Rapid Genotyping of Swine Influenza Viruses | CDC EID

EID Journal Home > Volume 17, Number 4–April 2011

Volume 17, Number 4–April 2011
Dispatch
Rapid Genotyping of Swine Influenza Viruses
Polly W.Y. Mak, Chloe K.S. Wong, Olive T.W. Li, Kwok Hung Chan, Chung Lam Cheung, Edward S. Ma, Richard J. Webby, Yi Guan, Joseph S. Malik Peiris, and Leo L.M. Poon

Author affiliations: The University of Hong Kong, Hong Kong Special Administrative Region, People's Republic of China (P.W.Y. Mak, C.K.S. Wong, O.T.W. Li, K.H. Chan, C.L. Cheung, E.S. Ma, Y. Guan, J.S.M. Peiris, L.L.M. Poon); St. Jude Children's Research Hospital, Memphis, Tennessee, USA (R.J. Webby); and Hong Kong University–Pasteur Research Centre, Hong Kong (J.S.M. Peiris)

Suggested citation for this article

Abstract
The emergence of pandemic (H1N1) 2009 virus highlighted the need for enhanced surveillance of swine influenza viruses. We used real-time reverse–transcription PCR–based genotyping and found that this rapid and simple genotyping method may identify reassortants derived from viruses of Eurasian avian-like, triple reassortant-like, and pandemic (H1N1) 2009 virus lineages.

Co-infection of influenza A viruses enables viral gene reassortments, thereby generating progeny viruses with novel genotypes. Such reassortants may pose a serious public health threat, as exemplified by the emergence of pandemic influenza (H1N1) in 2009 (1). Transmission of pandemic (H1N1) 2009 virus from humans to pigs has been reported (2–5). We recently identified a reassortment between pandemic (H1N1) 2009 virus and swine influenza viruses in pigs (6). These results emphasize the potential role of pigs as a mixing vessel for influenza viruses and the need for screening tests that can identify major reassortment events in pigs.

We previously developed 8 monoplex SYBR green–based quantitative reverse transcription–PCRs to detect all 8 gene segments derived from the pandemic (H1N1) 2009 virus or virus segments that are closely related to this lineage (i.e., neuraminidase [NA] and matrix protein from the Eurasian avian-like swine linage and polymerase basic protein [PB] 2, PB1, polymerase acidic protein [PA], hemagglutinin [HA], nucleocapsid protein [NP], and nonstructural protein [NS]) from triple reassortant swine linage (5). Using these PCRs, we identified swine viruses of atypical genotypes. However, with the exception of the HA-specific assay, the melting-curve signals of pandemic (H1N1) 2009 virus may be indistinguishable from the positive signals generated from its sister clade as indicated above. To differentiate between these closely related groups of viruses, we further optimized these assays by adding sequence-specific hydrolysis probes in the SYBR green assays.

full-text:
Rapid Genotyping of Swine Influenza Viruses | CDC EID


Suggested Citation for this Article
Mak PWY, Wong CKS, Li OTW, Chan KH, Cheung CL, Ma ES, et al. Rapid genotyping of swine influenza viruses. Emerg Infect Dis [serial on the Internet]. 2011 Apr [date cited].
http://www.cdc.gov/EID/content/17/4/691.htm


DOI: 10.3201/eid1704.101726


Comments to the Authors
Please use the form below to submit correspondence to the authors or contact them at the following address:

Leo L.M. Poon, Department of Microbiology, University Pathology Building, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China; email: llmpoon@hkucc.hku.hk