Rapid detection of respiratory tract viral infections and coinfections in patients with influenza-like illnesses by use of reverse transcription-PCR DNA microarray systems

Abstract

We prospectively tested 95 nasal swabs or nasopharyngeal aspirates taken from 56 adults and 39 children visiting the Reims University Medical Centre (northern France) for influenza-like illnesses (ILI) during the early stage of the French influenza A/H1N1v pandemic (October 2009). Respiratory samples were tested using a combination of two commercially available reverse transcription-PCR (RT-PCR) DNA microarray systems allowing rapid detection of influenza A virus strains, including the new A/H1N1v strain as well as 20 other common or newly discovered respiratory viruses. Concomitantly, a generic and classical real-time RT-PCR assay was performed to detect all circulating influenza A virus strains in the same samples. Of the 95 respiratory samples tested, 30 (31%) were positive for the detection of influenza A/H1N1v virus infection by both RT-PCR DNA microarray and classical real-time RT-PCR detection assays. Among the infections, 25 (83%) were monoinfections, whereas 5 (17%) were multiple infections associating influenza A/H1N1v virus with coronavirus (CoV), human bocavirus (HBoV), respiratory syncytial virus (RSV), or human rhinoviruses (HRVs). Of the 95 respiratory samples tested, 35 (37%) were positive for respiratory viruses other than influenza A/H1N1v virus. Among these infections, we observed 30 monoinfections (HRVs [63%], parainfluenza viruses [PIVs] [20%]), influenza A/H3N2 virus [6%], coronavirus [4%], and HBoV [4%]) and 5 multiple infections, in which HRVs and PIVs were the most frequently detected viruses. No specific single or mixed viral infections appeared to be associated significantly with secondary hospitalization in infectious disease or intensive care departments during the study period (P > 0.5). The use of RT-PCR DNA microarray systems in clinical virology practice allows the rapid and accurate detection of conventional and newly discovered viral respiratory pathogens in patients suffering from ILI and therefore could be of major interest for development of new epidemiological survey systems for respiratory viral infections.

FIG. 1.

Prevalence of detection of upper respiratory tract viral infections in patients with ILI by use of a combination of two RT-PCR DNA microarray systems. The distribution (%) of the total number of single (n = 55; 58%) and mixed (n = 10; 10.6%) viral infections among 95 respiratory samples from patients with ILI during the early stage of the French influenza A/H1N1v pandemic (October 2009) was determined using two RT-PCR DNA microarray systems. Only one respiratory sample was tested for each patient. HRV, human rhinovirus; PIV, parainfluenza viruses; CoV E-229, coronavirus E-229; RSV, respiratory syncytial virus; HBoV, human bocavirus.

FIG. 2.

Distribution (%) of positive respiratory viral infections by age class among patients with ILI during the early stage of the influenza A/H1N1v pandemic (northern France, October 2009). HRV, human rhinovirus; PIV, parainfluenza viruses; CoV E-229, coronavirus E-229; RSV, respiratory syncytial virus; HBoV, human bocavirus.