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

Detection of baloxavir resistant influenza A viruses using next generation sequencing and pyrosequencing methods. Antiviral Res. 2020 Aug 13;:104906 Authors: Patel MC, Mishin VP, De La Cruz JA, Chesnokov A, Nguyen HT, Wilson MM, Barnes J, Kondor RJG, Wentworth DE, Gubareva LV 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 ...
Source: Antiviral Research - Category: Virology Authors: Tags: Antiviral Res Source Type: research