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Funk M, Spronken MI, Bestebroer TM, de Bruin AC, Gultyaev AP, Fouchier RA, te Velthuis AJ, Richard M. Transient RNA structures underlie highly pathogenic avian influenza virus genesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.11.574333. [PMID: 38370829 PMCID: PMC10871305 DOI: 10.1101/2024.01.11.574333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Highly pathogenic avian influenza viruses (HPAIVs) cause severe disease and high fatality in poultry1. They emerge exclusively from H5 and H7 low pathogenic avian influenza viruses (LPAIVs)2. Although insertion of a furin-cleavable multibasic cleavage site (MBCS) in the hemagglutinin gene was identified decades ago as the genetic basis for LPAIV-to-HPAIV transition3,4, the exact mechanisms underlying said insertion have remained unknown. Here we used an innovative combination of bioinformatic models to predict RNA structures forming around the influenza virus RNA polymerase during replication, and circular sequencing5 to reliably detect nucleotide insertions. We show that transient H5 hemagglutinin RNA structures predicted to trap the polymerase on purine-rich sequences drive nucleotide insertions characteristic of MBCSs, providing the first strong empirical evidence of RNA structure involvement in MBCS acquisition. Insertion frequencies at the H5 cleavage site were strongly affected by substitutions in flanking genomic regions altering predicted transient RNA structures. Introduction of H5-like cleavage site sequences and structures into an H6 hemagglutinin resulted in MBCS-yielding insertions never observed before in H6 viruses. Our results demonstrate that nucleotide insertions that underlie H5 HPAIV emergence result from a previously unknown RNA-structure-driven diversity-generating mechanism, which could be shared with other RNA viruses.
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Affiliation(s)
- Mathis Funk
- Department of Viroscience; Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Monique I. Spronken
- Department of Viroscience; Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Theo M. Bestebroer
- Department of Viroscience; Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Anja C.M. de Bruin
- Department of Viroscience; Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands
| | - 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
| | - Ron A.M. Fouchier
- Department of Viroscience; Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Aartjan J.W. te Velthuis
- Lewis Thomas Laboratory, Department of Molecular Biology; Princeton University, 08544 New Jersey, United States
| | - Mathilde Richard
- Department of Viroscience; Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands
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2
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Influence of viral genome properties on polymerase fidelity. Trends Genet 2023; 39:9-14. [PMID: 36402624 DOI: 10.1016/j.tig.2022.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 10/27/2022] [Accepted: 10/30/2022] [Indexed: 11/17/2022]
Abstract
The first step of viral evolution takes place during genome replication via the error-prone viral polymerase. Among the mutants that arise through this process, only a few well-adapted variants will be selected by natural selection, renewing the viral genome population. Viral polymerase-mediated errors are thought to occur stochastically. However, accumulating evidence suggests that viral polymerase-mediated mutations are heterogeneously distributed throughout the viral genome. Here, we review work that supports this concept and provides mechanistic insights into how specific features of the viral genome could modulate viral polymerase-mediated errors. A predisposition to accumulate viral polymerase-mediated errors at specific loci in the viral genome may guide evolution to specific pathways, thus opening new directions of research to better understand viral evolutionary dynamics.
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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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Glycine Nano-Selenium Enhances Immunoglobulin and Cytokine Production in Mice Immunized with H9N2 Avian Influenza Virus Vaccine. Int J Mol Sci 2022; 23:ijms23147914. [PMID: 35887267 PMCID: PMC9317336 DOI: 10.3390/ijms23147914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/13/2022] [Accepted: 07/15/2022] [Indexed: 02/01/2023] Open
Abstract
This study was performed to investigate the immune enhancement effect of glycine nano-selenium, a microelement on H9N2 avian influenza virus vaccine (H9N2 AIV vaccine) in mice. Fifty (50) Specific Pathogen Free Kunming mice aged 4−6 weeks (18−20 g Body weight) were randomly divided into five groups: control normal group, which received no immunization + 0.5 mL 0.9% normal saline, positive control group, which received H9N2 AIV vaccine + 0.5 mL 0.9% normal saline, 0.25 mg/kg selenium group, which received H9N2 AIV vaccine + 0.5 mL 0.25 mg/kg selenium solution, 0.5 mg/kg selenium group, which received H9N2 AIV vaccine + 0.5 mL 0.5 mg/kg selenium solution, and 1 mg/kg selenium group, which received H9N2 AIV vaccine + 0.5 mL 1 mg/kg selenium solution. Hematoxylin and eosin staining, enzyme linked immunosorbent assay (ELISA), and quantitative real time polymerase chain reaction (qRT-PCR) methods were used to investigate the pathological changes, immunoglobulin levels, and cytokine gene expressions in this study. The results showed that all tested doses (0.25 mg/kg, 0.5 mg/kg and 1.00 mg/kg) of glycine nano-selenium did not lead to poisoning in mice. In addition, when compared to the positive control group, glycine nano-selenium increased the immunoglobin indexes (IgA, IgG, IgM and AIV-H9 IgG in serum) as well as the mRNA levels of IL-1β, IL-6 and INF-γ in the liver, lungs, and spleen (p < 0.05). In summary, glycine nano-selenium could enhance the efficacy of avian influenza vaccine.
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Funk M, de Bruin ACM, Spronken MI, Gultyaev AP, Richard M. In Silico Analyses of the Role of Codon Usage at the Hemagglutinin Cleavage Site in Highly Pathogenic Avian Influenza Genesis. Viruses 2022; 14:v14071352. [PMID: 35891333 PMCID: PMC9316147 DOI: 10.3390/v14071352] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 06/10/2022] [Accepted: 06/13/2022] [Indexed: 02/01/2023] Open
Abstract
A vast diversity of 16 influenza hemagglutinin (HA) subtypes are found in birds. Interestingly, viruses from only two subtypes, H5 and H7, have so far evolved into highly pathogenic avian influenza viruses (HPAIVs) following insertions or substitutions at the HA cleavage site by the viral polymerase. The mechanisms underlying this striking subtype specificity are still unknown. Here, we compiled a comprehensive dataset of 20,488 avian influenza virus HA sequences to investigate differences in nucleotide and amino acid usage at the HA cleavage site between subtypes and how these might impact the genesis of HPAIVs by polymerase stuttering and realignment. We found that sequences of the H5 and H7 subtypes stand out by their high purine content at the HA cleavage site. In addition, fewer substitutions were necessary in H5 and H7 HAs than in HAs from other subtypes to acquire an insertion-prone HA cleavage site sequence, as defined based on in vitro and in vivo data from the literature. Codon usage was more favorable for HPAIV genesis in sequences of viruses isolated from species or geographical regions in which HPAIV genesis is more frequently observed in nature. The results of the present analyses suggest that the subtype restriction of HPAIV genesis to H5 and H7 influenza viruses might be due to the particular codon usage at the HA cleavage site in these subtypes.
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Affiliation(s)
- Mathis Funk
- Department of Viroscience, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands; (M.F.); (A.C.M.d.B.); (M.I.S.); (A.P.G.)
| | - Anja C. M. de Bruin
- Department of Viroscience, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands; (M.F.); (A.C.M.d.B.); (M.I.S.); (A.P.G.)
| | - Monique I. Spronken
- Department of Viroscience, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands; (M.F.); (A.C.M.d.B.); (M.I.S.); (A.P.G.)
| | - Alexander P. Gultyaev
- Department of Viroscience, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands; (M.F.); (A.C.M.d.B.); (M.I.S.); (A.P.G.)
- Group Imaging and Bioinformatics, Leiden Institute of Advanced Computer Science (LIACS), Leiden University, 2300 RA Leiden, The Netherlands
| | - Mathilde Richard
- Department of Viroscience, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands; (M.F.); (A.C.M.d.B.); (M.I.S.); (A.P.G.)
- Correspondence:
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6
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Genomic determinants of Furin cleavage in diverse European SARS-related bat coronaviruses. Commun Biol 2022; 5:491. [PMID: 35637279 PMCID: PMC9151638 DOI: 10.1038/s42003-022-03421-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 04/27/2022] [Indexed: 12/11/2022] Open
Abstract
The furin cleavage site (FCS) in SARS-CoV-2 is unique within the Severe acute respiratory syndrome–related coronavirus (SrC) species. We re-assessed diverse SrC from European horseshoe bats and analyzed the spike-encoding genomic region harboring the FCS in SARS-CoV-2. We reveal molecular features in SrC such as purine richness and RNA secondary structures that resemble those required for FCS acquisition in avian influenza viruses. We discuss the potential acquisition of FCS through molecular mechanisms such as nucleotide substitution, insertion, or recombination, and show that a single nucleotide exchange in two European bat-associated SrC may suffice to enable furin cleavage. Furthermore, we show that FCS occurrence is variable in bat- and rodent-borne counterparts of human coronaviruses. Our results suggest that furin cleavage sites can be acquired in SrC via conserved molecular mechanisms known in other reservoir-bound RNA viruses and thus support a natural origin of SARS-CoV-2. Genomic analyses of spike glycoprotein genes of European bat SARS-related coronaviruses suggest that furin cleavage sites can be acquired in the bat reservoir via conserved molecular mechanisms, supporting a natural origin of SARS-CoV-2.
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7
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Putative Host-Derived Insertions in the Genomes of Circulating SARS-CoV-2 Variants. mSystems 2022; 7:e0017922. [PMID: 35582907 PMCID: PMC9239191 DOI: 10.1128/msystems.00179-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Insertions in the SARS-CoV-2 genome have the potential to drive viral evolution, but the source of the insertions is often unknown. Recent proposals have suggested that human RNAs could be a source of some insertions, but the small size of many insertions makes this difficult to confirm. Through an analysis of available direct RNA sequencing data from SARS-CoV-2-infected cells, we show that viral-host chimeric RNAs are formed through what are likely stochastic RNA-dependent RNA polymerase template-switching events. Through an analysis of the publicly available GISAID SARS-CoV-2 genome collection, we identified two genomic insertions in circulating SARS-CoV-2 variants that are identical to regions of the human 18S and 28S rRNAs. These results provide direct evidence of the formation of viral-host chimeric sequences and the integration of host genetic material into the SARS-CoV-2 genome, highlighting the potential importance of host-derived insertions in viral evolution. IMPORTANCE Throughout the COVID-19 pandemic, the sequencing of SARS-CoV-2 genomes has revealed the presence of insertions in multiple globally circulating lineages of SARS-CoV-2, including the Omicron variant. The human genome has been suggested to be the source of some of the larger insertions, but evidence for this kind of event occurring is still lacking. Here, we leverage direct RNA sequencing data and SARS-CoV-2 genomes to show that host-viral chimeric RNAs are generated in infected cells and two large genomic insertions have likely been formed through the incorporation of host rRNA fragments into the SARS-CoV-2 genome. These host-derived insertions may increase the genetic diversity of SARS-CoV-2 and expand its strategies to acquire genetic material, potentially enhancing its adaptability, virulence, and spread.
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8
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Yang Y, Dufault-thompson K, Fontenele RS, Jiang X. Putative host-derived insertions in the genomes of circulating SARS-CoV-2 variants.. [PMID: 35043112 PMCID: PMC8764720 DOI: 10.1101/2022.01.04.474799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Insertions in the SARS-CoV-2 genome have the potential to drive viral evolution, but the source of the insertions is often unknown. Recent proposals have suggested that human RNAs could be a source of some insertions, but the small size of many insertions makes this difficult to confirm. Through an analysis of available direct RNA sequencing data from SARS-CoV-2 infected cells, we show that viral-host chimeric RNAs are formed through what are likely stochastic RNA-dependent RNA polymerase template switching events. Through an analysis of the publicly available GISAID SARS-CoV-2 genome collection, we identified two genomic insertions in circulating SARS-CoV-2 variants that are identical to regions of the human 18S and 28S rRNAs. These results provide direct evidence of the formation of viral-host chimeric sequences and the integration of host genetic material into the SARS-CoV-2 genome, highlighting the potential importance of host-derived insertions in viral evolution.
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9
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Kida Y, Okuya K, Saito T, Yamagishi J, Ohnuma A, Hattori T, Miyamoto H, Manzoor R, Yoshida R, Nao N, Kajihara M, Watanabe T, Takada A. Structural Requirements in the Hemagglutinin Cleavage Site-Coding RNA Region for the Generation of Highly Pathogenic Avian Influenza Virus. Pathogens 2021; 10:1597. [PMID: 34959552 PMCID: PMC8707032 DOI: 10.3390/pathogens10121597] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/08/2021] [Accepted: 12/08/2021] [Indexed: 11/25/2022] Open
Abstract
Highly pathogenic avian influenza viruses (HPAIVs) with H5 and H7 hemagglutinin (HA) subtypes are derived from their low pathogenic counterparts following the acquisition of multiple basic amino acids in their HA cleavage site. It has been suggested that consecutive adenine residues and a stem-loop structure in the viral RNA region that encodes the cleavage site are essential for the acquisition of the polybasic cleavage site. By using a reporter assay to detect non-templated nucleotide insertions, we found that insertions more frequently occurred in the RNA region (29 nucleotide-length) encoding the cleavage site of an H5 HA gene that was predicted to have a stem-loop structure containing consecutive adenines than in a mutated corresponding RNA region that had a disrupted loop structure with fewer adenines. In virus particles generated by using reverse genetics, nucleotide insertions that created additional codons for basic amino acids were found in the RNA region encoding the cleavage site of an H5 HA gene but not in the mutated RNA region. We confirmed the presence of virus clones with the ability to replicate without trypsin in a plaque assay and to cause lethal infection in chicks. These results demonstrate that the stem-loop structure containing consecutive adenines in HA genes is a key molecular determinant for the emergence of H5 HPAIVs.
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Affiliation(s)
- Yurie Kida
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan; (Y.K.); (K.O.); (T.S.); (T.H.); (H.M.); (R.M.); (R.Y.); (M.K.)
| | - Kosuke Okuya
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan; (Y.K.); (K.O.); (T.S.); (T.H.); (H.M.); (R.M.); (R.Y.); (M.K.)
| | - Takeshi Saito
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan; (Y.K.); (K.O.); (T.S.); (T.H.); (H.M.); (R.M.); (R.Y.); (M.K.)
| | - Junya Yamagishi
- Division of Collaboration and Education, International Institute for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan;
| | - Aiko Ohnuma
- Technical Office, International Institute for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan;
| | - Takanari Hattori
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan; (Y.K.); (K.O.); (T.S.); (T.H.); (H.M.); (R.M.); (R.Y.); (M.K.)
| | - Hiroko Miyamoto
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan; (Y.K.); (K.O.); (T.S.); (T.H.); (H.M.); (R.M.); (R.Y.); (M.K.)
| | - Rashid Manzoor
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan; (Y.K.); (K.O.); (T.S.); (T.H.); (H.M.); (R.M.); (R.Y.); (M.K.)
| | - Reiko Yoshida
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan; (Y.K.); (K.O.); (T.S.); (T.H.); (H.M.); (R.M.); (R.Y.); (M.K.)
| | - Naganori Nao
- Division of International Research Promotion, International Institute for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan;
- One Health Research Center, Hokkaido University, Sapporo 060-0818, Japan
| | - Masahiro Kajihara
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan; (Y.K.); (K.O.); (T.S.); (T.H.); (H.M.); (R.M.); (R.Y.); (M.K.)
| | - Tokiko Watanabe
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan;
| | - Ayato Takada
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan; (Y.K.); (K.O.); (T.S.); (T.H.); (H.M.); (R.M.); (R.Y.); (M.K.)
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan
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Dupré G, Hoede C, Figueroa T, Bessière P, Bertagnoli S, Ducatez M, Gaspin C, Volmer R. Phylodynamic Study of the Conserved RNA Structure Encompassing the Hemagglutinin Cleavage Site Encoding Region of H5 and H7 Low Pathogenic Avian Influenza Viruses. Virus Evol 2021; 7:veab093. [PMID: 35299790 PMCID: PMC8923263 DOI: 10.1093/ve/veab093] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 10/07/2021] [Accepted: 10/29/2021] [Indexed: 11/14/2022] Open
Abstract
Abstract
Highly Pathogenic Avian Influenza Viruses (HPAIV) evolve from Low Pathogenic Avian Influenza Viruses (LPAIV) of the H5 and H7 subtypes. This evolution is characterized by the acquisition of a multi-basic cleavage site (MBCS) motif in the hemagglutinin (HA) that leads to an extended viral tropism and severe disease in poultry. One key unanswered question is whether the risk of transition to HPAIV is similar for all LPAIV H5 or H7 strains, or whether specific determinants in the HA sequence of some H5 or H7 LPAIV strains correlate with a higher risk of transition to HPAIV. Here we determined if specific features of the conserved RNA stem loop located at the hemagglutinin cleavage site-encoding region could be detected along the LPAIV to HPAIV evolutionary pathway. Analysis of the thermodynamic stability of the predicted RNA structures showed no specific patterns common to HA sequences leading to HPAIV and distinct from those remaining LPAIV. However, RNA structure clustering analysis revealed that most of the American lineage ancestors leading to H7 emergences via recombination shared the same vRNA structure topology at the HA1/HA2 boundary region. Our study thus identified predicted secondary RNA structures present in the HA of H7 viruses, which could promote genetic recombination and acquisition of a MBCS.
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Affiliation(s)
- Gabriel Dupré
- Ecole nationale vétérinaire de Toulouse, Université de Toulouse, ENVT, INRAE, IHAP, UMR 1225, Toulouse, France
| | - Claire Hoede
- INRAE, UR875 Mathématiques et Informatique Appliquées Toulouse, Plateforme GenoToul BioInfo, F-31326 Castanet-Tolosan, France
| | - Thomas Figueroa
- Ecole nationale vétérinaire de Toulouse, Université de Toulouse, ENVT, INRAE, IHAP, UMR 1225, Toulouse, France
| | - Pierre Bessière
- Ecole nationale vétérinaire de Toulouse, Université de Toulouse, ENVT, INRAE, IHAP, UMR 1225, Toulouse, France
| | - Stéphane Bertagnoli
- Ecole nationale vétérinaire de Toulouse, Université de Toulouse, ENVT, INRAE, IHAP, UMR 1225, Toulouse, France
| | - Mariette Ducatez
- Ecole nationale vétérinaire de Toulouse, Université de Toulouse, ENVT, INRAE, IHAP, UMR 1225, Toulouse, France
| | - Christine Gaspin
- INRAE, UR875 Mathématiques et Informatique Appliquées Toulouse, Plateforme GenoToul BioInfo, F-31326 Castanet-Tolosan, France
| | - Romain Volmer
- Ecole nationale vétérinaire de Toulouse, Université de Toulouse, ENVT, INRAE, IHAP, UMR 1225, Toulouse, France
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