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      Swine influenza A virus isolates containing the pandemic H1N1 origin matrix gene elicit greater disease in the murine model

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          ABSTRACT

          Since the 1990s, endemic North American swine influenza A viruses (swFLUAVs) contained an internal gene segment constellation, the triple reassortment internal gene (TRIG) cassette. In 2009, the H1N1 pandemic (pdmH1N1) virus spilled back into swine but did not become endemic. However, the pdmH1N1 contributed the matrix gene (pdmM) to the swFLUAVs circulating in the pig population, which replaced the classical swine matrix gene (swM) found in the TRIG cassette, suggesting the pdmM has a fitness benefit. Others have shown that swFLUAVs containing the pdmM have greater transmission efficiency compared to viruses containing the swM gene segment. We hypothesized that the matrix (M) gene could also affect disease and utilized two infection models, resistant BALB/c and susceptible DBA/2 mice, to assess pathogenicity. We infected BALB/c and DBA/2 mice with H1 and H3 swFLUAVs containing the swM or pdmM and measured lung virus titers, morbidity, mortality, and lung histopathology. H1 influenza strains containing the pdmM gene caused greater morbidity and mortality in resistant and susceptible murine strains, while H3 swFLUAVs caused no clinical disease. However, both H1 and H3 swFLUAVs containing the pdmM replicated to higher viral titers in the lungs and pdmM containing H1 viruses induced greater histological changes compared to swM H1 viruses. While the surface glycoproteins and other gene segments may contribute to swFLUAV pathogenicity in mice, these data suggest that the origin of the matrix gene also contributes to pathogenicity of swFLUAV in mice, although we must be cautious in translating these conclusions to their natural host, swine.

          IMPORTANCE

          The 2009 pandemic H1N1 virus rapidly spilled back into North American swine, reassorting with the already genetically diverse swFLUAVs. Notably, the M gene segment quickly replaced the classical M gene segment, suggesting a fitness benefit. Here, using two murine models of infection, we demonstrate that swFLUAV isolates containing the pandemic H1N1 origin M gene caused increased disease compared to isolates containing the classical swine M gene. These results suggest that, in addition to other influenza virus gene segments, the swFLUAV M gene segment contributes to pathogenesis in mammals.

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          Most cited references72

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          Fast and accurate short read alignment with Burrows–Wheeler transform

          Motivation: The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A first generation of hash table-based methods has been developed, including MAQ, which is accurate, feature rich and fast enough to align short reads from a single individual. However, MAQ does not support gapped alignment for single-end reads, which makes it unsuitable for alignment of longer reads where indels may occur frequently. The speed of MAQ is also a concern when the alignment is scaled up to the resequencing of hundreds of individuals. Results: We implemented Burrows-Wheeler Alignment tool (BWA), a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps. BWA supports both base space reads, e.g. from Illumina sequencing machines, and color space reads from AB SOLiD machines. Evaluations on both simulated and real data suggest that BWA is ∼10–20× faster than MAQ, while achieving similar accuracy. In addition, BWA outputs alignment in the new standard SAM (Sequence Alignment/Map) format. Variant calling and other downstream analyses after the alignment can be achieved with the open source SAMtools software package. Availability: http://maq.sourceforge.net Contact: rd@sanger.ac.uk
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            Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data

            Massively-parallel cDNA sequencing has opened the way to deep and efficient probing of transcriptomes. Current approaches for transcript reconstruction from such data often rely on aligning reads to a reference genome, and are thus unsuitable for samples with a partial or missing reference genome. Here, we present the Trinity methodology for de novo full-length transcriptome reconstruction, and evaluate it on samples from fission yeast, mouse, and whitefly – an insect whose genome has not yet been sequenced. Trinity fully reconstructs a large fraction of the transcripts present in the data, also reporting alternative splice isoforms and transcripts from recently duplicated genes. In all cases, Trinity performs better than other available de novo transcriptome assembly programs, and its sensitivity is comparable to methods relying on genome alignments. Our approach provides a unified and general solution for transcriptome reconstruction in any sample, especially in the complete absence of a reference genome.
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              BLAT---The BLAST-Like Alignment Tool

              W. J. Kent (2002)
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                Author and article information

                Contributors
                Role: ConceptualizationRole: Formal analysisRole: InvestigationRole: MethodologyRole: VisualizationRole: Writing – original draftRole: Writing – review and editing
                Role: Formal analysisRole: InvestigationRole: MethodologyRole: VisualizationRole: Writing – review and editing
                Role: Formal analysisRole: MethodologyRole: Writing – review and editing
                Role: ConceptualizationRole: Writing – review and editing
                Role: Formal analysisRole: MethodologyRole: Writing – review and editing
                Role: ResourcesRole: SupervisionRole: Writing – review and editing
                Role: ConceptualizationRole: Funding acquisitionRole: MethodologyRole: ResourcesRole: SupervisionRole: VisualizationRole: Writing – review and editing
                Role: Editor
                Journal
                Microbiol Spectr
                Microbiol Spectr
                spectrum
                Microbiology Spectrum
                American Society for Microbiology (1752 N St., N.W., Washington, DC )
                2165-0497
                March 2024
                01 February 2024
                01 February 2024
                : 12
                : 3
                : e03386-23
                Affiliations
                [1 ]Department of Infectious Diseases, University of Georgia; , Athens, Georgia, USA
                [2 ]Center for Vaccines and Immunology, University of Georgia; , Athens, Georgia, USA
                [3 ]Emory-UGA Centers of Excellence for Influenza Research and Surveillance (CEIRS); , Athens, Georgia, USA
                [4 ]Department of Population Health, Poultry Diagnostic and Research Center, College of Veterinary Medicine, University of Georgia; , Athens, Georgia, USA
                [5 ]Department of Pathology, College of Veterinary Medicine, University of Georgia; , Athens, Georgia, USA
                Universiteit Utrecht; , the Netherlands
                Author notes
                Address correspondence to S. Mark Tompkins, smt@ 123456uga.edu

                Present address: Critical Care Medicine Department, National Institutes of Health, Bethesda, Maryland, USA

                Present address: Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA

                Present address: Department of Pathobiology, Sugg Laboratory, Auburn University, Alpharetta, Georgia, USA

                Shelly J. Curran and Emily F. Griffin contributed equally to this article. Author order was determined on the basis of initiating and completing the research and manuscript.

                The authors declare no conflict of interest.

                Author information
                https://orcid.org/0000-0002-6569-5689
                https://orcid.org/0000-0002-1523-5588
                Article
                03386-23 spectrum.03386-23
                10.1128/spectrum.03386-23
                10913740
                38299860
                472ebc31-ca22-4055-a802-a4d4940b9a4a
                Copyright © 2024 Curran et al.

                This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

                History
                : 22 September 2023
                : 08 January 2024
                Page count
                supplementary-material: 1, authors: 7, Figures: 5, References: 72, Pages: 17, Words: 10341
                Funding
                Funded by: HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID);
                Award ID: HHSN272201400004C
                Award Recipient :
                Categories
                Research Article
                virology, Virology
                Custom metadata
                March 2024

                influenza virus,pathogenesis,swine influenza,mouse model,matrix gene,pandemic influenza

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