1
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Beniston E, Skittrall JP. Locations and structures of influenza A virus packaging-associated signals and other functional elements via an in silico pipeline for predicting constrained features in RNA viruses. PLoS Comput Biol 2024; 20:e1012009. [PMID: 38648223 PMCID: PMC11034665 DOI: 10.1371/journal.pcbi.1012009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 03/18/2024] [Indexed: 04/25/2024] Open
Abstract
Influenza A virus contains regions of its segmented genome associated with ability to package the segments into virions, but many such regions are poorly characterised. We provide detailed predictions of the key locations within these packaging-associated regions, and their structures, by applying a recently-improved pipeline for delineating constrained regions in RNA viruses and applying structural prediction algorithms. We find and characterise other known constrained regions within influenza A genomes, including the region associated with the PA-X frameshift, regions associated with alternative splicing, and constraint around the initiation motif for a truncated PB1 protein, PB1-N92, associated with avian viruses. We further predict the presence of constrained regions that have not previously been described. The extra characterisation our work provides allows investigation of these key regions for drug target potential, and points towards determinants of packaging compatibility between segments.
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Affiliation(s)
- Emma Beniston
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
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2
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Szczesniak I, Baliga-Gil A, Jarmolowicz A, Soszynska-Jozwiak M, Kierzek E. Structural and Functional RNA Motifs of SARS-CoV-2 and Influenza A Virus as a Target of Viral Inhibitors. Int J Mol Sci 2023; 24:ijms24021232. [PMID: 36674746 PMCID: PMC9860923 DOI: 10.3390/ijms24021232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 12/28/2022] [Accepted: 12/29/2022] [Indexed: 01/11/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the COVID-19 pandemic, whereas the influenza A virus (IAV) causes seasonal epidemics and occasional pandemics. Both viruses lead to widespread infection and death. SARS-CoV-2 and the influenza virus are RNA viruses. The SARS-CoV-2 genome is an approximately 30 kb, positive sense, 5' capped single-stranded RNA molecule. The influenza A virus genome possesses eight single-stranded negative-sense segments. The RNA secondary structure in the untranslated and coding regions is crucial in the viral replication cycle. The secondary structure within the RNA of SARS-CoV-2 and the influenza virus has been intensively studied. Because the whole of the SARS-CoV-2 and influenza virus replication cycles are dependent on RNA with no DNA intermediate, the RNA is a natural and promising target for the development of inhibitors. There are a lot of RNA-targeting strategies for regulating pathogenic RNA, such as small interfering RNA for RNA interference, antisense oligonucleotides, catalytic nucleic acids, and small molecules. In this review, we summarized the knowledge about the inhibition of SARS-CoV-2 and influenza A virus propagation by targeting their RNA secondary structure.
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3
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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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4
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Evolution of the North American Lineage H7 Avian Influenza Viruses in Association with H7 Virus's Introduction to Poultry. J Virol 2022; 96:e0027822. [PMID: 35862690 PMCID: PMC9327676 DOI: 10.1128/jvi.00278-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The incursions of H7 subtype low-pathogenicity avian influenza virus (LPAIV) from wild birds into poultry and its mutations to highly pathogenic avian influenza virus (HPAIV) have been an ongoing concern in North America. Since 2000, 10 phylogenetically distinct H7 virus outbreaks from wild birds have been detected in poultry, six of which mutated to HPAIV. To study the molecular evolution of the H7 viruses that occurs when changing hosts from wild birds to poultry, we performed analyses of the North American H7 hemagglutinin (HA) genes to identify amino acid changes as the virus circulated in wild birds from 2000 to 2019. Then, we analyzed recurring HA amino acid changes and gene constellations of the viruses that spread from wild birds to poultry. We found six HA amino acid changes occurring during wild bird circulation and 10 recurring changes after the spread to poultry. Eight of the changes were in and around the HA antigenic sites, three of which were supported by positive selection. Viruses from each H7 outbreak had a unique genotype, with no specific genetic group associated with poultry outbreaks or mutation to HPAIV. However, the genotypes of the H7 viruses in poultry outbreaks tended to contain minor genetic groups less observed in wild bird H7 viruses, suggesting either a biased sampling of wild bird AIVs or a tendency of having reassortment with minor genetic groups prior to the virus's introduction to poultry. IMPORTANCE Wild bird-origin H7 subtype avian influenza viruses are a constant threat to commercial poultry, both directly by the disease they cause and indirectly through trade restrictions that can be imposed when the virus is detected in poultry. It is important to understand the genetic basis of why the North American lineage H7 viruses have repeatedly crossed the species barrier from wild birds to poultry. We examined the amino acid changes in the H7 viruses associated with poultry outbreaks and tried to determine gene reassortment related to poultry adaptation and mutations to HPAIV. The findings in this study increase the understanding of the evolutionary pathways of wild bird AIV before infecting poultry and the HA changes associated with adaptation of the virus in poultry.
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5
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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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6
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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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7
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Peterson JM, O'Leary CA, Moss WN. In silico analysis of local RNA secondary structure in influenza virus A, B and C finds evidence of widespread ordered stability but little evidence of significant covariation. Sci Rep 2022; 12:310. [PMID: 35013354 PMCID: PMC8748542 DOI: 10.1038/s41598-021-03767-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 12/02/2021] [Indexed: 12/13/2022] Open
Abstract
Influenza virus is a persistent threat to human health; indeed, the deadliest modern pandemic was in 1918 when an H1N1 virus killed an estimated 50 million people globally. The intent of this work is to better understand influenza from an RNA-centric perspective to provide local, structural motifs with likely significance to the influenza infectious cycle for therapeutic targeting. To accomplish this, we analyzed over four hundred thousand RNA sequences spanning three major clades: influenza A, B and C. We scanned influenza segments for local secondary structure, identified/modeled motifs of likely functionality, and coupled the results to an analysis of evolutionary conservation. We discovered 185 significant regions of predicted ordered stability, yet evidence of sequence covariation was limited to 7 motifs, where 3-found in influenza C-had higher than expected amounts of sequence covariation.
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Affiliation(s)
- Jake M Peterson
- Roy J. Carver Department of Biophysics, Biochemistry and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Collin A O'Leary
- Roy J. Carver Department of Biophysics, Biochemistry and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Walter N Moss
- Roy J. Carver Department of Biophysics, Biochemistry and Molecular Biology, Iowa State University, Ames, IA, 50011, USA.
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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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9
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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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10
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Lee DH, Criado MF, Swayne DE. Pathobiological Origins and Evolutionary History of Highly Pathogenic Avian Influenza Viruses. Cold Spring Harb Perspect Med 2021; 11:a038679. [PMID: 31964650 PMCID: PMC7849344 DOI: 10.1101/cshperspect.a038679] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
High-pathogenicity avian influenza (HPAI) viruses have arisen from low-pathogenicity avian influenza (LPAI) viruses via changes in the hemagglutinin proteolytic cleavage site, which include mutation of multiple nonbasic to basic amino acids, duplication of basic amino acids, or recombination with insertion of cellular or viral amino acids. Between 1959 and 2019, a total of 42 natural, independent H5 (n = 15) and H7 (n = 27) LPAI to HPAI virus conversion events have occurred in Europe (n = 16), North America (n = 9), Oceania (n = 7), Asia (n = 5), Africa (n = 4), and South America (n = 1). Thirty-eight of these HPAI outbreaks were limited in the number of poultry premises affected and were eradicated. However, poultry outbreaks caused by A/goose/Guangdong/1/1996 (H5Nx), Mexican H7N3, and Chinese H7N9 HPAI lineages have continued. Active surveillance and molecular detection and characterization efforts will provide the best opportunity for early detection and eradication from domestic birds.
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Affiliation(s)
- Dong-Hun Lee
- Department of Pathobiology & Veterinary Science, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Miria Ferreira Criado
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, Georgia 30605, USA
| | - David E Swayne
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, Georgia 30605, USA
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11
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Vandelli A, Monti M, Milanetti E, Armaos A, Rupert J, Zacco E, Bechara E, Delli Ponti R, Tartaglia GG. Structural analysis of SARS-CoV-2 genome and predictions of the human interactome. Nucleic Acids Res 2020. [PMID: 33068416 DOI: 10.1101/2020.03.28.013789] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023] Open
Abstract
Specific elements of viral genomes regulate interactions within host cells. Here, we calculated the secondary structure content of >2000 coronaviruses and computed >100 000 human protein interactions with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The genomic regions display different degrees of conservation. SARS-CoV-2 domain encompassing nucleotides 22 500-23 000 is conserved both at the sequence and structural level. The regions upstream and downstream, however, vary significantly. This part of the viral sequence codes for the Spike S protein that interacts with the human receptor angiotensin-converting enzyme 2 (ACE2). Thus, variability of Spike S is connected to different levels of viral entry in human cells within the population. Our predictions indicate that the 5' end of SARS-CoV-2 is highly structured and interacts with several human proteins. The binding proteins are involved in viral RNA processing, include double-stranded RNA specific editases and ATP-dependent RNA-helicases and have strong propensity to form stress granules and phase-separated assemblies. We propose that these proteins, also implicated in viral infections such as HIV, are selectively recruited by SARS-CoV-2 genome to alter transcriptional and post-transcriptional regulation of host cells and to promote viral replication.
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Affiliation(s)
- Andrea Vandelli
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain and Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- Systems Biology of Infection Lab, Department of Biochemistry and Molecular Biology, Biosciences Faculty, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Michele Monti
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain and Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen 83, 16152 Genoa, Italy
| | - Edoardo Milanetti
- Department of Physics, Sapienza University, Piazzale Aldo Moro 5, 00185 Rome, Italy
- Center for Life Nanoscience, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
| | - Alexandros Armaos
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain and Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen 83, 16152 Genoa, Italy
| | - Jakob Rupert
- Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen 83, 16152 Genoa, Italy
- Department of Biology 'Charles Darwin', Sapienza University of Rome, P.le A. Moro 5, Rome 00185, Italy
| | - Elsa Zacco
- Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen 83, 16152 Genoa, Italy
| | - Elias Bechara
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain and Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen 83, 16152 Genoa, Italy
| | - Riccardo Delli Ponti
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Gian Gaetano Tartaglia
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain and Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen 83, 16152 Genoa, Italy
- Department of Biology 'Charles Darwin', Sapienza University of Rome, P.le A. Moro 5, Rome 00185, Italy
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), 23 Passeig Lluis Companys, 08010 Barcelona, Spain
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Vandelli A, Monti M, Milanetti E, Armaos A, Rupert J, Zacco E, Bechara E, Delli Ponti R, Tartaglia G. Structural analysis of SARS-CoV-2 genome and predictions of the human interactome. Nucleic Acids Res 2020; 48:11270-11283. [PMID: 33068416 PMCID: PMC7672441 DOI: 10.1093/nar/gkaa864] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/15/2020] [Accepted: 09/25/2020] [Indexed: 12/17/2022] Open
Abstract
Specific elements of viral genomes regulate interactions within host cells. Here, we calculated the secondary structure content of >2000 coronaviruses and computed >100 000 human protein interactions with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The genomic regions display different degrees of conservation. SARS-CoV-2 domain encompassing nucleotides 22 500-23 000 is conserved both at the sequence and structural level. The regions upstream and downstream, however, vary significantly. This part of the viral sequence codes for the Spike S protein that interacts with the human receptor angiotensin-converting enzyme 2 (ACE2). Thus, variability of Spike S is connected to different levels of viral entry in human cells within the population. Our predictions indicate that the 5' end of SARS-CoV-2 is highly structured and interacts with several human proteins. The binding proteins are involved in viral RNA processing, include double-stranded RNA specific editases and ATP-dependent RNA-helicases and have strong propensity to form stress granules and phase-separated assemblies. We propose that these proteins, also implicated in viral infections such as HIV, are selectively recruited by SARS-CoV-2 genome to alter transcriptional and post-transcriptional regulation of host cells and to promote viral replication.
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Affiliation(s)
- Andrea Vandelli
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain and Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- Systems Biology of Infection Lab, Department of Biochemistry and Molecular Biology, Biosciences Faculty, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Michele Monti
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain and Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen 83, 16152 Genoa, Italy
| | - Edoardo Milanetti
- Department of Physics, Sapienza University, Piazzale Aldo Moro 5, 00185 Rome, Italy
- Center for Life Nanoscience, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
| | - Alexandros Armaos
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain and Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen 83, 16152 Genoa, Italy
| | - Jakob Rupert
- Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen 83, 16152 Genoa, Italy
- Department of Biology ‘Charles Darwin’, Sapienza University of Rome, P.le A. Moro 5, Rome 00185, Italy
| | - Elsa Zacco
- Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen 83, 16152 Genoa, Italy
| | - Elias Bechara
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain and Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen 83, 16152 Genoa, Italy
| | - Riccardo Delli Ponti
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Gian Gaetano Tartaglia
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain and Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen 83, 16152 Genoa, Italy
- Department of Biology ‘Charles Darwin’, Sapienza University of Rome, P.le A. Moro 5, Rome 00185, Italy
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), 23 Passeig Lluis Companys, 08010 Barcelona, Spain
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The Effects of Genetic Variation on H7N9 Avian Influenza Virus Pathogenicity. Viruses 2020; 12:v12111220. [PMID: 33126529 PMCID: PMC7693985 DOI: 10.3390/v12111220] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 10/18/2020] [Accepted: 10/26/2020] [Indexed: 12/12/2022] Open
Abstract
Since the H7N9 avian influenza virus emerged in China in 2013, there have been five seasonal waves which have shown human infections and caused high fatality rates in infected patients. A multibasic amino acid insertion seen in the HA of current H7N9 viruses occurred through natural evolution and reassortment, and created a high pathogenicity avian influenza (HPAI) virus from the low pathogenicity avian influenza (LPAI) in 2017, and significantly increased pathogenicity in poultry, resulting in widespread HPAI H7N9 in poultry, which along with LPAI H7N9, contributed to the severe fifth seasonal wave in China. H7N9 is a novel reassorted virus from three different subtypes of influenza A viruses (IAVs) which displays a great potential threat to public health and the poultry industry. To date, no sustained human-to-human transmission has been recorded by the WHO. However, the high ability of evolutionary adaptation of H7N9 and lack of pre-existing immunity in humans heightens the pandemic potential. Changes in IAVs proteins can affect the viral transmissibility, receptor binding specificity, pathogenicity, and virulence. The multibasic amino acid insertion, mutations in hemagglutinin, deletion and mutations in neuraminidase, and mutations in PB2 contribute to different virological characteristics. This review summarized the latest research evidence to describe the impacts of viral protein changes in viral adaptation and pathogenicity of H7N9, aiming to provide better insights for developing and enhancing early warning or intervention strategies with the goal of preventing highly pathogenic IAVs circulation in live poultry, and transmission to humans.
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