1
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Focosi D, Maggi F. Second-Generation SARS-CoV-2 Recombinants: Lessons from Other Viruses. Viruses 2023; 15:v15051063. [PMID: 37243149 DOI: 10.3390/v15051063] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 04/26/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
RNA viruses have developed notable strategies to evolve and escape host immunity [...].
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Affiliation(s)
- Daniele Focosi
- North-Western Tuscany Blood Bank, Pisa University Hospital, 56124 Pisa, Italy
| | - Fabrizio Maggi
- National Institute for Infectious Diseases "Lazzaro Spallanzani", 00149 Rome, Italy
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2
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de Bruin ACM, Funk M, Spronken MI, Gultyaev AP, Fouchier RAM, Richard M. Hemagglutinin Subtype Specificity and Mechanisms of Highly Pathogenic Avian Influenza Virus Genesis. Viruses 2022; 14:v14071566. [PMID: 35891546 PMCID: PMC9321182 DOI: 10.3390/v14071566] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 02/04/2023] Open
Abstract
Highly Pathogenic Avian Influenza Viruses (HPAIVs) arise from low pathogenic precursors following spillover from wild waterfowl into poultry populations. The main virulence determinant of HPAIVs is the presence of a multi-basic cleavage site (MBCS) in the hemagglutinin (HA) glycoprotein. The MBCS allows for HA cleavage and, consequently, activation by ubiquitous proteases, which results in systemic dissemination in terrestrial poultry. Since 1959, 51 independent MBCS acquisition events have been documented, virtually all in HA from the H5 and H7 subtypes. In the present article, data from natural LPAIV to HPAIV conversions and experimental in vitro and in vivo studies were reviewed in order to compile recent advances in understanding HA cleavage efficiency, protease usage, and MBCS acquisition mechanisms. Finally, recent hypotheses that might explain the unique predisposition of the H5 and H7 HA sequences to obtain an MBCS in nature are discussed.
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Affiliation(s)
- Anja C. M. de Bruin
- Department of Viroscience, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands; (A.C.M.d.B.); (M.F.); (M.I.S.); (A.P.G.); (R.A.M.F.)
| | - Mathis Funk
- Department of Viroscience, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands; (A.C.M.d.B.); (M.F.); (M.I.S.); (A.P.G.); (R.A.M.F.)
| | - Monique I. Spronken
- Department of Viroscience, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands; (A.C.M.d.B.); (M.F.); (M.I.S.); (A.P.G.); (R.A.M.F.)
| | - Alexander P. Gultyaev
- Department of Viroscience, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands; (A.C.M.d.B.); (M.F.); (M.I.S.); (A.P.G.); (R.A.M.F.)
- Group Imaging and Bioinformatics, Leiden Institute of Advanced Computer Science (LIACS), Leiden University, 2300 RA Leiden, The Netherlands
| | - Ron A. M. Fouchier
- Department of Viroscience, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands; (A.C.M.d.B.); (M.F.); (M.I.S.); (A.P.G.); (R.A.M.F.)
| | - Mathilde Richard
- Department of Viroscience, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands; (A.C.M.d.B.); (M.F.); (M.I.S.); (A.P.G.); (R.A.M.F.)
- Correspondence:
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3
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Affiliation(s)
- Farid Rahimi
- Research School of Biology, The Australian National University, Ngunnawal and Ngambri Country, Canberra, Australia
| | - Amin Talebi Bezmin Abadi
- Department of Bacteriology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran.
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4
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Zhou A, Zhang J, Li H, Xu Q, Chen Y, Li B, Liu W, Su G, Ren X, Lao G, Luo B, Liao M, Qi W. Combined insertion of basic and non-basic amino acids at hemagglutinin cleavage site of highly pathogenic H7N9 virus promotes replication and pathogenicity in chickens and mice. Virol Sin 2022; 37:38-47. [PMID: 35234617 PMCID: PMC8922421 DOI: 10.1016/j.virs.2022.01.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 07/22/2021] [Indexed: 12/22/2022] Open
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5
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Gultyaev AP, Spronken MI, Funk M, Fouchier RAM, Richard M. Insertions of codons encoding basic amino acids in H7 hemagglutinins of influenza A viruses occur by recombination with RNA at hotspots near snoRNA binding sites. RNA (NEW YORK, N.Y.) 2021; 27:123-132. [PMID: 33188057 PMCID: PMC7812872 DOI: 10.1261/rna.077495.120] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 11/06/2020] [Indexed: 06/11/2023]
Abstract
The presence of multiple basic amino acids in the protease cleavage site of the hemagglutinin (HA) protein is the main molecular determinant of virulence of highly pathogenic avian influenza (HPAI) viruses. Recombination of HA RNA with other RNA molecules of host or virus origin is a dominant mechanism of multibasic cleavage site (MBCS) acquisition for H7 subtype HA. Using alignments of HA RNA sequences from documented cases of MBCS insertion due to recombination, we show that such recombination with host RNAs is most likely to occur at particular hotspots in ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), and viral RNAs. The locations of these hotspots in highly abundant RNAs indicate that RNA recombination is facilitated by the binding of small nucleolar RNA (snoRNA) near the recombination points.
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MESH Headings
- Amino Acids, Basic/genetics
- Amino Acids, Basic/metabolism
- Animals
- Base Pairing
- Base Sequence
- Chickens/virology
- Codon
- Gene Expression Regulation
- Hemagglutinin Glycoproteins, Influenza Virus/genetics
- Hemagglutinin Glycoproteins, Influenza Virus/metabolism
- Host-Pathogen Interactions/genetics
- Humans
- Influenza A virus/genetics
- Influenza A virus/metabolism
- Influenza A virus/pathogenicity
- Influenza in Birds/virology
- Influenza, Human/virology
- Mutagenesis, Insertional
- RNA, Small Nucleolar/chemistry
- RNA, Small Nucleolar/genetics
- RNA, Small Nucleolar/metabolism
- RNA, Viral/chemistry
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Recombination, Genetic
- Sequence Alignment
- Virulence
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Affiliation(s)
- Alexander P Gultyaev
- Department of Viroscience, Erasmus Medical Center, 3000 CA Rotterdam, the Netherlands
- Group Imaging and Bioinformatics, Leiden Institute of Advanced Computer Science (LIACS), Leiden University, 2300 RA Leiden, the Netherlands
| | - Monique I Spronken
- Department of Viroscience, Erasmus Medical Center, 3000 CA Rotterdam, the Netherlands
| | - Mathis Funk
- Department of Viroscience, Erasmus Medical Center, 3000 CA Rotterdam, the Netherlands
| | - Ron A M Fouchier
- Department of Viroscience, Erasmus Medical Center, 3000 CA Rotterdam, the Netherlands
| | - Mathilde Richard
- Department of Viroscience, Erasmus Medical Center, 3000 CA Rotterdam, the Netherlands
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6
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Cárdenas M, Galleguillos C, Acevedo K, Ananias C, Alarcón J, Michelson S, Toledo J, Montoya M, Meneses C, Castro-Nallar E, Vásquez-Martínez Y, Cortez-San Martin M. Rapid sequence modification in the highly polymorphic region (HPR) of the hemagglutinin gene of the infectious salmon anaemia virus (ISAV) suggests intra-segmental template switching recombination. JOURNAL OF FISH DISEASES 2020; 43:1483-1496. [PMID: 32955147 DOI: 10.1111/jfd.13242] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 07/11/2020] [Accepted: 07/13/2020] [Indexed: 06/11/2023]
Abstract
The ISAV has a genome composed of eight segments of (-)ssRNA, segment 6 codes for the hemagglutinin-esterase protein, and has the most variable region of the genome, the highly polymorphic region (HPR), which is unique among orthomyxoviruses. The HPR has been associated with virulence, infectivity and pathogenicity. The full length of the HPR is called HPR0 and the strain with this HPR is avirulent, in contrast to strains with deleted HPR that are virulent to varying degrees. The molecular mechanism that gives rise to the different HPRs remains unclear. Here, we studied in vitro the evolution of reassortant recombinant ISAV (rISAV) in Atlantic salmon head kidney (ASK) cells. To this end, we rescued and cultivated a set of rISAV with different segment 6-HPR genotypes using a reverse genetics system and then sequencing HPR regions of the viruses. Our results show rapid multiple recombination events in ISAV, with sequence insertions and deletions in the HPR, indicating a dynamic process. Inserted sequences can be found in four segments of the ISAV genome (segments 1, 5, 6, and 8). The results suggest intra-segmental heterologous recombination, probably by class I and class II template switching, similar to the proposed segment 5 recombination mechanism.
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Affiliation(s)
- Matías Cárdenas
- Molecular Virology and Pathogen Control Laboratory, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Claudia Galleguillos
- Molecular Virology and Pathogen Control Laboratory, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Karina Acevedo
- Molecular Virology and Pathogen Control Laboratory, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Catarina Ananias
- Molecular Virology and Pathogen Control Laboratory, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Javiera Alarcón
- Molecular Virology and Pathogen Control Laboratory, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Sofía Michelson
- Molecular Virology and Pathogen Control Laboratory, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Jorge Toledo
- Biotechnology and Biopharmaceutical Laboratory, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Margarita Montoya
- Cell Biochemistry Laboratory, Department of Biology, Faculty of Chemistry and Biology, University of Santiago, Santiago, Chile
| | - Claudio Meneses
- Plant Biotechnology Center, Andres Bello University, Santiago, Chile
| | - Eduardo Castro-Nallar
- Center of Bioinformatics and Integrative Biology, Faculty of Life Sciences, University Andrés Bello, Santiago, Chile
| | - Yesseny Vásquez-Martínez
- Molecular Virology and Pathogen Control Laboratory, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago, Chile
- Programa Centro de Investigaciones Biomédicas Aplicadas, Facultad de Ciencias Médicas, University of Santiago de Chile, Santiago, Chile
| | - Marcelo Cortez-San Martin
- Molecular Virology and Pathogen Control Laboratory, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago, Chile
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7
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Emergence of highly pathogenic H5N2 and H7N1 influenza A viruses from low pathogenic precursors by serial passage in ovo. PLoS One 2020; 15:e0240290. [PMID: 33031421 PMCID: PMC7544131 DOI: 10.1371/journal.pone.0240290] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 09/24/2020] [Indexed: 02/01/2023] Open
Abstract
Highly pathogenic (HPAI) strains emerge from their low pathogenic (LPAI) precursors and cause severe disease in poultry with enormous economic losses, and zoonotic potential. Understanding the mechanisms involved in HPAI emergence is thus an important goal for risk assessments. In this study ostrich-origin H5N2 and H7N1 LPAI progenitor viruses were serially passaged seventeen times in 14-day old embryonated chicken eggs and Ion Torrent ultra-deep sequencing was used to monitor the incremental changes in the consensus genome sequences. Both virus strains increased in virulence with successive passages, but the H7N1 virus attained a virulent phenotype sooner. Mutations V63M, E228V and D272G in the HA protein, Q357K in the nucleoprotein (NP) and H155P in the neuraminidase protein correlated with the increased pathogenicity of the H5N2 virus; whereas R584H and L589I substitutions in the polymerase B2 protein, A146T and Q220E in HA plus D231N in the matrix 1 protein correlated with increased pathogenicity of the H7N1 virus in embryos. Enzymatic cleavage of HA protein is the critical virulence determinant, and HA cleavage site motifs containing multibasic amino acids were detected at the sub-consensus level. The motifs PQERRR/GLF and PQRERR/GLF were first detected in passages 11 and 15 respectively of the H5N2 virus, and in the H7N1 virus the motifs PELPKGKK/GLF and PELPKRR/GLF were detected as early as passage 7. Most significantly, a 13 nucleotide insert of unknown origin was identified at passage 6 of the H5N2 virus, and at passage 17 a 42 nucleotide insert derived from the influenza NP gene was identified. This is the first report of non-homologous recombination at the HA cleavage site in an H5 subtype virus. This study provides insights into how HPAI viruses emerge from low pathogenic precursors and demonstrated the pathogenic potential of H5N2 and H7N1 strains that have not yet been implicated in HPAI outbreaks.
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8
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Abstract
The earliest recorded cases of what was likely high-pathogenicity AIV in poultry were reported in Italy in the 1870s. Avian influenza infection has been recognized in domestic poultry through the modern era of poultry production. Infection of poultry with either low pathogenic (LP) or highly pathogenic (HP) avian influenza viruses (AIVs) can result in substantial economic consequences. Productivity can be reduced directly and indirectly because of disease leading to decreased egg or meat yield, mortality, vaccination costs, and restricted trade. Aquatic birds are the natural hosts for AIV, and infection tends to be subclinical, although some strains of HPAIV can cause losses in domestic ducks. Biosecurity and vaccination are the most common methods of preventing infection of poultry. Approaches to AIV control vary widely, but elimination of the disease in poultry is a common goal. The basics of AIV biology, clinical disease, molecular aspects, and AIV detection are briefly reviewed.
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Affiliation(s)
- Erica Spackman
- Exotic and Emerging Avian Viral Diseases Unit, US National Poultry Research Center, US Department of Agriculture, Agricultural Research Service, Athens, GA, USA.
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9
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Evolution of Influenza A Virus by Mutation and Re-Assortment. Int J Mol Sci 2017; 18:ijms18081650. [PMID: 28783091 PMCID: PMC5578040 DOI: 10.3390/ijms18081650] [Citation(s) in RCA: 179] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Revised: 07/20/2017] [Accepted: 07/24/2017] [Indexed: 12/13/2022] Open
Abstract
Influenza A virus (IAV), a highly infectious respiratory pathogen, has continued to be a significant threat to global public health. To complete their life cycle, influenza viruses have evolved multiple strategies to interact with a host. A large number of studies have revealed that the evolution of influenza A virus is mainly mediated through the mutation of the virus itself and the re-assortment of viral genomes derived from various strains. The evolution of influenza A virus through these mechanisms causes worldwide annual epidemics and occasional pandemics. Importantly, influenza A virus can evolve from an animal infected pathogen to a human infected pathogen. The highly pathogenic influenza virus has resulted in stupendous economic losses due to its morbidity and mortality both in human and animals. Influenza viruses fall into a category of viruses that can cause zoonotic infection with stable adaptation to human, leading to sustained horizontal transmission. The rapid mutations of influenza A virus result in the loss of vaccine optimal efficacy, and challenge the complete eradication of the virus. In this review, we highlight the current understanding of influenza A virus evolution caused by the mutation and re-assortment of viral genomes. In addition, we discuss the specific mechanisms by which the virus evolves.
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10
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De A, Sarkar T, Nandy A. Bioinformatics studies of Influenza A hemagglutinin sequence data indicate recombination-like events leading to segment exchanges. BMC Res Notes 2016; 9:222. [PMID: 27083561 PMCID: PMC4832483 DOI: 10.1186/s13104-016-2017-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 03/31/2016] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND The influenza genome is highly variable due primarily to two mechanisms: antigenic drift and antigenic shift. A third mechanism for genetic change, known as copy choice or template switching, can arise during replication when, if two viral strains infect a cell, a part of a gene from the second viral strain can be copied into the growing progeny of a gene of the first viral strain as replacement leading to a new variety of the virus. This template switching between the same genes of the two strains is known as homologous recombination. While genetic drift and shift are well-understood, the presence or absence of intra-segment homologous recombination in influenza genomes is controversial. CONTEXT AND PURPOSE OF STUDY We are interested to study the possibility of subunit-wise homologous recombination. The idea is that where well-defined subunits are separated by consensus sequences, it might be possible for template switching to take place at such junctions. The influenza hemagglutinin gene has basically two subunits, HA1 and HA2, with HA1 being mostly surface exposed and containing the active site for binding to cells, while HA2 secures the hemagglutinin to the viral coat. We undertook a thorough search of the major human infecting influenza hemagglutinin gene sequences, viz., the H1N1, H5N1, H3N2 and H7N9 subtypes, over the period 2010-2014 in Asia to determine if certain sequences could be identified that had HA1 from a previous strain and HA2 from another. RESULTS Our search yielded several instances where sequence identities between segments of various strains could be interpreted as indicating possibilities of segment exchange. In some cases, on closer examination they turn out to differ by a few mutations in each segment, due perhaps to the short time span of our database. CONCLUSIONS AND POTENTIAL IMPLICATIONS The study reported here, and in combination with our earlier observations on the neuraminidase, shows that subunit-wise recombination-like events in the influenza genes may be occurring more often than have been accounted for and merits further detailed studies.
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Affiliation(s)
- Antara De
- Centre for Interdisciplinary Research and Education, 404B Jodhpur Park, Kolkata, 700068, India.
| | - Tapati Sarkar
- Physics Department, Jadavpur University, Jadavpur, Kolkata, 700032, India
| | - Ashesh Nandy
- Centre for Interdisciplinary Research and Education, 404B Jodhpur Park, Kolkata, 700068, India
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11
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Sun X, Belser JA, Tumpey TM. A novel eight amino acid insertion contributes to the hemagglutinin cleavability and the virulence of a highly pathogenic avian influenza A (H7N3) virus in mice. Virology 2015; 488:120-8. [PMID: 26629952 DOI: 10.1016/j.virol.2015.10.032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Revised: 10/15/2015] [Accepted: 10/29/2015] [Indexed: 01/01/2023]
Abstract
In 2012, an avian influenza A H7N3 (A/Mexico/InDRE7218/2012; Mx/7218) virus was responsible for two confirmed cases of human infection and led to the death or culling of more than 22 million chickens in Jalisco, Mexico. Interestingly, this virus acquired an 8-amino acid (aa)-insertion (..PENPK-DRKSRHRR-TR/GLF) near the hemagglutinin (HA) cleavage site by nonhomologous recombination with host rRNA. It remains unclear which specific residues at the cleavage site contribute to the virulence of H7N3 viruses in mammals. Using loss-of-function approaches, we generated a series of cleavage site mutant viruses by reverse genetics and characterized the viruses in vitro and in vivo. We found that the 8-aa insertion and the arginine at position P4 of the Mx/7218 HA cleavage site are essential for intracellular HA cleavage in 293T cells, but have no effect on the pH of membrane fusion. However, we identified a role for the histidine residue at P5 position in viral fusion pH. In mice, the 8-aa insertion is required for Mx/7218 virus virulence; however, the basic residues upstream of the P4 position are dispensable for virulence. Overall, our study provides the first line of evidence that the insertion in the Mx/7218 virus HA cleavage site confers its intracellular cleavability, and consequently contributes to enhanced virulence in mice.
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Affiliation(s)
- Xiangjie Sun
- Immunology and Pathogenesis Branch, Influenza Division, National Center for Immunology and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Jessica A Belser
- Immunology and Pathogenesis Branch, Influenza Division, National Center for Immunology and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Terrence M Tumpey
- Immunology and Pathogenesis Branch, Influenza Division, National Center for Immunology and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA.
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12
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Luczo JM, Stambas J, Durr PA, Michalski WP, Bingham J. Molecular pathogenesis of H5 highly pathogenic avian influenza: the role of the haemagglutinin cleavage site motif. Rev Med Virol 2015; 25:406-30. [PMID: 26467906 PMCID: PMC5057330 DOI: 10.1002/rmv.1846] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 06/09/2015] [Accepted: 06/11/2015] [Indexed: 11/22/2022]
Abstract
The emergence of H5N1 highly pathogenic avian influenza has caused a heavy socio‐economic burden through culling of poultry to minimise human and livestock infection. Although human infections with H5N1 have to date been limited, concerns for the pandemic potential of this zoonotic virus have been greatly intensified following experimental evidence of aerosol transmission of H5N1 viruses in a mammalian infection model. In this review, we discuss the dominance of the haemagglutinin cleavage site motif as a pathogenicity determinant, the host‐pathogen molecular interactions driving cleavage activation, reverse genetics manipulations and identification of residues key to haemagglutinin cleavage site functionality and the mechanisms of cell and tissue damage during H5N1 infection. We specifically focus on the disease in chickens, as it is in this species that high pathogenicity frequently evolves and from which transmission to the human population occurs. With >75% of emerging infectious diseases being of zoonotic origin, it is necessary to understand pathogenesis in the primary host to explain spillover events into the human population. © 2015 The Authors. Reviews in Medical Virology published by John Wiley & Sons Ltd.
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Affiliation(s)
- Jasmina M Luczo
- Australian Animal Health Laboratory, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Geelong, Victoria, Australia.,School of Medicine, Deakin University, Geelong, Victoria, Australia
| | - John Stambas
- School of Medicine, Deakin University, Geelong, Victoria, Australia
| | - Peter A Durr
- Australian Animal Health Laboratory, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Geelong, Victoria, Australia
| | - Wojtek P Michalski
- Australian Animal Health Laboratory, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Geelong, Victoria, Australia
| | - John Bingham
- Australian Animal Health Laboratory, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Geelong, Victoria, Australia
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13
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Bulla I, Schultz AK, Chesneau C, Mark T, Serea F. A model-based information sharing protocol for profile Hidden Markov Models used for HIV-1 recombination detection. BMC Bioinformatics 2014; 15:205. [PMID: 24946781 PMCID: PMC4230192 DOI: 10.1186/1471-2105-15-205] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 06/04/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In many applications, a family of nucleotide or protein sequences classified into several subfamilies has to be modeled. Profile Hidden Markov Models (pHMMs) are widely used for this task, modeling each subfamily separately by one pHMM. However, a major drawback of this approach is the difficulty of dealing with subfamilies composed of very few sequences. One of the most crucial bioinformatical tasks affected by the problem of small-size subfamilies is the subtyping of human immunodeficiency virus type 1 (HIV-1) sequences, i.e., HIV-1 subtypes for which only a small number of sequences is known. RESULTS To deal with small samples for particular subfamilies of HIV-1, we introduce a novel model-based information sharing protocol. It estimates the emission probabilities of the pHMM modeling a particular subfamily not only based on the nucleotide frequencies of the respective subfamily but also incorporating the nucleotide frequencies of all available subfamilies. To this end, the underlying probabilistic model mimics the pattern of commonality and variation between the subtypes with regards to the biological characteristics of HI viruses. In order to implement the proposed protocol, we make use of an existing HMM architecture and its associated inference engine. CONCLUSIONS We apply the modified algorithm to classify HIV-1 sequence data in the form of partial HIV-1 sequences and semi-artificial recombinants. Thereby, we demonstrate that the performance of pHMMs can be significantly improved by the proposed technique. Moreover, we show that our algorithm performs significantly better than Simplot and Bootscanning.
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Affiliation(s)
- Ingo Bulla
- Institut für Mathematik und Informatik, Universität Greifswald, Walther-Rathenau-Straße 47, 17487 Greifswald, Germany.
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14
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Abstract
Avian influenza virus (AIV) causes a disease of high economic importance for poultry production worldwide. The earliest recorded cases of probable high-pathogenicity AIV in poultry were reported in Italy in the 1870s, and avian influenza has been recognized in domestic poultry through the modern era of poultry production. Approaches to control vary widely, but elimination of the disease in poultry is a common goal. The basics of AIV biology, clinical disease, molecular aspects, and AIV detection are briefly reviewed.
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Affiliation(s)
- Erica Spackman
- Exotic and Emerging Avian Viral Diseases Unit, Southeast Poultry Research Laboratory, US Department of Agriculture, ARS, 934 College Station Rd., Athens, GA, 30605, USA,
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15
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Böttcher-Friebertshäuser E, Garten W, Matrosovich M, Klenk HD. The hemagglutinin: a determinant of pathogenicity. Curr Top Microbiol Immunol 2014; 385:3-34. [PMID: 25031010 DOI: 10.1007/82_2014_384] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The hemagglutinin (HA) is a prime determinant of the pathogenicity of influenza A viruses. It initiates infection by binding to cell surface receptors and by inducing membrane fusion. The fusion capacity of HA depends on cleavage activation by host proteases, and it has long been known that highly pathogenic avian influenza viruses displaying a multibasic cleavage site differ in protease sensitivity from low pathogenic avian and mammalian influenza viruses with a monobasic cleavage site. Evidence is increasing that there are also variations in proteolytic activation among the viruses with a monobasic cleavage site, and several proteases have been identified recently that activate these viruses in a natural setting. Differences in protease sensitivity of HA and in tissue specificity of the enzymes are important determinants for virus tropism in the respiratory tract and for systemic spread of infection. Protease inhibitors that interfere with cleavage activation have the potential to be used for antiviral therapy and attenuated viruses have been generated by mutation of the cleavage site that can be used for the development of inactivated and live vaccines. It has long been known that human and avian influenza viruses differ in their specificity for sialic acid-containing cell receptors, and it is now clear that human tissues contain also receptors for avian viruses. Differences in receptor-binding specificity of seasonal and zoonotic viruses and differential expression of receptors for these viruses in the human respiratory tract account, at least partially, for the severity of disease. Receptor binding and fusion activation are modulated by HA glycosylation, and interaction of the glycans of HA with cellular lectins also affects virus infectivity. Interestingly, some of the mechanisms underlying pathogenicity are determinants of host range and transmissibility, as well.
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16
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Warren S, Wan XF, Conant G, Korkin D. Extreme evolutionary conservation of functionally important regions in H1N1 influenza proteome. PLoS One 2013; 8:e81027. [PMID: 24282564 PMCID: PMC3839886 DOI: 10.1371/journal.pone.0081027] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2013] [Accepted: 10/08/2013] [Indexed: 12/31/2022] Open
Abstract
The H1N1 subtype of influenza A virus has caused two of the four documented pandemics and is responsible for seasonal epidemic outbreaks, presenting a continuous threat to public health. Co-circulating antigenically divergent influenza strains significantly complicates vaccine development and use. Here, by combining evolutionary, structural, functional, and population information about the H1N1 proteome, we seek to answer two questions: (1) do residues on the protein surfaces evolve faster than the protein core residues consistently across all proteins that constitute the influenza proteome? and (2) in spite of the rapid evolution of surface residues in influenza proteins, are there any protein regions on the protein surface that do not evolve? To answer these questions, we first built phylogenetically-aware models of the patterns of surface and interior substitutions. Employing these models, we found a single coherent pattern of faster evolution on the protein surfaces that characterizes all influenza proteins. The pattern is consistent with the events of inter-species reassortment, the worldwide introduction of the flu vaccine in the early 80's, as well as the differences caused by the geographic origins of the virus. Next, we developed an automated computational pipeline to comprehensively detect regions of the protein surface residues that were 100% conserved over multiple years and in multiple host species. We identified conserved regions on the surface of 10 influenza proteins spread across all avian, swine, and human strains; with the exception of a small group of isolated strains that affected the conservation of three proteins. Surprisingly, these regions were also unaffected by genetic variation in the pandemic 2009 H1N1 viral population data obtained from deep sequencing experiments. Finally, the conserved regions were intrinsically related to the intra-viral macromolecular interaction interfaces. Our study may provide further insights towards the identification of novel protein targets for influenza antivirals.
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Affiliation(s)
- Samantha Warren
- Department of Computer Science, University of Missouri, Columbia, Missouri, United States of America
| | - Xiu-Feng Wan
- Department of Basic Sciences, Mississippi State University, Mississippi State, Mississippi, United States of America
| | - Gavin Conant
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, United States of America
- Informatics Institute, University of Missouri, Columbia, Missouri, United States of America
| | - Dmitry Korkin
- Department of Computer Science, University of Missouri, Columbia, Missouri, United States of America
- Informatics Institute, University of Missouri, Columbia, Missouri, United States of America
- Bond Life Science Center, University of Missouri, Columbia, Missouri, United States of America
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Abdelwhab ESM, Veits J, Mettenleiter TC. Genetic changes that accompanied shifts of low pathogenic avian influenza viruses toward higher pathogenicity in poultry. Virulence 2013; 4:441-52. [PMID: 23863606 PMCID: PMC5359749 DOI: 10.4161/viru.25710] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 07/09/2013] [Accepted: 07/10/2013] [Indexed: 11/19/2022] Open
Abstract
Avian influenza viruses (AIV) of H5 and H7 subtypes exhibit two different pathotypes in poultry: infection with low pathogenic (LP) strains results in minimal, if any, health disturbances, whereas highly pathogenic (HP) strains cause severe morbidity and mortality. LPAIV of H5 and H7 subtypes can spontaneously mutate into HPAIV. Ten outbreaks caused by HPAIV are known to have been preceded by circulation of a predecessor LPAIV in poultry. Three of them were caused by H5N2 subtype and seven involved H7 subtype in combination with N1, N3, or N7. Here, we review those outbreaks and summarize the genetic changes which resulted in the transformation of LPAIV to HPAIV under natural conditions. Mutations that were found directly in those outbreaks are more likely to be linked to virulence, pathogenesis, and early adaptation of AIV.
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Affiliation(s)
- El-Sayed M Abdelwhab
- Friedrich-Loeffler-Institut; Federal Research Institute for Animal Health; Institute of Molecular Biology; Greifswald-Insel Riems, Germany
| | - Jutta Veits
- Friedrich-Loeffler-Institut; Federal Research Institute for Animal Health; Institute of Molecular Biology; Greifswald-Insel Riems, Germany
| | - Thomas C Mettenleiter
- Friedrich-Loeffler-Institut; Federal Research Institute for Animal Health; Institute of Molecular Biology; Greifswald-Insel Riems, Germany
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18
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Wang HI, Chang CH, Lin PH, Fu HC, Tang C, Yeh HH. Application of motif-based tools on evolutionary analysis of multipartite single-stranded DNA viruses. PLoS One 2013; 8:e71565. [PMID: 23936517 PMCID: PMC3735576 DOI: 10.1371/journal.pone.0071565] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 07/01/2013] [Indexed: 11/19/2022] Open
Abstract
Multipartite viruses contain more than one distinctive genome component, and the origin of multipartite viruses has been suggested to evolve from a non-segmented wild-type virus. To explore whether recombination also plays a role in the evolution of the genomes of multipartite viruses, we developed a systematic approach that employs motif-finding tools to detect conserved motifs from divergent genomic regions and applies statistical approaches to select high-confidence motifs. The information that this approach provides helps us understand the evolution of viruses. In this study, we compared our motif-based strategy with current alignment-based recombination-detecting methods and applied our methods to the analysis of multipartite single-stranded plant DNA viruses, including bipartite begomoviruses, Banana bunchy top virus (BBTV) (consisting of 6 genome components) and Faba bean necrotic yellows virus (FBNYV) (consisting of 8 genome components). Our analysis revealed that recombination occurred between genome components in some begomoviruses, BBTV and FBNYV. Our data also show that several unusual recombination events have contributed to the evolution of BBTV genome components. We believe that similar approaches can be applied to resolve the evolutionary history of other viruses.
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Affiliation(s)
- Hsiang-Iu Wang
- Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan
| | - Chih-Hung Chang
- Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan
| | - Po-Heng Lin
- Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan
| | - Hui-Chuan Fu
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, Taiwan
| | - ChuanYi Tang
- Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan
- Department of Computer Science and Information Engineering, Providence University, Taichung City, Taiwan
| | - Hsin-Hung Yeh
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, Taiwan
- Research Center for Plant Medicine, National Taiwan University, Taipei, Taiwan
- * E-mail:
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19
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Characterization of the 2012 highly pathogenic avian influenza H7N3 virus isolated from poultry in an outbreak in Mexico: pathobiology and vaccine protection. J Virol 2013; 87:9086-96. [PMID: 23760232 DOI: 10.1128/jvi.00666-13] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In June of 2012, an H7N3 highly pathogenic avian influenza (HPAI) virus was identified as the cause of a severe disease outbreak in commercial laying chicken farms in Mexico. The purpose of this study was to characterize the Mexican 2012 H7N3 HPAI virus (A/chicken/Jalisco/CPA1/2012) and determine the protection against the virus conferred by different H7 inactivated vaccines in chickens. Both adult and young chickens intranasally inoculated with the virus became infected and died at between 2 and 4 days postinoculation (p.i.). High virus titers and viral replication in many tissues were demonstrated at 2 days p.i. in infected birds. The virus from Jalisco, Mexico, had high sequence similarity of greater than 97% to the sequences of wild bird viruses from North America in all eight gene segments. The hemagglutinin gene of the virus contained a 24-nucleotide insert at the hemagglutinin cleavage site which had 100% sequence identity to chicken 28S rRNA, suggesting that the insert was the result of nonhomologous recombination with the host genome. For vaccine protection studies, both U.S. H7 low-pathogenic avian influenza (LPAI) viruses and a 2006 Mexican H7 LPAI virus were tested as antigens in experimental oil emulsion vaccines and injected into chickens 3 weeks prior to challenge. All H7 vaccines tested provided ≥90% protection against clinical disease after challenge and decreased the number of birds shedding virus and the titers of virus shed. This study demonstrates the pathological consequences of the infection of chickens with the 2012 Mexican lineage H7N3 HPAI virus and provides support for effective programs of vaccination against this virus in poultry.
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The highly pathogenic H7N3 avian influenza strain from July 2012 in Mexico acquired an extended cleavage site through recombination with host 28S rRNA. Virol J 2013; 10:139. [PMID: 23635025 PMCID: PMC3673898 DOI: 10.1186/1743-422x-10-139] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Accepted: 04/25/2013] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND A characteristic difference between highly and non-highly pathogenic avian influenza strains is the presence of an extended, often multibasic, cleavage motif insertion in the hemagglutinin protein. Such motif is found in H7N3 strains from chicken farm outbreaks in 2012 in Mexico. METHODS Through phylogenetic, sequence and structural analysis, we try to shed light on the role, prevalence, likelihood of appearance and origin of the inserted cleavage motifs in these H7N3 avian influenza strains. RESULTS The H7N3 avian influenza strain which caused outbreaks in chicken farms in June/July 2012 in Mexico has a new extended cleavage site which is the likely reason for its high pathogenicity in these birds. This cleavage site appears to have been naturally acquired and was not present in the closest low pathogenic precursors. Structural modeling shows that insertion of a productive cleavage site is quite flexible to accept insertions of different length and with sequences from different possible origins. Different from recent cleavage site insertions, the origin of the insert here is not from the viral genome but from host 28S ribosomal RNA (rRNA) instead. This is a novelty for a natural acquisition as a similar insertion has so far only been observed in a laboratory strain before. Given the abundance of viral and host RNA in infected cells, the acquisition of a pathogenicity-enhancing extended cleavage site through a similar route by other low-pathogenic avian strains in future does not seem unlikely. Important for surveillance of these H7N3 strains, the structural sites known to enhance mammalian airborne transmission are dominated by the characteristic avian residues and the risk of human to human transmission should currently be low but should be monitored for future changes accordingly. CONCLUSIONS This highly pathogenic H7N3 avian influenza strain acquired a novel extended cleavage site which likely originated from recombination with 28S rRNA from the avian host. Notably, this new virus can infect humans but currently lacks critical host receptor adaptations that would facilitate human to human transmission.
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Pathogenesis, transmissibility, and ocular tropism of a highly pathogenic avian influenza A (H7N3) virus associated with human conjunctivitis. J Virol 2013; 87:5746-54. [PMID: 23487452 DOI: 10.1128/jvi.00154-13] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
H7 subtype influenza A viruses, responsible for numerous outbreaks in land-based poultry in Europe and the Americas, have caused over 100 cases of confirmed or presumed human infection over the last decade. The emergence of a highly pathogenic avian influenza H7N3 virus in poultry throughout the state of Jalisco, Mexico, resulting in two cases of human infection, prompted us to examine the virulence of this virus (A/Mexico/InDRE7218/2012 [MX/7218]) and related avian H7 subtype viruses in mouse and ferret models. Several high- and low-pathogenicity H7N3 and H7N9 viruses replicated efficiently in the respiratory tract of mice without prior adaptation following intranasal inoculation, but only MX/7218 virus caused lethal disease in this species. H7N3 and H7N9 viruses were also detected in the mouse eye following ocular inoculation. Virus from both H7N3 and H7N9 subtypes replicated efficiently in the upper and lower respiratory tracts of ferrets; however, only MX/7218 virus infection caused clinical signs and symptoms and was capable of transmission to naive ferrets in a direct-contact model. Similar to other highly pathogenic H7 viruses, MX/7218 replicated to high titers in human bronchial epithelial cells, yet it downregulated numerous genes related to NF-κB-mediated signaling transduction. These findings indicate that the recently isolated North American lineage H7 subtype virus associated with human conjunctivitis is capable of causing severe disease in mice and spreading to naive-contact ferrets, while concurrently retaining the ability to replicate within ocular tissue and allowing the eye to serve as a portal of entry.
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22
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Suzuki Y, Kobayashi Y. Evolution of complementary nucleotides in 5' and 3' untranslated regions of influenza A virus genomic segments. INFECTION GENETICS AND EVOLUTION 2012; 13:175-9. [PMID: 23146832 DOI: 10.1016/j.meegid.2012.10.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 09/29/2012] [Accepted: 10/08/2012] [Indexed: 10/27/2022]
Abstract
The genome of influenza A virus comprises 8 segments (segments 1-8) of single-stranded RNA (virion RNA: vRNA) with negative-polarity. All vRNAs share 13 and 12 terminal nucleotides in the 5' and 3' untranslated regions (UTRs), respectively, which are partially complementary and constitute panhandle and corkscrew structures. Here, it is shown, from the analysis of genomic sequences for 506 strains of influenza A virus, that the number of contiguous complementary nucleotides in the 5' and 3' UTRs varies from 4 to 7 among segments. Complementary nucleotides were segment specific and highly conserved in all segments except for segment 6, where in the phylogenetic analysis co-evolution was observed to have occurred between and within subtypes of neuraminidase (NA). Mutations in the terminal sequences sometimes appeared to have caused convergence between subtypes, involving changes in multiple nucleotide positions. These observations suggest that intra-segmental (homologous) recombinations may have taken place for transferring terminal sequences in segment 6.
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Affiliation(s)
- Yoshiyuki Suzuki
- Graduate School of Natural Sciences, Nagoya City University, 1 Yamanohata, Nagoya-shi, Aichi-ken 467-8501, Japan.
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23
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Rapid PCR-based molecular pathotyping of H5 and H7 avian influenza viruses. J Clin Microbiol 2011; 49:3860-73. [PMID: 21900520 DOI: 10.1128/jcm.01179-11] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
While the majority of avian influenza virus (AIV) subtypes are classified as low-pathogenicity avian influenza viruses (LPAIV), the H5 and H7 subtypes have the ability to mutate to highly pathogenic avian influenza viruses (HPAIV) in poultry and therefore are the etiological agents of notifiable AIV (NAIV). It is of great importance to distinguish HPAIV from LPAIV variants during H5/H7 outbreaks and surveillance. To this end, a novel and fast strategy for the molecular pathotyping of H5/H7 AIVs is presented. The differentiation of the characteristic hemagglutinin (HA) protein cleavage sites (CSs) of HPAIVs and LPAIVs is achieved by a novel PCR method where the samples are interrogated for all existing CSs with a 484-plex primer mixture directly targeting the CS region. CSs characteristic for HP or LP H5/H7 viruses are distinguished in a seminested duplex real-time PCR format using plexor fluorogenic primers. Eighty-six laboratory isolates and 60 characterized NAIV-positive clinical specimens from poultry infected with H5/H7 both experimentally and in the field were successfully pathotyped in the validation. The method has the potential to substitute CS sequencing in the HA gene for the determination of the molecular pathotype, thereby providing a rapid means to acquire additional information concerning NAIV outbreaks, which may be critical to their management. The new assay may be extended to the LP/HP differentiation of previously unknown H5/H7 isolates. It may be considered for integration into surveillance and control programs in both domestic and wild bird populations.
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24
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Homologous recombination in negative sense RNA viruses. Viruses 2011; 3:1358-73. [PMID: 21994784 PMCID: PMC3185808 DOI: 10.3390/v3081358] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Revised: 07/12/2011] [Accepted: 07/22/2011] [Indexed: 01/05/2023] Open
Abstract
Recombination is an important process that influences biological evolution at many different levels. More and more homologous recombination events have been reported among negative sense RNA viruses recently. While sporadic authentic examples indicate that homologous recombination does occur, recombination seems to be generally rare or even absent in most negative sense RNA viruses, and most of the homologous recombination events reported in the literature were likely generated artificially due to lab contamination or inappropriate bioinformatics methods. Homologous recombination in negative sense RNA viruses should be reported with caution in the future, and only after stringent quality control efforts. Moreover, co-infection experiments should be performed to confirm whether recombination can occur.
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Abstract
Influenza is a highly contagious respiratory pathogen that continues to evolve and threaten both veterinary and human public health. Influenza A viruses are continually undergoing molecular changes through mutations, reassortment, and, in rare instances, recombination. While they generally cause benign enteric infection in their natural reservoir of wild aquatic birds, they can cause catastrophic and potentially lethal disease outbreaks in humans, domestic poultry, and pigs when they cross the host species barrier. The continuing circulation of highly pathogenic (HP) H5N1 influenza viruses in domestic poultry in parts of Eurasia and the emergence and global spread of pandemic H1N1 2009 are current examples of influenza evolution. The spread of both HP H5N1 and pandemic H1N1 to multiple hosts emphasizes the potential for continued evolution. In this review, we discuss the current understanding of influenza A virus structure and strategies of variation, with a specific focus on the HP H5N1 and pandemic H1N1 influenza viruses. Additionally, we attempt to identify the gaps in our knowledge of H5N1 and pandemic H1N1 influenza viruses. These gaps include (i) an understanding of the molecular determinants of influenza virus and the host that permit efficient transmissibility and pandemic potential, (ii) the urgent need for prospective surveillance in apparently healthy swine, (iii) the molecular determinants of high pathogenicity in poultry, pigs, and people, (iv) the genetic basis of host susceptibility, (v) antigenic variability, (vi) the use of vaccine to control influenza, (vii) the role of wild birds as the reservoir of highly pathogenic avian influenza, (viii) the problems with vaccines, (ix) seasonality, (x) co-infections, and (xi) anti-influenza drug resistance. Our failure to eradicate HP H5N1 globally and to explain why H5N1 does not transmit efficiently in humans while an H1N1 pandemic virus of swine origin spread globally in months are key examples that emphasize the critical need to bridge these knowledge gaps. Future directions in influenza research that will help us resolve each of the above-mentioned knowledge gaps include complete genomic and proteomic analysis of both the virus and the host with the prospect of designing new control strategies and the development of genetically resistant hosts.
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26
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Bioinformatic analysis of the genome of infectious salmon anemia virus associated with outbreaks with high mortality in Chile. J Virol 2010; 84:11916-28. [PMID: 20810724 DOI: 10.1128/jvi.01202-10] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The infectious salmon anemia virus (ISAV), an orthomyxovirus, is the major cause of outbreaks of high mortality rates in salmon in Chile. It has been proposed that the virulence of ISAV isolates lies mainly in hemagglutinin-esterase and fusion glycoproteins. However, based on current information, the contribution of other viral genes cannot be ruled out. To study this, we isolated and determined the complete coding sequence of two high-prevalence Chilean isolates associated with outbreaks of high mortality rates: ISAV752_09 and ISAV901_09. These isolates were compared to 15 Norwegian isolates that exhibit differences in their virulence. For this purpose, we performed bioinformatic analyses of (i) functional domains, (ii) specific mutations, (iii) Bayesian phylogenetics, and (iv) structural comparisons between ISAV and influenza virus glycoproteins by using molecular modeling. Phylogenetic analysis shows two genogroups for each protein, one of them containing the Chilean isolates. The gene sequence of the polymerase complex and nucleoprotein indicated that they are closely related to homologues from highly pathogenic Norwegian viruses. Notably, seven of the eight mutations that are present only in the Chilean isolates are on the polymerase complex and nucleoprotein. Structural modeling of hemagglutinin-esterase shows patches of variable residues on its surface. Fusion protein modeling shows that insertions are flexible regions that could affect proteolytic processing, increasing either the accessibility or the number of recognition sites for specific proteases. We found antigenic drift processes related to insertion into the isolated segment 5 of the ISAV752_09. Our results confirm the European origin of Chilean isolates to be the result of reassortments from Norwegian ancestors.
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27
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Boni MF, de Jong MD, van Doorn HR, Holmes EC. Guidelines for identifying homologous recombination events in influenza A virus. PLoS One 2010; 5:e10434. [PMID: 20454662 PMCID: PMC2862710 DOI: 10.1371/journal.pone.0010434] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2010] [Accepted: 04/06/2010] [Indexed: 11/22/2022] Open
Abstract
The rapid evolution of influenza viruses occurs both clonally and non-clonally through a variety of genetic mechanisms and selection pressures. The non-clonal evolution of influenza viruses comprises relatively frequent reassortment among gene segments and a more rarely reported process of non-homologous RNA recombination. Homologous RNA recombination within segments has been proposed as a third such mechanism, but to date the evidence for the existence of this process among influenza viruses has been both weak and controversial. As homologous recombination has not yet been demonstrated in the laboratory, supporting evidence, if it exists, may come primarily from patterns of phylogenetic incongruence observed in gene sequence data. Here, we review the necessary criteria related to laboratory procedures and sample handling, bioinformatic analysis, and the known ecology and evolution of influenza viruses that need to be met in order to confirm that a homologous recombination event occurred in the history of a set of sequences. To determine if these criteria have an effect on recombination analysis, we gathered 8307 publicly available full-length sequences of influenza A segments and divided them into those that were sequenced via the National Institutes of Health Influenza Genome Sequencing Project (IGSP) and those that were not. As sample handling and sequencing are executed to a very high standard in the IGSP, these sequences should be less likely to be exposed to contamination by other samples or by laboratory strains, and thus should not exhibit laboratory-generated signals of homologous recombination. Our analysis shows that the IGSP data set contains only two phylogenetically-supported single recombinant sequences and no recombinant clades. In marked contrast, the non-IGSP data show a very large amount of potential recombination. We conclude that the presence of false positive signals in the non-IGSP data is more likely than false negatives in the IGSP data, and that given the evidence to date, homologous recombination seems to play little or no role in the evolution of influenza A viruses.
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Affiliation(s)
- Maciej F Boni
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.
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28
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Bulla I, Schultz AK, Schreiber F, Zhang M, Leitner T, Korber B, Morgenstern B, Stanke M. HIV classification using the coalescent theory. ACTA ACUST UNITED AC 2010; 26:1409-15. [PMID: 20400454 DOI: 10.1093/bioinformatics/btq159] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
MOTIVATION Existing coalescent models and phylogenetic tools based on them are not designed for studying the genealogy of sequences like those of HIV, since in HIV recombinants with multiple cross-over points between the parental strains frequently arise. Hence, ambiguous cases in the classification of HIV sequences into subtypes and circulating recombinant forms (CRFs) have been treated with ad hoc methods in lack of tools based on a comprehensive coalescent model accounting for complex recombination patterns. RESULTS We developed the program ARGUS that scores classifications of sequences into subtypes and recombinant forms. It reconstructs ancestral recombination graphs (ARGs) that reflect the genealogy of the input sequences given a classification hypothesis. An ARG with maximal probability is approximated using a Markov chain Monte Carlo approach. ARGUS was able to distinguish the correct classification with a low error rate from plausible alternative classifications in simulation studies with realistic parameters. We applied our algorithm to decide between two recently debated alternatives in the classification of CRF02 of HIV-1 and find that CRF02 is indeed a recombinant of Subtypes A and G. AVAILABILITY ARGUS is implemented in C++ and the source code is available at http://gobics.de/software.
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Affiliation(s)
- Ingo Bulla
- Abteilung Bioinformatik, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Goldschmidtstrasse 1, 37077 Göttingen, Germany.
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Bokhari SH, Janies DA. Reassortment networks for investigating the evolution of segmented viruses. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2010; 7:288-298. [PMID: 20431148 DOI: 10.1109/tcbb.2008.73] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Many viruses of interest, such as influenza A, have distinct segments in their genome. The evolution of these viruses involves mutation and reassortment, where segments are interchanged between viruses that coinfect a host. Phylogenetic trees can be constructed to investigate the mutation-driven evolution of individual viral segments. However, reassortment events among viral genomes are not well depicted in such bifurcating trees. We propose the concept of reassortment networks to analyze the evolution of segmented viruses. These are layered graphs in which the layers represent evolutionary stages such as a temporal series of seasons in which influenza viruses are isolated. Nodes represent viral isolates and reassortment events between pairs of isolates. Edges represent evolutionary steps, while weights on edges represent edit costs of reassortment and mutation events. Paths represent possible transformation series among viruses. The length of each path is the sum edit cost of the events required to transform one virus into another. In order to analyze tau stages of evolution of n viruses with segments of maximum length m, we first compute the pairwise distances between all corresponding segments of all viruses in O(m2n2) time using dynamic programming. The reassortment network, with O(taun2) nodes, is then constructed using these distances. The ancestors and descendents of a specific virus can be traced via shortest paths in this network, which can be found in O(taun3) time.
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Affiliation(s)
- Shahid H Bokhari
- Department of Biomedical Informatics, Ohio State University, 3190 Graves Hall, 333 W. 10th Ave. Columbus, OH 43210, USA.
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30
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Pasick J, Berhane Y, Hisanaga T, Kehler H, Hooper-McGrevy K, Handel K, Neufeld J, Argue C, Leighton F. Diagnostic Test Results and Pathology Associated with the 2007 Canadian H7N3 Highly Pathogenic Avian Influenza Outbreak. Avian Dis 2010; 54:213-9. [DOI: 10.1637/8822-040209-reg.1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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31
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Arias CF, Escalera-Zamudio M, de los Dolores Soto-Del Río M, Georgina Cobián-Güemes A, Isa P, López S. Molecular Anatomy of 2009 Influenza Virus A (H1N1). Arch Med Res 2009; 40:643-54. [DOI: 10.1016/j.arcmed.2009.10.007] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2009] [Accepted: 10/08/2009] [Indexed: 01/29/2023]
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32
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Kibenge FSB, Godoy MG, Wang Y, Kibenge MJT, Gherardelli V, Mansilla S, Lisperger A, Jarpa M, Larroquete G, Avendaño F, Lara M, Gallardo A. Infectious salmon anaemia virus (ISAV) isolated from the ISA disease outbreaks in Chile diverged from ISAV isolates from Norway around 1996 and was disseminated around 2005, based on surface glycoprotein gene sequences. Virol J 2009. [PMID: 19558648 DOI: 10.1186/1743-1422x-1186-1188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2023] Open
Abstract
BACKGROUND Infectious salmon anaemia (ISA) virus (ISAV) is a pathogen of marine-farmed Atlantic salmon (Salmo salar); a disease first diagnosed in Norway in 1984. For over 25 years ISAV has caused major disease outbreaks in the Northern hemisphere, and remains an emerging fish pathogen because of the asymptomatic infections in marine wild fish and the potential for emergence of new epidemic strains. ISAV belongs to the family Orthomyxoviridae, together with influenza viruses but is sufficiently different to be assigned to its own genus, Isavirus. The Isavirus genome consists of eight single-stranded RNA species, and the virions have two surface glycoproteins; fusion (F) protein encoded on segment 5 and haemagglutinin-esterase (HE) protein encoded on segment 6. However, comparison between different ISAV isolates is complicated because there is presently no universally accepted nomenclature system for designation of genetic relatedness between ISAV isolates. The first outbreak of ISA in marine-farmed Atlantic salmon in the Southern hemisphere occurred in Chile starting in June 2007. In order to describe the molecular characteristics of the virus so as to understand its origins, how ISAV isolates are maintained and spread, and their virulence characteristics, we conducted a study where the viral sequences were directly amplified, cloned and sequenced from tissue samples collected from several ISA-affected fish on the different fish farms with confirmed or suspected ISA outbreaks in Chile. This paper describes the genetic characterization of a large number of ISAV strains associated with extensive outbreaks in Chile starting in June 2007, and their phylogenetic relationships with selected European and North American isolates that are representative of the genetic diversity of ISAV. RESULTS RT-PCR for ISAV F and HE glycoprotein genes was performed directly on tissue samples collected from ISA-affected fish on different farms among 14 fish companies in Chile during the ISA outbreaks that started in June 2007. The genes of the F and HE glycoproteins were cloned and sequenced for 51 and 78 new isolates, respectively. An extensive comparative analysis of ISAV F and HE sequence data, including reference isolates sampled from Norway, Faroe Islands, Scotland, USA, and Canada was performed. Based on phylogenetic analysis of concatenated ISAV F and HE genes of 103 individual isolates, the isolates from the ISA outbreaks in Chile grouped in their own cluster of 7 distinct strains within Genotype I (European genotype) of ISAV, with the closest relatedness to Norwegian ISAVs isolated in 1997. The phylogenetic software program, BACKTRACK, estimated the Chile isolates diverged from Norway isolates about 1996 and, therefore, had been present in Chile for some time before the recent outbreaks. Analysis of the deduced F protein sequence showed 43 of 51 Chile isolates with an 11-amino acid insert between 265N and 266Q, with 100% sequence identity with Genotype I ISAV RNA segment 2. Twenty four different HE-HPRs, including HPR0, were detected, with HPR7b making up 79.7%. This is considered a manifestation of ISAV quasispecies HE protein sequence diversity. CONCLUSION Taken together, these findings suggest that the ISA outbreaks were caused by virus that was already present in Chile that mutated to new strains. This is the first comprehensive report tracing ISAV from Europe to South America.
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Affiliation(s)
- Frederick S B Kibenge
- Department of Pathology and Microbiology, OIE Reference Laboratory for ISA, Atlantic Veterinary College, University of Prince Edward Island, 550 University Ave., Charlottetown, P.E.I., C1A 4P3, Canada.
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Kibenge FSB, Godoy MG, Wang Y, Kibenge MJT, Gherardelli V, Mansilla S, Lisperger A, Jarpa M, Larroquete G, Avendaño F, Lara M, Gallardo A. Infectious salmon anaemia virus (ISAV) isolated from the ISA disease outbreaks in Chile diverged from ISAV isolates from Norway around 1996 and was disseminated around 2005, based on surface glycoprotein gene sequences. Virol J 2009; 6:88. [PMID: 19558648 PMCID: PMC2710322 DOI: 10.1186/1743-422x-6-88] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2009] [Accepted: 06/26/2009] [Indexed: 11/23/2022] Open
Abstract
Background Infectious salmon anaemia (ISA) virus (ISAV) is a pathogen of marine-farmed Atlantic salmon (Salmo salar); a disease first diagnosed in Norway in 1984. For over 25 years ISAV has caused major disease outbreaks in the Northern hemisphere, and remains an emerging fish pathogen because of the asymptomatic infections in marine wild fish and the potential for emergence of new epidemic strains. ISAV belongs to the family Orthomyxoviridae, together with influenza viruses but is sufficiently different to be assigned to its own genus, Isavirus. The Isavirus genome consists of eight single-stranded RNA species, and the virions have two surface glycoproteins; fusion (F) protein encoded on segment 5 and haemagglutinin-esterase (HE) protein encoded on segment 6. However, comparision between different ISAV isolates is complicated because there is presently no universally accepted nomenclature system for designation of genetic relatedness between ISAV isolates. The first outbreak of ISA in marine-farmed Atlantic salmon in the Southern hemisphere occurred in Chile starting in June 2007. In order to describe the molecular characteristics of the virus so as to understand its origins, how ISAV isolates are maintained and spread, and their virulence characteristics, we conducted a study where the viral sequences were directly amplified, cloned and sequenced from tissue samples collected from several ISA-affected fish on the different fish farms with confirmed or suspected ISA outbreaks in Chile. This paper describes the genetic characterization of a large number of ISAV strains associated with extensive outbreaks in Chile starting in June 2007, and their phylogenetic relationships with selected European and North American isolates that are representative of the genetic diversity of ISAV. Results RT-PCR for ISAV F and HE glycoprotein genes was performed directly on tissue samples collected from ISA-affected fish on different farms among 14 fish companies in Chile during the ISA outbreaks that started in June 2007. The genes of the F and HE glycoproteins were cloned and sequenced for 51 and 78 new isolates, respectively. An extensive comparative analysis of ISAV F and HE sequence data, including reference isolates sampled from Norway, Faroe Islands, Scotland, USA, and Canada was performed. Based on phylogenetic analysis of concatenated ISAV F and HE genes of 103 individual isolates, the isolates from the ISA outbreaks in Chile grouped in their own cluster of 7 distinct strains within Genotype I (European genotype) of ISAV, with the closest relatedness to Norwegian ISAVs isolated in 1997. The phylogenetic software program, BACKTRACK, estimated the Chile isolates diverged from Norway isolates about 1996 and, therefore, had been present in Chile for some time before the recent outbreaks. Analysis of the deduced F protein sequence showed 43 of 51 Chile isolates with an 11-amino acid insert between 265N and 266Q, with 100% sequence identity with Genotype I ISAV RNA segment 2. Twenty four different HE-HPRs, including HPR0, were detected, with HPR7b making up 79.7%. This is considered a manifestation of ISAV quasispecies HE protein sequence diversity. Conclusion Taken together, these findings suggest that the ISA outbreaks were caused by virus that was already present in Chile that mutated to new strains. This is the first comprehensive report tracing ISAV from Europe to South America.
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Affiliation(s)
- Frederick S B Kibenge
- Department of Pathology and Microbiology, OIE Reference Laboratory for ISA, Atlantic Veterinary College, University of Prince Edward Island, 550 University Ave., Charlottetown, P.E.I., C1A 4P3, Canada.
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He CQ, Xie ZX, Han GZ, Dong JB, Wang D, Liu JB, Ma LY, Tang XF, Liu XP, Pang YS, Li GR. Homologous recombination as an evolutionary force in the avian influenza A virus. Mol Biol Evol 2008; 26:177-87. [PMID: 18931384 DOI: 10.1093/molbev/msn238] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Avian influenza A viruses (AIVs), including the H5N1, H9N2, and H7N7 subtypes, have been directly transmitted to humans, raising concerns over the possibility of a new influenza pandemic. To prevent a future avian influenza pandemic, it is very important to fully understand the molecular basis driving the change in AIV virulence and host tropism. Although virulent variants of other viruses have been generated by homologous recombination, the occurrence of homologous recombination within AIV segments is controversial and far from proven. This study reports three circulating H9N2 AIVs with similar mosaic PA genes descended from H9N2 and H5N1. Additionally, many homologous recombinants are also found deposited in GenBank. Recombination events can occur in PB2, PB1, PA, HA, and NP segments and between lineages of the same/different serotype. These results collectively demonstrate that intragenic recombination plays a role in driving the evolution of AIVs, potentially resulting in effects on AIV virulence and host tropism changes.
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Affiliation(s)
- Cheng-Qiang He
- Department of Biotechnology College of Life Science, Shandong Normal University, Shandong Province, Jinan, China.
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He CQ, Han GZ, Wang D, Liu W, Li GR, Liu XP, Ding NZ. Homologous recombination evidence in human and swine influenza A viruses. Virology 2008; 380:12-20. [DOI: 10.1016/j.virol.2008.07.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2008] [Revised: 05/06/2008] [Accepted: 07/15/2008] [Indexed: 12/26/2022]
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Godoy MG, Aedo A, Kibenge MJT, Groman DB, Yason CV, Grothusen H, Lisperguer A, Calbucura M, Avendaño F, Imilán M, Jarpa M, Kibenge FSB. First detection, isolation and molecular characterization of infectious salmon anaemia virus associated with clinical disease in farmed Atlantic salmon (Salmo salar) in Chile. BMC Vet Res 2008; 4:28. [PMID: 18680586 PMCID: PMC2519066 DOI: 10.1186/1746-6148-4-28] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2008] [Accepted: 08/04/2008] [Indexed: 11/29/2022] Open
Abstract
Background Infectious salmon anaemia (ISA) is a viral disease of marine-farmed Atlantic salmon (Salmo salar) caused by ISA virus (ISAV), which belongs to the genus Isavirus, family Orthomyxoviridae. The virus is considered to be carried by marine wild fish and for over 25 years has caused major disease outbreaks in marine-farmed Atlantic salmon in the Northern hemisphere. In the Southern hemisphere, ISAV was first detected in Chile in 1999 in marine-farmed Coho salmon (Oncorhynchus kisutch). In contrast to the classical presentation of ISA in Atlantic salmon, the presence of ISAV in Chile until now has only been associated with a clinical condition called Icterus Syndrome in Coho salmon and virus isolation has not always been possible. During the winter of 2007, unexplained mortalities were registered in market-size Atlantic salmon in a grow-out site located in Chiloé in Region X of Chile. We report here the diagnostic findings of the first significant clinical outbreak of ISA in marine-farmed Atlantic salmon in Chile and the first characterization of the ISAV isolated from the affected fish. Results In mid-June 2007, an Atlantic salmon marine farm site located in central Chiloé Island in Region X of Chile registered a sudden increase in mortality following recovery from an outbreak of Pisciricketsiosis, which rose to a cumulative mortality of 13.6% by harvest time. Based on the clinical signs and lesions in the affected fish, and laboratory tests performed on the fish tissues, a confirmatory diagnosis of ISA was made; the first time ISA in its classical presentation and for the first time affecting farmed Atlantic salmon in Chile. Rapid sequencing of the virus-specific RT-PCR products amplified from the fish tissues identified the virus to belong to the European genotype (Genotype I) of the highly polymorphic region (HPR) group HPR 7b, but with an 11-amino acid insert in the fusion glycoprotein, and ability to cause cytopathic effects (CPE) in CHSE-214 cell line, characteristics which make it distinct from common European Genotype ISAV isolates from Europe and North America. Conclusion In conclusion, the present work constitutes the first report of a case of ISA in farmed Atlantic salmon in Chile. The clinical signs and lesions are consistent with the classical descriptions of the disease in marine-farmed Atlantic salmon in the Northern hemisphere. The outbreak was caused by ISAV of European genotype (or Genotype I) of HPR 7b but distinct from common European Genotype ISAV isolates.
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Han GZ, Liu XP, Li SS. Homologous recombination is unlikely to play a major role in influenza B virus evolution. Virol J 2008; 5:65. [PMID: 18505573 PMCID: PMC2474605 DOI: 10.1186/1743-422x-5-65] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2008] [Accepted: 05/27/2008] [Indexed: 11/30/2022] Open
Abstract
Influenza B viruses cause a significant amount of morbidity and mortality. The occurrence of homologous recombination in influenza viruses is controversial. To determine the extent of homologous recombination in influenza B viruses, recombination analyses of 2,650 sequences representing all eight segments of the influenza B viruses were carried out. Only four sequences were indentified as putative recombinants, which were verified using phylogenetic methods. However, the mosaics detected here were much likely to represent cases of laboratory-generated artificial recombinants. As in other myxoviruses, it is unlikely that homologous recombination plays a major role in influenza B virus evolution.
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Affiliation(s)
- Guan-Zhu Han
- National Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China.
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Boni MF, Zhou Y, Taubenberger JK, Holmes EC. Homologous recombination is very rare or absent in human influenza A virus. J Virol 2008; 82:4807-11. [PMID: 18353939 PMCID: PMC2346757 DOI: 10.1128/jvi.02683-07] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2007] [Accepted: 02/26/2008] [Indexed: 11/20/2022] Open
Abstract
To determine the extent of homologous recombination in human influenza A virus, we assembled a data set of 13,852 sequences representing all eight segments and both major circulating subtypes, H3N2 and H1N1. Using an exhaustive search and a nonparametric test for mosaic structure, we identified 315 sequences (approximately 2%) in five different RNA segments that, after a multiple-comparison correction, had statistically significant mosaic signals compatible with homologous recombination. Of these, only two contained recombinant regions of sufficient length (>100 nucleotides [nt]) that the occurrence of homologous recombination could be verified using phylogenetic methods, with the rest involving very short sequence regions (15 to 30 nt). Although this secondary analysis revealed patterns of phylogenetic incongruence compatible with the action of recombination, neither candidate recombinant was strongly supported. Given our inability to exclude the occurrence of mixed infection and template switching during amplification, laboratory artifacts provide an alternative and likely explanation for the occurrence of phylogenetic incongruence in these two cases. We therefore conclude that, if it occurs at all, homologous recombination plays only a very minor role in the evolution of human influenza A virus.
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Affiliation(s)
- Maciej F Boni
- Resources for the Future, 1616 P St. NW, Washington, DC 20036, USA.
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Markussen T, Jonassen CM, Numanovic S, Braaen S, Hjortaas M, Nilsen H, Mjaaland S. Evolutionary mechanisms involved in the virulence of infectious salmon anaemia virus (ISAV), a piscine orthomyxovirus. Virology 2008; 374:515-27. [PMID: 18280528 DOI: 10.1016/j.virol.2008.01.019] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2007] [Accepted: 01/04/2008] [Indexed: 11/25/2022]
Abstract
Infectious salmon anaemia virus (ISAV) is an orthomyxovirus causing a multisystemic, emerging disease in Atlantic salmon. Here we present, for the first time, detailed sequence analyses of the full-genome sequence of a presumed avirulent isolate displaying a full-length hemagglutinin-esterase (HE) gene (HPR0), and compare this with full-genome sequences of 11 Norwegian ISAV isolates from clinically diseased fish. These analyses revealed the presence of a virulence marker right upstream of the putative cleavage site R267 in the fusion (F) protein, suggesting a Q266-->L266 substitution to be a prerequisite for virulence. To gain virulence in isolates lacking this substitution, a sequence insertion near the cleavage site seems to be required. This strongly suggests the involvement of a protease recognition pattern at the cleavage site of the fusion protein as a determinant of virulence, as seen in highly pathogenic influenza A virus H5 or H7 and the paramyxovirus Newcastle disease virus.
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Affiliation(s)
- Turhan Markussen
- Department of Food Safety and Infection Biology, Norwegian School of Veterinary Science, P.O. Box 8146 Dep., N-0033 Oslo, Norway.
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Boni MF, Posada D, Feldman MW. An exact nonparametric method for inferring mosaic structure in sequence triplets. Genetics 2007; 176:1035-47. [PMID: 17409078 PMCID: PMC1894573 DOI: 10.1534/genetics.106.068874] [Citation(s) in RCA: 570] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2006] [Accepted: 03/18/2007] [Indexed: 11/18/2022] Open
Abstract
Statistical tests for detecting mosaic structure or recombination among nucleotide sequences usually rely on identifying a pattern or a signal that would be unlikely to appear under clonal reproduction. Dozens of such tests have been described, but many are hampered by long running times, confounding of selection and recombination, and/or inability to isolate the mosaic-producing event. We introduce a test that is exact, nonparametric, rapidly computable, free of the infinite-sites assumption, able to distinguish between recombination and variation in mutation/fixation rates, and able to identify the breakpoints and sequences involved in the mosaic-producing event. Our test considers three sequences at a time: two parent sequences that may have recombined, with one or two breakpoints, to form the third sequence (the child sequence). Excess similarity of the child sequence to a candidate recombinant of the parents is a sign of recombination; we take the maximum value of this excess similarity as our test statistic Delta(m,n,b). We present a method for rapidly calculating the distribution of Delta(m,n,b) and demonstrate that it has comparable power to and a much improved running time over previous methods, especially in detecting recombination in large data sets.
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Affiliation(s)
- Maciej F Boni
- Stanford Genome Technology Center, Palo Alto, California 94304, USA.
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Abstract
Recent developments in complete-genome sequencing, antigenic mapping and epidemiological modelling are greatly improving our knowledge of the evolution of human influenza virus at the epidemiological scale. In particular, recent studies have revealed a more complex relationship between antigenic evolution, natural selection and reassortment than previously realized. Despite these advances, there is much that remains to be understood about the epidemiology of influenza virus, particularly the processes that determine the virus's strong seasonality. We argue that a complete understanding of the evolutionary biology of this important human pathogen will require a genomic view of genetic diversity, including the acquisition of polymorphism data from within individual hosts and from geographical regions, particularly the tropics, which have been poorly surveyed to date.
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Affiliation(s)
- Martha I Nelson
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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Abstract
The Arenaviridae family contains 22 recognized virus species, each of them strongly associated with a rodent species (except Tacaribe virus which is associated with a species of bat), suggesting an ancient co-evolutionary process. Although the concept of co-evolution between rodents and arenaviruses is now largely accepted, little has been uncovered in terms of dating the phenomenon and the mechanisms of evolution, including speciation and pathogenicity. These questions are targeted in the present chapter. Old World arenaviruses are associated with the Eurasian rodents in the family Muridae. New World arenaviruses are associated with American rodents in the subfamily Sigmodontinae. The correlation between the rodent host phylogeny and the viruses suggests a long association and a co-evolutionary process. Furthermore, three distinct New World arenaviruses share a common ancestor, demonstrating a unique recombination event that probably occurred in that ancestor. This shows that recombination among arenaviruses of different lineages might occur in nature. Recombination and co-evolutionary adaptation appear as the main mechanisms of arenavirus evolution, generating a high degree of diversity. The diversity among rodent host reservoir and virus species and the potential to exchange genomic material provide a basis for the emergence of new viruses and the risk of these becoming pathogenic for humans.
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Affiliation(s)
- James E. Childs
- Department of Epidemiology and Public Health and Center for Eco-Epidemiolog, Yale University School of Medicine, 60 College St, 208034, 06520-8034 New Haven, CT USA
| | - John S. Mackenzie
- Centre for Emerging Infectious Diseases, Australian Biosecurity Cooperative Research Centre, Curtin University of Technology, U1987, 6845 Perth, WA Australia
| | - Jürgen A. Richt
- Virus and Prion Diseases of Livestock Research Unit, National Animal Disease Center USDA, 2300 Dayton Ave Ames, 50010 IA USA
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Finke S, Conzelmann KK. Recombinant rhabdoviruses: vectors for vaccine development and gene therapy. Curr Top Microbiol Immunol 2005; 292:165-200. [PMID: 15981472 DOI: 10.1007/3-540-27485-5_8] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
The establishment of methods to recover rhabdoviruses from cDNA, so-called reverse genetics systems, has made it possible to genetically engineer rhabdoviruses and to study all aspects of the virus life cycle by introducing defined mutations into the viral genomes. It has also opened the way to make use of the viruses in biomedical applications such as vaccination, gene therapy, or oncolytic virotherapy. The typical gene expression mode of rhabdoviruses, a high genetic stability, and the propensity to tolerate changes in the virus envelope have made rhabdoviruses attractive, targetable gene expression vectors. This chapter provides an overview on the possibilities to manipulate biological properties of the rhabdoviruses that may be important for further development of vaccine vectors and examples of recombinant rhabdoviruses expressing foreign genes and antigens.
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Affiliation(s)
- S Finke
- Max von Pettenkofer-Institut & Genzentrum, Ludwig-Maximilians-Universität, Feodor-Lynen-Str. 25, 81377 Munich, Germany.
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Pasick J, Handel K, Robinson J, Copps J, Ridd D, Hills K, Kehler H, Cottam-Birt C, Neufeld J, Berhane Y, Czub S. Intersegmental recombination between the haemagglutinin and matrix genes was responsible for the emergence of a highly pathogenic H7N3 avian influenza virus in British Columbia. J Gen Virol 2005; 86:727-731. [PMID: 15722533 DOI: 10.1099/vir.0.80478-0] [Citation(s) in RCA: 149] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In February 2004 a highly pathogenic avian influenza (HPAI) outbreak erupted in British Columbia. Investigations indicated that the responsible HPAI H7N3 virus emerged suddenly from a low pathogenic precursor. Analysis of the haemagglutinin (HA) genes of the low and high pathogenic viruses isolated from the index farm revealed the only difference to be a 21 nt insert at the HA cleavage site of the highly pathogenic avian influenza virus. It was deduced that this insert most probably arose as a result of non-homologous recombination between the HA and matrix genes of the same virus. Over the course of the outbreak, a total of 37 isolates with, and 3 isolates without inserts were characterized. The events described here appear very similar to those which occurred in Chile in 2002 where the virulence shift of another H7N3 virus was attributed to non-homologous recombination between the HA and nucleoprotein genes.
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Affiliation(s)
- John Pasick
- Canadian Food Inspection Agency, National Centre for Foreign Animal Disease, 1015 Arlington Street, Winnipeg, Manitoba, Canada R3E 3M4
| | - Katherine Handel
- Canadian Food Inspection Agency, National Centre for Foreign Animal Disease, 1015 Arlington Street, Winnipeg, Manitoba, Canada R3E 3M4
| | - John Robinson
- Animal Health Centre, British Columbia Ministry of Agriculture and Food, 1767 Angus Campbell Road, Abbotsford, British Columbia, Canada V3G 2M3
| | - John Copps
- Canadian Food Inspection Agency, National Centre for Foreign Animal Disease, 1015 Arlington Street, Winnipeg, Manitoba, Canada R3E 3M4
| | - Deidre Ridd
- Canadian Food Inspection Agency, National Centre for Foreign Animal Disease, 1015 Arlington Street, Winnipeg, Manitoba, Canada R3E 3M4
| | - Kevin Hills
- Canadian Food Inspection Agency, National Centre for Foreign Animal Disease, 1015 Arlington Street, Winnipeg, Manitoba, Canada R3E 3M4
| | - Helen Kehler
- Canadian Food Inspection Agency, National Centre for Foreign Animal Disease, 1015 Arlington Street, Winnipeg, Manitoba, Canada R3E 3M4
| | - Colleen Cottam-Birt
- Canadian Food Inspection Agency, National Centre for Foreign Animal Disease, 1015 Arlington Street, Winnipeg, Manitoba, Canada R3E 3M4
| | - James Neufeld
- Canadian Food Inspection Agency, National Centre for Foreign Animal Disease, 1015 Arlington Street, Winnipeg, Manitoba, Canada R3E 3M4
| | - Yohannes Berhane
- Canadian Food Inspection Agency, National Centre for Foreign Animal Disease, 1015 Arlington Street, Winnipeg, Manitoba, Canada R3E 3M4
| | - Stefanie Czub
- Canadian Food Inspection Agency, National Centre for Foreign Animal Disease, 1015 Arlington Street, Winnipeg, Manitoba, Canada R3E 3M4
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Plyusnina A, Plyusnin A. Recombinant Tula hantavirus shows reduced fitness but is able to survive in the presence of a parental virus: analysis of consecutive passages in a cell culture. Virol J 2005; 2:12. [PMID: 15725355 PMCID: PMC552329 DOI: 10.1186/1743-422x-2-12] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2005] [Accepted: 02/22/2005] [Indexed: 11/10/2022] Open
Abstract
Tula hantavirus carrying recombinant S RNA segment (recTULV) grew in a cell culture to the same titers as the original cell adapted variant but presented no real match to the parental virus. Our data showed that the lower competitiveness of recTULV could not be increased by pre-passaging in the cell culture. Nevertheless, the recombinant virus was able to survive in the presence of the parental virus during five consecutive passages. The observed survival time seems to be sufficient for transmission of newly formed recombinant hantaviruses in nature.
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Affiliation(s)
- Angelina Plyusnina
- Haartman Institute, Department of Virology, University of Helsinki POB 21, FIN-00014, Helsinki, Finland
| | - Alexander Plyusnin
- Haartman Institute, Department of Virology, University of Helsinki POB 21, FIN-00014, Helsinki, Finland
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Hirst M, Astell CR, Griffith M, Coughlin SM, Moksa M, Zeng T, Smailus DE, Holt RA, Jones S, Marra MA, Petric M, Krajden M, Lawrence D, Mak A, Chow R, Skowronski DM, Tweed SA, Goh S, Brunham RC, Robinson J, Bowes V, Sojonky K, Byrne SK, Li Y, Kobasa D, Booth T, Paetzel M. Novel avian influenza H7N3 strain outbreak, British Columbia. Emerg Infect Dis 2005; 10:2192-5. [PMID: 15663859 PMCID: PMC3323367 DOI: 10.3201/eid1012.040743] [Citation(s) in RCA: 152] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Genome sequences of chicken (low pathogenic avian influenza [LPAI] and highly pathogenic avian influenza [HPAI]) and human isolates from a 2004 outbreak of H7N3 avian influenza in Canada showed a novel insertion in the HA0 cleavage site of the human and HPAI isolate. This insertion likely occurred by recombination between the hemagglutination and matrix genes in the LPAI virus.
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Affiliation(s)
- Martin Hirst
- British Columbia Cancer Agency (BCCA) Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Caroline R. Astell
- British Columbia Cancer Agency (BCCA) Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Malachi Griffith
- British Columbia Cancer Agency (BCCA) Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Shaun M. Coughlin
- British Columbia Cancer Agency (BCCA) Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Michelle Moksa
- British Columbia Cancer Agency (BCCA) Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Thomas Zeng
- British Columbia Cancer Agency (BCCA) Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Duane E. Smailus
- British Columbia Cancer Agency (BCCA) Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Robert A. Holt
- British Columbia Cancer Agency (BCCA) Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Steven Jones
- British Columbia Cancer Agency (BCCA) Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Marco A. Marra
- British Columbia Cancer Agency (BCCA) Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Martin Petric
- British Columbia Centre for Disease Control and University of British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
| | - Mel Krajden
- British Columbia Centre for Disease Control and University of British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
| | - David Lawrence
- British Columbia Centre for Disease Control and University of British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
| | - Annie Mak
- British Columbia Centre for Disease Control and University of British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
| | - Ron Chow
- British Columbia Centre for Disease Control and University of British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
| | - Danuta M. Skowronski
- British Columbia Centre for Disease Control and University of British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
| | - S. Aleina Tweed
- British Columbia Centre for Disease Control and University of British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
| | - SweeHan Goh
- British Columbia Centre for Disease Control and University of British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
| | - Robert C. Brunham
- British Columbia Centre for Disease Control and University of British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
| | - John Robinson
- Ministry of Agriculture, Abbotsford, British Columbia, Canada
| | - Victoria Bowes
- Ministry of Agriculture, Abbotsford, British Columbia, Canada
| | - Ken Sojonky
- Ministry of Agriculture, Abbotsford, British Columbia, Canada
| | - Sean K. Byrne
- Ministry of Agriculture, Abbotsford, British Columbia, Canada
| | - Yan Li
- Canadian Centre for Human and Animal Health, Winnipeg, Manitoba, Canada
| | - Darwyn Kobasa
- Canadian Centre for Human and Animal Health, Winnipeg, Manitoba, Canada
| | - Tim Booth
- Canadian Centre for Human and Animal Health, Winnipeg, Manitoba, Canada
| | - Mark Paetzel
- Simon Fraser University, Burnaby, British Columbia, Canada
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47
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Suarez DL, Senne DA, Banks J, Brown IH, Essen SC, Lee CW, Manvell RJ, Mathieu-Benson C, Moreno V, Pedersen JC, Panigrahy B, Rojas H, Spackman E, Alexander DJ. Recombination resulting in virulence shift in avian influenza outbreak, Chile. Emerg Infect Dis 2004; 10:693-9. [PMID: 15200862 PMCID: PMC3323103 DOI: 10.3201/eid1004.030396] [Citation(s) in RCA: 251] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Influenza A viruses occur worldwide in wild birds and are occasionally associated with outbreaks in commercial chickens and turkeys. However, avian influenza viruses have not been isolated from wild birds or poultry in South America. A recent outbreak in chickens of H7N3 low pathogenic avian influenza (LPAI) occurred in Chile. One month later, after a sudden increase in deaths, H7N3 highly pathogenic avian influenza (HPAI) virus was isolated. Sequence analysis of all eight genes of the LPAI virus and the HPAI viruses showed minor differences between the viruses except at the hemagglutinin (HA) cleavage site. The LPAI virus had a cleavage site similar to other low pathogenic H7 viruses, but the HPAI isolates had a 30 nucleotide insert. The insertion likely occurred by recombination between the HA and nucleoprotein genes of the LPAI virus, resulting in a virulence shift. Sequence comparison of all eight gene segments showed the Chilean viruses were also distinct from all other avian influenza viruses and represent a distinct South American clade.
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Affiliation(s)
- David L Suarez
- Southeast Poultry Research Laboratory, Athens, Georgia, USA.
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48
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Chare ER, Gould EA, Holmes EC. Phylogenetic analysis reveals a low rate of homologous recombination in negative-sense RNA viruses. J Gen Virol 2003; 84:2691-2703. [PMID: 13679603 DOI: 10.1099/vir.0.19277-0] [Citation(s) in RCA: 205] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recombination is increasingly seen as an important means of shaping genetic diversity in RNA viruses. However, observed recombination frequencies vary widely among those viruses studied to date, with only sporadic occurrences reported in RNA viruses with negative-sense genomes. To determine the extent of homologous recombination in negative-sense RNA viruses, phylogenetic analyses of 79 gene sequence alignments from 35 negative-sense RNA viruses (a total of 2154 sequences) were carried out. Powerful evidence was found for recombination, in the form of incongruent phylogenetic trees between different gene regions, in only five sequences from Hantaan virus, Mumps virus and Newcastle disease virus. This is the first report of recombination in these viruses. More tentative evidence for recombination, where conflicting phylogenetic trees were observed (but were without strong bootstrap support) and/or where putative recombinant regions were very short, was found in three alignments from La Crosse virus and Puumala virus. Finally, patterns of sequence variation compatible with the action of recombination, but not definitive evidence for this process, were observed in a further ten viruses: Canine distemper virus, Crimean-Congo haemorrhagic fever virus, Influenza A virus, Influenza B virus, Influenza C virus, Lassa virus, Pirital virus, Rabies virus, Rift Valley Fever virus and Vesicular stomatitis virus. The possibility of recombination in these viruses should be investigated further. Overall, this study reveals that rates of homologous recombination in negative-sense RNA viruses are very much lower than those of mutation, with many viruses seemingly clonal on current data. Consequently, recombination rate is unlikely to be a trait that is set by natural selection to create advantageous or purge deleterious mutations.
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Affiliation(s)
- Elizabeth R Chare
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
| | - Ernest A Gould
- Centre for Ecology and Hydrology, Mansfield Road, Oxford, UK
| | - Edward C Holmes
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
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49
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Abstract
Influenza A viruses contain genomes composed of eight separate segments of negative-sense RNA. Circulating human strains are notorious for their tendency to accumulate mutations from one year to the next and cause recurrent epidemics. However, the segmented nature of the genome also allows for the exchange of entire genes between different viral strains. The ability to manipulate influenza gene segments in various combinations in the laboratory has contributed to its being one of the best characterized viruses, and studies on influenza have provided key contributions toward the understanding of various aspects of virology in general. However, the genetic plasticity of influenza viruses also has serious potential implications regarding vaccine design, pathogenicity, and the capacity for novel viruses to emerge from natural reservoirs and cause global pandemics.
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Affiliation(s)
- David A Steinhauer
- Department of Microbiology and Immunology, Emory University School of Medicine, Rollins Research Center, Atlanta, Georgia 30322, USA.
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50
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Reina J. [Factors affecting the virulence and pathogenicity of avian and human viral strains (influenza virus type A)]. Enferm Infecc Microbiol Clin 2002; 20:346-53. [PMID: 12237002 DOI: 10.1016/s0213-005x(02)72814-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Most studies performed in avian viral strains seem to indicate that virulence is a polygenic phenomenon. However, hemagglutinin and neuraminidase and the genes codifying these substances (genes 4 and 6) play an essential role in viral pathogenesis. Avian strains can be classified as avirulent or virulent according to the ability of hemagglutinin to be activated by endoproteases of the respiratory tract only or by proteases from other tissues. This ability is based on the progressive development of mutations that lead to the substitution of the normal amino acids at the point of hemagglutinin hydrolysis by the other basic amino acids that determine the amplification of the spectrum of hydrolysis and activation. Neuraminidase participates in the acquisition of virulence through its capacity to bind to plasminogen and by increasing the concentration of activating proteases. Adaptation to the host, through recognition of the cell receptor, is another factor determining the virulence and interspecies transmission of avian strains. From an epidemiological point of view, viral strains should be subtyped and the activating capacity of hemagglutinin should be determined to identify their degree of virulence.
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Affiliation(s)
- Jordi Reina
- Unidad de Virología, Servicio de Microbiología Clínica, Hospital Universitario Son Dureta, Palma de Mallorca, España.
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