About: Detection of baloxavir resistant influenza A viruses using next generation sequencing and pyrosequencing methods

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About: Detection of baloxavir resistant influenza A viruses using next generation sequencing and pyrosequencing methods Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : covidontheweb.inria.fr associated with source document(s)

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type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Detection of baloxavir resistant influenza A viruses using next generation sequencing and pyrosequencing methods
Creator	Barnes, John Gubareva, Larisa Patel, M Mishin, Vasiliy Wentworth, David Patel, Mira Wilson, Malania Cruz, La De, Juan Nguyen, A Nguyen, Ha Wilson, H Chesnokov, Anton Chesnokov, J De, V Gubareva, D Kondor, J Kondor, Rebecca Wentworth, R
Source	Elsevier; Medline; PMC
abstract	Abstract Baloxavir, a new antiviral drug targeting cap-dependent endonuclease activity of polymerase acidic (PA) protein of influenza viruses, is now approved in multiple countries. Several substitutions at isoleucine 38 in PA protein (e.g., PA-I38T) have been associated with decreased baloxavir susceptibility in vitro and in vivo. In recent years, next generation sequencing (NGS) analysis and pyrosequencing have been used by CDC and U.S. Public Health Laboratories to monitor drug susceptibility of influenza viruses. Here we described an improved pyrosequencing assay for detecting influenza A viruses carrying substitutions at PA-38. Cyclic and customized orders of nucleotide dispensation were evaluated, and pyrosequencing results were compared to those generated using NGS. Our data showed that the customized nucleotide dispensation has improved the pyrosequencing assay performance in identification of double mixtures (e.g., PA-38I/T); however, identification of PA-38 variants in triple mixtures remains a challenge. While NGS analysis indicated the presence of PA-I38K in one clinical specimen and isolate, our attempts to detect this mutation by pyrosequencing or recover the virus carrying PA-I38K in cell culture were unsuccessful, raising a possibility of a rarely occurring sequencing error. Overall, pyrosequencing provides a convenient means to detect baloxavir resistant influenza viruses when NGS is unavailable or a faster turnaround time is required.
has issue date	2020-08-14(xsd:dateTime)
bibo:doi	10.1016/j.antiviral.2020.104906
bibo:pmid	32798601
has license	els-covid
sha1sum (hex)	9c07423388d2a07d947d574a43379bef6e30f78f
schema:url	https://doi.org/10.1016/j.antiviral.2020.104906
resource representing a document's title	Detection of baloxavir resistant influenza A viruses using next generation sequencing and pyrosequencing methods
has PubMed Central identifier	PMC7426223
has PubMed identifier	32798601
schema:publication	Antiviral Research
resource representing a document's body	covid:9c07423388d2a07d947d574a43379bef6e30f78f#body_text
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