation(s)
- Kevin Ciminski
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Wei Ran
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Marco Gorka
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald, Germany
| | - Jinhwa Lee
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Ashley Malmlov
- Arthropod Borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Jan Schinköthe
- Department of Experimental Animal Facilities and Biorisk Management, Friedrich-Loeffler-Institut, Greifswald, Germany
| | - Miles Eckley
- Arthropod Borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Reyes A Murrieta
- Arthropod Borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Tawfik A Aboellail
- Arthropod Borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Corey L Campbell
- Arthropod Borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Gregory D Ebel
- Arthropod Borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Jingjiao Ma
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Anne Pohlmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald, Germany
| | - Kati Franzke
- Institute of Infectology, Friedrich-Loeffler-Institut, Greifswald, Germany
| | - Reiner Ulrich
- Department of Experimental Animal Facilities and Biorisk Management, Friedrich-Loeffler-Institut, Greifswald, Germany
| | - Donata Hoffmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald, Germany
| | - Adolfo García-Sastre
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Wenjun Ma
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA.
| | - Tony Schountz
- Arthropod Borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA.
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald, Germany.
| | - Martin Schwemmle
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany. .,Faculty of Medicine, University of Freiburg, Freiburg, Germany.
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29
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Ciminski K, Pulvermüller J, Adam J, Schwemmle M. Human MxA is a potent interspecies barrier for the novel bat-derived influenza A-like virus H18N11. Emerg Microbes Infect 2019; 8:556-563. [PMID: 30945621 PMCID: PMC6455144 DOI: 10.1080/22221751.2019.1599301] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The human innate immune factor MxA represents an effective interspecies barrier for zoonotic influenza A viruses (IAVs) of animal origin. Accordingly, human but not avian IAVs efficiently escape the antiviral activity of MxA due to adaptive mutations in their viral nucleoprotein. Partial MxA resistance can be acquired in intermediate hosts such as swine, which possess an antivirally active Mx1 protein. Intriguingly, Mx1 of the bat Carollia perspicillata, a host of the recently discovered bat influenza A-like virus H18N11, is antivirally active against avian IAVs, thus raising the question whether H18N11 has undergone a preadaptation to human MxA. Here, by utilizing a chimeric bat influenza virus, PR8-H18N11, we demonstrate that MxA efficiently blocks viral replication in vitro as well as in MxA transgenic mice. Nevertheless, the H18N11 nucleoprotein exhibits partial MxA resistance in a polymerase reconstitution assay, suggesting that a certain degree of MxA preadaptation occurred. Together, our data indicate a currently reduced risk for H18N11 to overcome the human restriction factor MxA. Further adaptive mutations in NP are required to facilitate full MxA escape.
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Affiliation(s)
- Kevin Ciminski
- a Institute of Virology, Medical Center - University of Freiburg , Freiburg , Germany.,b Faculty of Medicine , University of Freiburg , Freiburg , Germany
| | - Johanna Pulvermüller
- a Institute of Virology, Medical Center - University of Freiburg , Freiburg , Germany.,b Faculty of Medicine , University of Freiburg , Freiburg , Germany
| | - Julia Adam
- a Institute of Virology, Medical Center - University of Freiburg , Freiburg , Germany.,b Faculty of Medicine , University of Freiburg , Freiburg , Germany
| | - Martin Schwemmle
- a Institute of Virology, Medical Center - University of Freiburg , Freiburg , Germany.,b Faculty of Medicine , University of Freiburg , Freiburg , Germany
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30
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Sreenivasan CC, Thomas M, Kaushik RS, Wang D, Li F. Influenza A in Bovine Species: A Narrative Literature Review. Viruses 2019; 11:v11060561. [PMID: 31213032 PMCID: PMC6631717 DOI: 10.3390/v11060561] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 06/10/2019] [Accepted: 06/14/2019] [Indexed: 12/17/2022] Open
Abstract
It is quite intriguing that bovines were largely unaffected by influenza A, even though most of the domesticated and wild animals/birds at the human-animal interface succumbed to infection over the past few decades. Influenza A occurs on a very infrequent basis in bovine species and hence bovines were not considered to be susceptible hosts for influenza until the emergence of influenza D. This review describes a multifaceted chronological review of literature on influenza in cattle which comprises mainly of the natural infections/outbreaks, experimental studies, and pathological and seroepidemiological aspects of influenza A that have occurred in the past. The review also sheds light on the bovine models used in vitro and in vivo for influenza-related studies over recent years. Despite a few natural cases in the mid-twentieth century and seroprevalence of human, swine, and avian influenza viruses in bovines, the evolution and host adaptation of influenza A virus (IAV) in this species suffered a serious hindrance until the novel influenza D virus (IDV) emerged recently in cattle across the world. Supposedly, certain bovine host factors, particularly some serum components and secretory proteins, were reported to have anti-influenza properties, which could be an attributing factor for the resilient nature of bovines to IAV. Further studies are needed to identify the host-specific factors contributing to the differential pathogenetic mechanisms and disease progression of IAV in bovines compared to other susceptible mammalian hosts.
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Affiliation(s)
- Chithra C Sreenivasan
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA.
| | - Milton Thomas
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD 57007, USA.
| | - Radhey S Kaushik
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA.
| | - Dan Wang
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA.
- BioSystems Networks and Translational Research Center (BioSNTR), Brookings, SD 57007, USA.
| | - Feng Li
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA.
- BioSystems Networks and Translational Research Center (BioSNTR), Brookings, SD 57007, USA.
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31
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Ren C, Chen Y, Zhang M, Zhang T, Bao D, Lu C, Xue R, Zhang Y, Liu W, Chen H, Teng Q, Yang J, Li X, Li Z, Liu Q. Limited adaptation of chimeric H9N2 viruses containing internal genes from bat influenza viruses in chickens. Vet Microbiol 2019; 232:151-155. [PMID: 31030840 PMCID: PMC7117387 DOI: 10.1016/j.vetmic.2019.04.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 04/11/2019] [Accepted: 04/12/2019] [Indexed: 01/26/2023]
Abstract
Influenza virus-like sequences of H17N10 and H18N11 were identified in bats, despite there has been no live virus isolated. The genetic analysis indicated that they have distinct but relatively close evolutionary relationships to known influenza A viruses. However, the infectivity and adaptation of bat influenza viruses in avian species remain unclear. In this study, two modified bat influenza viruses cH9cN2/H17 and cH9cN2/H18 containing HA and NA coding regions replaced with those of H9N2 influenza A virus were generated in the background of the H17N10 or H18N11 viruses. These two modified viruses replicated less efficiently than wild type H9N2 virus in cultured chicken cells. The mini-genome assay showed that viral ribonucleoproteins (vRNPs) of H9N2 has significantly higher polymerase activity than that of bat influenza viruses in avian cells. In chicken study, compared with H9N2 virus, which replicated and transmitted efficiently in chickens, the cH9cN2/H17 and cH9cN2/H18 viruses only replicated in chicken tracheas with lower titers. Pathological examination showed that the H9N2 caused severer lesions in lung and trachea than the modified bat influenza viruses. Notably, the cH9cN2/H18 transmitted among chickens, but not cH9cN2/H17, and chicken IFN-β antagonism results showed that H18N11 NS1 protein inhibited chicken IFN-β response more efficiently than H17N10 NS1 protein in avian cells. Taken together, our data indicated that the internal genes of bat influenza viruses adapted poorly to chickens, while the internal genes of H18N11 seemed to adapt to chickens better than H17N10.
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Affiliation(s)
- Chaochao Ren
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Yinyin Chen
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Min Zhang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Ting Zhang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Danqi Bao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Chenyang Lu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Ruixue Xue
- Shandong Provincial Center for Animal Disease Control and Prevention, Jinan, Shandong, China
| | - Yanjie Zhang
- College of Animal Husbandry and Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Wenhua Liu
- College of Animal Husbandry and Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Hongjun Chen
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Qiaoyang Teng
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Jianmei Yang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Xuesong Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Zejun Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China.
| | - Qinfang Liu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China.
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