1
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Miura T, Kadoya SS, Miura Y, Takino H, Akiba M, Sano D, Masuda T. Pepper mild mottle virus intended for use as a process indicator for drinking water treatment: Present forms and quantitative relations to norovirus and rotavirus in surface water. WATER RESEARCH 2024; 257:121713. [PMID: 38733963 DOI: 10.1016/j.watres.2024.121713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 03/19/2024] [Accepted: 05/01/2024] [Indexed: 05/13/2024]
Abstract
Pepper mild mottle virus (PMMoV) has been proposed as a potential indicator of human enteric viruses in environmental water and for viral removal during drinking water treatment. To investigate the occurrence and present forms of PMMoV and quantitative relations to norovirus GII and rotavirus A (RVA) in surface waters, 147 source water samples were collected from 21 drinking water treatment plants (DWTPs) in Japan between January 2018 and January 2021, and the concentrations of viruses in suspended and dissolved fractions were measured using real-time RT-PCR. PMMoV was detected in 81-100 % of samples in each sample month and observed concentrations ranged from 3.0 to 7.0 log10 copies/L. The concentrations of PMMoV were higher in dissolved fraction compared to suspended fractions, while different partitioning was observed for NoV GII depending on seasons. The concentrations of PMMoV were basically higher than those of norovirus GII (1.9-5.3 log10 copies/L) and RVA (1.9-6.6 log10 copies/L), while in 18 samples, RVA presented higher concentrations than PMMoV. Partial regions of VP7, VP4, and VP6 of the RVA in the 18 samples were amplified using nested PCR, and the genotypes were determined using an amplicon-based next-generation sequencing approach. We found that these source water samples included not only human RVA but also various animal RVA and high genetic diversity due to the existence of animal RVA was associated with a higher RVA concentration than PMMoV. Our findings suggest that PMMoV can be used as an indicator of norovirus GII and human RVA in drinking water sources and that the indicator performance should be evaluated by comparing to zoonotic viruses as well as human viruses.
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Affiliation(s)
- Takayuki Miura
- Department of Environmental Health, National Institute of Public Health, Wako, Japan.
| | - Syun-Suke Kadoya
- Department of Civil and Environmental Engineering, Tohoku University, Japan; Department of Urban Engineering, The University of Tokyo, Japan
| | - Yohei Miura
- Department of Civil and Environmental Engineering, Tohoku University, Japan
| | - Hiroyuki Takino
- Department of Environmental Health, National Institute of Public Health, Wako, Japan
| | - Michihiro Akiba
- Department of Environmental Health, National Institute of Public Health, Wako, Japan
| | - Daisuke Sano
- Department of Civil and Environmental Engineering, Tohoku University, Japan
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2
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Staller E, Carrique L, Swann OC, Fan H, Keown JR, Sheppard CM, Barclay WS, Grimes JM, Fodor E. Structures of H5N1 influenza polymerase with ANP32B reveal mechanisms of genome replication and host adaptation. Nat Commun 2024; 15:4123. [PMID: 38750014 PMCID: PMC11096171 DOI: 10.1038/s41467-024-48470-3] [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: 01/05/2024] [Accepted: 05/01/2024] [Indexed: 05/18/2024] Open
Abstract
Avian influenza A viruses (IAVs) pose a public health threat, as they are capable of triggering pandemics by crossing species barriers. Replication of avian IAVs in mammalian cells is hindered by species-specific variation in acidic nuclear phosphoprotein 32 (ANP32) proteins, which are essential for viral RNA genome replication. Adaptive mutations enable the IAV RNA polymerase (FluPolA) to surmount this barrier. Here, we present cryo-electron microscopy structures of monomeric and dimeric avian H5N1 FluPolA with human ANP32B. ANP32B interacts with the PA subunit of FluPolA in the monomeric form, at the site used for its docking onto the C-terminal domain of host RNA polymerase II during viral transcription. ANP32B acts as a chaperone, guiding FluPolA towards a ribonucleoprotein-associated FluPolA to form an asymmetric dimer-the replication platform for the viral genome. These findings offer insights into the molecular mechanisms governing IAV genome replication, while enhancing our understanding of the molecular processes underpinning mammalian adaptations in avian-origin FluPolA.
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Affiliation(s)
- Ecco Staller
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Loïc Carrique
- Division of Structural Biology, Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Olivia C Swann
- Section of Molecular Virology, Imperial College London, London, UK
| | - Haitian Fan
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- School of Basic Medical Sciences, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
| | - Jeremy R Keown
- Division of Structural Biology, Centre for Human Genetics, University of Oxford, Oxford, UK
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Carol M Sheppard
- Section of Molecular Virology, Imperial College London, London, UK
| | - Wendy S Barclay
- Section of Molecular Virology, Imperial College London, London, UK
| | - Jonathan M Grimes
- Division of Structural Biology, Centre for Human Genetics, University of Oxford, Oxford, UK.
| | - Ervin Fodor
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
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3
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Padykula I, Damodaran L, Young KT, Krunkosky M, Griffin EF, North JF, Neasham PJ, Pliasas VC, Siepker CL, Stanton JB, Howerth EW, Bahl J, Kyriakis CS, Tompkins SM. Pandemic Risk Assessment for Swine Influenza A Virus in Comparative In Vitro and In Vivo Models. Viruses 2024; 16:548. [PMID: 38675891 PMCID: PMC11053818 DOI: 10.3390/v16040548] [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: 02/29/2024] [Revised: 03/17/2024] [Accepted: 03/18/2024] [Indexed: 04/28/2024] Open
Abstract
Swine influenza A viruses pose a public health concern as novel and circulating strains occasionally spill over into human hosts, with the potential to cause disease. Crucial to preempting these events is the use of a threat assessment framework for human populations. However, established guidelines do not specify which animal models or in vitro substrates should be used. We completed an assessment of a contemporary swine influenza isolate, A/swine/GA/A27480/2019 (H1N2), using animal models and human cell substrates. Infection studies in vivo revealed high replicative ability and a pathogenic phenotype in the swine host, with replication corresponding to a complementary study performed in swine primary respiratory epithelial cells. However, replication was limited in human primary cell substrates. This contrasted with our findings in the Calu-3 cell line, which demonstrated a replication profile on par with the 2009 pandemic H1N1 virus. These data suggest that the selection of models is important for meaningful risk assessment.
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Affiliation(s)
- Ian Padykula
- Center for Vaccines and Immunology, University of Georgia, Athens, GA 30602, USA
- Department of Infectious Diseases, University of Georgia, Athens, GA 30602, USA
- Emory-UGA Centers of Excellence for Influenza Research and Surveillance (CEIRS), Athens, GA 30602, USA
| | - Lambodhar Damodaran
- Department of Infectious Diseases, University of Georgia, Athens, GA 30602, USA
- Emory-UGA Centers of Excellence for Influenza Research and Surveillance (CEIRS), Athens, GA 30602, USA
| | - Kelsey T. Young
- Department of Pathology, University of Georgia, Athens, GA 30602, USA
| | - Madelyn Krunkosky
- Center for Vaccines and Immunology, University of Georgia, Athens, GA 30602, USA
- Department of Infectious Diseases, University of Georgia, Athens, GA 30602, USA
- Emory-UGA Centers of Excellence for Influenza Research and Surveillance (CEIRS), Athens, GA 30602, USA
| | - Emily F. Griffin
- Center for Vaccines and Immunology, University of Georgia, Athens, GA 30602, USA
- Department of Infectious Diseases, University of Georgia, Athens, GA 30602, USA
- Emory-UGA Centers of Excellence for Influenza Research and Surveillance (CEIRS), Athens, GA 30602, USA
| | - James F. North
- Emory-UGA Centers of Excellence for Influenza Research and Surveillance (CEIRS), Athens, GA 30602, USA
- Department of Pathobiology, Auburn University, Auburn, AL 36849, USA
| | - Peter J. Neasham
- Emory-UGA Centers of Excellence for Influenza Research and Surveillance (CEIRS), Athens, GA 30602, USA
- Department of Pathobiology, Auburn University, Auburn, AL 36849, USA
| | - Vasilis C. Pliasas
- Emory-UGA Centers of Excellence for Influenza Research and Surveillance (CEIRS), Athens, GA 30602, USA
- Department of Pathobiology, Auburn University, Auburn, AL 36849, USA
| | - Chris L. Siepker
- Department of Pathology, University of Georgia, Athens, GA 30602, USA
| | - James B. Stanton
- Department of Pathology, University of Georgia, Athens, GA 30602, USA
| | | | - Justin Bahl
- Department of Infectious Diseases, University of Georgia, Athens, GA 30602, USA
| | - Constantinos S. Kyriakis
- Emory-UGA Centers of Excellence for Influenza Research and Surveillance (CEIRS), Athens, GA 30602, USA
- Department of Pathobiology, Auburn University, Auburn, AL 36849, USA
| | - Stephen Mark Tompkins
- Center for Vaccines and Immunology, University of Georgia, Athens, GA 30602, USA
- Department of Infectious Diseases, University of Georgia, Athens, GA 30602, USA
- Emory-UGA Centers of Excellence for Influenza Research and Surveillance (CEIRS), Athens, GA 30602, USA
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4
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Willett JDS, Gravel A, Dubuc I, Gudimard L, Dos Santos Pereira Andrade AC, Lacasse É, Fortin P, Liu JL, Cervantes JA, Galvez JH, Djambazian HHV, Zwaig M, Roy AM, Lee S, Chen SH, Ragoussis J, Flamand L. SARS-CoV-2 rapidly evolves lineage-specific phenotypic differences when passaged repeatedly in immune-naïve mice. Commun Biol 2024; 7:191. [PMID: 38365933 PMCID: PMC10873417 DOI: 10.1038/s42003-024-05878-3] [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: 05/21/2023] [Accepted: 02/01/2024] [Indexed: 02/18/2024] Open
Abstract
The persistence of SARS-CoV-2 despite the development of vaccines and a degree of herd immunity is partly due to viral evolution reducing vaccine and treatment efficacy. Serial infections of wild-type (WT) SARS-CoV-2 in Balb/c mice yield mouse-adapted strains with greater infectivity and mortality. We investigate if passaging unmodified B.1.351 (Beta) and B.1.617.2 (Delta) 20 times in K18-ACE2 mice, expressing the human ACE2 receptor, in a BSL-3 laboratory without selective pressures, drives human health-relevant evolution and if evolution is lineage-dependent. Late-passage virus causes more severe disease, at organism and lung tissue scales, with late-passage Delta demonstrating antibody resistance and interferon suppression. This resistance co-occurs with a de novo spike S371F mutation, linked with both traits. S371F, an Omicron-characteristic mutation, is co-inherited at times with spike E1182G per Nanopore sequencing, existing in different within-sample viral variants at others. Both S371F and E1182G are linked to mammalian GOLGA7 and ZDHHC5 interactions, which mediate viral-cell entry and antiviral response. This study demonstrates SARS-CoV-2's tendency to evolve with phenotypic consequences, its evolution varying by lineage, and suggests non-dominant quasi-species contribution.
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Affiliation(s)
- Julian Daniel Sunday Willett
- Quantitative Life Sciences Ph.D. Program, McGill University, Montreal, QC, Canada
- McGill Genome Centre, McGill University, Montreal, QC, Canada
- Lady Davis Institute, Jewish General Hospital, Montreal, QC, Canada
| | - Annie Gravel
- Axe maladies infectieuses et immunitaires, Centre de Recherche du Centre Hospitalier Universitaire de Québec- Université Laval, Québec, Canada
| | - Isabelle Dubuc
- Axe maladies infectieuses et immunitaires, Centre de Recherche du Centre Hospitalier Universitaire de Québec- Université Laval, Québec, Canada
| | - Leslie Gudimard
- Axe maladies infectieuses et immunitaires, Centre de Recherche du Centre Hospitalier Universitaire de Québec- Université Laval, Québec, Canada
| | | | - Émile Lacasse
- Axe maladies infectieuses et immunitaires, Centre de Recherche du Centre Hospitalier Universitaire de Québec- Université Laval, Québec, Canada
| | - Paul Fortin
- Axe maladies infectieuses et immunitaires, Centre de Recherche du Centre Hospitalier Universitaire de Québec- Université Laval, Québec, Canada
- Centre de Recherche ARThrite-Arthrite, Recherche et Traitements, Université Laval, Québec, QC, Canada
- Division of Rheumatology, Department of Medicine, CHU de Québec-Université Laval, Québec, QC, Canada
| | - Ju-Ling Liu
- McGill Genome Centre, McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Jose Avila Cervantes
- McGill Genome Centre, McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Jose Hector Galvez
- Canadian Centre for Computational Genomics, McGill University, Montreal, QC, Canada
| | - Haig Hugo Vrej Djambazian
- McGill Genome Centre, McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Melissa Zwaig
- McGill Genome Centre, McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Anne-Marie Roy
- McGill Genome Centre, McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Sally Lee
- McGill Genome Centre, McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Shu-Huang Chen
- McGill Genome Centre, McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Jiannis Ragoussis
- McGill Genome Centre, McGill University, Montreal, QC, Canada.
- Department of Human Genetics, McGill University, Montreal, QC, Canada.
| | - Louis Flamand
- Axe maladies infectieuses et immunitaires, Centre de Recherche du Centre Hospitalier Universitaire de Québec- Université Laval, Québec, Canada.
- Département de microbiologie-infectiologie et d'immunologie, Université Laval, Québec, QC, Canada.
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5
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Sheppard CM, Goldhill DH, Swann OC, Staller E, Penn R, Platt OK, Sukhova K, Baillon L, Frise R, Peacock TP, Fodor E, Barclay WS. An Influenza A virus can evolve to use human ANP32E through altering polymerase dimerization. Nat Commun 2023; 14:6135. [PMID: 37816726 PMCID: PMC10564888 DOI: 10.1038/s41467-023-41308-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 06/09/2023] [Indexed: 10/12/2023] Open
Abstract
Human ANP32A and ANP32B are essential but redundant host factors for influenza virus genome replication. While most influenza viruses cannot replicate in edited human cells lacking both ANP32A and ANP32B, some strains exhibit limited growth. Here, we experimentally evolve such an influenza A virus in these edited cells and unexpectedly, after 2 passages, we observe robust viral growth. We find two mutations in different subunits of the influenza polymerase that enable the mutant virus to use a novel host factor, ANP32E, an alternative family member, which is unable to support the wild type polymerase. Both mutations reside in the symmetric dimer interface between two polymerase complexes and reduce polymerase dimerization. These mutations have previously been identified as adapting influenza viruses to mice. Indeed, the evolved virus gains the ability to use suboptimal mouse ANP32 proteins and becomes more virulent in mice. We identify further mutations in the symmetric dimer interface which we predict allow influenza to adapt to use suboptimal ANP32 proteins through a similar mechanism. Overall, our results suggest a balance between asymmetric and symmetric dimers of influenza virus polymerase that is influenced by the interaction between polymerase and ANP32 host proteins.
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Affiliation(s)
- Carol M Sheppard
- Department of Infectious Disease, Imperial College London, London, UK.
| | - Daniel H Goldhill
- Department of Infectious Disease, Imperial College London, London, UK
- Department of Pathobiology and Population Sciences, Royal Veterinary College, London, UK
| | - Olivia C Swann
- Department of Infectious Disease, Imperial College London, London, UK
| | - Ecco Staller
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Rebecca Penn
- Department of Infectious Disease, Imperial College London, London, UK
| | - Olivia K Platt
- Department of Infectious Disease, Imperial College London, London, UK
| | - Ksenia Sukhova
- Department of Infectious Disease, Imperial College London, London, UK
| | - Laury Baillon
- Department of Infectious Disease, Imperial College London, London, UK
| | - Rebecca Frise
- Department of Infectious Disease, Imperial College London, London, UK
| | - Thomas P Peacock
- Department of Infectious Disease, Imperial College London, London, UK
| | - Ervin Fodor
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Wendy S Barclay
- Department of Infectious Disease, Imperial College London, London, UK.
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6
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Zhao C, Pu J. Influence of Host Sialic Acid Receptors Structure on the Host Specificity of Influenza Viruses. Viruses 2022; 14:v14102141. [PMID: 36298694 PMCID: PMC9608321 DOI: 10.3390/v14102141] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/20/2022] [Accepted: 09/23/2022] [Indexed: 11/23/2022] Open
Abstract
Influenza viruses need to use sialic acid receptors to invade host cells, and the α-2,3 and α-2,6 sialic acids glycosidic bonds linking the terminal sialic acids are generally considered to be the most important factors influencing the cross-species transmission of the influenza viruses. The development of methods to detect the binding of influenza virus HA proteins to sialic acid receptors, as well as the development of glycobiological techniques, has led to a richer understanding of the structure of the sialylated glycan in influenza virus hosts. It was found that, in addition to the sialic acid glycosidic bond, sialic acid variants, length of the sialylated glycan, Gal-GlcNAc-linked glycosidic bond within the sialylated glycan, and sulfation/fucosylation of the GlcNAc within the sialylated glycan all affect the binding properties of influenza viruses to the sialic acid receptors, thus indirectly affecting the host specificity of influenza viruses. This paper will review the sialic acid variants, internal structural differences of sialylated glycan molecules that affect the host specificity of influenza viruses, and distribution characteristics of sialic acid receptors in influenza virus hosts, in order to provide a more reliable theoretical basis for the in-depth investigation of cross-species transmission of influenza viruses and the development of new antiviral drugs.
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7
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Kadoya SS, Urayama SI, Nunoura T, Hirai M, Takaki Y, Kitajima M, Nakagomi T, Nakagomi O, Okabe S, Nishimura O, Sano D. The Intrapopulation Genetic Diversity of RNA Virus May Influence the Sensitivity of Chlorine Disinfection. Front Microbiol 2022; 13:839513. [PMID: 35668760 PMCID: PMC9163991 DOI: 10.3389/fmicb.2022.839513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 04/22/2022] [Indexed: 11/13/2022] Open
Abstract
RNA virus populations are not clonal; rather, they comprise a mutant swarm in which sequences are slightly different from the master sequence. Genetic diversity within a population (intrapopulation genetic diversity) is critical for RNA viruses to survive under environmental stresses. Disinfection has become an important practice in the control of pathogenic viruses; however, the impact of intrapopulation genetic diversity on the sensitivity of disinfection, defined as -log10 (postdisinfected infectious titer/predisinfected titer), has not been elucidated. In this study, we serially passaged populations of rhesus rotavirus. We demonstrated that populations with reduced chlorine sensitivity emerged at random and independently of chlorine exposure. Sequencing analysis revealed that compared with sensitive populations, less-sensitive ones had higher non-synonymous genetic diversity of the outer capsid protein gene, suggesting that changes in the amino acid sequences of the outer capsid protein were the main factors influencing chlorine sensitivity. No common mutations were found among less-sensitive populations, indicating that rather than specific mutations, the diversity of the outer capsid protein itself was associated with the disinfection sensitivity and that the disinfection sensitivity changed stochastically. Simulation results suggest that the disinfection sensitivity of a genetically diverse population is destabilized if cooperative viral clusters including multiple sequences are formed. These results advocate that any prevention measures leading to low intrapopulation genetic diversity are important to prevent the spread and evolution of pathogenic RNA viruses in society.
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Affiliation(s)
- Syun-suke Kadoya
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
- Department of Urban Engineering, The University of Tokyo, Tokyo, Japan
| | - Syun-ichi Urayama
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Research Center for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Miho Hirai
- Super-Cutting-Edge Grand and Advanced Research Program, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Yoshihiro Takaki
- Super-Cutting-Edge Grand and Advanced Research Program, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Masaaki Kitajima
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, Sapporo, Japan
| | - Toyoko Nakagomi
- Department of Molecular Microbiology and Immunology, Nagasaki University, Nagasaki, Japan
| | - Osamu Nakagomi
- Department of Molecular Microbiology and Immunology, Nagasaki University, Nagasaki, Japan
| | - Satoshi Okabe
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, Sapporo, Japan
| | - Osamu Nishimura
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - Daisuke Sano
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
- Department of Frontier Sciences for Advanced Environment, Graduate School of Environmental Studies, Tohoku University, Sendai, Japan
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8
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Swine H1N1 Influenza Virus Variants with Enhanced Polymerase Activity and HA Stability Promote Airborne Transmission in Ferrets. J Virol 2022; 96:e0010022. [DOI: 10.1128/jvi.00100-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Diverse IAVs circulate in animals, yet few acquire the viral traits needed to start a human pandemic. A stabilized HA and mammalian-adapted polymerase have been shown to promote the adaptation of IAVs to humans and ferrets (the gold-standard model for IAV replication, pathogenicity, and transmissibility).
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9
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Barnard KN, Wasik BR, Alford BK, Hayward JJ, Weichert WS, Voorhees IEH, Holmes EC, Parrish CR. Sequence dynamics of three influenza A virus strains grown in different MDCK cell lines, including those expressing different sialic acid receptors. J Evol Biol 2021; 34:1878-1900. [PMID: 34114711 DOI: 10.1111/jeb.13890] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 06/02/2021] [Accepted: 06/08/2021] [Indexed: 12/12/2022]
Abstract
Viruses are often cultured in cell lines for research and vaccine development, and those often differ from the natural hosts or tissues. Cell lines can also differ in the presence of virus receptors, such as the sialic acid (Sia) receptors used by influenza A viruses (IAV), which can vary in linkage (α2,3- or α2,6-linkage) and form (N-glycolylneuraminic acid [Neu5Gc] or N-acetylneuraminic acid [Neu5Ac]). The selective pressures resulting from passaging viruses in cell types with host-specific variations in viral receptors are still only partially understood. IAV are commonly cultured in MDCK cells which are both derived from canine kidney tubule epithelium and inherently heterogeneous. MDCK cells naturally present Neu5Ac and α2,3-linked Sia forms. Here, we examine natural MDCK variant lineages, as well as engineered variants that synthesize Neu5Gc and/or α2,6-linkages. We determined how viral genetic variation occurred within human H3N2, H1N1 pandemic and canine H3N2 IAV populations when serially passaged in MDCK cell lines that vary in cell type (MDCK-Type I or MDCK-Type II clones) and in Sia display. Deep sequencing of viral genomes showed small numbers of consensus-level mutations, mostly within the hemagglutinin (HA) gene. Both human IAV showed variants in the HA stem and the HA receptor-binding site of populations passaged in cells displaying Neu5Gc. Canine H3N2 showed variants near the receptor-binding site when passaged in cells displaying Neu5Gc or α2,6-linkages. Viruses replicated to low titres in MDCK-Type II cells, suggesting that not all cell types in heterogeneous MDCK cell populations are equally permissive to infection.
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Affiliation(s)
- Karen N Barnard
- Department of Microbiology and Immunology, College of Veterinary Medicine, Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA.,Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Brian R Wasik
- Department of Microbiology and Immunology, College of Veterinary Medicine, Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA
| | - Brynn K Alford
- Department of Microbiology and Immunology, College of Veterinary Medicine, Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA
| | - Jessica J Hayward
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Wendy S Weichert
- Department of Microbiology and Immunology, College of Veterinary Medicine, Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA
| | - Ian E H Voorhees
- Department of Microbiology and Immunology, College of Veterinary Medicine, Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Biological Sciences and School of Medical Sciences, University of Sydney, Sydney, NSW, Australia
| | - Colin R Parrish
- Department of Microbiology and Immunology, College of Veterinary Medicine, Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA
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10
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Plant EP, Manukyan H, Laassri M, Ye Z. Insights from the comparison of genomic variants from two influenza B viruses grown in the presence of human antibodies in cell culture. PLoS One 2020; 15:e0239015. [PMID: 32925936 PMCID: PMC7489522 DOI: 10.1371/journal.pone.0239015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 08/27/2020] [Indexed: 12/25/2022] Open
Abstract
Understanding the extent and limitation of viral genome evolution can provide insight about potential drug and vaccine targets. Influenza B Viruses (IBVs) infect humans in a seasonal manner and causes significant morbidity and mortality. IBVs are negative-sense single-stranded RNA viruses with a segmented genome and can be divided into two antigenically distinct lineages. The two lineages have been circulating and further evolving for almost four decades. The immune response to IBV infection can lead to antibodies that target the strain causing the infection. Some antibodies are cross-reactive and are able to bind strains from both lineages but, because of antigenic drift and immunodominance, both lineages continue to evolve and challenge human health. Here we investigate changes in the genomes of an IBVs from each lineage after passage in tissue culture in the presence of human sera containing polyclonal antibodies directed toward antigenically and temporally distinct viruses. Our previous analysis of the fourth segment, which encodes the major surface protein HA, revealed a pattern of change in which signature sequences from one lineage mutated to the signature sequences of the other lineage. Here we analyze genes from the other genomic segments and observe that most of the quasispecies’ heterogeneity occurs at the same loci in each lineage. The nature of the variants at these loci are investigated and possible reasons for this pattern are discussed. This work expands our understanding of the extent and limitations of genomic change in IBV.
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Affiliation(s)
- Ewan P. Plant
- Office of Vaccine Research and Review, US Food and Drug Administration, Silver Spring, Maryland, United States of America
- * E-mail:
| | - Hasmik Manukyan
- Office of Vaccine Research and Review, US Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Majid Laassri
- Office of Vaccine Research and Review, US Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Zhiping Ye
- Office of Vaccine Research and Review, US Food and Drug Administration, Silver Spring, Maryland, United States of America
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11
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Kadoya SS, Urayama SI, Nunoura T, Hirai M, Takaki Y, Kitajima M, Nakagomi T, Nakagomi O, Okabe S, Nishimura O, Sano D. Bottleneck Size-Dependent Changes in the Genetic Diversity and Specific Growth Rate of a Rotavirus A Strain. J Virol 2020; 94:e02083-19. [PMID: 32132235 PMCID: PMC7199400 DOI: 10.1128/jvi.02083-19] [Citation(s) in RCA: 12] [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: 12/16/2019] [Accepted: 02/21/2020] [Indexed: 12/24/2022] Open
Abstract
RNA viruses form a dynamic distribution of mutant swarms (termed "quasispecies") due to the accumulation of mutations in the viral genome. The genetic diversity of a viral population is affected by several factors, including a bottleneck effect. Human-to-human transmission exemplifies a bottleneck effect, in that only part of a viral population can reach the next susceptible hosts. In the present study, two lineages of the rhesus rotavirus (RRV) strain of rotavirus A were serially passaged five times at a multiplicity of infection (MOI) of 0.1 or 0.001, and three phenotypes (infectious titer, cell binding ability, and specific growth rate) were used to evaluate the impact of a bottleneck effect on the RRV population. The specific growth rate values of lineages passaged under the stronger bottleneck (MOI of 0.001) were higher after five passages. The nucleotide diversity also increased, which indicated that the mutant swarms of the lineages under the stronger bottleneck effect were expanded through the serial passages. The random distribution of synonymous and nonsynonymous substitutions on rotavirus genome segments indicated that almost all mutations were selectively neutral. Simple simulations revealed that the presence of minor mutants could influence the specific growth rate of a population in a mutant frequency-dependent manner. These results indicate a stronger bottleneck effect can create more sequence spaces for minor sequences.IMPORTANCE In this study, we investigated a bottleneck effect on an RRV population that may drastically affect the viral population structure. RRV populations were serially passaged under two levels of a bottleneck effect, which exemplified human-to-human transmission. As a result, the genetic diversity and specific growth rate of RRV populations increased under the stronger bottleneck effect, which implied that a bottleneck created a new space in a population for minor mutants originally existing in a hidden layer, which includes minor mutations that cannot be distinguished from a sequencing error. The results of this study suggest that the genetic drift caused by a bottleneck in human-to-human transmission explains the random appearance of new genetic lineages causing viral outbreaks, which can be expected according to molecular epidemiology using next-generation sequencing in which the viral genetic diversity within a viral population is investigated.
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Affiliation(s)
- Syun-Suke Kadoya
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Aoba-ku, Sendai, Miyagi, Japan
| | - Syun-Ichi Urayama
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Miho Hirai
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Yoshihiro Takaki
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Masaaki Kitajima
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Toyoko Nakagomi
- Department of Molecular Microbiology and Immunology, Nagasaki University, Nagasaki, Japan
| | - Osamu Nakagomi
- Department of Molecular Microbiology and Immunology, Nagasaki University, Nagasaki, Japan
| | - Satoshi Okabe
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Osamu Nishimura
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Aoba-ku, Sendai, Miyagi, Japan
| | - Daisuke Sano
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Aoba-ku, Sendai, Miyagi, Japan
- Department of Environmental Studies, Tohoku University, Aoba-ku, Sendai, Miyagi, Japan
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12
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Barnard KN, Alford-Lawrence BK, Buchholz DW, Wasik BR, LaClair JR, Yu H, Honce R, Ruhl S, Pajic P, Daugherity EK, Chen X, Schultz-Cherry SL, Aguilar HC, Varki A, Parrish CR. Modified Sialic Acids on Mucus and Erythrocytes Inhibit Influenza A Virus Hemagglutinin and Neuraminidase Functions. J Virol 2020; 94:e01567-19. [PMID: 32051275 PMCID: PMC7163148 DOI: 10.1128/jvi.01567-19] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 02/04/2020] [Indexed: 12/13/2022] Open
Abstract
Sialic acids (Sia) are the primary receptors for influenza viruses and are widely displayed on cell surfaces and in secreted mucus. Sia may be present in variant forms that include O-acetyl modifications at C-4, C-7, C-8, and C-9 positions and N-acetyl or N-glycolyl at C-5. They can also vary in their linkages, including α2-3 or α2-6 linkages. Here, we analyze the distribution of modified Sia in cells and tissues of wild-type mice or in mice lacking CMP-N-acetylneuraminic acid hydroxylase (CMAH) enzyme, which synthesizes N-glycolyl (Neu5Gc) modifications. We also examined the variation of Sia forms on erythrocytes and in saliva from different animals. To determine the effect of Sia modifications on influenza A virus (IAV) infection, we tested for effects on hemagglutinin (HA) binding and neuraminidase (NA) cleavage. We confirmed that 9-O-acetyl, 7,9-O-acetyl, 4-O-acetyl, and Neu5Gc modifications are widely but variably expressed in mouse tissues, with the highest levels detected in the respiratory and gastrointestinal (GI) tracts. Secreted mucins in saliva and surface proteins of erythrocytes showed a high degree of variability in display of modified Sia between different species. IAV HAs from different virus strains showed consistently reduced binding to both Neu5Gc- and O-acetyl-modified Sia; however, while IAV NAs were inhibited by Neu5Gc and O-acetyl modifications, there was significant variability between NA types. The modifications of Sia in mucus may therefore have potent effects on the functions of IAV and may affect both pathogens and the normal flora of different mucosal sites.IMPORTANCE Sialic acids (Sia) are involved in numerous different cellular functions and are receptors for many pathogens. Sia come in chemically modified forms, but we lack a clear understanding of how they alter interactions with microbes. Here, we examine the expression of modified Sia in mouse tissues, on secreted mucus in saliva, and on erythrocytes, including those from IAV host species and animals used in IAV research. These Sia forms varied considerably among different animals, and their inhibitory effects on IAV NA and HA activities and on bacterial sialidases (neuraminidases) suggest a host-variable protective role in secreted mucus.
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Affiliation(s)
- Karen N Barnard
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Brynn K Alford-Lawrence
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - David W Buchholz
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Brian R Wasik
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Justin R LaClair
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Hai Yu
- Department of Chemistry, University of California-Davis, Davis, California, USA
| | - Rebekah Honce
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
- Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Stefan Ruhl
- Department of Oral Biology, University at Buffalo, Buffalo, New York, USA
| | - Petar Pajic
- Department of Oral Biology, University at Buffalo, Buffalo, New York, USA
| | - Erin K Daugherity
- Center for Animal Resources and Education, Cornell University, Ithaca, New York, USA
| | - Xi Chen
- Department of Chemistry, University of California-Davis, Davis, California, USA
| | - Stacey L Schultz-Cherry
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Hector C Aguilar
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Ajit Varki
- Glycobiology Research and Training Center, University of California, San Diego, California, USA
| | - Colin R Parrish
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
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13
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Identification and Characterization of Novel Compounds with Broad-Spectrum Antiviral Activity against Influenza A and B Viruses. J Virol 2020; 94:JVI.02149-19. [PMID: 31941776 DOI: 10.1128/jvi.02149-19] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 12/24/2019] [Indexed: 12/23/2022] Open
Abstract
Influenza A (IAV) and influenza B (IBV) viruses are highly contagious pathogens that cause fatal respiratory disease every year, with high economic impact. In addition, IAV can cause pandemic infections with great consequences when new viruses are introduced into humans. In this study, we evaluated 10 previously described compounds with antiviral activity against mammarenaviruses for their ability to inhibit IAV infection using our recently described bireporter influenza A/Puerto Rico/8/34 (PR8) H1N1 (BIRFLU). Among the 10 tested compounds, eight (antimycin A [AmA], brequinar [BRQ], 6-azauridine, azaribine, pyrazofurin [PF], AVN-944, mycophenolate mofetil [MMF], and mycophenolic acid [MPA]), but not obatoclax or Osu-03012, showed potent anti-influenza virus activity under posttreatment conditions [median 50% effective concentration (EC50) = 3.80 nM to 1.73 μM; selective index SI for 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide (MTT) assay, >28.90 to 13,157.89]. AmA, 6-azauridine, azaribine, and PF also showed potent inhibitory effect in pretreatment (EC50 = 0.14 μM to 0.55 μM; SI-MTT = 70.12 to >357.14) or cotreatment (EC50 = 34.69 nM to 7.52 μM; SI-MTT = 5.24 to > 1,441.33) settings. All of the compounds tested inhibited viral genome replication and gene transcription, and none of them affected host cellular RNA polymerase II activities. The antiviral activity of the eight identified compounds against BIRFLU was further confirmed with seasonal IAVs (A/California/04/2009 H1N1 and A/Wyoming/3/2003 H3N2) and an IBV (B/Brisbane/60/2008, Victoria lineage), demonstrating their broad-spectrum prophylactic and therapeutic activity against currently circulating influenza viruses in humans. Together, our results identified a new set of antiviral compounds for the potential treatment of influenza viral infections.IMPORTANCE Influenza viruses are highly contagious pathogens and are a major threat to human health. Vaccination remains the most effective tool to protect humans against influenza infection. However, vaccination does not always guarantee complete protection against drifted or, more noticeably, shifted influenza viruses. Although U.S. Food and Drug Administration (FDA) drugs are approved for the treatment of influenza infections, influenza viruses resistant to current FDA antivirals have been reported and continue to emerge. Therefore, there is an urgent need to find novel antivirals for the treatment of influenza viral infections in humans, a search that could be expedited by repurposing currently approved drugs. In this study, we assessed the influenza antiviral activity of 10 compounds previously shown to inhibit mammarenavirus infection. Among them, eight drugs showed antiviral activities, providing a new battery of drugs that could be used for the treatment of influenza infections.
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14
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Wasik BR, Voorhees IEH, Barnard KN, Alford-Lawrence BK, Weichert WS, Hood G, Nogales A, Martínez-Sobrido L, Holmes EC, Parrish CR. Influenza Viruses in Mice: Deep Sequencing Analysis of Serial Passage and Effects of Sialic Acid Structural Variation. J Virol 2019; 93:e01039-19. [PMID: 31511393 PMCID: PMC6854484 DOI: 10.1128/jvi.01039-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 09/09/2019] [Indexed: 12/19/2022] Open
Abstract
Influenza A viruses have regularly jumped to new host species to cause epidemics or pandemics, an evolutionary process that involves variation in the viral traits necessary to overcome host barriers and facilitate transmission. Mice are not a natural host for influenza virus but are frequently used as models in studies of pathogenesis, often after multiple passages to achieve higher viral titers that result in clinical disease such as weight loss or death. Here, we examine the processes of influenza A virus infection and evolution in mice by comparing single nucleotide variations of a human H1N1 pandemic virus, a seasonal H3N2 virus, and an H3N2 canine influenza virus during experimental passage. We also compared replication and sequence variation in wild-type mice expressing N-glycolylneuraminic acid (Neu5Gc) with those seen in mice expressing only N-acetylneuraminic acid (Neu5Ac). Viruses derived from plasmids were propagated in MDCK cells and then passaged in mice up to four times. Full-genome deep sequencing of the plasmids, cultured viruses, and viruses from mice at various passages revealed only small numbers of mutational changes. The H3N2 canine influenza virus showed increases in frequency of sporadic mutations in the PB2, PA, and NA segments. The H1N1 pandemic virus grew well in mice, and while it exhibited the maintenance of some minority mutations, there was no clear evidence for adaptive evolution. The H3N2 seasonal virus did not establish in the mice. Finally, there were no clear sequence differences associated with the presence or absence of Neu5Gc.IMPORTANCE Mice are commonly used as a model to study the growth and virulence of influenza A viruses in mammals but are not a natural host and have distinct sialic acid receptor profiles compared to humans. Using experimental infections with different subtypes of influenza A virus derived from different hosts, we found that evolution of influenza A virus in mice did not necessarily proceed through the linear accumulation of host-adaptive mutations, that there was variation in the patterns of mutations detected in each repetition, and that the mutation dynamics depended on the virus examined. In addition, variation in the viral receptor, sialic acid, did not affect influenza virus evolution in this model. Overall, our results show that while mice provide a useful animal model for influenza virus pathology, host passage evolution will vary depending on the specific virus tested.
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Affiliation(s)
- Brian R Wasik
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Ian E H Voorhees
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Karen N Barnard
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Brynn K Alford-Lawrence
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Wendy S Weichert
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Grace Hood
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
- College of Veterinary Medicine, University of Queensland, Gatton, Queensland, Australia
| | - Aitor Nogales
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Luis Martínez-Sobrido
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Biological Sciences and Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Colin R Parrish
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
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