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Review

Influenza genome analysis using pyrosequencing method: current applications for a moving target

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Pages 493-509 | Published online: 09 Jan 2014

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Matteo Samuele Pizzuto, Cristian De Battisti, Sabrina Marciano, Ilaria Capua & Giovanni Cattoli. (2010) Pyrosequencing analysis for a rapid classification of fowl adenovirus species. Avian Pathology 39:5, pages 391-398.
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Cristina Andrés, Margarita del Cuerpo, Núria Rabella, Maria Piñana, Manuel Jesús Iglesias-Cabezas, Alejandra González-Sánchez, Juliana Esperalba, Ariadna Rando, Maria Carmen Martín, Francisco Fuentes, Susana Rubio, Narcís Saubi, Tomàs Pumarola & Andrés Antón. (2023) Detection of reassortant influenza B strains from 2004 to 2015 seasons in Barcelona (Catalonia, Spain) by whole genome sequencing. Virus Research 330, pages 199089.
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Omid Rashidi, Afagh Moattari, Neda Pirbonyeh, Amir Emami, Mohammad Rahim Kadivar, Nahid Tavakoli Movaghar & Fahimeh Edalat. (2021) Investigation of genetic variation: Neuraminidase gene of influenza A  virus H1N1/pdm09, Shiraz, Iran (2015–2016) . Journal of Medical Virology 93:8, pages 4763-4772.
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E. A. Stepanova, E. V. Krutikova, I. V. Kiseleva & L. G. Rudenko. (2018) Development of Pyrosequencing-Based Assay for Analyzing the Origin of Genes in Preparing Reassortant LAIV Candidates. Molecular Genetics, Microbiology and Virology 33:2, pages 131-138.
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E. A. Stepanova, E. V. Krutikova, I. V. Kiseleva & L. G. Rudenko. (2018) Development of pyrosequencing-based assay for the analysis of the origin of genes in preparing reassortant laiv candidates. Molecular Genetics Microbiology and Virology (Russian version) 36:2, pages 98.
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Scott H. James & Richard J. Whitley. 2017. Infectious Diseases. Infectious Diseases 1465 1471.e1 .
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Christine C. Ginocchio. 2016. Molecular Pathology in Clinical Practice. Molecular Pathology in Clinical Practice 755 778 .
Daisuke Tamura, Margaret Okomo-Adhiambo, Vasiliy P. Mishin, Zhu Guo, Xiyan Xu, Julie Villanueva, Alicia M. Fry, James Stevens & Larisa V. Gubareva. (2015) Application of a Seven-Target Pyrosequencing Assay To Improve the Detection of Neuraminidase Inhibitor-Resistant Influenza A(H3N2) Viruses. Antimicrobial Agents and Chemotherapy 59:4, pages 2374-2379.
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Katia Corrêa de Oliveira Santos, Daniela Bernardes Borges da Silva, Margarete Aparecida Benega, Renato de Sousa Paulino, Elian Reis E Silva Jr, Dejanira dos Santos Pereira, Aparecida Duarte Hg Mussi, Valéria Cristina da Silva, Larissa V. Gubareva & Terezinha Maria de Paiva. (2015) INFLUENZA VIRUS SURVEILLANCE BY THE INSTITUTO ADOLFO LUTZ, INFLUENZA SEASON 2014: ANTIVIRAL RESISTANCE. Revista do Instituto de Medicina Tropical de São Paulo 57:1, pages 92-92.
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Irene Latorre, Verónica Saludes, Juana Díez & Andreas Meyerhans. 2014. Nucleic Acids as Molecular Diagnostics. Nucleic Acids as Molecular Diagnostics 201 216 .
Miguel E. Quiñones-Mateu, Santiago Avila, Gustavo Reyes-Teran & Miguel A. Martinez. (2014) Deep sequencing: Becoming a critical tool in clinical virology. Journal of Clinical Virology 61:1, pages 9-19.
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Dawid Nidzworski, Joanna Dobkowska, Marcin Hołysz, Beata Gromadzka & Bogusław Szewczyk. (2014) A multiplex real-time PCR assay for detection of oseltamivir-resistant strains of influenza virus. Open Life Sciences 9:6, pages 628-633.
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Jennifer Laplante & Kirsten St. George. (2014) Antiviral Resistance in Influenza Viruses. Clinics in Laboratory Medicine 34:2, pages 387-408.
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Turhan Markussen, Hilde Sindre, Christine Monceyron Jonassen, Torstein Tengs, Anja B. Kristoffersen, Jon Ramsell, Sanela Numanovic, Monika J. Hjortaas, Debes H. Christiansen, Ole Bendik Dale & Knut Falk. (2013) Ultra-Deep Pyrosequencing of Partial Surface Protein Genes from Infectious Salmon Anaemia Virus (ISAV) Suggest Novel Mechanisms Involved in Transition to Virulence. PLoS ONE 8:11, pages e81571.
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Margaret Okomo-Adhiambo, Katrina Sleeman, Colleen Lysén, Ha T. Nguyen, Xiyan Xu, Yan Li, Alexander I. Klimov & Larisa V. Gubareva. (2013) Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. Influenza and Other Respiratory Viruses 7:5, pages 645-658.
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Margaret Okomo-Adhiambo, Tiffany G. Sheu & Larisa V. Gubareva. (2013) Assays for monitoring susceptibility of influenza viruses to neuraminidase inhibitors. Influenza and Other Respiratory Viruses 7, pages 44-49.
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A. M. Fry & L. V. Gubareva. (2012) Understanding Influenza Virus Resistance to Antiviral Agents; Early Warning Signs for Wider Community Circulation. Journal of Infectious Diseases 206:2, pages 145-147.
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Aeron C. Hurt, Margaret Okomo-Adhiambo & Larisa V. Gubareva. 2012. Influenza Virus. Influenza Virus 115 125 .
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Christian Renaud, Jane Kuypers & Janet A. Englund. (2011) Emerging oseltamivir resistance in seasonal and pandemic influenza A/H1N1. Journal of Clinical Virology 52:2, pages 70-78.
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Steven Y. C. Tong, Farshid Dakh, Aeron C. Hurt, Yi-Mo Deng, Kevin Freeman, Peter K. Fagan, Ian G. Barr & Philip M. Giffard. (2011) Rapid Detection of the H275Y Oseltamivir Resistance Mutation in Influenza A/H1N1 2009 by Single Base Pair RT-PCR and High-Resolution Melting. PLoS ONE 6:6, pages e21446.
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Shao-Min Yan & Guang Wu. (2011) Fitting evolutionary process of influenza a virus nucleoproteins using analytical solution of system of differential equations. Interdisciplinary Sciences: Computational Life Sciences 3:2, pages 128-137.
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Marnie Levine, Tiffany G. Sheu, Larisa V. Gubareva & Vasiliy P. Mishin. (2011) Detection of Hemagglutinin Variants of the Pandemic Influenza A (H1N1) 2009 Virus by Pyrosequencing. Journal of Clinical Microbiology 49:4, pages 1307-1312.
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Elodie Ghedin, Jennifer Laplante, Jay DePasse, David E. Wentworth, Roberto P. Santos, Martha L. Lepow, Joanne Porter, Kathleen Stellrecht, Xudong Lin, Darwin Operario, Sara Griesemer, Adam Fitch, Rebecca A. Halpin, Timothy B. Stockwell, David J. Spiro, Edward C. Holmes & Kirsten St. George. (2011) Deep Sequencing Reveals Mixed Infection with 2009 Pandemic Influenza A (H1N1) Virus Strains and the Emergence of Oseltamivir Resistance. The Journal of Infectious Diseases 203:2, pages 168-174.
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Tiffany G. Sheu, Alicia M. Fry, Rebecca J. Garten, Varough M. Deyde, Thein Shwe, Lesley Bullion, Patrick J. Peebles, Yan Li, Alexander I. Klimov & Larisa V. Gubareva. (2011) Dual Resistance to Adamantanes and Oseltamivir Among Seasonal Influenza A(H1N1) Viruses: 2008–2010. The Journal of Infectious Diseases 203:1, pages 13-17.
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Larisa V Gubareva, A Angelica Trujillo, Margaret Okomo-Adhiambo, Vasiliy P Mishin, Varough M Deyde, Katrina Sleeman, Ha T Nguyen, Tiffany G Sheu, Rebecca J Garten, Michael W Shaw, Alicia M Fry & Alexander I Klimov. (2010) Comprehensive assessment of 2009 Pandemic Influenza a (H1N1) Virus Drug Susceptibility in vitro . Antiviral Therapy 15:8, pages 1151-1159.
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