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The hemagglutinin (HA) is a major influenza virus antigen, which, once recognized by antibodies and substitutions in HA genes, helps virus in escaping the human immune response. It is therefore critical to perform genetic and phylogenetic analysis of HA in circulating influenza viruses. We performed phylogenetic and genetic analysis of isolates from Ukraine, the vaccine strain and reference strains were used to phylogenetically identify trends in mutation locations and substitutions. Ukrainian isolates were collected between 2009&ndash, 2017 and clustered in the influenza genetic groups 2, 6, 7, and 8. Genetic changes were observed in each of the antigenic sites: Sa &ndash, S162T, K163Q, K163I, Sb &ndash, S185T, A186T, S190G, S190R, Ca1 &ndash, S203T, R205K, E235V, E235D, S236P, Ca2 &ndash, P137H, H138R, A141T, D222G, D222N, Cb &ndash, A73S, S74R, S74N. In spite of detected mutations in antigenic sites, Ukrainian isolates retained similarity to the vaccine strain A/California/07/09 circulated during 2009&ndash, 2017. However, WHO recommended a new vaccine strain A/Michigan/45/2015 for the Southern Hemisphere after the emergence of the new genetic groups 6B.1 and 6B.2. Our study demonstrated genetic variability of HA protein of A(H1N1)pdm09 viruses isolated in 2009&ndash, 2017 in Ukraine. Influenza surveillance is very important for understanding epidemiological situations.

A broad range of naturally occurring antigenic variants of the influenza virus is caused by its rapid evolutionary variability. The survival of viable influenza virus variants occurs through natural selection. The treatment of influenza infection with modern antiviral drugs – neuraminidase (NA) inhibitors – leads to the occurrence of mutations in the NA gene, which thereby result in the emergence of virus resistance to these drugs. The goal of this study was to determine the selection pressure on the NA protein of influenza viruses isolated in Ukraine from 2009 to 2015. The main method for assessing the selection pressure on proteins is to quantify the ratio of substitution rates at nonsynonymous (dN) and synonymous (dS) sites. With the help of this method, we showed that only a few codons in the NA gene were under positive selection resulting in mutations at the following sites: for influenza A viruses of the A(H1N1)pdm09 subtype – site 40, for viruses of the A(H3N2) subtype – sites 93 and 402, for Influenza B viruses of the B/Yamagata lineage – sites 74, 99, and 268, and for the viruses of the B/Victoria lineage – sites 358, 288, and 455. These sites are not associated with the NA active site, transmembrane domain, or the antigenic sites of this protein. We concluded that NA inhibitors are not a significant factor in the process of selection of the influenza viruses in Ukraine because the sites associated with the resistance of influenza viruses to NA inhibitors were not affected by positive selection. This finding could be explained by the limited use of NA inhibitors for the treatment of influenza infections in Ukraine.

Aim. To perform a phylogenetic and molecular-genetic analysis of the HA genes of influenza viruses that circulated in Ukraine during the 2016–2017 epidemic season, and to compare them with those that circulated in the world. Methods. Samples (nasopharyngeal swabs from patients) were analyzed using the real-time polymerase chain reaction (RT-PCR). Phylogenetic trees were constructed using MEGA 7 software. 3D structures were constructed in Chimera 1.11.2rc software. Results. Ukrainian isolates from the 2016–2017 season have substitutions in the antigenic sites which were not detected earlier; they and can influence the antigenic properties of viruses. Otherwise the A(H3N2) and B/Victoria viruses retained the similarity to the vaccine strains. For the A(H1N1)pdm09, a higher similarity to the vaccine strain recommended for the 2017–2018 epidemic season was observed. Conclusions. In the 2016–2017 epidemic season, all influenza viruses –A(H3N2), A(H1N1)pdm09 and B/Victoria acquired a number of unique amino-acid substitutions in the HA gene. The results of this study reaffirm the continuous genetic variability of circulating seasonal influenza viruses and the need for continued systematic antigenic and molecular surveillance. Мета. провести філогенетичний та молекулярно-генетичний аналіз генів НА вірусів грипу, що циркулювали на території України протягом епідемічного сезону 2016–2017 років та порівняти їх з тими, що циркулювали в світі. Методи. Зразки (назофаригіальні змиви від паціентів) були проаналізовані методом полімеразної ланцюгової реакції в реальному часі (ЗТ-ПЛР). Філогенетичні дерева будували в програмі MEGA7. 3D структури будували в програмі Chimera 1.11.2rc. Результати. Українські ізоляти мали заміни в антигенних сайтах, що виникли в попердніх сезонах та епідемічному сезоні 2016–2017 років і не виявлялись раніше, які можуть мати вплив на антигенні властивості вірусу. Не дивлячись на це, віруси грипу A(H3N2) та B/Victoria зберегли подібність до вакцинних штамів. Для вірусів грипу A(H1N1)pdm09 була показана вища подібність до вакцинного штаму, рекомендованого на епідемічний сезон 2017–2018 років. Висновки. В епідемічному сезоні 2016-2017 років всі віруси грипу – A(H3N2), A(H1N1)pdm09 та B/Victoria набули значну кількість унікальних амінокислотних заміщень в гені гемаглютиніну. Результати цього дослідження підтверджують постійну генетичну мінливість циркулюючих вірусів сезонного грипу та необхідність постійного систематичного антигенного та молекулярного нагляду. Цель. Провести филогенетический и молекулярно-генетический анализ генов НА вирусов грипа, которые циркулировали на территории Украины в эпидемическом сезоне 2016–2017 годов и сравнить их с теми, что циркулировали в мире. Методы. Образцы (назофаригиальные смывы от пациентов) были проанализированы методом полимеразной цепной реакции в реальном времени (ОТ-ПЦР). Филогенетические деревья строили в программе MEGA7. 3D структуры строили в программе Chimera 1.11.2rc. Результаты. Украинские изоляты имели замены в антигенных сайтах, возникшие в предыдущих сезонах и эпидемическом сезоне 2016–2017 годов и не выявлялись ранее, которые могут повлиять на антигенные свойства вируса. Несмотря на это, вирусы гриппа A (H3N2) и B / Victoria сохранили сходство с вакцинными штаммами. Для вирусов гриппа A (H1N1) pdm09 было показано сходство с вакцинным штаммом, рекомендованным на эпидемический сезон 2017–2018 годов. Выводы. В эпидемическом сезоне 2016–2017 годов все вирусы гриппа –A(H3N2), A(H1N1)pdm09 и B/Victoria приобрели значительное количество уникальных аминокислотных замещений в гене гемагглютинина. Результаты этого исследования подтверждают постоянную генетическую изменчивость циркулирующих вирусов сезонного гриппа и необходимость постоянного систематического антигенного и молекулярного надзора.

Background Several eastern European countries reported a severe influenza season to the World Health Organization (WHO) during late 2015. A country-specific rapid risk assessment for Ukraine was conducted to assess the season's severity and inform public health action. Methods The exposure and hazard were assessed using acute respiratory infection (ARI), severe acute respiratory infection (SARI), laboratory surveillance, virological and vaccine data from weeks 40/2015 to 7/2016 with comparison to 4 previous seasons to describe the influenza season start (5-week consecutive increase in ARI or SARI), predominant virus types, geographical spread and affected age groups. Results The exposure was characterised by an earlier and steeper increase in SARI (week 1/2016) and ARI (week 2/2016) compared to the previous 4 seasons. Transmission was across Ukraine with an increase in ARI and SARI cases aged 30-64 years compared to 2014/15. Laboratory-confirmed deaths increased from 11 in 2014/2015 to 342 in 2015/2016; the majority were 30-64 years old and unvaccinated; and 63.5% had underlying conditions. Total population vaccination coverage was 0.3%. The hazard assessment found influenza virus A(H1N1)pdm09 accounted for >95% of viruses detected. Ukrainian virus strains (n = 62) were antigenically similar to vaccine strains and susceptible to neuraminidase inhibitors. Conclusions The first weeks of the 2015/16 influenza season were more severe than previous seasons, with an earlier and steeper increase in severe cases and deaths, particularly in younger adults. Influenza A(H1N1)pdm09 was the predominant strain and was closely related to the seasonal vaccine strain with no evidence of resistance to antiviral drugs.

Free PMC article: https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/31513690/ We describe the epidemiological characteristics, pattern of circulation, and geographical distribution of influenza B viruses and its lineages using data from the Global Influenza B Study. We included over 1.8 million influenza cases occurred in thirty-one countries during 2000-2018. We calculated the proportion of cases caused by influenza B and its lineages; determined the timing of influenza A and B epidemics; compared the age distribution of B/Victoria and B/Yamagata cases; and evaluated the frequency of lineage-level mismatch for the trivalent vaccine. The median proportion of influenza cases caused by influenza B virus was 23.4%, with a tendency (borderline statistical significance, p = 0.060) to be higher in tropical vs. temperate countries. Influenza B was the dominant virus type in about one every seven seasons. In temperate countries, influenza B epidemics occurred on average three weeks later than influenza A epidemics; no consistent pattern emerged in the tropics. The two B lineages caused a comparable proportion of influenza B cases globally, however the B/Yamagata was more frequent in temperate countries, and the B/Victoria in the tropics (p = 0.048). B/Yamagata patients were significantly older than B/Victoria patients in almost all countries. A lineage-level vaccine mismatch was observed in over 40% of seasons in temperate countries and in 30% of seasons in the tropics. The type B virus caused a substantial proportion of influenza infections globally in the 21st century, and its two virus lineages differed in terms of age and geographical distribution of patients. These findings will help inform health policy decisions aiming to reduce disease burden associated with seasonal influenza. info:eu-repo/semantics/publishedVersion

Aim. 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. Мета. Молекулярний та філогенетичний аналіз пандемічних вірусів грипу A(H1N1), що циркулювали в Україні протягом сезо-ну 2014-2015 років. Методи. Зразки були проаналізовані методом полімеразної ланцюгової реакції (ПЛР) в реальному часі. Філогенетичні дерева будували в програмі MEGA 6. Результати. Сиквенси українських ізолятів вірусів грипу A(H1N1)pdm були подібними до вакцинного штаму A/California/07/2009. Більшість штамів належали до кладу 6В. Серед досліджуваних ізолятів виявили мутацію H275Y в гені нейрамінідази, яка зумовлює стійкість до озельтамівіру. Висновки. Базуючись на сиквенсах генів HA і NA вірусів грипу побудували філогенетичні дерева. Український вірус, виділений в сезоні 2014-2015 років мав специфічну мутацію, яку асоціюють з стійкістю до противірусних препаратів, таких як озельтамівір. Цель. Молекулярный и филогенетический анализ пандемических вирусов гриппа A(H1N1), которые циркулировали в Украине на протяжении 2014-2015 годов. Методы. Образцы были проанализированы методом полимеразной цепной реакции (ПЦР) в реальном времени. Филогенетические деревья построили в программе MEGA 6. Результаты. Сиквенсы украинских изолятов вирусов гриппа A(H1N1)pdm были подобными к вакцинному штамму A/California/07/2009. Большинство штаммов принадлежа-ли к клайду 6В. Среди исследованных изолятов обнаружили мутацию H275Y в гене нейраминидазы. Выводы. Основываясь на сиквенсах генов HA и NA вирусов гриппа, построили филогенетические деревья. Украинский вирус, изолированный в сезоне 2014-2015 годов имел специфическую мутацию, которую ассоциируют с устойчивостью к противовирусным препаратам, таким как осельтамивир.