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Antimicrobial Agents and Chemotherapy, March 2009, p. 1039-1047, Vol. 53, No. 3
0066-4804/09/$08.00+0     doi:10.1128/AAC.01446-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

Detection of Molecular Markers of Antiviral Resistance in Influenza A (H5N1) Viruses Using a Pyrosequencing Method{triangledown}

Varough M. Deyde,1,# Tung Nguyen,2,# Rick A. Bright,1,{dagger} Amanda Balish,1 Bo Shu,1 Stephen Lindstrom,1 Alexander I. Klimov,1 and Larisa V. Gubareva1*

Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia,1 National Centre for Veterinary Diagnostics, DAH11-78th lane, Giai Phong str Phuong Mai, Dong Da, Hanoi, Vietnam2

Received 29 October 2008/ Returned for modification 8 December 2008/ Accepted 23 December 2008

Resistance of influenza viruses to antiviral drugs can emerge following medication or may result from natural variation. Two classes of anti-influenza virus drugs targeting either the M2 protein (amantadine and rimantadine) or neuraminidase (NA; oseltamivir and zanamivir) are currently licensed. These drugs are expected to be important in controlling the early stages of a potential pandemic. In the present study, we describe how a pyrosequencing method can be used to rapidly detect established molecular markers of resistance to M2 blockers and NA inhibitors in influenza A (H5N1) viruses. The residues L26, V27, A30, S31, and G34 in the M2 protein were targeted for pyrosequencing. The NA residues for pyrosequencing analysis included the established markers of drug resistance (H274 and N294), as well as residues of less certain relevance (V116, I117, Q136, K150, and I222). A single pair of pyro-reverse transcription (RT)-PCR primers was designed to allow amplification of an approximately 600-nucleotide-long amplicon of the NA genes of H5N1 viruses from various clades/subclades associated with infections in humans. The sensitivity of the assay was demonstrated by the successful pyrosequencing of RNA extracted from samples of serially diluted (10–5 to 10–7) virus stocks with initial concentrations ranging from 105 to 108 PFU/ml. The markers of resistance were detected in samples with threshold cycle values ranging from 32 to 37, as determined by real-time RT-PCR. The pyrosequencing approach may provide a valuable tool for rapid detection of markers of drug resistance in H5N1 viruses and facilitate the elucidation of the role of such changes in natural and acquired drug resistance.

* Corresponding author. Mailing address: Mail Stop G-16, 1600 Clifton Road, Atlanta, GA 30333. Phone: (404) 639-3204. Fax: (404) 639-0080. E-mail: lqg3{at}cdc.gov

{triangledown} Published ahead of print on 5 January 2009.

# V. M. Deyde and T. Nguyen contributed equally to the study.

{dagger} Present address: PATH, 1800 K Street NW, Suite 800, Washington, DC 20006.

Antimicrobial Agents and Chemotherapy, March 2009, p. 1039-1047, Vol. 53, No. 3
0066-4804/09/$08.00+0     doi:10.1128/AAC.01446-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.



This article has been cited by other articles:

  • McSharry, J. J., Weng, Q., Brown, A., Kulawy, R., Drusano, G. L. (2009). Prediction of the Pharmacodynamically Linked Variable of Oseltamivir Carboxylate for Influenza A Virus Using an In Vitro Hollow-Fiber Infection Model System. Antimicrob. Agents Chemother. 53: 2375-2381 [Abstract] [Full Text]  


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