Measles outbreaks in 2017-2019 - molecular surveillance started in the Czech Republic.

OBJECTIVE: Between 2017 and 2019, measles virus spread globally, causing a large measles epidemic that suddenly ended in 2020. Measles outbreaks also occurred in the Czech Republic (CR) as part of the global public health problem. In the recent alarming epidemiological situation, molecular surveillance is becoming increasingly important as it plays a vital role in the identification of imported cases and in the monitoring of virus transmission. Molecular surveillance makes it possible to obtain evidence of the discontinuation of the endemic spread and is indispensable for the verification of measles elimination. The study aim is to find out whether any of measles virus genotypes circulated in the CR for more than 12 months in order to either confirm or refute the endemic spread of measles virus in the country in relation to the recent loss of the measles elimination status. Another aim is to assess the current laboratory diagnosis from the perspective of recent measles outbreaks and the obligation to refer samples for confirmation and genotyping. MATERIAL AND METHODS: In total, 243 positive nasopharyngeal swabs collected from outbreak patients from all over the CR in 2018 and 2019 were analysed by molecular methods. The most variable part of the measles virus genome, the nucleoprotein gene (N-450), was sequenced according to the WHO protocol. The sequence analysis was performed by Sanger method using the Applied Biosystems 3 500 sequencer, and sequence data were analysed by the bioinformatics programe Geneious. RESULTS: In the CR, only two genotypes were found in measles outbreaks in 2018-2019, eight variants of the dominant D8 and six B3 variants, while genotype A was detected in eight samples. The dominant genotype of 2017 (D8, 4283) was identified for the first time in the CR in January 2018. Four months later, it was replaced by genotype D8, 4683, occurring in the CR from March 2018 to June 2019. This genotype was identified in 170 of 243 samples (70%). There was a 3-month window between the first and the second detection of this genotype, which does not imply that in the meantime the virus did not circulate in the population. The analysis of seven samples from 2017 conducted by the collaborating Regional Reference Laboratory at the Robert Koch Institute (RRL RKI) in Berlin assigned five samples from Ostrava to genotype B3 and detected two variants of genotype D8 (Praha, Liberec). Laboratory diagnosis was facilitated by a higher proportion of clinical specimens available for direct detection of the virus, which increased from 18% in 2017 to 43% in 2019. Samples were referred to the National Reference Laboratory (NRL) in Prague for sequencing in accordance with the set legal rules. Between 2018 - 2019, laboratories sent 424 samples. Two hundred and forty-three samples (60%) were successfully sequenced, while the sequencing of the remaining samples failed due to low viral load. CONCLUSIONS: Measles virus sequencing was introduced in the Czech Republic as a necessary part of molecular surveillance, and almost 60% of positive samples were analysed. The sequencing analysis confirmed the endemic spread of measles virus, with genotype D8, 4683 MVs/GirSomnath.IND/42.16 found to circulate in the CR for 16 months between 2018 and 2019. Laboratory diagnosis is recently focusing more on direct detection of the virus, which along with genotyping extended to include another part of the genome will improve molecular surveillance.

[Phylogenetic and molecular analysis of A/H1N1pdm influenza viruses isolated in the epidemic season 2012/2013 from hospitalised patients with -symptoms of influenza-like illness]. / Fylogenetická a molekulární analýza viru chripky A/H1N1pdm izolovaných v epidemické sezone 2012/2013 od pacientu hospitalizovaných s príznaky ILI.

AIM: To perform phylogenetic and molecular analysis of A/H1N1pdm influenza viruses isolated in the epidemic season 2012/2013 from hospitalised patients with symptoms of influenza-like illness (ILI). MATERIAL AND METHODS: The study set included 34 strains of the A/H1N1pdm influenza virus isolated in the Czech Republic in the epidemic season 2012/2013. The strains were analysed by partial or whole-genome sequencing. The genome segments were compared at the nucleotide and amino acid levels, absolute and percentage sequence identity were determined, and phylogenetic relations were identified. The last steps were the comparison of the H1 molecule with that of the most recent vaccine strain and identification of the genotypic structure and molecular markers linked to the pathogenicity and antiviral resistance. RESULTS: Phylogenetic analysis of the H1 molecule suggested that all 34 A/H1N1pdm isolates from the 2012/2013 season in the Czech Republic should be assigned to H1 group 6 divided into sublineages 6A and 6B. The comparison of the known antigenic regions of the H1 molecule with those in the most recent vaccine strain revealed two stable changes in antigenic regions Sb and Ca1. Furthermore, sporadic mutations were identified in antigenic regions Ca2, Cb, and Sb. Genotyping revealed co-circulation of two related but clearly distiguishable genotypes of A/H1N1pdm. All isolates showed sensitivity to oseltamivir. One strain consisted of two N1 sub-populations, one oseltamivir sensitive and the other oseltamivir resistant, in nearly equimolar proportions. CONCLUSION: All A/H1N1pdm isolates from the epidemic season 2012/2013 in the Czech Republic formed a phenotypically uniform group. At the nucleotide level, the divergence was relatively more pronounced and H1 sublineages and discrete genotypes were possible to identify. H1 molecules were highly identical to those of the vaccine strain A/California/7/2009 (H1N1) which showed that the current vaccine was protective enough. All strains were sensitive to oseltamivir; however, the selection of oseltamivir resistant N1 subpopulations was observed.

[Clinical and epidemiological characteristics of patients hospitalized with severe influenza in the season 2012-2013]. / Klinické a epidemiologické charakteristiky pacientu hospitalizovaných pro tezký prubeh chripky v sezone 2012-2013.

AIM OF THE STUDY: To characterize the clinical and epidemiological features of patients hospitalized with moderate to severe influenza infection at the infec-tious diseases department of a tertiary care hospital in the epidemic season 2012-2013. MATERIAL AND METHODS: A prospective observational study of patients hospitalized with influenza infection in the season 2012-2013 was carried out at the Infectious Diseases Department, Na Bulovce Hospital in Prague. Influenza infection was diagnosed by real-time quantitative polymerase chain reaction (RT-qPCR) in nasopharyngeal swab or tracheal aspirate specimens. Demographic, clinical, and laboratory data were recorded along with the disease course and outcome. RESULTS: One hundred and ninety-nine patients, 85 females and 114 males (age median 47, range 1-87 years), were hospitalized with confirmed influenza in the epidemic season 2012-2013. Only seven of them got the influenza vaccine. Altogether 136 patients were diagnosed with influenza type A (91 with H1N1pdm, 33 with H3N2, and 12 with an unknown subtype), 66 patients with type B, and three patients with both types A and B. One hundred and eight patients (54%) had an underlying chronic disease, most often cardiovascular or pulmonary. The main symptoms of influenza were fever, cough, headache, myalgia, and arthralgia. Pneumonia was the most common complication: twenty-one patients suffered from primary viral pneumonia and 35 from bacterial pneumonia. Twenty-three patients (12%) needed intensive care. Six patients died and the leading cause of death was heart failure. CONCLUSION: During the epidemic influenza season 2012-2013, more patients were hospitalized than in the pandemic season 2009-2010. Also the proportions of complicated cases and case fatality ratios were fully comparable in both seasons. The fact that most patients were not vaccinated clearly supports the recommendation to vaccinate every year both the individuals at high risk of complications due to comorbidities and the healthy population.

DNA persistence after treatment of Lyme borreliosis.

One hundred twenty-four patients-53 with neuroborreliosis, 48 with erythema migrans, and 23 with Lyme arthritis-were tested in a prospective study for the presence of the DNA of Borrelia burgdorferi sensu lato in plasma, cerebrospinal fluid (CSF), urine, and synovial fluid by nested polymerase chain reaction (PCR). Specific DNA was detected using five amplification systems simultaneously: three targeted chromosomal genes encoding 16S rDNA, flagellin, and p66; and two plasmid sequences of OspA and OspC. Patients were examined clinically and by PCR before and after treatment and again after 3 and 6 months. Before treatment, the specific DNA was detected in 78 patients (62.9 %). Forty-one neuroborreliosis patients were DNA-positive (77.4 %), with CSF positivity in 26 patients, urine in 25, and plasma in 16. Twenty-six erythema migrans patients were DNA-positive (54.2 %), with plasma positivity in 18 cases and urine in 14. Eleven Lyme arthritis cases (47.8 %) were DNA positive (six in urine, five in plasma, and four in synovial fluid). The frequency of PCR positives was comparable in CSF and urine, and it was lower by approximately 50 % in plasma. Specific DNA was also found in a significant number of patients in later testing periods: 48 patients after treatment, 29 patients after 3 months, and 6 patients after 6 months. The prolonged PCR positivity was not explainable by persistent infection according to the clinical manifestations of the disease. Possible explanations of the problem are discussed.

[Scoring systems to evaluate prognosis of community-acquired pneumonias]. / Skórovací systémy hodnotící prognózu komunitních pneumonií

Several expert systems were developed for assessment of community-acquired pneumonia (CAP) and its severity in individual patients. Scoring systems PSI, CURB-65, and CRB-65 are widely used. They were primarily designed for easier decision on need of CAP patients hospitalization. Newer scoring systems evaluate especially severity of CAP and need of intensive care. This group of systems comprise ATS/IDSA recommendations, CURXO-8O, SMART-COP, and SMRT-CO. The last one appears to be the most appropriate for common practice but more studies are necessary to confirm this opinion. Regardless of the scoring systems the authors recommend more extensive usage of pulse oxymetry in the care of CAP patients.