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Use of Sequence-Independent, Single-Primer-Amplification (SISPA) for rapid detection, identification, and characterization of avian RNA viruses

Current technologies with next generation sequencing have revolutionized metagenomics analysis of clinical samples. To achieve the non-selective amplification and recovery of low abundance genetic sequences, a simplified Sequence-Independent, Single-Primer Amplification (SISPA) technique in combinat...

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Autores principales: Chrzastek, Klaudia, Lee, Dong-hun, Smith, Diane, Sharma, Poonam, Suarez, David L., Pantin-Jackwood, Mary, Kapczynski, Darrell R.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Academic Press 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7111618/
https://www.ncbi.nlm.nih.gov/pubmed/28646651
http://dx.doi.org/10.1016/j.virol.2017.06.019
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author Chrzastek, Klaudia
Lee, Dong-hun
Smith, Diane
Sharma, Poonam
Suarez, David L.
Pantin-Jackwood, Mary
Kapczynski, Darrell R.
author_facet Chrzastek, Klaudia
Lee, Dong-hun
Smith, Diane
Sharma, Poonam
Suarez, David L.
Pantin-Jackwood, Mary
Kapczynski, Darrell R.
author_sort Chrzastek, Klaudia
collection PubMed
description Current technologies with next generation sequencing have revolutionized metagenomics analysis of clinical samples. To achieve the non-selective amplification and recovery of low abundance genetic sequences, a simplified Sequence-Independent, Single-Primer Amplification (SISPA) technique in combination with MiSeq platform was applied to target negative- and positive-sense single-stranded RNA viral sequences. This method allowed successful sequence assembly of full or near full length avian influenza virus (AIV), infectious bronchitis virus (IBV), and Newcastle disease virus (NDV) viral genome. Moreover, SISPA analysis applied to unknown clinical cases of mixed viral infections produced genome assemblies comprising 98% NDV and 99% of IBV genomes. Complete or near complete virus genome sequence was obtained with titers at or above 10(4.5) EID(50)/ml (50% embryo infectious dose), and virus identification could be detected with titers at or above 10(3) EID(50)/ml. Taken together, these studies demonstrate a simple template enrichment protocol for rapid detection and accurate characterization of avian RNA viruses.
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spelling pubmed-71116182020-04-02 Use of Sequence-Independent, Single-Primer-Amplification (SISPA) for rapid detection, identification, and characterization of avian RNA viruses Chrzastek, Klaudia Lee, Dong-hun Smith, Diane Sharma, Poonam Suarez, David L. Pantin-Jackwood, Mary Kapczynski, Darrell R. Virology Article Current technologies with next generation sequencing have revolutionized metagenomics analysis of clinical samples. To achieve the non-selective amplification and recovery of low abundance genetic sequences, a simplified Sequence-Independent, Single-Primer Amplification (SISPA) technique in combination with MiSeq platform was applied to target negative- and positive-sense single-stranded RNA viral sequences. This method allowed successful sequence assembly of full or near full length avian influenza virus (AIV), infectious bronchitis virus (IBV), and Newcastle disease virus (NDV) viral genome. Moreover, SISPA analysis applied to unknown clinical cases of mixed viral infections produced genome assemblies comprising 98% NDV and 99% of IBV genomes. Complete or near complete virus genome sequence was obtained with titers at or above 10(4.5) EID(50)/ml (50% embryo infectious dose), and virus identification could be detected with titers at or above 10(3) EID(50)/ml. Taken together, these studies demonstrate a simple template enrichment protocol for rapid detection and accurate characterization of avian RNA viruses. Academic Press 2017-09 2017-06-21 /pmc/articles/PMC7111618/ /pubmed/28646651 http://dx.doi.org/10.1016/j.virol.2017.06.019 Text en Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.
spellingShingle Article
Chrzastek, Klaudia
Lee, Dong-hun
Smith, Diane
Sharma, Poonam
Suarez, David L.
Pantin-Jackwood, Mary
Kapczynski, Darrell R.
Use of Sequence-Independent, Single-Primer-Amplification (SISPA) for rapid detection, identification, and characterization of avian RNA viruses
title Use of Sequence-Independent, Single-Primer-Amplification (SISPA) for rapid detection, identification, and characterization of avian RNA viruses
title_full Use of Sequence-Independent, Single-Primer-Amplification (SISPA) for rapid detection, identification, and characterization of avian RNA viruses
title_fullStr Use of Sequence-Independent, Single-Primer-Amplification (SISPA) for rapid detection, identification, and characterization of avian RNA viruses
title_full_unstemmed Use of Sequence-Independent, Single-Primer-Amplification (SISPA) for rapid detection, identification, and characterization of avian RNA viruses
title_short Use of Sequence-Independent, Single-Primer-Amplification (SISPA) for rapid detection, identification, and characterization of avian RNA viruses
title_sort use of sequence-independent, single-primer-amplification (sispa) for rapid detection, identification, and characterization of avian rna viruses
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7111618/
https://www.ncbi.nlm.nih.gov/pubmed/28646651
http://dx.doi.org/10.1016/j.virol.2017.06.019
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