1
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McAdams Z, Gustafson K, Ericsson A. The Effect of Common Viral Inactivation Techniques on 16S rRNA Amplicon-Based Analysis of the Gut Microbiota. Microorganisms 2021; 9:1755. [PMID: 34442834 PMCID: PMC8400488 DOI: 10.3390/microorganisms9081755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/05/2021] [Accepted: 08/13/2021] [Indexed: 11/25/2022] Open
Abstract
Research investigating the gut microbiome (GM) during a viral infection may necessitate inactivation of the fecal viral load. Here, we assess how common viral inactivation techniques affect 16S rRNA-based analysis of the gut microbiome. Five common viral inactivation methods were applied to cross-matched fecal samples from sixteen female CD-1 mice of the same GM background prior to fecal DNA extraction. The V4 region of the 16S rRNA gene was amplified and sequenced from extracted DNA. Treatment-dependent effects on DNA yield, genus-level taxonomic abundance, and alpha and beta diversity metrics were assessed. A sodium dodecyl sulfate (SDS)-based inactivation method and Holder pasteurization had no effect on measures of microbial richness, while two Buffer AVL-based inactivation methods resulted in a decrease in detected richness. SDS inactivation, Holder pasteurization, and the AVL-based inactivation methods had no effect on measures of alpha diversity within samples or beta diversity between samples. Fecal DNA extracted with TRIzol-treated samples failed to amplify and sequence, making it unsuitable for microbiome analysis. These results provide guidance in the 16S rRNA microbiome analysis of fecal samples requiring viral inactivation.
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Affiliation(s)
- Zachary McAdams
- Molecular Pathogenesis and Therapeutics Program, University of Missouri, Columbia, MO 65211, USA;
| | - Kevin Gustafson
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA;
- Comparative Medicine Program, University of Missouri, Columbia, MO 65211, USA
| | - Aaron Ericsson
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA;
- Comparative Medicine Program, University of Missouri, Columbia, MO 65211, USA
- Metagenomics Center, University of Missouri, Columbia, MO 65211, USA
- Mutant Mouse Resource and Research Center, University of Missouri, Columbia, MO 65211, USA
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2
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Al Khatib HA, Coyle PV, Al Maslamani MA, Al Thani AA, Pathan SA, Yassine HM. Molecular and biological characterization of influenza A viruses isolated from human fecal samples. INFECTION GENETICS AND EVOLUTION 2021; 93:104972. [PMID: 34153546 DOI: 10.1016/j.meegid.2021.104972] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 06/12/2021] [Accepted: 06/15/2021] [Indexed: 01/14/2023]
Abstract
Human influenza viruses are occasionally detected in the stools of influenza patients. OBJECTIVES Here, we investigated the molecular and biological characteristics of intestinal influenza viruses and their potential role in virus transmission. METHODS Fecal samples were first screened for the presence of influenza viral RNA using RT-qPCR. Positive fecal samples were subjected to cell culture. Isolated viruses were then sequenced using MiSeq platform. Replication kinetics and receptor binding affinity were also evaluated. RESULTS Influenza RNA was detected in stool samples of 41% (36/87) of influenza A positive patients. Among the 36 stool samples subjected to viral isolation, 5 showed virus growth. Sequence analysis of isolated viruses revealed two distinct mutation patterns in fecal viruses. Set I viruses was able to replicate to higher titers in cell culture despite the limited number of mutations (6 mutations) compared to set II viruses (>10 mutations). Functional analysis of both sets revealed the ability to replicate efficiently in differentiated human bronchial cells. Receptor binding testing has also demonstrated their ability to bind α 2,3 and α 2,6 sialic acid receptors. CONCLUSION The ability of fecal influenza viruses to replicate in intestinal cells and human 3D bronchial cells might suggest their possible contribution in virus transmission.
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Affiliation(s)
| | - Peter V Coyle
- Virology Laboratory, Hamad Medical Corporation, Doha 3050, Qatar.
| | | | - Asmaa A Al Thani
- Biomedical Research Center, Qatar University, Doha 2713, Qatar; Department of Biomedical Sciences, College of Health Sciences-QU Health, Qatar University, Doha 2713, Qatar.
| | - Sameer A Pathan
- Emergency Medicine, Hamad Medical Corporation, Doha 3050, Qatar
| | - Hadi M Yassine
- Biomedical Research Center, Qatar University, Doha 2713, Qatar; Department of Biomedical Sciences, College of Health Sciences-QU Health, Qatar University, Doha 2713, Qatar.
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3
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Russell CJ. Hemagglutinin Stability and Its Impact on Influenza A Virus Infectivity, Pathogenicity, and Transmissibility in Avians, Mice, Swine, Seals, Ferrets, and Humans. Viruses 2021; 13:746. [PMID: 33923198 PMCID: PMC8145662 DOI: 10.3390/v13050746] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 04/21/2021] [Accepted: 04/23/2021] [Indexed: 12/13/2022] Open
Abstract
Genetically diverse influenza A viruses (IAVs) circulate in wild aquatic birds. From this reservoir, IAVs sporadically cause outbreaks, epidemics, and pandemics in wild and domestic avians, wild land and sea mammals, horses, canines, felines, swine, humans, and other species. One molecular trait shown to modulate IAV host range is the stability of the hemagglutinin (HA) surface glycoprotein. The HA protein is the major antigen and during virus entry, this trimeric envelope glycoprotein binds sialic acid-containing receptors before being triggered by endosomal low pH to undergo irreversible structural changes that cause membrane fusion. The HA proteins from different IAV isolates can vary in the pH at which HA protein structural changes are triggered, the protein causes membrane fusion, or outside the cell the virion becomes inactivated. HA activation pH values generally range from pH 4.8 to 6.2. Human-adapted HA proteins tend to have relatively stable HA proteins activated at pH 5.5 or below. Here, studies are reviewed that report HA stability values and investigate the biological impact of variations in HA stability on replication, pathogenicity, and transmissibility in experimental animal models. Overall, a stabilized HA protein appears to be necessary for human pandemic potential and should be considered when assessing human pandemic risk.
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Affiliation(s)
- Charles J Russell
- Department of Infectious Diseases, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105-3678, USA
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4
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Minodier L, Masse S, Capai L, Blanchon T, Ceccaldi PE, van der Werf S, Hanslik T, Charrel R, Falchi A. Risk factors for seasonal influenza virus detection in stools of patients consulting in general practice for acute respiratory infections in France, 2014-2016. Influenza Other Respir Viruses 2019; 13:398-406. [PMID: 29144593 PMCID: PMC6586184 DOI: 10.1111/irv.12523] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/06/2017] [Indexed: 11/29/2022] Open
Abstract
Background Previous studies reported detection of influenza RNA in stools of patients with seasonal influenza infection. While this detection may have a clinical significance, other factors may influence the stool positivity for influenza viruses. Objectives The objective of this study was to investigate demographical, clinical, and microbiological factors which could favor the presence of influenza viral RNA in the stools of patients with laboratory‐confirmed influenza infection. Methods Acute respiratory infection (ARI) patients were enrolled by general practitioners (GP) during two winter seasons (2014‐2016). Nasopharyngeal swabs, stool specimens, and clinical data were collected. Samples were tested for 12 respiratory pathogen groups (nasopharyngeal and stool specimens) and for 12 enteric pathogens (stool specimens). Results Among the 331 patients with ARI enrolled by GP, 114 (34.4%) presented influenza infection. Influenza RNA was detected in stool samples of 21% (24/114) of the 114 stool specimens analyzed. Hospitalization (adjusted odds ratio (aOR) = 7.8 (95% confidence interval (CI)) [1.7‐33.7], P = .02), age between 45 and 64 years (aOR = 4.8 [1.7‐14.5], P = .01), consumption of raw shellfish and/or mollusks (aOR = 16.7 [3.6‐90.9], P = .00), and use of antibiotics (aOR = 6.4 [2.1‐19.8], P = .006) or antiviral treatment (aOR = 7.4 [1.9‐29], P = .01) were significantly associated with an increased odds of the detection of influenza RNA in stools. Among the 24 stool samples subjected to viral isolation, no one showed virus growth. Conclusions These findings will be useful to studies investigating the dissemination route of influenza viruses to gastrointestinal tract.
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Affiliation(s)
- Laëtitia Minodier
- EA7310, Laboratoire de Virologie, Université de Corse-Inserm, Corte, France
| | - Shirley Masse
- EA7310, Laboratoire de Virologie, Université de Corse-Inserm, Corte, France
| | - Lisandru Capai
- EA7310, Laboratoire de Virologie, Université de Corse-Inserm, Corte, France
| | - Thierry Blanchon
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, France
| | - Pierre-Emmanuel Ceccaldi
- Pasteur Institute, Virology Department, Epidemiology and Physiopathology of Oncogenic Viruses Unit, Paris, France.,UMR CNRS 3569, Paris, France.,Sorbonne Paris Cité, Institut Pasteur, Cellule Pasteur, Université Paris Diderot, Paris, France
| | - Sylvie van der Werf
- UMR CNRS 3569, Paris, France.,Pasteur Institute, Virology Department, Molecular Genetics of RNA Viruses Unit, Paris, France.,Unité de Génétique Moléculaire des Virus à ARN, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Thomas Hanslik
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, France.,Université Versailles Saint Quentin en Yvelines, UFR de Médecine, Versailles, France.,Hôpital universitaire Ambroise Paré APHP, Service de médecine interne, Boulogne-Billancourt, France
| | - Remi Charrel
- UMR "Emergence des Pathologies Virales" (EPV: Aix-Marseille Univ - IRD 190 - Inserm 1207 - EHESP) & Fondation IHU Méditerranée Infection, APHM Public Hospitals of Marseille, Marseille, France
| | - Alessandra Falchi
- EA7310, Laboratoire de Virologie, Université de Corse-Inserm, Corte, France
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5
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Minodier L, Masse S, Capai L, Blanchon T, Ceccaldi PE, van der Werf S, Hanslik T, Charrel R, Falchi A. Clinical and virological factors associated with gastrointestinal symptoms in patients with acute respiratory infection: a two-year prospective study in general practice medicine. BMC Infect Dis 2017; 17:729. [PMID: 29166867 PMCID: PMC5700681 DOI: 10.1186/s12879-017-2823-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 11/06/2017] [Indexed: 02/07/2023] Open
Abstract
Background Gastrointestinal (GI) symptoms, such as diarrhea, vomiting, abdominal pain and nausea are not an uncommon manifestation of an acute respiratory infection (ARI). We therefore evaluated clinical and microbiological factors associated with the presence of GI symptoms in patients consulting a general practitioner (GP) for ARI. Methods Nasopharyngeal swabs, stool specimens and clinical data from patients presenting to GPs with an ARI were prospectively collected during two winter seasons (2014-2016). Samples were tested by quantitative real-time PCR for 12 respiratory pathogen groups and for 12 enteric pathogens. Results Two hundred and four of 331 included patients (61.6%) were positive for at least one respiratory pathogen. Sixty-nine stools (20.8%) were positive for at least one pathogen (respiratory and/or enteric). GI symptoms were more likely declared in case of laboratory confirmed-enteric infection (adjusted odds ratio (aOR) = 3.2; 95% confidence interval [CI] [1.2–9.9]; p = 0.02) or human coronavirus (HCoV) infection (aOR = 2.7; [1.2–6.8]; p = 0.02). Consumption of antipyretic medication before the consultation seemed to reduce the risk of developing GI symptoms for patients with laboratory-confirmed influenza (aOR = 0.3; [0.1–0.6]; p = 0.002). Conclusions The presence of GI symptoms in ARI patients could not be explained by the detection of respiratory pathogens in stools. However, the detection of enteric pathogens in stool samples could explained by the presence of GI symptoms in some of ARI cases. The biological mechanisms explaining the association between the presence of HCoVs in nasopharynx and GI symptoms need to be explored. Electronic supplementary material The online version of this article (10.1186/s12879-017-2823-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Laetitia Minodier
- EA7310, Laboratoire de Virologie, Université de Corse-Inserm, 20250, Corte, France
| | - Shirley Masse
- EA7310, Laboratoire de Virologie, Université de Corse-Inserm, 20250, Corte, France
| | - Lisandru Capai
- EA7310, Laboratoire de Virologie, Université de Corse-Inserm, 20250, Corte, France
| | - Thierry Blanchon
- Institut Pierre Louis d'Epidémiologie et de Santé Publique, Sorbonne Universités, UPMC Univ Paris 06, UMR_S 1136, 56, Boulevard Vincent Auriol, 81393-75646, Paris, France.,INSERM, UMR_S 1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, 56, Boulevard Vincent Auriol, 81393-75646, Paris, France
| | - Pierre-Emmanuel Ceccaldi
- Pasteur Institute, Virology Department, Epidemiology and Physiopathology of Oncogenic Viruses Unit, F-75015, Paris, France.,UMR CNRS 3569, 75015, Paris, France.,Sorbonne Paris Cité, Cellule Pasteur, Université Paris Diderot, Institut Pasteur, 75015, Paris, France
| | - Sylvie van der Werf
- UMR CNRS 3569, 75015, Paris, France.,Pasteur Institute, Virology Department, Molecular Genetics of RNA Viruses Unit, F-75015, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Unité de Génétique Moléculaire des Virus à ARN, EA302, F-75015, Paris, France
| | - Thomas Hanslik
- Sorbonne Université, UPMC Université Paris 06, Institut Pierre-Louis d'Épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, France.,Hôpital Ambroise Paré, service de médecine interne, Boulogne-Billancourt, France.,UFR des Sciences de la Santé Simone-Veil, Université Versailles Saint Quentin en Yvelines, Versailles, France
| | - Remi Charrel
- UMR "Emergence des Pathologies Virales" (EPV: Aix-Marseille Univ - IRD 190 - Inserm 1207 - EHESP) & Fondation IHU Méditerranée Infection, APHM Public Hospitals of Marseille, Marseille, France
| | - Alessandra Falchi
- EA7310, Laboratoire de Virologie, Université de Corse-Inserm, 20250, Corte, France.
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6
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Bourret V, Lyall J, Frost SDW, Teillaud A, Smith CA, Leclaire S, Fu J, Gandon S, Guérin JL, Tiley LS. Adaptation of avian influenza virus to a swine host. Virus Evol 2017; 3:vex007. [PMID: 28458917 PMCID: PMC5399929 DOI: 10.1093/ve/vex007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The emergence of pathogenic RNA viruses into new hosts can have dramatic consequences for both livestock and public health. Here we characterize the viral genetic changes that were observed in a previous study which experimentally adapted a field isolate of duck influenza virus to swine respiratory cells. Both pre-existing and de novo mutations were selected during this adaptation. We compare the in vitro growth dynamics of the adapted virus with those of the original strain as well as all possible reassortants using reverse genetics. This full factorial design showed that viral gene segments are involved in complex epistatic interactions on virus fitness, including negative and sign epistasis. We also identify two point mutations at positions 67 and 113 of the HA2 subunit of the hemagglutinin protein conferring a fast growth phenotype on the naïve avian virus in swine cells. These HA2 mutations enhance the pH dependent, HA-mediated membrane fusion. A global H1 maximum-likelihood phylogenetic analysis, combined with comprehensive ancestry reconstruction and tests for directional selection, confirmed the field relevance of the mutation at position 113 of HA2. Most notably, this mutation was associated with the establishment of the H1 'avian-like' swine influenza lineage, regarded as the most likely to cause the next influenza pandemic in humans. This multidisciplinary approach to study the genetics of viral adaptation provides unique insights on the underlying processes leading to influenza emergence in a new host species, and identifies specific targets for future surveillance and functional studies.
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Affiliation(s)
- Vincent Bourret
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
- Université de Toulouse, INP, ENVT, Toulouse, France
- INRA, UMR 1225, IHAP, Toulouse, France
| | - Jon Lyall
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Simon D W Frost
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Angélique Teillaud
- Université de Toulouse, INP, ENVT, Toulouse, France
- INRA, UMR 1225, IHAP, Toulouse, France
| | - Catherine A Smith
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Sarah Leclaire
- Centre d’Ecologie Fonctionnelle et Evolutive, UMR CNRS 5175, Montpellier, France
| | - JinQi Fu
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Sylvain Gandon
- Centre d’Ecologie Fonctionnelle et Evolutive, UMR CNRS 5175, Montpellier, France
| | - Jean-Luc Guérin
- Université de Toulouse, INP, ENVT, Toulouse, France
- INRA, UMR 1225, IHAP, Toulouse, France
| | - Laurence S Tiley
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
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7
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Meliopoulos VA, Karlsson EA, Schultz-Cherry S. What can imaging tell us about influenza virus transmission and protection? Future Virol 2016. [DOI: 10.2217/fvl-2016-0062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The emergence of zoonotic influenza infections is a constant threat to public health. One of the major determinants of pandemic potential is the ability to transmit from animal to human and/or human to human via respiratory droplets. Understanding viral tropism and spread is crucial for predicting which viruses represent the most threatening to human health. Recently, a replication-competent influenza reporter virus was described that permitted in vivo imaging and visualization of infection in ferrets for the first time. This review will focus on the applications of luminescent reporter viruses toward understanding transmission of influenza viruses and development of therapeutic interventions.
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Affiliation(s)
- Victoria A Meliopoulos
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Erik A Karlsson
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Stacey Schultz-Cherry
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN 38105, USA
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8
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Minodier L, Charrel RN, Ceccaldi PE, van der Werf S, Blanchon T, Hanslik T, Falchi A. Prevalence of gastrointestinal symptoms in patients with influenza, clinical significance, and pathophysiology of human influenza viruses in faecal samples: what do we know? Virol J 2015; 12:215. [PMID: 26651485 PMCID: PMC4676820 DOI: 10.1186/s12985-015-0448-4] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 12/04/2015] [Indexed: 12/14/2022] Open
Abstract
This review provides for the first time an assessment of the current understanding about the occurrence and the clinical significance of gastrointestinal (GI) symptoms in influenza patients, and their correlation with the presence of human influenza viruses in stools of patients with confirmed influenza virus infection. Studies exploring how human influenza viruses spread to the patient’s GI tract after a primary respiratory infection have been summarized. We conducted a systematic search of published peer-reviewed literature up to June 2015 with regard to the above-mentioned aspects, focusing on human influenza viruses (A(H1N1), A(H1N1)pdm09, A(H3N2), and B). Forty-four studies were included in this systematic review and meta-analysis. The pooled prevalence of any digestive symptoms ranged from 30.9 % (95 % CI, 9.8 to 57.5; I2 = 97.5 %) for A(H1N1)pdm09 to 2.8 % (95 % CI, 0.6 to 6.5; I2 = 75.4 %) for A(H1N1). The pooled prevalence of influenza viruses in stool was 20.6 % (95 % CI, 8.9 to 35.5; I2 = 96.8 %), but their correlation with GI symptoms has rarely been explored. The presence of viral RNA in stools because of haematogenous dissemination to organs via infected lymphocytes is likely, but the potential to cause direct intestinal infection and faecal–oral transmission warrants further investigation. This review highlights the gaps in our knowledge, and the high degree of uncertainty about the prevalence and significance of GI symptoms in patients with influenza and their correlation with viral RNA positivity in stool because of the high level of heterogeneity among studies.
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Affiliation(s)
- Laetitia Minodier
- EA 7310, laboratory of virology, University of Corsica-Inserm, 20250, Corte, France.
| | - Remi N Charrel
- Aix Marseille Université, IRD French Institute of Research for Development, INSERM U1207, EHESP French School of Public Health, EPV UMR_D 190 "Emergence des Pathologies Virales", & IHU Méditerranée Infection, APHM Public Hospitals of Marseille, Marseille, France.
| | - Pierre-Emmanuel Ceccaldi
- Unité EPVO, Institut Pasteur, Paris-UMR CNRS 3569-Université Paris Diderot, Paris Sorbonne Cité, Cellule Pasteur, Paris, France.
| | - Sylvie van der Werf
- Unit of Molecular Genetics of RNA viruses, Institut Pasteur-UMR CNRS 3569-Université Paris Diderot-Sorbonne Paris Cité, Paris, France. .,Coordinating Center of the National Reference Center for influenza viruses, National Influenza Center (Northern-France), Institut Pasteur, Paris, France.
| | - Thierry Blanchon
- Sorbonne Universités, UPMC Univ Paris 06, UMR_S 1136, Paris, France. .,INSERM, UMR_S 1136, Paris, France.
| | - Thomas Hanslik
- INSERM, UMR_S 1136, Paris, France. .,Université Versailles Saint Quentin en Yvelines, UFR de Médecine Paris-Ile-de-France-Ouest, 9 boulevard d'Alembert, 78280, Guyancourt, France. .,Service de médecine interne, Hôpital Ambroise Paré, Assistance Publique-Hôpitaux de Paris, 92100, Boulogne Billancourt, France.
| | - Alessandra Falchi
- EA 7310, laboratory of virology, University of Corsica-Inserm, 20250, Corte, France.
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9
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Koçer ZA, Carter R, Wu G, Zhang J, Webster RG. The Genomic Contributions of Avian H1N1 Influenza A Viruses to the Evolution of Mammalian Strains. PLoS One 2015. [PMID: 26208281 PMCID: PMC4514870 DOI: 10.1371/journal.pone.0133795] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Among the influenza A viruses (IAVs) in wild aquatic birds, only H1, H2, and H3 subtypes have caused epidemics in humans. H1N1 viruses of avian origin have also caused 3 of 5 pandemics. To understand the reappearance of H1N1 in the context of pandemic emergence, we investigated whether avian H1N1 IAVs have contributed to the evolution of human, swine, and 2009 pandemic H1N1 IAVs. On the basis of phylogenetic analysis, we concluded that the polymerase gene segments (especially PB2 and PA) circulating in North American avian H1N1 IAVs have been reintroduced to swine multiple times, resulting in different lineages that led to the emergence of the 2009 pandemic H1N1 IAVs. Moreover, the similar topologies of hemagglutinin and nucleoprotein and neuraminidase and matrix gene segments suggest that each surface glycoprotein coevolved with an internal gene segment within the H1N1 subtype. The genotype of avian H1N1 IAVs of Charadriiformes origin isolated in 2009 differs from that of avian H1N1 IAVs of Anseriformes origin. When the antigenic sites in the hemagglutinin of all 31 North American avian H1N1 IAVs were considered, 60%-80% of the amino acids at the antigenic sites were identical to those in 1918 and/or 2009 pandemic H1N1 viruses. Thus, although the pathogenicity of avian H1N1 IAVs could not be inferred from the phylogeny due to the small dataset, the evolutionary process within the H1N1 IAV subtype suggests that the circulation of H1N1 IAVs in wild birds poses a continuous threat for future influenza pandemics in humans.
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Affiliation(s)
- Zeynep A. Koçer
- Department of Infectious Diseases, Division of Virology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Robert Carter
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Gang Wu
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Robert G. Webster
- Department of Infectious Diseases, Division of Virology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- * E-mail:
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10
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Possible basis for the emergence of H1N1 viruses with pandemic potential from avian hosts. Emerg Microbes Infect 2015; 4:e40. [PMID: 26251829 PMCID: PMC4522614 DOI: 10.1038/emi.2015.40] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 05/20/2015] [Accepted: 05/22/2015] [Indexed: 01/04/2023]
Abstract
Influenza A viruses of the H1N1 subtype have emerged from the avian influenza gene pool in aquatic birds and caused human pandemics at least twice during the past century. Despite this fact, surprisingly little is known about the H1N1 gene pool in the aquatic bird reservoir. A preliminary study showed that an H1N1 virus from a shorebird of the Charadriiformes order was transmitted between animals through the airborne route of infection, whereas an H1N1 virus from a bird of the Anseriformes order was not. Here we show that two of the three H1N1 viruses isolated from Charadriiformes species in 2009 were transmitted between animals through the airborne route of infection, and five H1N1 isolates from Anseriformes species were not. The one H1N1 virus from a Charadriiformes species that failed to transmit through the airborne route was a reassortant possessing multiple internal gene segments from Anseriformes species. The molecular differences between the airborne-transmissible and non-airborne-transmissible H1N1 viruses were multigenic, involving the selection of virus with human-like receptor-binding specificity (α2-6 sialic acid) and multiple differences in the polymerase complex, mainly in the PB2, PB1-F2, and nonstructural genes.
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11
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Greig DJ, Gulland FMD, Smith WA, Conrad PA, Field CL, Fleetwood M, Harvey JT, Ip HS, Jang S, Packham A, Wheeler E, Hall AJ. Surveillance for zoonotic and selected pathogens in harbor seals Phoca vitulina from central California. DISEASES OF AQUATIC ORGANISMS 2014; 111:93-106. [PMID: 25266897 DOI: 10.3354/dao02762] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The infection status of harbor seals Phoca vitulina in central California, USA, was evaluated through broad surveillance for pathogens in stranded and wild-caught animals from 2001 to 2008, with most samples collected in 2007 and 2008. Stranded animals from Mendocino County to San Luis Obispo County were sampled at a rehabilitation facility: The Marine Mammal Center (TMMC, n = 175); wild-caught animals were sampled at 2 locations: San Francisco Bay (SF, n = 78) and Tomales Bay (TB, n = 97), that differed in degree of urbanization. Low prevalences of Salmonella, Campylobacter, Giardia, and Cryptosporidium were detected in the feces of stranded and wild-caught seals. Clostridium perfringens and Escherichia coli were more prevalent in the feces of stranded (58% [78 out of 135] and 76% [102 out of 135]) than wild-caught (42% [45 out of 106] and 66% [68 out of 106]) seals, whereas Vibrio spp. were 16 times more likely to be cultured from the feces of seals from SF than TB or TMMC (p < 0.005). Brucella DNA was detected in 3.4% of dead stranded harbor seals (2 out of 58). Type A influenza was isolated from feces of 1 out of 96 wild-caught seals. Exposure to Toxoplasma gondii, Sarcocystis neurona, and type A influenza was only detected in the wild-caught harbor seals (post-weaning age classes), whereas antibody titers to Leptospira spp. were detected in stranded and wild-caught seals. No stranded (n = 109) or wild-caught (n = 217) harbor seals had antibodies to phocine distemper virus, although a single low titer to canine distemper virus was detected. These results highlight the role of harbor seals as sentinel species for zoonotic and terrestrial pathogens in the marine environment.
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Affiliation(s)
- Denise J Greig
- Sea Mammal Research Unit, Scottish Oceans Institute, University of St Andrews, St Andrews KY16 8LB, UK
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