Detection of multiple respiratory pathogens during primary respiratory infection: nasal swab versus nasopharyngeal aspirate using real-time polymerase chain reaction.

In this study, we present the multiple detection of respiratory viruses in infants during primary respiratory illness, investigate the sensitivity of nasal swabs and nasopharyngeal aspirates, and assess whether patient characteristics and viral load played a role in the sensitivity. Healthy infants were included at signs of first respiratory tract infection. Paired nasopharyngeal aspirates and nasal swabs were collected. Real-time polymerase chain reaction (PCR) was carried out for 11 respiratory pathogens. Paired nasopharyngeal aspirates and nasal swabs were collected in 98 infants. Rhinovirus (n = 67) and respiratory syncytial virus (n = 39) were the most frequently detected. Co-infection occurred in 48% (n = 45) of the infants. The sensitivity of the nasal swab was lower than the nasopharyngeal aspirate, in particular, for respiratory syncytial virus (51% vs. 100%) and rhinovirus (75% vs. 97%). The sensitivity of the nasal swab was strongly determined by the cycle threshold (CT) value (p < 0.001). The sensitivity of the swab for respiratory syncytial virus, but not rhinovirus, was 100% in children with severe symptoms (score >or=11). It is concluded that, for community-based studies and surveillance purposes, the nasal swab can be used, though the sensitivity is lower than the aspirate, in particular, for the detection of mild cases of respiratory syncytial virus (RSV) infection.

Oseltamivir-resistant influenza A(H1N1) viruses detected in Europe during season 2007-8 had epidemiologic and clinical characteristics similar to co-circulating susceptible A(H1N1) viruses.

During the 2007-08 influenza season, high levels of oseltamivir resistance were detected among influenza A(H1N1) viruses ina number of European countries. We used surveillance data to describe influenza A(H1N1) cases for whom antiviral resistance testing was performed. We pooled data from national studies to identify possible risk factors for infection with a resistant virus and to ascertain whether such infections led to influenza illness of different severity. Information on demographic and clinical variables was obtained from patients or their physicians. Odds ratios for infection with an oseltamivir resistant virus and relative risks for developing certain clinical outcomes were computed and adjusted through multivariable analysis. Overall, 727 (24.3%) of 2,992 tested influenza A(H1N1) viruses from 22 of 30 European countries were oseltamivir-resistant. Levels of resistance ranged from 1% in Italy to 67% in Norway. Five countries provided detailed case-based data on 373 oseltamivir resistant and 796 susceptible cases. By multivariable analysis, none of the analysed factors was significantly associated with an increased risk of infection with anoseltamivir-resistant virus. Similarly, infection with an oseltamivir-resistant virus was not significantly associated with a different risk of pneumonia, hospitalisation or any clinical complication. The large-scale emergence of oseltamivir-resistant viruses in Europe calls for a review of guidelines for influenza treatment.

Progress in the surveillance of respiratory syncytial virus (RSV) in Europe: 2001-2008.

Respiratory syncytial virus (RSV) surveillance is important to get insight into the burden of disease and epidemic pattern of RSV infection. This information is useful for healthcare resource allocation as well as the timing of preventive messages and palivizumab prophylaxis. For influenza surveillance the European Influenza Surveillance Scheme (EISS) was established in 1996, but no surveillance platform is available for RSV. To improve surveillance an RSV Task Group was established in 2003 and recommendations for RSV surveillance were developed. By 2008, progress was made for four out of six recommendations: the number of European countries testing specimens for RSV increased from six to fourteen; nose and/or throat swabs were generally used for detection of influenza and RSV; a total of 25 laboratories performed molecular testing for diagnosis and participated in a quality control assessment for RSV with an overall good performance; four of the ten countries that joined EISS in 2004 started reporting RSV detections in addition to influenza in the period 2004-8. Limited progress was achieved for standardising methods and the development of a sentinel surveillance system of representative hospitals. Improving RSV surveillance is possible by further harmonising the data collection and increased reporting of RSV.

The impact of laboratory characteristics on molecular detection of respiratory syncytial virus in a European multicentre quality control study.

The performance of nucleic acid amplification techniques for detecting respiratory syncytial virus (RSV) was evaluated in 25 laboratories across Europe by an external quality assessment study. In addition, factors related to the diagnostic performance of laboratories were explored. The results of this quality control study show that the performance of laboratories for RSV diagnosis in Europe is good, with an overall correct score of 88%. The type of assay (nested or real-time PCR vs. commercial tests) was identified as a significant factor (OR 8.39; 95% CI 1.91-36.78) in predicting a correct result.

Epidemiological and virological assessment of influenza activity in Europe, during the 2006-2007 winter.

Influenza surveillance in Europe is based on influenza surveillance networks that cooperate and share information through the European Influenza Surveillance Scheme (EISS). EISS collected clinical and virological data on influenza in 33 countries during the 2006-2007 winter. Influenza activity started around 1 January and first occurred in Greece, Scotland and Spain. It then moved gradually across Europe from south to north and lasted until the end of March. In 29 out of 33 countries, the consultation rates for influenza-like-illness or acute respiratory infections in the winter of 2006-2007 were similar or somewhat higher than in the 2005-2006 winter. The highest consultation rates for influenzal ike-illness were generally observed among children aged 0-4 years and 5-14 years. The predominant virus strain was influenza A (97% of total detections) of the H3 subtype (93% of H-subtyped A viruses; 7% were A(H1)). The influenza A(H3) and A(H1) viruses were similar to the vaccine reference strains for the 2006-2007 season, A/Wisconsin/67/2005 (H3N2) and A/New Caledonia/20/99 (H1N1) respectively. The majority of the influenza B viruses were similar to the reference strain B/Malaysia/2506/2004, included in the 2006-2007 vaccine. In conclusion, the 2006-2007 influenza season in Europe was characterised by moderate clinical activity, a south to north spread pattern across Europe, and a dominance of influenza A(H3). Overall there was a good match between the vaccine virus strains and the reported virus strains.

Epidemiological and virological assessment of influenza activity in Europe during the winter 2005-2006.

Influenza activity in Europe during the winter 2005-2006 started late January - early February 2006 and first occurred in the Netherlands, France, Greece and England. Subsequently, countries were affected in a random pattern across Europe and the period of influenza activity lasted till the end of April. In contrast to the winter seasons in the period 2001-2005, no west-east pattern was detected. In 12 out of 23 countries, the consultation rates for influenza-like illness or acute respiratory infection in the winter 2005-2006 were similar or higher than in the winter 2004-2005, despite a dominance of influenza B viruses that normally cause milder disease than influenza A viruses. In the remaining 11 countries the consultation rates were lower to much lower than in the winter 2004-2005. The highest consultation rates were usually observed among children aged 0-14. The circulating influenza virus types and subtypes were distributed heterogeneously across Europe. Although the figures for total virus detections in Europe indicated a predominance of influenza B virus (58% of all virus detections), in many countries influenza B virus was predominant only early in the winter, whilst later there was a marked increase in influenza A virus detections. Among the countries where influenza A viruses were co-dominant with B viruses (9/29) or were predominant (4/29), the dominant influenza A subtype was H3 in seven countries and H1 in four countries. The vast majority of characterised influenza B viruses (90%) were similar to the B/Victoria/2/87 lineage of influenza B viruses that re-emerged in Europe in the winter 2004-2005 but were not included in the vaccine for the influenza season 2005-2006. This might help to explain the dominance of influenza B viruses in many countries in Europe during the winter 2005-2006. The influenza A(H3) and A(H1) viruses were similar to the reference strains included in the 2005-2006 vaccine, A/California/7/2004 (H3N2) and A/New Caledonia/20/99 (H1N1), respectively. In conclusion, the 2005-2006 influenza epidemic in Europe was characterised by moderate clinical activity, a heterogeneous spread pattern across Europe, and a variable virus dominance by country, although an overall dominance of influenza B viruses that did not match the virus strain included in the vaccine was observed.

Epidemiological and virological assessment of influenza activity in Europe, during the 2004-2005 winter.

The 2004-2005 influenza season in Europe started in late December 2004 and the first influenza activity occurred in the west and southwest (Spain, United Kingdom and Ireland). Influenza activity then moved gradually east across Europe during January and early February 2005, and from late February until late March, most movement was south to north. The intensity of clinical influenza activity in ten out of 23 countries was higher than during the 2003-2004 season, and lower or equal to the 2003-2004 season in the other 13 countries. The highest consultation rates were generally observed among children aged 0-14 years. However, the peak consultation rates due to influenza-like illness or acute respiratory infection were not especially high when compared with historical data. The predominant virus strain was influenza A (83% of total detections) of the H3 subtype (85% of H-subtyped A viruses), with fewer influenza B (17% of total detections) or A(H1) viruses (15 % of H-subtyped A viruses) detected. The vast majority of A(H3) viruses were similar to the reference strains A/Wellington/1/2004 (H3N2) and, subsequently, A/California/7/2004 (H3N2) that are closely related drift variants of the A/Fujian/411/2002 (H3N2) prototype vaccine strain. The B viruses co-circulated with A viruses during the whole influenza season in 11 out of 24 countries. Seven of these were located in the northeast of Europe and in these countries the proportion of B viruses was higher (range: 31-60%) than in the rest of Europe (range: 6-26%). In 13 out of 24 countries the B viruses circulated relatively late in the season. About 43% of all antigenically characterised B viruses were B/Hong Kong/330/2001-like (B/Victoria/2/87 lineage), a strain that is distinguishable from the vaccine influenza B strain, which was a B/Yamagata/16/88 lineage virus. Based on the viruses detected worldwide until February 2005, the World Health Organization modified the composition of the 2005-2006 influenza vaccine from the 2004-2005 season vaccine to include a new A(H3N2) component: an A/California/7/2004 (H3N2)-like virus.

Epidemiological and virological assessment of influenza activity in Europe, during the 2004-2005 winter.

The 2004-2005 influenza season in Europe started in late December 2004 and the first influenza activity occurred in the west and southwest (Spain, United Kingdom and Ireland). Influenza activity then moved gradually east across Europe during January and early February 2005, and from late February until late March, most movement was south to north. The intensity of clinical influenza activity in ten out of 23 countries was higher than during the 2003-2004 season, and lower or equal to the 2003-2004 season in the other 13 countries. The highest consultation rates were generally observed among children aged 0-14 years. However, the peak consultation rates due to influenza-like illness or acute respiratory infection were not especially high when compared with historical data. The predominant virus strain was influenza A (83% of total detections) of the H3 subtype (85% of H-subtyped A viruses), with fewer influenza B (17% of total detections) or A(H1) viruses (15 % of H-subtyped A viruses) detected. The vast majority of A(H3) viruses were similar to the reference strains A/Wellington/1/2004 (H3N2) and, subsequently, A/California/7/2004 (H3N2) that are closely related drift variants of the A/Fujian/411/2002 (H3N2) prototype vaccine strain. The B viruses co-circulated with A viruses during the whole influenza season in 11 out of 24 countries. Seven of these were located in the northeast of Europe and in these countries the proportion of B viruses was higher (range: 31-60%) than in the rest of Europe (range: 6-26%). In 13 out of 24 countries the B viruses circulated relatively late in the season. About 43% of all antigenically characterised B viruses were B/Hong Kong/330/2001-like (B/Victoria/2/87 lineage), a strain that is distinguishable from the vaccine influenza B strain, which was a B/Yamagata/16/88 lineage virus. Based on the viruses detected worldwide until February 2005, the World Health Organization modified the composition of the 2005-2006 influenza vaccine from the 2004-2005 season vaccine to include a new A(H3N2) component: an A/California/7/2004 (H3N2)-like virus.

Epidemiological and virological assessment of influenza activity in Europe during the 2003-2004 season.

The 2003-2004 influenza season in Europe was dominated by the spread of the new drift variant A/Fujian/411/2002 (H3N2)-like virus which was not perfectly matched with the A(H3N2) component of the influenza vaccine. Sporadic cases of this virus were detected in Europe at the end of the 2002-2003 season and influenza activity associated with this virus began relatively early during the 2003-2004 season. Generally, influenza activity first occurred in the west of Europe (Ireland, the United Kingdom and the Iberian Peninsula) in October/November and gradually moved east across Europe, affecting Latvia, Lithuania and Poland during the months of January and February 2004. In general, the intensity of clinical activity was higher than during the 2002-2003 season (in 13 out of 20 networks) and, in countries reporting age specific data, the highest consultation incidences were observed among children aged 0-14. However, despite the emergence of the A(H3N2) drift variant, clinical incidences were not especially high compared with historical data. The composition of the 2004-2005 influenza vaccine has been modified compared with the 2003-2004 season and includes an A/Fujian/411/2002 (H3N2)-like virus strain and a new B virus strain (a B/Shanghai/361/2002-like virus).

Epidemiological and virological assessment of influenza activity in Europe during the 2003-2004 season.

The 2003-2004 influenza season in Europe was dominated by the spread of the new drift variant A/Fujian/411/2002 (H3N2)-like virus which was not perfectly matched with the A(H3N2) component of the influenza vaccine. Sporadic cases of this virus were detected in Europe at the end of the 2002-2003 season and influenza activity associated with this virus began relatively early during the 2003-2004 season. Generally, influenza activity first occurred in the west of Europe (Ireland, the United Kingdom and the Iberian Peninsula) in October/November and gradually moved east across Europe, affecting Latvia, Lithuania and Poland during the months of January and February 2004. In general, the intensity of clinical activity was higher than during the 2002-2003 season (in 13 out of 20 networks) and, in countries reporting age specific data, the highest consultation incidences were observed among children aged 0-14. However, despite the emergence of the A(H3N2) drift variant, clinical incidences were not especially high compared with historical data. The composition of the 2004-2005 influenza vaccine has been modified compared with the 2003-2004 season and includes an A/Fujian/411/2002 (H3N2)-like virus strain and a new B virus strain (a B/Shanghai/361/2002-like virus).

Harmonising the virological surveillance of influenza in Europe: results of an 18-country survey.

The European influenza surveillance scheme (EISS) is based on a surveillance model that combines clinical and virological data in the general population. Eighteen countries in Europe report weekly influenza activity to EISS (http://www.eiss.org). A questionnaire on the virological data collection was sent electronically to the EISS members. Questions on the specimen collection, representativity, laboratory diagnosis of influenza, reporting of variants, testing for other respiratory infections, serological testing, near-patient tests and preparedness for a pandemic were included. The results of the survey showed that for the typing of influenza, the methods polymerase chain reaction (PCR), enzyme-linked immunosorbent assay (ELISA) and haemagglutination inhibition (HAI) methods are used most frequently. For the subtyping of influenza, HAI and PCR are used most often. An east-west divide was seen for the use of PCR in typing and subtyping (more PCR use in the west). Differences in the virological surveillance systems in Europe can make direct comparisons difficult because detection rates may differ by test. For the reporting of other respiratory infections besides influenza, many networks (68%) collect information on RSV. This is important because RSV causes similar clinical symptoms as influenza and can have a similar impact in terms of burden of disease. With the collection of RSV data, EISS is moving to a broader spectrum of viral respiratory diseases. The findings of this survey will be used to better harmonise laboratory methods in EISS in order to obtain more reliable and comparable information on influenza activity in Europe.

Methods for sentinel virological surveillance of influenza in Europe - an 18-country survey.

The European Influenza Surveillance Scheme (EISS) is based on an integrated clinical and virological surveillance model. To assess the comparability of virological data, a questionnaire was sent to participants in June 2002 enquiring about specimen collection, laboratory diagnosis of influenza and tests for other respiratory infections. The results showed differences, but also uniformity in virological data collection methods. Similarities were reported for the specimen collection procedures; the type of swab and the transport conditions were comparable. The diagnostic methods were diverse; differences were seen in the (sub)typing methods, with PCR used most often in western countries. The findings will be helpful for the interpretation of virological data collected by sentinel physicians and for the creation of a Community Network of Reference Laboratories for Human Influenza in Europe. Important objectives of the Community Network include the harmonisation of virological methods and the application of quality assurance assessments for the national reference laboratories.

Heterogeneous influenza activity across Europe during the winter of 2002-2003.

Influenza activity varied across Europe during the 2002-2003 season both in terms of the intensity of clinical activity and the circulating virus types/subtypes. Influenza B was generally predominant in the 'western' parts of Europe (Portugal, Spain, the United Kingdom and Ireland) and influenza A (H3N2) in the 'central' and 'eastern' areas (Germany, Italy, Denmark, Switzerland, Poland, Slovenia, the Slovak Republic, the Netherlands). A number of countries experienced mixed seasons, first experiencing activity associated with influenza B and then with influenza A (Belgium, France and Spain). Generally, countries where influenza B was predominant had low (compared to historical data) levels of intensity (a mild season) and longer periods of influenza activity compared to countries where influenza A (H3N2) was predominant. A number of countries, all where influenza A (H3N2) was predominant, reported high levels of intensity compared to historical data: the Czech Republic, Denmark, Germany and Poland. In the six countries where age-specific incidence rates were available, the highest rates were observed among those aged 0-14 years. The influenza virus strains circulating in Europe had a good match with the virus strains in the influenza vaccine. A small number of isolates (A/Fujian/411/2002 (H3N2)-like) were reported at the end of the season that had a reduced reactivity to anti-sera of the vaccine strain. The composition of the 2003-2004 influenza vaccine is the same as during the 2002-2003 season.

Mild to moderate influenza activity in Europe and the detection of novel A(H1N2) and B viruses during the winter of 2001-02.

Influenza activity in Europe during the 2001-02 influenza season was mild to moderate. Compared to historical data, the intensity was low in six countries, medium in eleven and high in one country (Spain). The dominant virus circulating in Europe was influenza A(H3N2). Two novel influenza virus strains were isolated during the 2001-02 season: influenza A(H1N2) viruses (mainly isolated in the United Kingdom and Ireland, but also in Belgium, France, Germany, the Netherlands, Portugal, Sweden, Switzerland and Romania), and influenza B viruses belonging to the B/Victoria/2/87 lineage (mainly isolated in Germany, but also sporadically in France, Italy, the Netherlands and Norway). With the exception of H1N2 virus detections in England, and Ireland and the influenza B viruses belonging to the B/Victoria/2/87 lineage in Germany, these two viruses did not circulate widely in Europe and did not play an important role in influenza activity during the 2001-02 season. An influenza B virus belonging to the B/Victoria/2/87 lineage will be included in the 2002-03 influenza vaccine. The new subtype influenza A(H1N2) is covered by the 2002-03 vaccine, as the haemagglutinin and neuraminidase components of the H1N2 viruses are antigenically similar to the vaccine components (H1N1 and H3N2).