Dataset Information

Rapid spread of influenza A(H1N1)pdm09 viruses with a new set of specific mutations in the internal genes in the beginning of 2015/2016 epidemic season in Moscow and Saint Petersburg (Russian Federation).

ABSTRACT: A dramatic increase of influenza activity in Russia since week 3 of 2016 significantly differs from previous seasons in terms of the incidence of influenza and acute respiratory infection (ARI) and in number of lethal cases. We performed antigenic analysis of 108 and whole-genome sequencing of 77 influenza A(H1N1)pdm09 viruses from Moscow and Saint Petersburg. Most of the viruses were antigenically related to the vaccine strain. Whole-genome analysis revealed a composition of specific mutations in the internal genes (D2E and M83I in NEP, E125D in NS1, M105T in NP, Q208K in M1, and N204S in PA-X) that probably emerged before the beginning of 2015/2016 epidemic season.

SUBMITTER: Komissarov A

PROVIDER: S-EPMC4910175 | biostudies-literature | 2016 Jul

REPOSITORIES: biostudies-literature

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Rapid spread of influenza A(H1N1)pdm09 viruses with a new set of specific mutations in the internal genes in the beginning of 2015/2016 epidemic season in Moscow and Saint Petersburg (Russian Federation).

Komissarov Andrey A Komissarov Andrey A Fadeev Artem A Sergeeva Maria M Petrov Sergey S Sintsova Kseniya K Egorova Anna A Pisareva Maria M Buzitskaya Zhanna Z Musaeva Tamila T Danilenko Daria D Konovalova Nadezhda N Petrova Polina P Stolyarov Kirill K Smorodintseva Elizaveta E Burtseva Elena E Krasnoslobodtsev Kirill K Kirillova Elena E Karpova Lyudmila L Eropkin Mikhail M Sominina Anna A Grudinin Mikhail M

Influenza and other respiratory viruses 20160527 4

A dramatic increase of influenza activity in Russia since week 3 of 2016 significantly differs from previous seasons in terms of the incidence of influenza and acute respiratory infection (ARI) and in number of lethal cases. We performed antigenic analysis of 108 and whole-genome sequencing of 77 influenza A(H1N1)pdm09 viruses from Moscow and Saint Petersburg. Most of the viruses were antigenically related to the vaccine strain. Whole-genome analysis revealed a composition of specific mutations ...[more]

PMID: 26992820

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Project description:Background and aimsHIV infection and mortality in Eastern Europe are driven by unsafe injection drug use. We sought to compare engagement in care from HIV testing through receipt of antiretroviral treatment among HIV-positive people who inject drugs (PWID) in St Petersburg, Russian Federation (RF) and Kohtla-Järve, Estonia and identify factors associated significantly with failure to progress at each stage of the HIV treatment cascade.DesignCross-sectional biobehavioral surveys of PWID with an analysis stratified by location-two Russian-speaking regions with similar HIV epidemic histories and current prevalence.SettingField-based surveys conducted in St Petersburg, RF and Kohtla-Järve, Estonia.ParticipantsWe recruited 452 HIV-positive PWID in St Petersburg (November 2012 to June 2013) and 370 HIV-positive PWID in Kohtla-Järve (June-August 2012) using respondent-driven sampling.MeasurementsParticipants were tested for antibodies to HIV, and administered a questionnaire focusing on participants' medical care histories. Engagement in care was categorized as a cascade of five transitional steps through six stages, ranging from HIV testing to current receipt of antiretroviral medications.FindingsProgress along the cascade was greater in Kohtla Järve (32.7% were receiving antiretroviral medications) than in St Petersburg (9.7%). In both locations, we found the steps with high failure rates were the transitions from being aware of one's HIV diagnosis to being in regular care and initiation of highly active antiretroviral therapy (HAART). Factors associated significantly with transition failure in both locations and across steps included high alcohol consumption, variables associated with drug choice and injection frequency and lack of basic medical insurance.ConclusionThe two steps in treatment cascade for HIV-positive PWID in St Petersburg, RF and Kohtla-Järve, Estonia requiring greatest improvement are retention in regular care and initiation of HAART. Both individual behavioral and structural factors are associated with failure to transition along the cascade.

Project description:The spatiotemporal patterns of spread of influenza A(H1N1)pdm09 viruses on a countrywide scale are unclear in many tropical/subtropical regions mainly because spatiotemporally representative sequence data are lacking. We isolated, sequenced, and analyzed 383 A(H1N1)pdm09 viral genomes from hospitalized patients between 2009 and 2018 from seven locations across Kenya. Using these genomes and contemporaneously sampled global sequences, we characterized the spread of the virus in Kenya over several seasons using phylodynamic methods. The transmission dynamics of A(H1N1)pdm09 virus in Kenya were characterized by (i) multiple virus introductions into Kenya over the study period, although only a few of those introductions instigated local seasonal epidemics that then established local transmission clusters, (ii) persistence of transmission clusters over several epidemic seasons across the country, (iii) seasonal fluctuations in effective reproduction number (Re) associated with lower number of infections and seasonal fluctuations in relative genetic diversity after an initial rapid increase during the early pandemic phase, which broadly corresponded to epidemic peaks in the northern and southern hemispheres, (iv) high virus genetic diversity with greater frequency of seasonal fluctuations in 2009-2011 and 2018 and low virus genetic diversity with relatively weaker seasonal fluctuations in 2012-2017, and (v) virus spread across Kenya. Considerable influenza virus diversity circulated within Kenya, including persistent viral lineages that were unique to the country, which may have been capable of dissemination to other continents through a globally migrating virus population. Further knowledge of the viral lineages that circulate within understudied low-to-middle-income tropical and subtropical regions is required to understand the full diversity and global ecology of influenza viruses in humans and to inform vaccination strategies within these regions.

Dataset Information

Rapid spread of influenza A(H1N1)pdm09 viruses with a new set of specific mutations in the internal genes in the beginning of 2015/2016 epidemic season in Moscow and Saint Petersburg (Russian Federation).

Publications

Rapid spread of influenza A(H1N1)pdm09 viruses with a new set of specific mutations in the internal genes in the beginning of 2015/2016 epidemic season in Moscow and Saint Petersburg (Russian Federation).

Similar Datasets

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