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Pellegrini F, Buonavoglia A, Omar AH, Diakoudi G, Lucente MS, Odigie AE, Sposato A, Augelli R, Camero M, Decaro N, Elia G, Bányai K, Martella V, Lanave G. A Cold Case of Equine Influenza Disentangled with Nanopore Sequencing. Animals (Basel) 2023; 13:ani13071153. [PMID: 37048408 PMCID: PMC10093709 DOI: 10.3390/ani13071153] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 03/13/2023] [Accepted: 03/21/2023] [Indexed: 03/29/2023] Open
Abstract
Massive sequencing techniques have allowed us to develop straightforward approaches for the whole genome sequencing of viruses, including influenza viruses, generating information that is useful for improving the levels and dimensions of data analysis, even for archival samples. Using the Nanopore platform, we determined the whole genome sequence of an H3N8 equine influenza virus, identified from a 2005 outbreak in Apulia, Italy, whose origin had remained epidemiologically unexplained. The virus was tightly related (>99% at the nucleotide level) in all the genome segments to viruses identified in Poland in 2005–2008 and it was seemingly introduced locally with horse trading for the meat industry. In the phylogenetic analysis based on the eight genome segments, strain ITA/2005/horse/Bari was found to cluster with sub-lineage Florida 2 in the HA and M genes, whilst in the other genes it clustered with strains of the Eurasian lineage, revealing a multi-reassortant nature.
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Affiliation(s)
- Francesco Pellegrini
- Department of Veterinary Medicine, University of Bari, 70010 Valenzano, Italy (G.L.)
| | - Alessio Buonavoglia
- Department of Veterinary Medicine, University of Bari, 70010 Valenzano, Italy (G.L.)
| | - Ahmed H. Omar
- Department of Veterinary Medicine, University of Bari, 70010 Valenzano, Italy (G.L.)
| | - Georgia Diakoudi
- Department of Veterinary Medicine, University of Bari, 70010 Valenzano, Italy (G.L.)
| | - Maria S. Lucente
- Department of Veterinary Medicine, University of Bari, 70010 Valenzano, Italy (G.L.)
| | - Amienwanlen E. Odigie
- Department of Veterinary Medicine, University of Bari, 70010 Valenzano, Italy (G.L.)
| | - Alessio Sposato
- Department of Veterinary Medicine, University of Bari, 70010 Valenzano, Italy (G.L.)
| | | | - Michele Camero
- Department of Veterinary Medicine, University of Bari, 70010 Valenzano, Italy (G.L.)
| | - Nicola Decaro
- Department of Veterinary Medicine, University of Bari, 70010 Valenzano, Italy (G.L.)
| | - Gabriella Elia
- Department of Veterinary Medicine, University of Bari, 70010 Valenzano, Italy (G.L.)
| | - Krisztián Bányai
- Veterinary Medical Research Institute, 1143 Budapest, Hungary
- Department of Pharmacology and Toxicology, University of Veterinary Medicine, 1400 Budapest, Hungary
| | - Vito Martella
- Department of Veterinary Medicine, University of Bari, 70010 Valenzano, Italy (G.L.)
- Correspondence:
| | - Gianvito Lanave
- Department of Veterinary Medicine, University of Bari, 70010 Valenzano, Italy (G.L.)
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2
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From Clinical Specimen to Whole Genome Sequencing of A(H3N2) Influenza Viruses: A Fast and Reliable High-Throughput Protocol. Vaccines (Basel) 2022; 10:vaccines10081359. [PMID: 36016246 PMCID: PMC9412868 DOI: 10.3390/vaccines10081359] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 08/11/2022] [Accepted: 08/11/2022] [Indexed: 11/29/2022] Open
Abstract
(1) Background: Over the last few years, there has been growing interest in the whole genome sequencing (WGS) of rapidly mutating pathogens, such as influenza viruses (IVs), which has led us to carry out in-depth studies on viral evolution in both research and diagnostic settings. We aimed at describing and determining the validity of a WGS protocol that can obtain the complete genome sequence of A(H3N2) IVs directly from clinical specimens. (2) Methods: RNA was extracted from 80 A(H3N2)-positive respiratory specimens. A one-step RT-PCR assay, based on the use of a single set of specific primers, was used to retro-transcribe and amplify the entire IV type A genome in a single reaction, thus avoiding additional enrichment approaches and host genome removal treatments. Purified DNA was quantified; genomic libraries were prepared and sequenced by using Illumina MiSeq platform. The obtained reads were evaluated for sequence quality and read-pair length. (3) Results: All of the study specimens were successfully amplified, and the purified DNA concentration proved to be suitable for NGS (at least 0.2 ng/µL). An acceptable coverage depth for all eight genes of influenza A(H3N2) virus was obtained for 90% (72/80) of the clinical samples with viral loads >105 genome copies/mL. The mean depth of sequencing ranged from 105 to 200 reads per position, with the majority of the mean depth values being above 103 reads per position. The total turnaround time per set of 20 samples was four working days, including sequence analysis. (4) Conclusions: This fast and reliable high-throughput sequencing protocol should be used for influenza surveillance and outbreak investigation.
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3
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Rattanaburi S, Sawaswong V, Nimsamer P, Mayuramart O, Sivapornnukul P, Khamwut A, Chanchaem P, Kongnomnan K, Suntronwong N, Poovorawan Y, Payungporn S. Genome characterization and mutation analysis of human influenza A virus in Thailand. Genomics Inform 2022; 20:e21. [PMID: 35794701 PMCID: PMC9299564 DOI: 10.5808/gi.21077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 04/05/2022] [Indexed: 11/20/2022] Open
Abstract
The influenza A viruses have high mutation rates and cause a serious health problem worldwide. Therefore, this study focused on genome characterization of the viruses isolated from Thai patients based on the next-generation sequencing technology. The nasal swabs were collected from patients with influenza-like illness in Thailand during 2017-2018. Then, the influenza A viruses were detected by reverse transcription-quantitative polymerase chain reaction and isolated by MDCK cells. The viral genomes were amplified and sequenced by Illumina MiSeq platform. Whole genome sequences were used for characterization, phylogenetic construction, mutation analysis and nucleotide diversity of the viruses. The result revealed that 90 samples were positive for the viruses including 44 of A/H1N1 and 46 of A/H3N2. Among these, 43 samples were successfully isolated and then the viral genomes of 25 samples were completely amplified. Finally, 17 whole genomes of the viruses (A/H1N1, n=12 and A/H3N2, n=5) were successfully sequenced with an average of 232,578 mapped reads and 1,720 genome coverage per sample. Phylogenetic analysis demonstrated that the A/H1N1 viruses were distinguishable from the recommended vaccine strains. However, the A/H3N2 viruses from this study were closely related to the recommended vaccine strains. The nonsynonymous mutations were found in all genes of both viruses, especially in HA and NA genes. The nucleotide diversity analysis revealed negative selection in the PB1, PA, hemagglutinin (HA) and neuraminidase (NA) genes of the A/H1N1 viruses. High-throughput data in this study allow for genetic characterization of circulating influenza viruses which would be crucial for preparation against pandemic and epidemic outbreaks in the future.
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Affiliation(s)
- Somruthai Rattanaburi
- Interdisciplinary Program of Biomedical Sciences, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand.,Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Vorthon Sawaswong
- Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Pattaraporn Nimsamer
- Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Oraphan Mayuramart
- Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Pavaret Sivapornnukul
- Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand.,Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Ariya Khamwut
- Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Prangwalai Chanchaem
- Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Kritsada Kongnomnan
- Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Nungruthai Suntronwong
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Yong Poovorawan
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Sunchai Payungporn
- Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand.,Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
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4
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Sansone M, Andersson M, Gustavsson L, Andersson LM, Nordén R, Westin J. Extensive Hospital In-Ward Clustering Revealed By Molecular Characterization of Influenza A Virus Infection. Clin Infect Dis 2021; 71:e377-e383. [PMID: 32011654 DOI: 10.1093/cid/ciaa108] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 01/31/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Nosocomial transmission of influenza A virus (InfA) infection is not fully recognized. The aim of this study was to describe the characteristics of hospitalized patients with InfA infections during an entire season and to investigate in-ward transmission at a large, acute-care hospital. METHODS During the 2016-17 season, all hospitalized patients ≥18 years old with laboratory-verified (real-time polymerase chain reaction) InfA were identified. Cases were characterized according to age; sex; comorbidity; antiviral therapy; viral load, expressed as cycle threshold values; length of hospital stay; 30-day mortality; and whether the InfA infection met criteria for a health care-associated influenza A infection (HCAI). Respiratory samples positive for InfA that were collected at the same wards within 7 days were chosen for whole-genome sequencing (WGS) and a phylogenetic analysis was performed to detect clustering. For reference, concurrent InfA strains from patients with community-acquired infection were included. RESULTS We identified a total of 435 InfA cases, of which 114 (26%) met the HCAI criteria. The overall 30-day mortality rate was higher among patients with HCAI (9.6% vs 4.6% among non-HCAI patients), although the difference was not statistically significant in a multivariable analysis, where age was the only independent risk factor for death (P < .05). We identified 8 closely related clusters (involving ≥3 cases) and another 10 pairs of strains, supporting in-ward transmission. CONCLUSIONS We found that the in-ward transmission of InfA occurs frequently and that HCAI may have severe outcomes. WGS may be used for outbreak investigations, as well as for evaluations of the effects of preventive measures.
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Affiliation(s)
- Martina Sansone
- Department of Clinical Microbiology, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Maria Andersson
- Department of Clinical Microbiology, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden.,Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Lars Gustavsson
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Infectious Diseases, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Lars-Magnus Andersson
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Infectious Diseases, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Rickard Nordén
- Department of Clinical Microbiology, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden.,Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Johan Westin
- Department of Clinical Microbiology, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden.,Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Infectious Diseases, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden
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5
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Mikhaylova YV, Shelenkov AA, Yanushevich YG, Shagin DA. Increasing the Uniformity of Genome Fragment Coverage for High-Throughput Sequencing of Influenza A Virus. Mol Biol 2021. [DOI: 10.1134/s0026893320060084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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6
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Southgate JA, Bull MJ, Brown CM, Watkins J, Corden S, Southgate B, Moore C, Connor TR. Influenza classification from short reads with VAPOR facilitates robust mapping pipelines and zoonotic strain detection for routine surveillance applications. Bioinformatics 2020; 36:1681-1688. [PMID: 31693070 PMCID: PMC7703727 DOI: 10.1093/bioinformatics/btz814] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 08/18/2019] [Accepted: 10/30/2019] [Indexed: 11/23/2022] Open
Abstract
Motivation Influenza viruses represent a global public health burden due to annual epidemics and pandemic potential. Due to a rapidly evolving RNA genome, inter-species transmission, intra-host variation, and noise in short-read data, reads can be lost during mapping, and de novo assembly can be time consuming and result in misassembly. We assessed read loss during mapping and designed a graph-based classifier, VAPOR, for selecting mapping references, assembly validation and detection of strains of non-human origin. Results Standard human reference viruses were insufficient for mapping diverse influenza samples in simulation. VAPOR retrieved references for 257 real whole-genome sequencing samples with a mean of >99.8% identity to assemblies, and increased the proportion of mapped reads by up to 13.3% compared to standard references. VAPOR has the potential to improve the robustness of bioinformatics pipelines for surveillance and could be adapted to other RNA viruses. Availability and implementation VAPOR is available at https://github.com/connor-lab/vapor. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Joel A Southgate
- Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
| | - Matthew J Bull
- Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK.,Public Health Wales, University Hospital of Wales, Cardiff CF14 4XW, UK
| | - Clare M Brown
- Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
| | - Joanne Watkins
- Public Health Wales, University Hospital of Wales, Cardiff CF14 4XW, UK
| | - Sally Corden
- Public Health Wales, University Hospital of Wales, Cardiff CF14 4XW, UK
| | - Benjamin Southgate
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh EH16 4UU, UK
| | - Catherine Moore
- Public Health Wales, University Hospital of Wales, Cardiff CF14 4XW, UK
| | - Thomas R Connor
- Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK.,Public Health Wales, University Hospital of Wales, Cardiff CF14 4XW, UK
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7
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The use of host factors in microbial forensics. MICROBIAL FORENSICS 2020. [PMCID: PMC7153337 DOI: 10.1016/b978-0-12-815379-6.00014-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Advances have been made in the forensic analysis of microbes and toxins. An underdeveloped and underutilized area in microbial forensics is how the host interacts with microorganisms in a way that provides unique signatures for forensic use. For forensic purposes, an immediate goal is to distinguish a potential victim and innocent person from a perpetrator, and to distinguish between a naturally acquired or intentional infection. Principal methods that are sufficiently developed are characterization of the humoral immune response to microbial antigens including vaccine-induced immunity and detection of antibiotics that may be present in a possible perpetrator. This chapter presents central elements of the host response in a simplified fashion and describes a representative example, which, in the appropriate context, has a high potential of providing evidence that may aid an investigation to distinguish a perpetrator from a victim. This chapter also presents information about the immune system so that the interested reader can have a fuller understanding of the immune response in general.
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8
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Lewandowski K, Xu Y, Pullan ST, Lumley SF, Foster D, Sanderson N, Vaughan A, Morgan M, Bright N, Kavanagh J, Vipond R, Carroll M, Marriott AC, Gooch KE, Andersson M, Jeffery K, Peto TEA, Crook DW, Walker AS, Matthews PC. Metagenomic Nanopore Sequencing of Influenza Virus Direct from Clinical Respiratory Samples. J Clin Microbiol 2019; 58:e00963-19. [PMID: 31666364 PMCID: PMC6935926 DOI: 10.1128/jcm.00963-19] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 10/21/2019] [Indexed: 01/11/2023] Open
Abstract
Influenza is a major global public health threat as a result of its highly pathogenic variants, large zoonotic reservoir, and pandemic potential. Metagenomic viral sequencing offers the potential for a diagnostic test for influenza virus which also provides insights on transmission, evolution, and drug resistance and simultaneously detects other viruses. We therefore set out to apply the Oxford Nanopore Technologies sequencing method to metagenomic sequencing of respiratory samples. We generated influenza virus reads down to a limit of detection of 102 to 103 genome copies/ml in pooled samples, observing a strong relationship between the viral titer and the proportion of influenza virus reads (P = 4.7 × 10-5). Applying our methods to clinical throat swabs, we generated influenza virus reads for 27/27 samples with mid-to-high viral titers (cycle threshold [CT ] values, <30) and 6/13 samples with low viral titers (CT values, 30 to 40). No false-positive reads were generated from 10 influenza virus-negative samples. Thus, Nanopore sequencing operated with 83% sensitivity (95% confidence interval [CI], 67 to 93%) and 100% specificity (95% CI, 69 to 100%) compared to the current diagnostic standard. Coverage of full-length virus was dependent on sample composition, being negatively influenced by increased host and bacterial reads. However, at high influenza virus titers, we were able to reconstruct >99% complete sequences for all eight gene segments. We also detected a human coronavirus coinfection in one clinical sample. While further optimization is required to improve sensitivity, this approach shows promise for the Nanopore platform to be used in the diagnosis and genetic analysis of influenza virus and other respiratory viruses.
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Affiliation(s)
- Kuiama Lewandowski
- Public Health England, National infection Service, Porton Down, Salisbury, United Kingdom
| | - Yifei Xu
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom
- Oxford NIHR BRC, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Steven T Pullan
- Public Health England, National infection Service, Porton Down, Salisbury, United Kingdom
| | - Sheila F Lumley
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Dona Foster
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom
- Oxford NIHR BRC, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Nicholas Sanderson
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom
- Oxford NIHR BRC, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Alison Vaughan
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom
- Oxford NIHR BRC, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Marcus Morgan
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Nicole Bright
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - James Kavanagh
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Richard Vipond
- Public Health England, National infection Service, Porton Down, Salisbury, United Kingdom
| | - Miles Carroll
- Public Health England, National infection Service, Porton Down, Salisbury, United Kingdom
| | - Anthony C Marriott
- Public Health England, National infection Service, Porton Down, Salisbury, United Kingdom
| | - Karen E Gooch
- Public Health England, National infection Service, Porton Down, Salisbury, United Kingdom
| | - Monique Andersson
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Katie Jeffery
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Timothy E A Peto
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, United Kingdom
- Oxford NIHR BRC, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Derrick W Crook
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, United Kingdom
- Oxford NIHR BRC, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - A Sarah Walker
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Philippa C Matthews
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, United Kingdom
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Oxford NIHR BRC, John Radcliffe Hospital, Headington, Oxford, United Kingdom
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9
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Blackburn RM, Frampton D, Smith CM, Fragaszy EB, Watson SJ, Ferns RB, Binter Š, Coen PG, Grant P, Shallcross LJ, Kozlakidis Z, Pillay D, Kellam P, Hué S, Nastouli E, Hayward AC. Nosocomial transmission of influenza: A retrospective cross-sectional study using next generation sequencing at a hospital in England (2012-2014). Influenza Other Respir Viruses 2019; 13:556-563. [PMID: 31536169 PMCID: PMC6800305 DOI: 10.1111/irv.12679] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 08/21/2019] [Accepted: 08/25/2019] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND The extent of transmission of influenza in hospital settings is poorly understood. Next generation sequencing may improve this by providing information on the genetic relatedness of viral strains. OBJECTIVES We aimed to apply next generation sequencing to describe transmission in hospital and compare with methods based on routinely-collected data. METHODS All influenza samples taken through routine care from patients at University College London Hospitals NHS Foundation Trust (September 2012 to March 2014) were included. We conducted Illumina sequencing and identified genetic clusters. We compared nosocomial transmission estimates defined using classical methods (based on time from admission to sample) and genetic clustering. We identified pairs of cases with space-time links and assessed genetic relatedness. RESULTS We sequenced influenza sampled from 214 patients. There were 180 unique genetic strains, 16 (8.8%) of which seeded a new transmission chain. Nosocomial transmission was indicated for 32 (15.0%) cases using the classical definition and 34 (15.8%) based on genetic clustering. Of the 50 patients in a genetic cluster, 11 (22.0%) had known space-time links with other cases in the same cluster. Genetic distances between pairs of cases with space-time links were lower than for pairs without spatial links (P < .001). CONCLUSIONS Genetic data confirmed that nosocomial transmission contributes significantly to the hospital burden of influenza and elucidated transmission chains. Prospective next generation sequencing could support outbreak investigations and monitor the impact of infection and control measures.
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Affiliation(s)
| | | | | | - Ellen B. Fragaszy
- Institute of Health InformaticsUCLLondonUK
- Department of Infectious Disease EpidemiologyFaculty of Epidemiology and Population HealthLondon School of Hygiene and Tropical MedicineLondonUK
| | - Simon J. Watson
- Wellcome Trust Sanger InstituteWellcome Trust Genome CampusHinxtonUK
| | - R. Bridget Ferns
- Clinical Microbiology and VirologyUniversity College London Hospitals NHS Foundation TrustLondonUK
| | - Špela Binter
- Wellcome Trust Sanger InstituteWellcome Trust Genome CampusHinxtonUK
| | - Pietro G. Coen
- Infection Control DepartmentUniversity College London HospitalsNHS Foundation TrustLondonUK
| | - Paul Grant
- Clinical Microbiology and VirologyUniversity College London Hospitals NHS Foundation TrustLondonUK
| | | | - Zisis Kozlakidis
- Institute of Health InformaticsUCLLondonUK
- International Agency for Research on CancerWorld Health OrganizationLyonFrance
| | - Deenan Pillay
- Division of Infection and ImmunityUCLLondonUK
- Africa Health Research InstituteDurbanSouth Africa
| | - Paul Kellam
- Wellcome Trust Sanger InstituteWellcome Trust Genome CampusHinxtonUK
| | - Stéphane Hué
- Department of Infectious Disease EpidemiologyFaculty of Epidemiology and Population HealthLondon School of Hygiene and Tropical MedicineLondonUK
| | - Eleni Nastouli
- Clinical Microbiology and VirologyUniversity College London Hospitals NHS Foundation TrustLondonUK
- Department of Population, Policy and PracticeUCL Institute of Child HealthLondonUK
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10
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Genomic analysis of respiratory syncytial virus infections in households and utility in inferring who infects the infant. Sci Rep 2019; 9:10076. [PMID: 31296922 PMCID: PMC6624209 DOI: 10.1038/s41598-019-46509-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 06/26/2019] [Indexed: 12/18/2022] Open
Abstract
Infants (under 1-year-old) are at most risk of life threatening respiratory syncytial virus (RSV) disease. RSV epidemiological data alone has been insufficient in defining who acquires infection from whom (WAIFW) within households. We investigated RSV genomic variation within and between infected individuals and assessed its potential utility in tracking transmission in households. Over an entire single RSV season in coastal Kenya, nasal swabs were collected from members of 20 households every 3-4 days regardless of symptom status and screened for RSV nucleic acid. Next generation sequencing was used to generate >90% RSV full-length genomes for 51.1% of positive samples (191/374). Single nucleotide polymorphisms (SNPs) observed during household infection outbreaks ranged from 0-21 (median: 3) while SNPs observed during single-host infection episodes ranged from 0-17 (median: 1). Using the viral genomic data alone there was insufficient resolution to fully reconstruct within-household transmission chains. For households with clear index cases, the most likely source of infant infection was via a toddler (aged 1 to <3 years-old) or school-aged (aged 6 to <12 years-old) co-occupant. However, for best resolution of WAIFW within households, we suggest an integrated analysis of RSV genomic and epidemiological data.
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11
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Ferreri LM, Ortiz L, Geiger G, Barriga GP, Poulson R, Gonzalez-Reiche AS, Crum JA, Stallknecht D, Moran D, Cordon-Rosales C, Rajao D, Perez DR. Improved detection of influenza A virus from blue-winged teals by sequencing directly from swab material. Ecol Evol 2019; 9:6534-6546. [PMID: 31236242 PMCID: PMC6580304 DOI: 10.1002/ece3.5232] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 04/10/2019] [Accepted: 04/12/2019] [Indexed: 12/22/2022] Open
Abstract
Abstract The greatest diversity of influenza A virus (IAV) is found in wild aquatic birds of the orders Anseriformes and Charadriiformes. In these birds, IAV replication occurs mostly in the intestinal tract. Fecal, cloacal, and/or tracheal swabs are typically collected and tested by real-time RT-PCR (rRT-PCR) and/or by virus isolation in embryonated chicken eggs in order to determine the presence of IAV. Virus isolation may impose bottlenecks that select variant populations that are different from those circulating in nature, and such bottlenecks may result in artifactual representation of subtype diversity and/or underrepresented mixed infections. The advent of next-generation sequencing (NGS) technologies provides an opportunity to explore to what extent IAV subtype diversity is affected by virus isolation in eggs. In the present work, we evaluated the advantage of sequencing by NGS directly from swab material of IAV rRT-PCR-positive swabs collected during the 2013-14 surveillance season in Guatemala and compared to results from NGS after virus isolation. The results highlight the benefit of sequencing IAV genomes directly from swabs to better understand subtype diversity and detection of alternative amino acid motifs that could otherwise escape detection using traditional methods of virus isolation. In addition, NGS sequencing data from swabs revealed reduced presence of defective interfering particles compared to virus isolates. We propose an alternative workflow in which original swab samples positive for IAV by rRT-PCR are first subjected to NGS before attempting viral isolation. This approach should speed the processing of samples and better capture natural IAV diversity. OPEN RESEARCH BADGES This article has earned an Open Data Badge for making publicly available the digitally-shareable data necessary to reproduce the reported results. The data is available at https://doi.org/10.5061/dryad.3h2n106.
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Affiliation(s)
- Lucas M Ferreri
- Poultry Diagnostic and Research Center, Department of Population Health, College of Veterinary Medicine University of Georgia Athens Georgia
| | - Lucia Ortiz
- Poultry Diagnostic and Research Center, Department of Population Health, College of Veterinary Medicine University of Georgia Athens Georgia.,Centro de Estudios en Salud Universidad del Valle de Guatemala Guatemala City Guatemala
| | - Ginger Geiger
- Poultry Diagnostic and Research Center, Department of Population Health, College of Veterinary Medicine University of Georgia Athens Georgia
| | - Gonzalo P Barriga
- Laboratory of Emerging Viruses, Virology Program Institute of Biomedical Sciences, Faculty of Medicine Universidad de Chile Santiago Chile
| | - Rebecca Poulson
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine University of Georgia Athens Georgia
| | | | - Jo Anne Crum
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine University of Georgia Athens Georgia
| | - David Stallknecht
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine University of Georgia Athens Georgia
| | - David Moran
- Centro de Estudios en Salud Universidad del Valle de Guatemala Guatemala City Guatemala
| | - Celia Cordon-Rosales
- Centro de Estudios en Salud Universidad del Valle de Guatemala Guatemala City Guatemala
| | - Daniela Rajao
- Poultry Diagnostic and Research Center, Department of Population Health, College of Veterinary Medicine University of Georgia Athens Georgia
| | - Daniel R Perez
- Poultry Diagnostic and Research Center, Department of Population Health, College of Veterinary Medicine University of Georgia Athens Georgia
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12
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Evaluation of two workflows for whole genome sequencing-based typing of influenza A viruses. J Virol Methods 2019; 266:30-33. [PMID: 30677464 DOI: 10.1016/j.jviromet.2019.01.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 01/04/2019] [Accepted: 01/17/2019] [Indexed: 12/20/2022]
Abstract
We compared two sample preparation protocols for whole genome sequencing of influenza A viruses. Each protocol was assessed using cDNA quantity and quality and the resulting mean genome coverage after sequencing. Both protocols produced acceptable result for samples with high viral load, whereas one protocol performed slightly better with limited virus count.
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13
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Barbezange C, Jones L, Blanc H, Isakov O, Celniker G, Enouf V, Shomron N, Vignuzzi M, van der Werf S. Seasonal Genetic Drift of Human Influenza A Virus Quasispecies Revealed by Deep Sequencing. Front Microbiol 2018; 9:2596. [PMID: 30429836 PMCID: PMC6220372 DOI: 10.3389/fmicb.2018.02596] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 10/11/2018] [Indexed: 01/06/2023] Open
Abstract
After a pandemic wave in 2009 following their introduction in the human population, the H1N1pdm09 viruses replaced the previously circulating, pre-pandemic H1N1 virus and, along with H3N2 viruses, are now responsible for the seasonal influenza type A epidemics. So far, the evolutionary potential of influenza viruses has been mainly documented by consensus sequencing data. However, like other RNA viruses, influenza A viruses exist as a population of diverse, albeit related, viruses, or quasispecies. Interest in this quasispecies nature has increased with the development of next generation sequencing (NGS) technologies that allow a more in-depth study of the genetic variability. NGS deep sequencing methodologies were applied to determine the whole genome genetic heterogeneity of the three categories of influenza A viruses that circulated in humans between 2007 and 2012 in France, directly from clinical respiratory specimens. Mutation frequencies and single nucleotide polymorphisms were used for comparisons to address the level of natural intrinsic heterogeneity of influenza A viruses. Clear differences in single nucleotide polymorphism profiles between seasons for a given subtype also revealed the constant genetic drift that human influenza A virus quasispecies undergo.
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Affiliation(s)
- Cyril Barbezange
- Viral Populations and Pathogenesis, Department of Virology, Institut Pasteur, Paris, France
- Molecular Genetics of RNA Viruses, Department of Virology, Institut Pasteur, Paris, France
- UMR 3569, Centre National de la Recherche Scientifique, Paris, France
- Cellule Pasteur, Université Paris Diderot–Université Sorbonne Paris Cité, Paris, France
| | - Louis Jones
- Molecular Genetics of RNA Viruses, Department of Virology, Institut Pasteur, Paris, France
- UMR 3569, Centre National de la Recherche Scientifique, Paris, France
- Cellule Pasteur, Université Paris Diderot–Université Sorbonne Paris Cité, Paris, France
- Bioinformatics and Biostatistics HUB, The Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, Paris, France
| | - Hervé Blanc
- Viral Populations and Pathogenesis, Department of Virology, Institut Pasteur, Paris, France
- UMR 3569, Centre National de la Recherche Scientifique, Paris, France
| | - Ofer Isakov
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Gershon Celniker
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Vincent Enouf
- Molecular Genetics of RNA Viruses, Department of Virology, Institut Pasteur, Paris, France
- UMR 3569, Centre National de la Recherche Scientifique, Paris, France
- Cellule Pasteur, Université Paris Diderot–Université Sorbonne Paris Cité, Paris, France
| | - Noam Shomron
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Marco Vignuzzi
- Viral Populations and Pathogenesis, Department of Virology, Institut Pasteur, Paris, France
- UMR 3569, Centre National de la Recherche Scientifique, Paris, France
| | - Sylvie van der Werf
- Molecular Genetics of RNA Viruses, Department of Virology, Institut Pasteur, Paris, France
- UMR 3569, Centre National de la Recherche Scientifique, Paris, France
- Cellule Pasteur, Université Paris Diderot–Université Sorbonne Paris Cité, Paris, France
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14
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Houlihan CF, Frampton D, Ferns RB, Raffle J, Grant P, Reidy M, Hail L, Thomson K, Mattes F, Kozlakidis Z, Pillay D, Hayward A, Nastouli E. Use of Whole-Genome Sequencing in the Investigation of a Nosocomial Influenza Virus Outbreak. J Infect Dis 2018; 218:1485-1489. [PMID: 29873767 PMCID: PMC6151078 DOI: 10.1093/infdis/jiy335] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 06/04/2018] [Indexed: 11/14/2022] Open
Abstract
Traditional epidemiological investigation of nosocomial transmission of influenza involves the identification of patients who have the same influenza virus type and who have overlapped in time and place. This method may misidentify transmission where it has not occurred or miss transmission when it has. We used influenza virus whole-genome sequencing (WGS) to investigate an outbreak of influenza A virus infection in a hematology/oncology ward and identified 2 separate introductions, one of which resulted in 5 additional infections and 79 bed-days lost. Results from WGS are becoming rapidly available and may supplement traditional infection control procedures in the investigation and management of nosocomial outbreaks.
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Affiliation(s)
- Catherine F Houlihan
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Dan Frampton
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - R Bridget Ferns
- Division of Infection and Immunity, University College London, London, United Kingdom
- National Institute for Health Research Biomedical Research Centre, London, United Kingdom
| | - Jade Raffle
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Paul Grant
- Department of Clinical Virology, UCL Hospitals National Health Service Foundation Trust, London, United Kingdom
| | - Myriam Reidy
- Infection Control Service, UCL Hospitals National Health Service Foundation Trust, London, United Kingdom
| | - Leila Hail
- Infection Control Service, UCL Hospitals National Health Service Foundation Trust, London, United Kingdom
| | - Kirsty Thomson
- Department of Blood Diseases, UCL Hospitals National Health Service Foundation Trust, London, United Kingdom
| | - Frank Mattes
- Department of Clinical Virology, UCL Hospitals National Health Service Foundation Trust, London, United Kingdom
| | - Zisis Kozlakidis
- Division of Infection and Immunity, University College London, London, United Kingdom
- Department of Infectious Disease Informatics, Farr Institute of Health Informatics Research, London, United Kingdom
| | - Deenan Pillay
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Andrew Hayward
- Institute of Epidemiology and Health Care, University College London, London, United Kingdom
- Department of Infectious Disease Informatics, Farr Institute of Health Informatics Research, London, United Kingdom
| | - Eleni Nastouli
- Department of Population, Policy, and Practice, Great Ormond Street Institute of Child Health, University College London (UCL), London, United Kingdom
- Department of Clinical Virology, UCL Hospitals National Health Service Foundation Trust, London, United Kingdom
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15
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Sansone M, Wiman Å, Karlberg ML, Brytting M, Bohlin L, Andersson LM, Westin J, Nordén R. Molecular characterization of a nosocomial outbreak of influenza B virus in an acute care hospital setting. J Hosp Infect 2018; 101:30-37. [PMID: 29909095 PMCID: PMC7114871 DOI: 10.1016/j.jhin.2018.06.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 06/04/2018] [Indexed: 01/21/2023]
Abstract
Aim To describe a hospital outbreak of influenza B virus (InfB) infection during season 2015/2016 by combining clinical and epidemiological data with molecular methods. Methods Twenty patients diagnosed with InfB from a hospital outbreak over a four-week-period were included. Nasopharyngeal samples (NPS) positive for InfB by multiplex real-time polymerase chain reaction were sent for lineage typing and whole genome sequencing (WGS). Medical records were reviewed retrospectively for data regarding patient characteristics, localization, exposure and outcome, and assembled into a timeline. In order to find possible connections to the hospital outbreak, all patients with a positive NPS for influenza from the region over an extended time period were also reviewed. Findings All 20 cases of InfB were of subtype B/Yamagata, and 17 of 20 patients could be linked to each other by either shared room or shared ward. WGS was successful or partially successful for 15 of the 17 viral isolates, and corroborated the epidemiological link supporting a close relationship. In the main affected ward, 19 of 75 inpatients were infected with InfB during the outbreak period, resulting in an attack rate of 25%. One probable case of influenza-related death was identified. Conclusion InfB may spread within an acute care hospital, and advanced molecular methods may facilitate assessment of the source and extent of the outbreak. A multi-faceted approach, including rapid diagnosis, early recognition of outbreak situations, simple rules for patient management and the use of regular infection control measures, may prevent nosocomial transmission of influenza virus.
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Affiliation(s)
- M Sansone
- Institute of Biomedicine, Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
| | - Å Wiman
- Public Health Agency of Sweden, Solna, Sweden
| | | | - M Brytting
- Public Health Agency of Sweden, Solna, Sweden
| | - L Bohlin
- Department of Internal Medicine, Kungalv Hospital, Kungalv, Sweden
| | - L-M Andersson
- Institute of Biomedicine, Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - J Westin
- Institute of Biomedicine, Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - R Nordén
- Institute of Biomedicine, Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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16
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Borges V, Pinheiro M, Pechirra P, Guiomar R, Gomes JP. INSaFLU: an automated open web-based bioinformatics suite "from-reads" for influenza whole-genome-sequencing-based surveillance. Genome Med 2018; 10:46. [PMID: 29954441 PMCID: PMC6027769 DOI: 10.1186/s13073-018-0555-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 06/07/2018] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND A new era of flu surveillance has already started based on the genetic characterization and exploration of influenza virus evolution at whole-genome scale. Although this has been prioritized by national and international health authorities, the demanded technological transition to whole-genome sequencing (WGS)-based flu surveillance has been particularly delayed by the lack of bioinformatics infrastructures and/or expertise to deal with primary next-generation sequencing (NGS) data. RESULTS We developed and implemented INSaFLU ("INSide the FLU"), which is the first influenza-oriented bioinformatics free web-based suite that deals with primary NGS data (reads) towards the automatic generation of the output data that are actually the core first-line "genetic requests" for effective and timely influenza laboratory surveillance (e.g., type and sub-type, gene and whole-genome consensus sequences, variants' annotation, alignments and phylogenetic trees). By handling NGS data collected from any amplicon-based schema, the implemented pipeline enables any laboratory to perform multi-step software intensive analyses in a user-friendly manner without previous advanced training in bioinformatics. INSaFLU gives access to user-restricted sample databases and projects management, being a transparent and flexible tool specifically designed to automatically update project outputs as more samples are uploaded. Data integration is thus cumulative and scalable, fitting the need for a continuous epidemiological surveillance during the flu epidemics. Multiple outputs are provided in nomenclature-stable and standardized formats that can be explored in situ or through multiple compatible downstream applications for fine-tuned data analysis. This platform additionally flags samples as "putative mixed infections" if the population admixture enrolls influenza viruses with clearly distinct genetic backgrounds, and enriches the traditional "consensus-based" influenza genetic characterization with relevant data on influenza sub-population diversification through a depth analysis of intra-patient minor variants. This dual approach is expected to strengthen our ability not only to detect the emergence of antigenic and drug resistance variants but also to decode alternative pathways of influenza evolution and to unveil intricate routes of transmission. CONCLUSIONS In summary, INSaFLU supplies public health laboratories and influenza researchers with an open "one size fits all" framework, potentiating the operationalization of a harmonized multi-country WGS-based surveillance for influenza virus. INSaFLU can be accessed through https://insaflu.insa.pt .
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Affiliation(s)
- Vítor Borges
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, Av. Padre Cruz, 1649-016 Lisbon, Portugal
| | - Miguel Pinheiro
- Institute of Biomedicine—iBiMED, Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Pedro Pechirra
- National Reference Laboratory for Influenza and other Respiratory Viruses, Department of Infectious Diseases, National Institute of Health, 1649-016 Lisbon, Portugal
| | - Raquel Guiomar
- National Reference Laboratory for Influenza and other Respiratory Viruses, Department of Infectious Diseases, National Institute of Health, 1649-016 Lisbon, Portugal
| | - João Paulo Gomes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, Av. Padre Cruz, 1649-016 Lisbon, Portugal
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