The present thesis aimed to determine the epidemiology of the main respiratory viruses circulating in our geographical area. The contribution of molecular techniques to the routine diagnosis of the infections caused by these viruses was also evaluated. Data of the respiratory viruses detected at Hospital de la Santa Creu i Sant Pau between January 1997 and December 2013 were collected. The circulation of respiratory viruses, including frequency and seasonal distribution, was analysed. The relationship between the viruses detected and the age and sex of the patients was also evaluated. The clinical specimens analysed included nasopharyngeal aspirates, nasal and pharyngeal exudates, bronchoalveolar lavages and lung biopsies. The virological studies were performed by cell culture (CC), immunochromatography and immunofluorescence (IF); a nucleic acid amplification technique (NAAT) for detection of Influenza viruses was also used. A total of 36,744 clinical specimens were studied. Of these, 13,201 (35. 9%) were positive for one virus or more than one. Overall 13,630 respiratory viruses were identified: RSV (29. 4%) was the most frequently detected, followed by FLUAV (28. 7%) and AdV (14. 7%). The other viruses were detected in a frequency under 10%: EV (9. 3%), FLUBV (6. 7%), hMPV (5. 1%), RV (4. 4%), PIV-3 (3%), PIV-1 (1. 1%) and PIV-2 ( 1%). A total of 428 co-detections were identified (3. 2%). RSV, FLUAV, AdV, EV and PIV-3 were detected every year. The other respiratory viruses had a heterogeneous distribution throughout the years under study. Overall the highest number of positive detections was obtained during the winter months and the fewest in summer. Some viruses followed a seasonal distribution showing a pick in definite months: RSV from November to January, hMPV from February to May, FLUAV from December to March, FLUBV from January to March, and PIV-2 from September to December. The remaining respiratory viruses under study were detected throughout the year. Co-detections were mainly found from October to March every year. Noteworthily during the influenza pandemic (2009-2010), FLUAV corresponded to only 43% of all the respiratory viruses. Respiratory viruses were more frequently identified in children. Viral detection was obtained in 37. 4%, 51. 2%, 50. 8%, 42. 7% and 32. 2% of the samples from children under 6 months of age, under 1 year, between 1 and 3 years, between 3 and 5 years, and between 5 and 18 years, respectively. The average of positivity in adults was 15%. Regarding the sex of the patients, 56. 1% and 43. 9% of viral detections corresponded to samples from men and women, respectively. The ratio men:woman over 1 was found in all age groups but young adults (ranging from 18 to 40 years). To determine the contribution of NAATs to the diagnosis of respiratory viral infection, two molecular techniques were compared: Seeplex® based on the DPO™ system (Dual Priming Oligonucleotide) and CLART®, based on microarray technology. These techniques were also compared to conventional techniques (IF/CC). Eighty nasopharyngeal aspirates were collected from children under six years of age attended for acute respiratory illness. The main finding was that both NAATs used to detect respiratory viruses yielded different results. NAATs and IF/CC results also differed. The number of positive samples was 40, 62 and 37 for Seeplex®, CLART® and IF/CC, respectively. Seeplex® and CLART® detected 11 and 57 viruses more than IF/CC, respectively. Considering those viruses detected only by PCR, about 72% corresponded to RV, hMPV, HCoV-OC43, PIV-4, FLUCV, and HBoV. Co-detections were detected in 30 samples by NAATs whereas none was detected by IF/CC. The main challenge posed by molecular techniques in the diagnosis of respiratory virus infections is the difficulty in determining whether a virus detected is related to the current symptoms of the patient.
| Date of Award | 27 Nov 2015 |
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| Original language | Catalan |
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| Awarding Institution | - Hospital de la Santa Creu i Sant Pau
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| Supervisor | Núria Rabella García (Director) & Ferran Navarro Risueño (Director) |
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