Estimation of the basic reproduction number of measles during an outbreak in a partially vaccinated population

From March to July 1996 a measles outbreak occurred in northern Luxembourg with 110 reported cases centered around two primary schools (85 cases) and the surrounding community (25 cases). Eighty four suspected cases were confirmed serologically. Vaccine coverage was estimated from questionnaire-based surveys at the two primary schools to be 70 and 76%, respectively. Vaccine efficacy during the outbreak was estimated to be 94.6% [95% confidence interval (CI) 90·4–97·0]. Using the information from the school surveys, we obtained estimates of the basic reproduction number of measles of 7·7 (95% CI 4·4–11·0) and 6·2 (95% CI 3·5–8·9), respectively. Assuming a 95% vaccine efficacy, these estimates correspond to minimal vaccine coverages of 91·6% (95% CI 81·4–95·7) and 88·3% (95% CI 75·5–93·4) which would have been necessary to minimize the chances of a major outbreak occurring. We can confirm that major outbreaks in similar school settings can only be prevented if vaccination coverage exceeds 90%

Human papillomavirus vaccination coverage in Luxembourg : implications of lowering and restricting target age groups

Background: In Luxembourg, a national Human Papillomavirus (HPV) vaccination programme was introduced in 2008, targeting 12-17 year old girls offering a choice of bivalent or quadrivalent vaccine free of charge. In 2015, the programme was changed offering the bivalent vaccine only to 11-13 year old girls. The aim of this study was to evaluate the HPV vaccination coverage, to assess the impact of age target changes and compare vaccination coverage to other European countries. Methods: Anonymous HPV vaccination records consisting of individual vaccine doses obtained free of charge in pharmacies between 2008 and 2016 were extracted from the Luxembourgish Social Security database. Additional aggregate tables by nationality and municipality were analysed. Results: Of the target cohort of 39,610 girls born between 1991 and 2003 residing in Luxembourg, 24,550 (62.0%) subjects obtained at least one dose, 22,082 (55.7%) obtained at least two doses, and 17,197 (43.4%) obtained three doses of HPV vaccine. The mean age at first dose was 13.7 years during 200814 and 12.7 years in 2016 after the age target change. Coverage varied significantly by nationality (p < 0.0001): Portuguese (80%), former Yugoslays (74%), Luxembourgish (54%), Belgian (52%), German (47%), French (39%) and other, nationalities (51%). Coverage varied also by geographical region, with lower rates (<50%) noted in some Northern and Central areas of Luxembourg (range: 38% to 78%). Conclusion: Overall HPV vaccination coverage in Luxembourg is moderate and varied by nationality and region. The policy changes in 2015 did not have a substantial impact except lowering age at initiating vaccination. Options to improve coverage deserve further investigation

Generalisation of COVID-19 incidences provides a biased view of the actual epidemiological situation.

peer reviewe

Complete genome sequence of a novel human gammapapillomavirus isolated from a cervical swab in Luxembourg

A novel human papillomavirus genotype was detected in a cervical swab specimen by next-generation sequencing after rolling circular amplification. It was fully cloned and characterized. The L1 open reading frame showed 77% nucleotide similarity with the closest genotype, HPV101, belonging to the gamma-6 species

Investigating Major Recurring Campylobacter jejuni Lineages in Luxembourg Using Four Core or Whole Genome Sequencing Typing Schemes

Campylobacter jejuni is the leading cause of bacterial gastroenteritis, which has motivated the monitoring of genetic profiles circulating in Luxembourg since 13 years. From our integrated surveillance using a genotyping strategy based on an extended MLST scheme including gyrA and porA markers, an unexpected endemic pattern was discovered in the temporal distribution of genotypes. We aimed to test the hypothesis of stable lineages occurrence by implementing whole genome sequencing (WGS) associated with comprehensive and internationally validated schemes. This pilot study assessed four WGS-based typing schemes to classify a panel of 108 strains previously identified as recurrent or sporadic profiles using this in-house typing system. The strain collection included four common lineages in human infection (N = 67) initially identified from recurrent combination of ST-gyrA-porA alleles also detected in non-human samples: veterinary (N = 19), food (N = 20), and environmental (N = 2) sources. An additional set of 19 strains belonging to sporadic profiles completed the tested panel. All the strains were processed by WGS by using Illumina technologies and by applying stringent criteria for filtering sequencing data; we ensure robustness in our genomic comparison. Four typing schemes were applied to classify the strains: (i) the cgMLST SeqSphere+ scheme of 637 loci, (ii) the cgMLST Oxford scheme of 1,343 loci, (iii) the cgMLST INNUENDO scheme of 678 loci, and (iv) the wgMLST INNUENDO scheme of 2,795 loci. A high concordance between the typing schemes was determined by comparing the calculated adjusted Wallace coefficients. After quality control and analyses with these four typing schemes, 60 strains were confirmed as members of the four recurrent lineages regardless of the method used (N = 32, 12, 7, and 9, respectively). Our results indicate that, regardless of the typing scheme used, epidemic or endemic signals were detected as reflected by lineage B (ST2254-gyrA9-porA1) in 2014 or lineage A (ST19-gyrA8-porA7), respectively. These findings support the clonal expansion of stable genomes in Campylobacter population exhibiting a multi-host profile and accounting for the majority of clinical strains isolated over a decade. Such recurring genotypes suggest persistence in reservoirs, sources or environment, emphasising the need to investigate their survival strategy in greater depth

Influenza surveillance in Europe: comparing intensity levels calculated using the moving epidemic method.

Although influenza-like illnesses (ILI) and acute respiratory illnesses (ARI) surveillance are well established in Europe, the comparability of intensity among countries and seasons remains an unresolved challenge. The objective is to compare the intensity of ILI and ARI in some European countries. Weekly ILI and ARI incidence rates and proportion of primary care consultations were modeled in 28 countries for the 1996/1997-2013/2014 seasons using the moving epidemic method (MEM). We calculated the epidemic threshold and three intensity thresholds, which delimit five intensity levels: baseline, low, medium, high, and very high. The intensity of 2013/2014 season is described and compared by country. The lowest ILI epidemic thresholds appeared in Sweden and Estonia (below 10 cases per 100 000) and the highest in Belgium, Denmark, Hungary, Poland, Serbia, and Slovakia (above 100 per 100 000). The 2009/2010 season was the most intense, with 35% of the countries showing high or very high intensity levels. The European epidemic period in season 2013/2014 started in January 2014 in Spain, Poland, and Greece. The intensity was between low and medium and only Greece reached the high intensity level, in weeks 7 to 9/2014. Some countries remained at the baseline level throughout the entire surveillance period. Epidemic and intensity thresholds varied by country. Influenza-like illnesses and ARI levels normalized by MEM in 2013/2014 showed that the intensity of the season in Europe was between low and medium in most of the countries. Comparing intensity among seasons or countries is essential for understanding patterns in seasonal epidemics. An automated standardized model for comparison should be implemented at national and international levels.This work has been funded by the National and International Public Institutions and the Regional Health Department of Castilla y León (Spain).S

Social Contacts and Mixing Patterns Relevant to the Spread of Infectious Diseases

Surveying 7,290 participants in eight European countries, Joël Mossong and colleagues determine patterns of person-to-person contact relevant to controlling pathogens spread by respiratory or close-contact routes

A standardised protocol for assessment of relative SARS-CoV-2 variant severity, with application to severity risk for COVID-19 cases infected with Omicron BA.1 compared to Delta variants in six European countries

Several SARS-CoV-2 variants that evolved during the COVID-19 pandemic have appeared to differ in severity, based on analyses of single-country datasets. With decreased SARS-CoV-2 testing and sequencing, international collaborative studies will become increasingly important for timely assessment of the severity of newly emerged variants. The Joint WHO Regional Office for Europe and ECDC Infection Severity Working Group was formed to produce and pilot a standardised study protocol to estimate relative variant case-severity in settings with individual-level SARS-CoV-2 testing and COVID-19 outcome data during periods when two variants were co-circulating. To assess feasibility, the study protocol and its associated statistical analysis code was applied by local investigators in Denmark, England, Luxembourg, Norway, Portugal and Scotland to assess the case-severity of Omicron BA.1 relative to Delta cases. After pooling estimates using meta-analysis methods (random effects estimates), the risk of hospital admission (adjusted hazard ratio [aHR]=0.41, 95% CI 0.31-0.54), ICU admission (aHR=0.12, 95% CI 0.05-0.27), and death (aHR=0.31, 95% CI 0.28-0.35) was lower for Omicron BA.1 compared to Delta cases. The aHRs varied by age group and vaccination status. In conclusion, this study has demonstrated the feasibility of conducting variant severity analyses in a multinational collaborative framework. The results add further evidence for the reduced severity of the Omicron BA.1 variant.Comment: 21 pages, 6 figures (excluding supplementary material