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Influenza A viral loads in respiratory samples collected from patients infected with pandemic H1N1, seasonal H1N1 and H3N2 viruses

Nathamon Ngaosuwankul1, Pirom Noisumdaeng1, Pisut Komolsiri1, Phisanu Pooruk1, Kulkanya Chokephaibulkit2, Tawee Chotpitayasunondh3, Chariya Sangsajja4, Charoen Chuchottaworn5, Jeremy Farrar6 and Pilaipan Puthavathana1*

Author Affiliations

1 Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand

2 Pediatrics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand

3 Queen Sirikit National Institute of Child Health, Bangkok 10400, Thailand

4 Bamrasnaradura Infectious Disease Institute, Nonthaburi 11000, Thailand

5 Chest Disease Institute, Nonthaburi 11000, Thailand

6 Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam

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Virology Journal 2010, 7:75  doi:10.1186/1743-422X-7-75

Published: 20 April 2010

Abstract

Background

Nasopharyngeal aspirate (NPA), nasal swab (NS), and throat swab (TS) are common specimens used for diagnosis of respiratory virus infections based on the detection of viral genomes, viral antigens and viral isolation. However, there is no documented data regarding the type of specimen that yields the best result of viral detection. In this study, quantitative real time RT-PCR specific for M gene was used to determine influenza A viral loads present in NS, NPA and TS samples collected from patients infected with the 2009 pandemic H1N1, seasonal H1N1 and H3N2 viruses. Various copy numbers of RNA transcripts derived from recombinant plasmids containing complete M gene insert of each virus strain were assayed by RT-PCR. A standard curve for viral RNA quantification was constructed by plotting each Ct value against the log quantity of each standard RNA copy number.

Results

Copy numbers of M gene were obtained through the extrapolation of Ct values of the test samples against the corresponding standard curve. Among a total of 29 patients with severe influenza enrolled in this study (12 cases of the 2009 pandemic influenza, 5 cases of seasonal H1N1 and 12 cases of seasonal H3N2 virus), NPA was found to contain significantly highest amount of viral loads and followed in order by NS and TS specimen. Viral loads among patients infected with those viruses were comparable regarding type of specimen analyzed.

Conclusion

Based on M gene copy numbers, we conclude that NPA is the best specimen for detection of influenza A viruses, and followed in order by NS and TS.