Severe influenza outbreak in Western Ukraine in 2009--a molecular-epidemiological study (original) (raw)
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Molecular Epidemiology Of Human Influenza Viruses In Thessaly During 2014-2015
2015
Influenza virus genotypes circulating in the Thessaly region of central Greece during the 2014-15 season were identified as genetically and antigenically similar to vaccine like viruses. Influenza A (H3N2) viruses were detected and isolated during December January and early February in 63% of the total number of positive for Influenza A and B samples. Influenza B viruses were detected and isolated during February and March 2015. There was found 100% correlation between rt-RT-PCR and cell culture results in the samples assayed. Sequence analysis of the hemagglutinin gene segment revealed a 97% homology to reference viruses in Genbank. These findings support the need for continuous influenza surveillance and underline the importance of influenza vaccine formulation according to the antigenic profile of circulating viral strains.
Microbiology Resource Announcements, 2021
Here, we report the coding-complete genome sequences of six influenza A (H1N1) strains that were detected in Vilnius, Lithuania, among patients exhibiting influenza-like symptoms during the 2009-2010 epidemic season, within national influenza surveillance. Several mutations were found in genes encoding hemagglutinin and neuraminidase, in comparison with the A/California/07/2009 reference strain (GenBank accession numbers NC_026433 and NC_026434). B elonging to the family Orthomyxoviridae, genus Alphainfluenzavirus, the influenza type A virus causes annual human and animal influenza. The manifestation of the disease may take the form of seasonal waves of cases, local epidemics, or global pandemics caused by the emergence of antigenically different strains (1). Lack of immunity to such strains in the human population is caused by continuous genetic variation of the virus, which is based on phenomena such as reassortment (exchange of genetic segments between two different viruses), antigenic shift (changes of genetic segments encoding the major surface antigens), and antigenic drift (slow accumulation of small variations in sequences encoding the major surface antigens) (2, 3). Therefore, it is important to not only keep tracking the current genetic diversity of these viruses but also take a look at changes that occurred in the past to have a full set of data for accurate estimation of the antigenic drift and what course it may take (4, 5). Viral RNA was isolated, using the RNeasy purification kit (Qiagen), from oropharyngeal swabs collected by the National Public Health Surveillance Laboratory of Lithuania during the 2009-2010 epidemic season from patients showing influenza symptoms such as fever, coughing, headache, and chills. The Vilnius Regional Bioethics Committee approved the study protocol; this was deemed minimal risk, and the requirement for written consent was waived. The samples were positively diagnosed as A(H1N1) with a reverse transcription-quantitative PCR (RT-qPCR) assay using primers and probes recommended by the World Health Organization (6, 7). For all A(H1N1) genomic segments, reverse transcription and PCR amplification were performed using PathAmp FluA reagents (8). Postreaction cleanup was done on Agencourt AMPure XP magnetic beads (Beckman Coulter). We performed full genome sequencing on the MiSeq platform (Illumina) with v3 sequencing chemistry. For genomic library preparation, a Nextera XT DNA sample preparation kit (Illumina) was used. Paired-end reads of the target size 2 Â 300 bp were generated (
Biopolymers and Cell, 2016
To analyze the pandemic influenza A(H1N1) strains that circulated in Ukraine during 2014-2015 epidemic season. Methods. Real-time polymerase chain reaction (RT-PCR). The phylogenetic trees were constructed using MEGA 6 software. Results. The strains, that were circulating in Ukraine were similar to those of the A/California/07/2009 (H1N1) vaccine strain. Most strains belonged to the clade 6B. The H275Y mutation in the neuraminidase (NA) gene was identified, that confers resistance to oseltamivir. Conclusions. Based on the nucleotide sequences of HA and NA genes, we constructed the influenza virus phylogenetic trees. The influenza virus isolated in 2014-2015 epidemic season had a specific mutation, associated with resistance to antiviral drugs such as oseltamivir. K e y w o r d s: A(H1N1)pdm influenza viruses, mutation, phylogenetic analysis, isolate.
Molecular Surveillance of Influenza Viruses in Iasi County
2017
Influenza viruses type A and B are responsible for epidemics often associated with increased rates of morbidity and mortality. As a result of their high genetic diversity, accurate diagnosis of influenza is difficult. Rapid and sensitive molecular assays play an important role in the diagnosis and surveillance of this disease. The aim of this study was to implement a qRT-PCR technique in the Microbiology Laboratory of the Regional Public Health Center Iasi that allows the identification of influenza types A and B, as part of the national surveillance program. We have included in the study 50 clinical specimens from Iasi County collected beginning with surveillance week 50/2015 until week 20/2016. PCR assay revealed, that 13 samples (26%) were positive for influenza A virus, which were subsequently identified as A (H1N1)pdm09 in National Institute of Research “Cantacuzino” Bucharest. Only one specimen (2%) was positive for influenza B virus. The highest number of positive cases was r...
American Journal of Infectious Diseases, 2013
Exchange of information on and sharing of influenza viruses through the GISRS network has great significance for understanding influenza virus evolution, recognition of a new pandemic virus emergence and for preparing annual WHO recommendations on influenza vaccine strain composition. Influenza surveillance in Russia is based on collaboration of two NICs with 59 Regional Bases. Most epidemiological and laboratory data are entered through the internet into the electronic database at the Research Institute of Influenza (RII), where they are analyzed and then reported to the Ministry of Public Health of Russia. Simultaneously, data are introduced into WHO's Flu Net and Euro Flu, both electronic databases. Annual influenza epidemics of moderate intensity were registered during four pre-pandemic seasons. Children aged 0-2 and 3-6 years were the most affected groups of the population. Influenza registered clinically among hospitalized patients with respiratory infections for the whole epidemic period varied between 1.3 and 5.4% and up but to 18.5-23.0% during the peak of the two pandemic waves caused by influenza A(H1N1) pdm 09 virus and to lesser extent (2.9 to 8.5%) during usual seasonal epidemics. Most epidemics were associated with influenza A(H1N1), A(H3N2) and B co-circulation. During the two pandemic waves (in 2009-2010 and 2010-2011) influenza A(H1N1) pdm 09 predominated. It was accompanied by a rapid growth of influenza morbidity with a significant increase of both hospitalization and mortality. The new pandemic virus displaced the previous seasonal A(H1N1) virus completely. As a rule, most of the influenza viruses circulating in Russia were antigenic ally related to the strains recommended by WHO for vaccine composition for the Northern hemisphere with the exception of two seasons when an unexpected replacement of the influenza B Victoria lineage by Yamagata lineage (2007-2008) and the following return of Victoria lineage viruses (2008-2009) was registered. Influenza surveillance in Russia was improved as a result of enhancing capacity to international standards and the introduction of new methods in NICs such as rRT-PCR diagnosis, regular testing of influenza viruses for susceptibility to antivirals, phylogenetic analysis as well as organization of sentinel surveillance in a number of Regional Base Laboratories. Improvements promoted rapid recognition of the appearance a new pandemic virus in the country and enhancement of confirmation tests in investigation of influenza related death cases.
The influenza epidemic in Russia in 2014–2015 season
Microbiology Independent Research journal, 2015
The goal of this study was to compare the data on the intensity of the influenza A(H3N2) and B epidemic (especially the death toll) in the 2014-2015 season with the previous epidemic of the 2013-2014 season. The data on weekly morbidity, hospitalization, deaths from influenza, and acute respiratory diseases in different age groups of inhabitants of 59 cities located in 7 Federal districts of the Russian Federation were collected using the database of the Research Institute of Influenza. Analysis of this data showed that the influenza epidemic in 2014-2015 began earlier (in December) compared to the epidemic of 2013-2014, and spread mainly from Europe through Russia to the East. The intensity of the epidemic of 2014-2015 was higher compared to the previous one. The epidemic was more prevalent by regions and cities and a wider engagement of different age groups (except children up to 2 years of age) was observed. At the peak of the epidemic, the morbidity level was higher, the average duration of the epidemic was longer, and the number of patients among cities' inhabitants (especially among children 7-14 years of age and adults) was higher than in the previous season. The rates of hospitalization with influenza and acute respiratory viral infections (ARVI) among patients older than 65 years were also higher (1.4 times) as well as the frequency of hospitalization with a diagnosis of "influenza" (2.7 times) and the number of deaths from laboratory confirmed influenza (1.8 times). Although the influenza pandemic virus strain A(H1N1)pdm09 was not the main causative agent of the 2015 epidemic and was distributed sporadically it still remained the leading cause of deaths from influenza in the course of this epidemic (45.5% of all cases). The deaths associated with this strain were recorded only in the European part of Russian Federation.
Virus Genes, 2021
Influenza viruses have a high potential for genetic changes. The objectives of this study were to analyse influenza virus circulation in Bulgaria during the 2019/2020 season, to perform a phylogenetic and molecular analyses of the haemagglutinin (HA) and neuraminidase (NA) sequences of representative influenza strains, and to identify amino acid substitutions compared to the current vaccine strains. Seasonal influenza viruses A(H3N2), A(H1N1)pdm09 and B/Victoria-lineage were detected using a real-time RT-PCR in 323 (23.3%), 149 (10.7%) and 138 (9.9%) out of 1387 patient samples studied, respectively. The HA genes of A(H3N2) viruses analysed belonged to clades 3C.3a (21 strains) and 3C.2a (5 strains): subclades 3C.2a1b + T131K, 3C.2a1b + T135K-B and 3C.2a1b + T135K-A. The clade 3C.3a and subclade 3C.2a1b viruses carried 5 and 14–17 substitutions in HA, as well as 3 and 9 substitutions in NA, respectively, in comparison with the A/Kansas/14/2017 vaccine virus, including some substitut...
Central European Journal of Public Health, 2016
Aim: Influenza virological surveillance is an essential tool for studying the evolution of influenza viruses as well as for annual updating of the vaccine composition. The aim of the present study is to analyse the circulation of the influenza viruses in Bulgaria during the four recent postpandemic seasons. Methods: A total of 3,681 respiratory samples from patients with influenza like illness (ILI) or acute respiratory illness (ARI) were tested for influenza viruses using Real Time RT-PCR. Results: Influenza viruses were detected in 1,367 (37%) samples. Of those viruses, 941 (69%) were of type A and 426 (31%) of type B. Among the subtyped A viruses, 543 (60%) were A(H1N1)pdm09 and 369 (40%) A(H3N2). Co-circulation of all seasonal influenza types/subtypes was registered during each season, with the exception of A(H1N1)pdm09 virus in the 2011/12 season. In this study, data gathered from the antigenic and genetic analyses of influenza viruses, their antiviral susceptibility, and the epidemiological and clinical characteristics of the infections are presented. Conclusions: Yearly variations in the distribution and frequency of influenza types/subtypes and an annual shift of the predominant type/subtype were observed. In the seasons with predominant spread of A(H1N1)pdm09 virus-2010/11 and 2013/14, a greater number of influenza-related pneumonia cases, ICU admissions and fatal cases was registered (p < 0.05). The results of the present study confirm the need for continuous and comprehensive influenza surveillance.