Advances in the diagnosis of respiratory virus infections

Molecular diagnosis of respiratory virus infections

The appearance of eight new respiratory viruses, including the SARS coronavirus in 2003 and swine-origin influenza A/H1N1 in 2009, in the human population in the past nine years has tested the ability of virology laboratories to develop diagnostic tests to identify these viruses. Nucleic acid based amplification tests (NATs) for respiratory viruses were first introduced two decades ago and today are utilized for the detection of both conventional and emerging viruses. These tests are more sensitive than other diagnostic approaches, including virus isolation in cell culture, shell vial culture (SVC), antigen detection by direct fluorescent antibody (DFA) staining, and rapid enzyme immunoassay (EIA), and now form the backbone of clinical virology laboratory testing around the world. NATs not only provide fast, accurate and sensitive detection of respiratory viruses in clinical specimens but also have increased our understanding of the epidemiology of both new emerging viruses such as the pandemic H1N1 influenza virus of 2009, and conventional viruses such as the common cold viruses, including rhinovirus and coronavirus. Multiplex polymerase chain reaction (PCR) assays introduced in the last five years detect up to 19 different viruses in a single test. Several multiplex PCR tests are now commercially available and tests are working their way into clinical laboratories. The final chapter in the evolution of respiratory virus diagnostics has been the addition of allelic discrimination and detection of single nucleotide polymorphisms associated with antiviral resistance. These assays are now being multiplexed with primary detection and subtyping assays, especially in the case of influenza virus. These resistance assays, together with viral load assays, will enable clinical laboratories to provide physicians with new and important information for optimal treatment of respiratory virus infections.

Is there any specific association between respiratory viruses and bacteria in acute otitis media of young children?

Background

Respiratory viral infections are usually preceding or coinciding with acute otitis media (AOM) in children. It is not known if a given viral infection would facilitate invasion of bacterial pathogens into the middle ear in a species-specific way. We reanalysed the microbiological results of the two prospective Finnish Otitis Media (FinOM) studies for this purpose.

Methods

The children had been followed from 2 months to 2 years of age in specific study clinics and all referred AOM events were analysed. Combined results of virus detection tests from middle ear fluid and nasopharyngeal aspirate and those of bacterial culture from middle ear fluid were cross-tabulated for 529 AOM events in the FinOM Cohort Study and for 364 events in the FinOM Vaccine Trial.

Results

In both studies the main bacterial pathogens were Streptococcus pneumoniae, Haemophilus influenzae and Moraxella catarrhalis while the main viruses detected were rhinoviruses and respiratory syncytial virus (plus enteroviruses in the Vaccine Trial). No distinct species-specific associations were observed between the viral and bacterial findings.

Conclusion

We did not find support to the theory that respiratory infection caused by a given viral species would favour growth of a certain bacterial pathogen in the MEF more than another.

The value of virus serology in epidemiological studies of acute otitis media in children

BACKGROUND

Acute otitis media (AOM) is a major health problem in young children. There is a general conception that AOM is a bacterial disease but with the availability of sensitive diagnostic methods, it has gradually become evident that viruses play an important role in the pathogenesis of AOM. Paired blood samples are seldom taken from infants although valuable information could be obtained by serological methods. During the recent Finnish Otitis Media (FinOM) Cohort Study, in addition to nasopharyngeal aspirates (NPA) and middle ear fluids (MEF), paired acute and convalescent serum samples were collected from children with AOM.

OBJECTIVES

To establish the diagnostic value of serological methods in etiological and epidemiological studies of AOM.

STUDY DESIGN

A complete set of NPA, MEF, and paired sera was collected during 447 events of AOM experienced by 179 children between 2 months and 2 years of age. Antigens of respiratory syncytial virus (RSV), adenoviruses, influenza A and B, and parainfluenza types 1-3 in NPAs and MEFs were detected by time-resolved fluoroimmunoassay (TR-FIA), and antibody titers were determined by complement fixation test (CFT) or by enzyme immunoassay.

RESULTS

A total of 163 virus-positive events were identified. Of those, only 34 were positive by TR-FIA and by serology. From 48 events a positive result was obtained only by TR-FIA and from 81 only by serology.

CONCLUSION

Although serological methods are usually of little use in clinical practice, epidemiological studies clearly gain value if serology is included. The number of virus-positive findings dramatically increased by including serological tests in the diagnostic work-up of these AOM events.

Development and application of a new method for amplification and detection of human rhinovirus RNA

A method based on nucleic acid sequence based amplification (NASBA) was developed for detection of rhinovirus RNA. Appropriate collection and storage conditions for maintenance of rhinovirus RNA integrity in clinical samples was determined. Two silica-based extraction methods were evaluated for preparation of RNA from virus isolates and clinical samples. Primers and probes were selected from the non-translated region at the 5' end and from VP4 of sequenced rhinoviruses. Amplified products were detected by 'in-solution' hybridization, with analysis by polyacrylamide gel electrophoresis (enzyme linked gel assay or ELGA), and by a microtitre-based plate hybridization assay. Using propagated picornavirus isolates in vitro the rhinovirus NASBA, with detection of amplified sequences by ELGA or plate hybridization, was confirmed as sensitive and specific for detection of rhinovirus RNA. The method was applied successfully to analysis of rhinovirus sequences in clinical samples from individuals with respiratory-tract symptoms. Rhinovirus NASBA will be useful for studies of the molecular epidemiology of respiratory infections and monitoring of response to anti-rhinovirus therapy.

Detection of respiratory syncytial virus, parainfluenzavirus 3, adenovirus and rhinovirus sequences in respiratory tract of infants by polymerase chain reaction and hybridization

BACKGROUND

Immunofluorescence assay (IFA) of viral antigens in nasal aspirates is largely used for the diagnosis of respiratory syncytial virus (RSV), parainfluenzavirus (PIV) type 3 and adenovirus (AdV) infections, whilst rhinovirus (RV) are detected by virus isolation technique (VIT) only. Using the two techniques, IFA and VIT, a significant number of specimens remain negative in spite of clinical and epidemiological presumptions of viral infection.

OBJECTIVES AND STUDY DESIGN

The polymerase chain reaction (PCR) should improve the sensitivity of viral detection in clinical specimens. From October 1995 to March 1996, 277 nasal aspirates from hospitalized infants were tested simultaneously by IFA, VIT, polymerase chain reaction and hybridization with a DNA enzyme immunoassay (PCR-EIA) for RSV, PIV-3, AdV and RV.

RESULTS

RSV were detected in 177 (64%) samples, PIV-3 in 23 (8%), RV in 40 (14%), and AdV in 30 (10%). PCR-EIA detected RSV in more samples 173 (62%) than IFA/VIT: 109 (39%) (P < 10(-7)). In most cases (79%), RSV-infected infants had lower respiratory tract disease, and routine and PCR techniques were positive. Out of the 23 PIV-3 infections, 12 were IFA/VIT- and PCR-EIA-positive, and 11 IFA/VIT-negative and PCR-EIA-positive. For RV, 35 (87%) specimens were PCR EIA-positive and 11 (27%) culture-positive; for AdV 30 samples were PCR-EIA-positive and four were culture-positive. Simultaneous viral infections were revealed in a significantly higher proportion than in conventional techniques: 18% (50/277) versus 2.5% (7/277); P < 10(-7). One RSV infection in four was associated with the presence of another virus, mainly PIV-3 (16 cases) and AdV (13 cases).

CONCLUSIONS

PCR-EIA detects more positive-specimens than IFA/VIT, 1.5 times more for RSV, 1.9 for PIV-3, 4 for RV and 10 for AdV, respectively. This increased sensitivity of viral detection by PCR-EIA compared to the IFA/VIT could suggest that samples containing low levels of virus are missed by routine methods IFA/VIT, and consequently, RSV or PIV-3, and above all RV or AdV are overlooked as agents of respiratory diseases. However, apart from the fact that the economic and convenient aspects of virus diagnostic cannot be missed, it is difficult to answer the following questions: what is the meaning of the detection of a viral sequences in nasal aspirates of infants, or may PCR have detected virus in patients who would not developed disease?