Sequencing and analysis of globally obtained human parainfluenza viruses 1 and 3 genomes
| Autor: | Martha I. Nelson, Neha Gupta, Paolo Amedeo, Kelly J. Henrickson, Christopher D. Town, Samuel Cordey, Daniel E. Noyola, Cristina Videla, Susmita Shrivastava, Tuckweng Kok, Astrid Vabret, Rebecca A. Halpin, Michael E. Bose, Nadia Fedorova, Hernan Lorenzi, Marietjie Venter, Amelia Buys, Jie He, Jayati Bera |
|---|---|
| Přispěvatelé: | Medical College of Wisconsin [Milwaukee] (MCW), J. Craig Venter Institute, Fogarty International Center, National Institutes of Health [Bethesda] (NIH), Universidad Autonoma de San Luis Potosi [México] (UASLP), Centro de Educación Médica e Investigaciones Clínicas (CEMIC), University of South Australia [Adelaide], National Institute for Communicable Diseases [Johannesburg] (NICD), University of Pretoria [South Africa], Groupe de Recherche sur l'Adaptation Microbienne (GRAM 2.0), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Université de Caen Normandie (UNICAEN), Normandie Université (NU), Service de Virologie [CHU Caen], CHU Caen, Normandie Université (NU)-Tumorothèque de Caen Basse-Normandie (TCBN)-Normandie Université (NU)-Tumorothèque de Caen Basse-Normandie (TCBN), Geneva University Hospital (HUG) |
| Jazyk: | angličtina |
| Rok vydání: | 2019 |
| Předmět: |
RNA viruses
0301 basic medicine medicine.disease_cause Genome Database and Informatics Methods Influenza A virus Genome Evolution Phylogeny Pathology and laboratory medicine ComputingMilieux_MISCELLANEOUS Data Management ddc:616 Recombination Genetic Genetics Multidisciplinary High-Throughput Nucleotide Sequencing Phylogenetic Analysis Genomics Medical microbiology 3. Good health Phylogenetics Human Parainfluenza Virus Viruses [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology Evolutionary Rate Medicine Pathogens Sequence Analysis Research Article Computer and Information Sciences Evolutionary Processes Bioinformatics Sequence analysis Science 030106 microbiology Genome Viral Biology Research and Analysis Methods Microbiology Molecular Evolution Virus Evolution Molecular 03 medical and health sciences Sequence Motif Analysis medicine Humans Influenza viruses Evolutionary Systematics Parainfluenza Virus 1 Human/genetics Selection Genetic Taxonomy Medicine and health sciences Evolutionary Biology Sequence Assembly Tools Organisms Viral pathogens Biology and Life Sciences Computational Biology Sequence Analysis DNA Ion semiconductor sequencing Genome Analysis [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology Genomics/methods Parainfluenza Virus 1 Human Parainfluenza Virus 3 Human Microbial pathogens 030104 developmental biology Parainfluenza Virus 3 Human/genetics Sequence Alignment Orthomyxoviruses |
| Zdroj: | PLoS ONE PLoS ONE, Public Library of Science, 2019, 14 (7), pp.e0220057. ⟨10.1371/journal.pone.0220057⟩ PLoS ONE, Vol 14, Iss 7, p e0220057 (2019) PLOS ONE, Vol. 14, No 7 (2019) P. e0220057 |
| ISSN: | 1932-6203 |
| Popis: | Human Parainfluenza viruses (HPIV) type 1 and 3 are important causes of respiratory tract infections in young children globally. HPIV infections do not confer complete protective immunity so reinfections occur throughout life. Since no effective vaccine is available for the two virus subtypes, comprehensive understanding of HPIV-1 and HPIV-3 genetic and epidemic features is important for diagnosis, prevention, and treatment of HPIV-1 and HPIV-3 infections. Relatively few whole genome sequences are available for both HPIV-1 and HPIV-3 viruses, so our study sought to provide whole genome sequences from multiple countries to further the understanding of the global diversity of HPIV at a whole-genome level. We collected HPIV-1 and HPIV-3 samples and isolates from Argentina, Australia, France, Mexico, South Africa, Switzerland, and USA from the years 2003-2011 and sequenced the genomes of 40 HPIV-1 and 75 HPIV-3 viruses with Sanger and next-generation sequencing with the Ion Torrent, Illumina, and 454 platforms. Phylogenetic analysis showed that the HPIV-1 genome is evolving at an estimated rate of 4.97 × 10-4 mutations/site/year (95% highest posterior density 4.55 × 10-4 to 5.38 × 10-4) and the HPIV-3 genome is evolving at a similar rate (3.59 × 10-4 mutations/site/year, 95% highest posterior density 3.26 × 10-4 to 3.94 × 10-4). There were multiple genetically distinct lineages of both HPIV-1 and 3 circulating on a global scale. Further surveillance and whole-genome sequencing are greatly needed to better understand the spatial dynamics of these important respiratory viruses in humans. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|