A universal primer-independent next-generation sequencing approach for investigations of norovirus outbreaks and novel variants.

Norovirus (NoV) is the most common cause of non-bacterial gastroenteritis and is a major agent associated with outbreaks of gastroenteritis. Conventional molecular genotyping analysis of NoV, used for the identification of transmission routes, relies on standard typing methods (STM) by Sanger-sequencing of only a limited part of the NoV genome, which could lead to wrong conclusions. Here, we combined a NoV capture method with next generation sequencing (NGS), which increased the proportion of norovirus reads by ~40 fold compared to NGS without prior capture. Of 15 NoV samples from 6 single-genotype outbreaks, near full-genome coverage (>90%) was obtained from 9 samples. Fourteen polymerase (RdRp) and 15 capsid (cap) genotypes were identified compared to 12 and 13 for the STM, respectively. Analysis of 9 samples from two mixed-genotype outbreaks identified 6 RdRp and 6 cap genotypes (two at >90% NoV genome coverage) compared to 4 and 2 for the STM, respectively. Furthermore, complete or partial sequences from the P2 hypervariable region were obtained from 7 of 8 outbreaks and a new NoV recombinant was identified. This approach could therefore strengthen outbreak investigations and could be applied to other important viruses in stool samples such as hepatitis A and enterovirus.

Influenza vaccine effectiveness in adults 65 years and older, Denmark, 2015/16 - a rapid epidemiological and virological assessment.

In Denmark, both influenza A(H1N1)pdm09 and influenza B co-circulated in the 2015/16 season. We estimated the vaccine effectiveness (VE) of the trivalent influenza vaccine in patients 65 years and older using the test-negative case-control design. The adjusted VE against influenza A(H1N1)pdm09 was 35.0% (95% confidence interval (CI): 11.1-52.4) and against influenza B 4.1% (95% CI: -22.0 to 24.7). The majority of influenza A(H1N1)pdm09 circulating in 2015/16 belonged to the new genetic subgroup subclade 6B.1.

Phylogenetic and epidemiological analysis of measles outbreaks in Denmark, 2013 to 2014.

Despite the introduction of safe, effective vaccines decades ago and joint global public health efforts to eliminate measles, this vaccine-preventable disease continues to pose threats to children's health worldwide. During 2013 and 2014, measles virus was introduced into Denmark through several independent importations. This resulted in a number of secondary cases (n=7), with two clusters in 2013 and one in 2014. In total, there were 44 cases of measles. Most cases (n=41) were laboratory confirmed by detection of measles virus genome by real-time reverse transcription (RT)-PCR and IgM antibodies. The viruses from confirmed cases were genotyped by sequencing. Only one genotype circulated each year, i.e. D8 and B3, respectively. Sequencing of measles virus from different clinical specimens from the same patients revealed that sequence variants of measles viruses might co-exist and co-transmit during an outbreak. The majority of the cases were unvaccinated (n=27) or recipients of one dose of measles-mumps-rubella (MMR) vaccine (n=7). In addition, two fully vaccinated adult cases were reported in 2014. We demonstrate the transmission of measles virus in a population in which the two-dose MMR vaccination coverage rate was 80% and how even vaccinated individuals may be at risk of contracting measles once transmission has been established.

Mumps resurgence in Denmark.

BACKGROUND: The past decade has witnessed a resurgence of parotitisvirus (mumps) in several countries where seemingly good mumps control otherwise had been achieved through vaccination. Recently detection of mumps has increased in Denmark. OBJECTIVES: To describe the age-specific changes and time trends of parotitisvirus detection in Denmark over a 10 year period. STUDY DESIGN: Retrospective cohort study based on national laboratory data for parotitisvirus typing surveillance and national epidemiology data for mumps reporting. RESULTS: The parotitisvirus detection rate has increased almost 10 times during the past 10 years from an incidence <0.1 per 100,000 in 2003 to 0.96 per 100,000 in 2013. The age distribution has shifted from children to young adults, and most cases are unvaccinated (54%) or vaccinated once (41%). The increase is due mainly to the existence of cohorts with low MMR vaccine coverage. CONCLUSION: Analysis of mumps surveillance data from Denmark documents that the incidence of mumps is increasing, and that the resurgence of parotitisvirus is primarily occurring among young Danish adults. Almost half of the infected clinical mumps cases had received the first dose of MMR.