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Detection of respiratory pathogens including coronaviruses using PCR

Abstract number: p643

Duerud  I., Jonassen  T.O., Steinbakk  M., Jonassen  C.M.

Objectives: 

We routinely use nucleic acid amplification tests to identify parainfluenza virus, influenza virus A and B, respiratory syncytial virus, human metapneumovirus, Chlamyophila pneumoniae, Mycoplasma pneumoniae and Bordetella pertussis in patient respiratory samples. In a 1-year period we also included a broad range PCR for detection of coronaviruses in the same samples. The aim of this study was to estimate the impact of coronaviruses as a respiratory pathogen in a Norwegian population.

Methods: 

A multiplex RT-PCR with subsequent probe hybridisation was used to identify parainfluenza virus, influenza virus A and B, respiratory syncytial virus and human metapneumovirus (Hexaplex, Prodesse, USA) in patient respiratory samples. The cDNA generated in the Hexaplex procedure was also amplified with coronavirus specific primers. Coronavirus PCR products were sequenced to identify the type of coronavirus. Real time PCRs for detection of Chlamyophila pneumoniae, Mycoplasma pneumoniae and Bordetella pertussis were performed on all samples.

Results: 

In the 1-year period from March 2004 about 2000 samples were analysed. In about two thirds of the samples no pathogen was found. In 12% of the samples one of the three bacteria were found. Infection with human metapneumovirus had a peak incidence in December–January with positive rates of 24 and 15% respectively. Infection with the influenza viruses had a peak incidence in February–March 2005 with positive rates of 24 and 29% respectively. In total 75 of the samples were positive for coronavirus, most of them OC43-like, with a peak incidence in January–February 2005 with positive rates of 9 and 14% respectively. In addition to the OC43 coronaviruses, three of type 229E, two of type NL63 and four of type HKU1 were detected. Very few samples contained more than one pathogen, but in 15 of the coronavirus positive samples another virus was also detected. All HKU1-like coronavirus positive samples also contained another respiratory pathogen.

Conclusion: 

In the winter months infection with coronavirus OC43 had a high incidence in this population of patients with respiratory illnesses. This suggests that this virus is an important cause of respiratory tract infections. As all of the coronavirus HKU1 positive samples also contained another respiratory pathogen, and the pathogenicity of coronavirus HKU1 is difficult to estimate from this study.

Session Details

Date: 01/08/2007
Time: 00:00-00:00
Session name: XXIst ISTH Congress
Subject:
Location: Oxford, UK
Presentation type:
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