Influenza A virus (IAV) is generally associated with the seasonal malady that causes brief respiratory illness during the winter months, known simply as "the flu." Most otherwise healthy individuals will suffer from mild fever, congestion, headaches and myalgia that are resolved within 5-7 days of onset. However, there are nearly 500,000 influenza-related deaths that occur world-wide every year. Many of these casualties and patients hospitalized with influenza also test positive for bacterial pneumonia, the most common agent being Streptococcus pneumoniae. Although all individuals are subject to this viral:bacterial synergistic disease, the young, elderly, and immunocompromised are the most susceptible. Previous studies have shown that viral infection creates a prolonged hyper-responsive pro-inflammatory state in the lungs, which increases susceptibility to secondary bacterial infection. Lethality is due to detrimental pulmonary damage from a dysregulated host inflammatory response, known as the "cytokine storm." However, the nature of dual infection has not been well-studied in the elderly demographic. Therefore, we aim to better define this disease synergy in an aged mouse model and explore potential therapeutic alternatives that could be beneficial for the aged and other vulnerable populations. Sphingolipid modulation has emerged as a potential target to ameliorate the excessive inflammation (cytokine storm) elicited by highly pathogenic influenza. There is particular emphasis on sphingosine 1-phosphate (S1P) signaling, as well as control of intracellular S1P levels via sphingosine kinases (SK). Sphingolipids are involved in a multitude of cellular processes, and are tightly regulated by their metabolizing enzymes. We hypothesize that manipulation of sphingolipid signaling and alteration of the internal sphingolipid milieu will diminish the inflammatory response elicited by IAV infection. Using fluorescence-activated cell sorting (FACS), real-time PCR and cytometric bead array (CBA) analysis, we evaluated the immunomodulatory effects of systemic sphingosine analog treatment within the lung microenvironment under homeostatic and influenza-infected conditions. FTY720 treatment caused transient, but significant lymphopenia, influx of neutrophils and efflux of macrophages in the lungs, which was enhanced during a mild influenza infectionGene expression in the lungs was generally unaltered, but protein levels showed increases in specific influenza-induced cytokines, suggesting these treatments may have post-transcriptional effects on cytokine expression. To evaluate sphingolipid modulation in specific pulmonary cell types, we next observed the effects of these compounds and sphingosine kinase (SK) inhibitors in epithelial and alveolar macrophage-like cell lines. SK inhibitors and Enigmol demonstrated anti-viral effects in A549 cells, decreasing viral loads by up to 1.5 logs. Real-time PCR and CBA analysis further demonstrated that these effects were associated with alterations in key cytokine expression, including CCL2, CCL5, CXCL10, IL-6, and IL-8. Collectively, these findings indicate that therapeutic sphingolipid modulation has the potential for creating a protective microenvironment in the lungs that could alleviate or even prevent viral:bacterial synergistic disease. / Master of Science

Der Eintritt von Influenza A Viren in Wirtszellen erfolgt anhand des Hämagglutinin (HA) Proteins. Neueste Entwicklungen zielen darauf ab, die fusionsinduzierende Konformations-änderung des HA und damit die Freisetzung des viralen Genoms in die Wirtszelle zu inhibieren. Der Fusionsprozess ist pH-abhängig da nur bei einem niedrigen pH-Wert (~5.0-6.0) die Protonierung bestimmter Reste innerhalb des HA eine Konformationsänderung, und somit die Membranfusion, auslöst. Die Identifizierung von konservierten, titrierbaren Resten und die Aufklärung der Strukturveränderungen im HA ermöglichen eine gezielte Entwicklung neuer antiviraler Medikamente. In dieser Arbeit wurden bestimmte Histidine im HA mittels umfassender experimenteller und theoretischer Methoden als potentielle pH-Sensoren untersucht. Dabei konnte das Histidin an Position 184 als wichtiger Schalter der pH-induzierten Konformationsänderung identifiziert werden. Außerdem bewirkte der Austausch des geladenen Rests an Position 216 in der Nähe des His184 eine Veränderung der pH-Abhängigkeit des H5 HA aufgrund der Beeinflussung des pKa-Werts des His184. Da die Mutation R216E im HA des hochpathogenen H5N1 Virus in allen Isolaten während der Vogelvirenseuche im Jahr 2003/04 detektiert wurde, deutet das Ergebnis daraufhin, dass diese Mutation zur Entstehung des hochvirulenten Vogelvirus und dessen Adaptierung an den Menschen beigetragen hat. In diesem Zusammenhang wurde auch der Einfluss der pH-Abhängigkeit des HA auf die Fusion und Infektiosität von Viren in lebenden Zellen getestet. Eine destabilisierende Mutation im HA eines rekombinanten WSN-H3 Virus reduzierte dessen Infektions- und Replikationseffizienz in MDCK-Zellen, was auf den endosomalen pH-Wert dieser Zellen zurückgeführt werden konnte. Die Messung der Virus-Endosom-Fusionskinetik in lebenden Zellen machte außerdem die Bedeutung der pH-Abhängigkeit des HA für den Zeitpunkt der Membranfusion und dessen Einfluss auf die Effizienz der Virusinfektion deutlich. / The entry of influenza A virus into host cells is established by the hemagglutinin (HA) protein. New antiviral strategies aim to inhibit the fusion inducing conformational change of HA and thereby liberation of the viral genome into the cell. This process is strictly pH dependent since the conformational change of HA initiating the fusion of membranes only occurs upon protonation of yet unknown residues within HA at low pH (~5.0-6.0). The identification of conserved titrable residues and better understanding of the sequential structural rearrangements within HA may facilitate the development of new broad-spectrum antivirals. In the present work His184 and His110 were characterized as potential pH sensors by a comprehensive mutational and computational analysis. The results suggest that His184, but not His110, is an important regulator of HA conformational change at low pH. Furthermore, an exchange of charge at position 216 in vicinity to His184 was shown to alter the pH dependence of conformational change and of fusion in correlation to the known pKa dependence of histidines on neighboring residues. The result advocates that the mutation R216E, which emerged in the highly pathogenic H5 HA in 2003-2004, contributed to an altered acid stability of H5 HA via its effect on His184 and thus to the adaptation of avian H5N1 viruses to the human host. Therefore, the role of an altered acid stability of HA for viral fusion and infectivity in living cells was assessed. Recombinant viruses containing a destabilizing mutation in the HA protein were found to have a reduced infectivity and replication efficiency in MDCK cells compared to the respective wild type. Studying virus-endosome fusion kinetics in these cells we could resolve a significant difference in the timing of fusion induction suggesting that the time-point of fusion is a critical determinant of viral infection efficiency which depends on the endosomal acidification as well as on the acid stability of HA.

Influenza A Viren besitzen ein segmentiertes, einzelsträngiges RNA-Genom, welches in Form viraler Ribonukleoprotein (vRNP)-Komplexe verpackt ist. Während das virale Genom im Zellkern repliziert wird, finden Assemblierung und Knospung reifer Viruspartikel an der apikalen Plasmamembran statt. Für die Virusbildung müssen die einzelnen viralen Komponenten hierher gebracht werden. Während intrinsische apikale Signale der viralen Transmembranproteine bekannt sind, sind der zielgerichtete Transport und der Einbau des viralen Genoms in neuentstehende Virionen noch wenig verstanden. In dieser Arbeit wurden potentielle Mechanismen des vRNP-Transportes untersucht, wie die Fähigkeit der vRNPs mit Lipidmembranen zu assoziieren und die intrinsische subzellulären Lokalisation des viralen Nukleoproteins (NP), eines Hauptbestandteils der vRNPs. Es konnte gezeigt werden, dass vRNPs nicht mit Lipidmembranen assoziieren, was mittels Flotation aufgereinigter vRNPs mit Liposomen unterschiedlicher Zusammensetzung untersucht wurde. Die Ergebnisse deuten jedoch darauf hin, dass das virale M1 in der Lage ist, Bindung von vRNPs an negativ-geladene Lipidmembranen zu vermitteln. Subzelluläre Lokalisation von NP wurde des Weiteren durch Expression fluoreszierender NP-Fusionsproteine und Fluoreszenzphotoaktivierung untersucht. Es konnte gezeigt werden, dass NP allein nicht mit zytoplasmatischen Strukturen assoziiert, stattdessen aber umfangreiche Interaktionen im Zellkern eingeht und mit hoher Affinität mit bestimmten Kerndomänen assoziiert, und zwar den Nukleoli sowie kleinen Kerndomänen, welche häufig in der Nähe von Cajal-Körperchen und PML-Körperchen zu finden waren. Schließlich wurde ein experimenteller Ansatz etabliert, welcher erlaubt, den Transport vRNP-ähnlicher Komplexe mittels Fluoreszenzdetektion aufzuzeichnen und Einzelpartikelverfolgungsanalysen durchzuführen. Unterschiedliche Phasen des vRNP-Transportes konnten beobachtet werden und ein 3-Phasen-Transportmodell wird skizziert. / Influenza A viruses have a segmented single-stranded RNA genome, which is packed in form of viral ribonucleoprotein (vRNP) complexes. While the viral genome is replicated and transcribed in the host cell nucleus, assembly and budding of mature virus particles take place at the apical plasma membrane. Efficient virus formation requires delivery of all viral components to this site. While intrinsic apical targeting signals of the viral transmembrane proteins have been identified, it still remains poorly understood how the viral genome is transported and targeted into progeny virus particles. In this study, potential targeting mechanisms were investigated like the ability of vRNPs to associate with lipid membranes and the intrinsic ability of the viral nucleoprotein (NP) – which is the major protein component of vRNPs – for subcellular targeting. It could be shown that vRNPs are not able to associate with model membranes in vitro, which was demonstrated by flotation of purified vRNPs with liposomes of different lipid compositions. Results indicated, however, that the matrix protein M1 can mediate binding of vRNPs to negatively charged lipid bilayers. Intrinsic subcellular targeting of NP was further investigated by expression of fluorescent NP fusion protein and fluorescence photoactivation, revealing that NP by itself does not target cytoplasmic structures. It was found to interact extensively with the nuclear compartment instead and to target specific nuclear domains with high affinity, in particular nucleoli and small interchromatin domains that frequently localized in close proximity to Cajal bodies and PML bodies. An experimental approach was finally established that allowed monitoring the transport of vRNP-like complexes in living infected cells by fluorescence detection. It was possible to perform single particle tracking and to describe different stages of vRNP transport between the nucleus and the plasma membrane. A model of three-stage transport is suggested.

學校停課在世界各國的流感大流行應對方案中常被列為一項社區緩疫措施，而這項措施亦在2009年H1N1流感大流行中被廣泛地使用。然而，這項緩疫措施經常被質疑是否恰當，原因是因為停課會對教育構成重大的影響，而且過往的流行病學硏究亦表示這項緩疫措施不一定有效。本論文硏究學校停課對2009年H1N1流感大流行在香港首5個月疫情中降低大流行流感傳播的效能。 / 在香港，在該大流行流感病毒於2009年4月在美國被發現後，香港政府實施了控疫措施(containment phase measures)，並開始對該流感大流行進行監測。為了判定大流行是否已在香港內蔓延，衛生防護中心設定了一個報告準則來讓本地醫生報告疑似大流行流感感染個案，並為每個懷疑個案作確診測試及為每個確診個案追溯感染源頭。當大流行流感在6月開始在香港內蔓延時，香港政府實施了緩疫措施(mitigation phase measures)。在緩疫措施底下，帶有流感病症的病人求診於指定流感診所和公共醫院急症室會被測試是否感染大流行流感，而停課措施亦在此時開始實行去減低大流行流感的傳播。停課措施一直維持至7月直至暑假開始，並經修改後於9月開學時繼續實行。在9月，鑑於已不再需要對流感大流行進行監測，對懷疑感染個案進行確診測試的政策止於該月下旬。確診個案中記錄了的病人資料，與及由學校停課和暑假所引起的學期變化，為這課題提供了一個理想硏究的機會。 / 在2009年的5月至9月，一共確診了27,687宗大流行流感個案。在確診個案中，所有個案都記錄了確診者的年歲和確診日期，而88%確診者提供了一個可定位的住宅地址。為了觀察學校停課的緩疫效果，本硏究定義了5個社會經濟年齡級別(socio-economic age classes) (當中包括有小學生和中學生)，並繪製了年齡級別與地域特定的疫情曲線(age-class-and-district-specific epidemic curves)。所有的疫情曲線在大流行流感在6月開始在香港蔓延後均穩步上升，而在屬於小學生和中學生的疫情曲線中能看到一個不尋常的上升出現在9月新學年開始時，意味著中小學生在學校的活動提升了大流行流感在他們之間的傳播。 / 先前，學校停課對減低2009年H1N1流感大流行在香港的傳播已被Wu et. al (2010a)進行了調查。透過使用一個具年齡結構的SIR模型(age-structured SIR model)來分析收集至8月27日的監測數據，該硏究表示流感大流行的傳播在暑假開始時減低了25%。在這研究中，我應用了Wu et. al (2010a)的方法來分析整個監測期間所收集的數據。在發現到該數學模型不能準確地擬合附加的監測數據後，我在該模型添加了兩個傳播特徵(當中包含兒童和成人之間的傳染在學校停課期間增加)去更準確地代表現實中的疫情。我的硏究顯示，學校停課雖然降低了兒童的感染率，但卻增加了成年人的感染率，令整體傳播在暑假開始時只減低了7.6%。這硏究結果表示，在將來的流感大流行中，封閉學校不大可能延遲流感大流行疫情至一個可令疫苗產生作用的程度，而且封閉學校可能會增加成人的感染率，從而有可能導致社會運作出現更混亂的情況。 / School closure is often included in national pandemic influenza response plans as a community mitigation measure and it was widely applied in Pandemic (H1N1) 2009. However, the appropriateness of this intervention is often questioned, as school closure causes major disruption to the education system and past epidemiological studies reveal this intervention is not necessarily effective. The present thesis evaluates the effect of school closure in mitigating transmission of Pandemic (H1N1) 2009 in Hong Kong in the initial 5 months of the pandemic. / In Hong Kong, following identification of the pandemic virus in US in April 2009, the government implemented containment phase measures and began surveillance on the pandemic. The Centre for Health Protection established a reporting criteria for doctors to report suspected cases of pandemic infection for laboratory confirmation, and the source of infection of confirmed cases was traced to determine if the pandemic was spreading locally. When local transmission of the pandemic began in June, the government began mitigation phase measures, in which patients with influenza-like- illness seeking treatment at designated flu clinics and public hospital emergency departments were tested for pandemic infection, and school closure was implemented for pandemic mitigation. The school closure policy lasted until summer holiday commenced in July, and was revised and continued in September when the new school season started. At the end of September, in view of pandemic surveillance was no longer useful, laboratory testing for suspected pandemic cases was halted. Patient demographic data collected from confirmed pandemic cases, together with temporal changes in school session induced by school closure and summer holiday, provided an ideal opportunity for investigation. / From May through September 2009, a total of 27,687 pandemic cases were confirmed, in which the age and confirmation date were recorded in all cases, and 88% provided a locatable residential address. To visualise the mitigative effect of school closure, 5 socio-economic age classes (which include primary and secondary school-aged children) were defined, and age-class-and-district-specific epidemic curves were constructed. All epidemic curves rose steadily after local transmission began in June, and an unusual upsurge in the epidemic curve of primary and secondary school-aged children is observed when schools resumed session in September, suggesting school session facilitated transmission amongst them. / Previously, the effect of school closure in mitigating Pandemic (H1N1) 2009 transmission in Hong Kong was investigated in Wu et al. (2010a). By analysing surveillance data collected as of 27 August with an age-structured susceptible- infectious-recovered (SIR) model, the study reported transmission was reduced by 25% when summer holiday commenced. In this study, I adapted the methodology in Wu et al. (2010a) to analyse data collected in the entire surveillance period. Upon observing the model fitted poorly to the additional data, I added 2 transmission features to the model (which include increased transmission between children and adults during school closure) to better represent the epidemic in reality. My analysis revealed that while school closure reduced incidence in children, it increased incidence in adults, leading to a reduction in overall transmission by only 7.6% when summer holiday started. The findings of this study suggest that school closure in a future influenza pandemic is unlikely to be able to delay the pandemic for vaccine to arrive in time, and that implementing this intervention may increase incidence in adults, which may lead to causing more disruption on the functioning of society. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Chau, Kwan Long. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2012. / Includes bibliographical references (leaves 148-154). / Abstracts also in Chinese. / Chapter Chapter 1 --- Introduction --- p.1 / Chapter 1.1 --- Influenza --- p.2 / Chapter 1.2 --- Public health response to pandemic influenza & School closure --- p.8 / Chapter 1.3 --- Pandemic (H1N1) 2009 --- p.13 / Chapter 1.4 --- Hong Kongs response to Pandemic (H1N1) 2009 --- p.17 / Chapter 1.5 --- Data and Research Objective --- p.24 / Chapter Chapter 2 --- Descriptive and Exploratory Analysis of Surveillance Data --- p.31 / Chapter 2.1 --- Introduction --- p.31 / Chapter 2.2 --- Methodology --- p.36 / Chapter 2.3 --- Results --- p.40 / Chapter 2.4 --- Discussion --- p.57 / Chapter Chapter 3 --- Evaluating the effect of School Closure by Modelling --- p.62 / Chapter 3.1 --- Introduction --- p.62 / Chapter 3.2 --- Methodology --- p.90 / Chapter 3.3 --- Results --- p.98 / Chapter 3.4 --- Discussion --- p.105 / Chapter Chapter 4 --- Discussion --- p.108 / Chapter 4.1 --- Study Findings --- p.108 / Chapter 4.2 --- Study Limitations --- p.109 / Chapter 4.3 --- Comments on using school closure in future influenza pandemics --- p.111 / Appendices --- p.116 / Bibliography --- p.148

This thesis explores the evolution of avian influenza A viruses (IAV), as well as host-pathogen interactions between these viruses and their main reservoir host, the Mallard (Anas platyrhynchos). IAV is a genetically diverse, multi-host virus and wild birds, particularly dabbling ducks, are the natural reservoir. At our study site, up to 30% of migratory Mallards are infected with IAV during an autumn season, and host a large number of virus subtypes. IAV diversity is driven by two main mechanisms: mutation, driving genetic drift; and reassortment following co-infection, resulting in genetic shift.   Reassortment is pervasive within an autumn season, both across multiple subtypes and within a single subtype. It is a key genetic feature in long-term maintenance of common subtypes, as it allows for independent lineage turn-over, generating novel genetic constellations. I hypothesize that the decoupling of successful constellations and generation of novel annual constellations enables viruses to escape herd immunity; these genetic changes must confer antigenic change for the process to be favourable. Indeed, in an experiment utilizing vaccines, circulating viruses escaped homosubtypic immunity, resulting in the proliferation of infections with the same subtype as the vaccine. While the host plays an important role in shaping IAV evolutionary genetics, one must consider that Mallards are infected with a multitude of other microorganisms. Here, Mallards were infected with IAV, gamma coronaviruses, and avian paramyxovirus type 1 simultaneously, and we found a putative synergistic interaction between IAV and gamma coronaviruses.   Mallards occupy the interface between humans, poultry, and wild birds, and are the reservoir of IAV diversity. New incursions of highly pathogenic H5 viruses to both Europe and North America reaffirms the role of wild birds, particularly waterfowl, in diffusion of viruses spatially. Using European low pathogenic viruses and Mallard model, this thesis contributes to aspects of epidemiology, ecology, and evolutionary dynamics of waterfowl viruses, particularly IAV

published_or_final_version / abstract / Microbiology / Master / Master of Philosophy

The influenza A virus non-structural (NS1) protein is multifunctional, and during virus-infection NS1 interacts with several factors in order to manipulate host-cell processes. This study reports that NS1 binds directly to p85β, a regulatory subunit of phosphoinositide 3-kinase (PI3K), but not to the related p85α. Expression of NS1 was sufficient to activate PI3K and cause the phosphorylation of a downstream mediator of PI3K signalling, Akt. However, in virus-infected MDCK cells, the kinetics of Akt phosphorylation did not correlate with NS1 expression, and suggested that negative regulation of this signalling pathway occurs subsequent to ~8h post-infection. Mapping studies showed that the NS1:p85β interaction is primarily mediated by the NS1 C-terminal domain and the p85β inter-SH2 (Src homology 2) domain. Additionally, the highly conserved tyrosine at residue 89 (Y89) of NS1 was found to be important for binding and activating PI3K in a phosphorylation-independent manner. The inter-SH2 domain of p85β is a coiled-coil structure that acts as a scaffold for the p110 catalytic subunit of PI3K. As NS1 does not displace p110 from the inter-SH2 domain, a model is proposed whereby NS1 forms an active heterotrimeric complex with PI3K, and disrupts the ability of p85β to control p110 function. Biological studies revealed that a mutant influenza A virus (Udorn/72) expressing NS1 with phenylalanine substituted for tyrosine-89 (Y89F) exhibited a small-plaque phenotype, and grew more slowly in MDCK cells than wild-type virus. Unexpectedly, another mutant influenza A virus strain (WSN/33) expressing NS1-Y89F was not attenuated in MDCK cells, yet appeared to be less pathogenic than wild-type in vivo. Overall, these data indicate a role for NS1-mediated PI3K activation in efficient influenza A virus replication. The potential application of this work to the design of novel anti-influenza drugs and vaccine production is discussed.

Introdução: Em 13 de Setembro de 2009, a OMS reportou que existiam mais de 296.471 casos confirmados laboratorialmente de infecção pelo p-H1N1 2009. Ainda assim muitas questões permanecem, incluindo o papel de regras de probabilidade clínica e escores de gravidade de pneumonia adquirida na comunidade nestes pacientes. Nós descrevemos as características clínicas e epidemiológicas de pacientes internados por pneumonia adquirida na comunidade com ou sem infecção pelo p-H1N1. Objetivos: Verificar a incidência e características clínicas da pneumonia adquirida na comunidade associada com infecção pelo p-H1N1 2009, comparado as pneumonias adquiridas na comunidade sem infecção pelo p-H1N1 2009 e a aplicação de regras de probabilidade clínica e escores de gravidade de pneumonia. Métodos: Estudo observacional prospectivo avaliando pacientes consecutivos hospitalizados por pneumonia adquirida na comunidade por mais de 24 horas no HC-FMUSP. A infecção pelo p-H1N1 foi confirmada utilizando ensaios realtime PCR (RT-PCR). Os dados coletados incluíam variáveis clínicas e laboratoriais e 3 escores de gravidade de pneumonia: PSI (Pneumonia Severity Index), CURB-65 e o SMART-COP. Resultados: De 12 de julho a 17 de agosto de 2009, um total de 118 pacientes com pneumonia foram hospitalizados e RT-PCR realizado em 105 pacientes, infecção pelo p-H1N1 foi identificada em 53 pacientes. Comparado com os 52 pacientes sem infecção pelo p-H1N1, o grupo p-H1N1 apresentou significativamente mais coriza [razão de chances (RC): 6,09;intervalo de confiança 95% (IC95%): 1,72-21,52) e infiltrado bilateral (RC: 11,08; IC95%: 3,48-35,2).Um modelo clínico baseado em nossos resultados, incluindo infiltrado bilateral, febre, coriza e idade menor que 65 anos, foi capaz de predizer infecção pelo p-H1N1 2009 com sensibilidade de 90,6% e acurácia de 82% e com uma área sobre a curva (AUC) de 0,82. Nós também verificamos que, em pacientes com infecção pelo p-H1N1 2009, apenas 9,52% com escore SMART-COP entre 0-2 foram admitidos em UTI ou evoluíram para óbito intra-hospitalar comparado a 36,84% dos pacientes com escore PSI 1-2 e 51% dos pacientes com escore CURB-65 de 0-1. O prognóstico da pneumonia foi similar nos grupos com ou sem infecção pelo p-H1N1 2009. Conclusões: A pneumonia associada com infecção pelo p-H1N1 2009 possui apresentação clínica diferente de pacientes sem infecção pelo p-H1N1, entretanto, possuem prognóstico similar. Escores tradicionais de gravidade de pneumonia como PSI e CURB-65 tiveram desempenho ruim em pacientes com infecção pelo p-H1N1 e o escore SMART-COP foi o melhor preditor de internação em UTI em pacientes com pneumonia e infecção pelo p-H1N1. / Introduction: As of September 13, 2009, the WHO had reported over 296.471 laboratory-confirmed cases of p-H1N1 2009. However many questions remain unanswered, including the role of clinical prediction rules and community-acquired pneumonia severity scores. We describe clinical and epidemiologic characteristics of patients hospitalized for pneumonia at our tertiary hospital with laboratory-confirmed and laboratory-excluded H1N1 infection. Objectives: Verify the incidence and clinical characteristics of community-acquired-pneumonia associated with p-H1N1 2009 infection compared with community-acquired pneumonia without p-H1N1 infection and the applicability of clinical prediction rules and pneumonia severity scores. Methods: We prospectively reviewed medical chart in daily basis to collect data on that patients. H1N1 infection was confirmed in specimens using a real-time reverse transcriptase-polymerase-chain-reaction (RT-PCR) assay. The data collected included clinical and laboratorial variables and three pneumonia severity scores: Pneumonia Severity Index, CURB-65 and the SMART-COP rule. Results: From 12 of July through August 17, 2009, a total of 118 cases of pneumonia were hospitalized, and RT-PCR was performed in 105, indentifying p-H1N1 infection in 53 patients. Compared with the 52 patients without p-H1N1 infection , the p-H1N1 group presented significantly more often with rhinorrhoea (OR 6,09 IC 95 1,72-21,52) and bilateral infiltrates ( OR 11,08 IC 95 3,48-35,2), a clinical model based on our results and using bilateral infiltrates, fever, rhinorrhoea and age less than 65 years was capable of predict p-H1N1 infection with 90,6% sensitivity, 82% accuracy and area under the ROC curve (AUC) being 0.82. We also find that in the patients with pneumonia and p-H1N1 infection, only 9.52% of those with SMART-COP score of 0-2 presented ICU admission/in-hospital mortality, compared with 36.84% of those with PSI score of 1-2 and 51% of those with CURB-65 score of 0-1. The prognosis of pneumonia was similar in the patients with and without p-H1N1 2009 infection. Conclusions: Pneumonia associated with p-H1N1 2009 has different clinical presentation than in pneumonia patients without p-H1N1 infection, but the prognosis is similar. Traditional pneumonia severity scores like PSI and CURB-65 performed poorly in patients with p-H1N1 infection and the SMART-COP rule was the best predictor of ICU admission in pneumonia patients with p-H1N1 infection.

<p>U radu je ispitana zastupljenost influenca A virusa, njihova antigenska i genetička svojstva i osetljivost na antivirotik oseltamivir.</p><p>Ispitivanje je sprovedeno u toku četiri uzastopne sezone, od 2010/2011 do 2013/2014 &nbsp;i obuhvatilo je 887 briseva nosa i grla pacijenata sa simptomima gripa, sa teritorije Južnobačkog okruga. Svi uzorci su&nbsp;testirani na prisustvo influenca A(H1N1)pdm09, A(H3N2), A(H1N1), A(H5) i A(H7) i influenca B virusa, real-time RT PCR testom. Pozitivni uzorci iz sezona 2012/2013 i 2013/2014, podvrgnuti su izolaciji na MDCK ćelijskim kulturama, a zatim je izvr&scaron;eno ispitivanje sposobnosti dobijenih izolata da aglutiniraju eritrocite koko&scaron;ke, čoveka i zamorca u reakciji virusne hemaglutinacije. Antigenska svojstva izolata sa hemaglutinacionim titrom &ge;40, ispitana su reakcijom inhibicije hemaglutinacije. Genetičkoj karakterizaciji, sekvenciranjem hemaglutinin i neuraminidaza gena, podvrgnuti su reprezentativni izolati iz sezona 2012/2013 i 2013/2014. Za ispitivanje osetljivosti odabranih izolata virusa na oseltamivir upotrebljen je hemiluminiscentni test inhibicije aktivnosti neuraminidaze.</p><p>Ukupno 46,3% (411/887) uzoraka bilo je influenca pozitivno, od čega je 73% (300/411) bilo influenca A pozitivno, a 27% (111/411)influenca B pozitivno (p&lt;0,0001). &nbsp;Influenca A(H1N1)pdm09 podtip je detektovan u 48% (144/300), a A(H3N2) podtip u&nbsp;52% (156/300) influenca Apozitivnih uzoraka. Najveći procenat influencaA pozitivnih zabeležen je u uzrastnoj grupi 5-14 godina (48,2%, 77/160) i kod pacijenata sa lak&scaron;im kliničkim manifestacijama gripa (43,7%, 153/350).</p><p>Influenca A(H1N1)pdm09 podtip preovladavao je u uzrastnoj grupi 15-29 godina (66%, 31/47, p=0,0400) i 30-64 godina (55,9%,71/127, p=0,0215), kao i kod pacijenata sa te&scaron;kom akutnom respiratornom bole&scaron;ću (63,5%, 80/126, p&lt;0,0001), fatalnih slučajeva (100%,9/9, p=0,0039) i pacijenata sa hroničnim bolestima i stanjima (68,8%, 84/122, p&lt;0,0001).&nbsp;</p><p>Influenca A(H3N2) podtip dominirao je kod dece uzrasta do 4 godine (72,2%,13/18, p=0,0381) i 5-14 godina (75,3%, 58/77, p&lt;0,0001), kod pacijenata sa lak&scaron;im oblikom bolesti (69,3%,106/153, p&lt;0,0001) i bez hroničnih bolesti ili stanja (66,3%, 118/178,&nbsp;p&lt;0,0001).</p><p>Najznačajniji predikcioni faktori komplikacija influence bili su: prisustvo hroničnih bolesti ili stanja i uzrast &ge;15 godina. Prisustvo hroničnih bolesti ili stanja nosilo je 34 puta, a uzrast &ge;15 godina 10 puta veći rizik od nastanka te&scaron;kih oblika bolesti.</p><p>Izolacija influenca virusa na MDCK ćelijskim kulturama, bila je uspe&scaron;na u 34,3% (70/204) slučajeva, pri čemu je u grupi uzoraka sa real-time RT-PCR Ct vrednostima &lt;30 ona iznosila 80,5% (62/77), kod uzoraka sa Ct vrednostima 30-34 svega 8,7% (8/92), a izolacija iz uzoraka sa Ct vrednostima &gt;34 nije bila moguća. U reakciji hemaglutinacije, najbolji rezultati su postignuti sa eritrocitima zamorca, koje je u titru &ge;40 aglutiniralo 56% (14/25) A(H1N1)pdm09 virusa i 62,5% (15/24) A(H3N2) virusa. Sa humanim eritrocitima dobar titar dalo je 16% (4/25) influenca A(H1N1)pdm09 i 8,3% (2/24) A(H3N2) virusa, a sa koko&scaron;ijim eritrocitima 8% (2/25) A(H1N1)pdm09 virusa i nijedan virus A(H3N2) podtipa.</p><p>Rezultati antigenske karakterizacije pokazali su da je svih 23 influenca virusa A(H1N1)pdm09 podtipa, iz sezona 2012/2013 i 2013/2014, antigenski bilo slično referentnom, vakcinalnom virusu A/California/7/2009. Nasuprot tome, samo 1 od 7 ispitanih A(H3N2) virusa iz sezone 2012/2013, antigenski je bio sličan vakcinalnom virusu A/Victoria/361/2011, a samo 2 od 20 iz sezone 2013/2014 antigenski je bilo slično vakcinalnom A/Texas /50/2012 virusu.</p><p>Filogenetska analiza hemaglutinin gena influenca A(H1N1)pdm09 virusa iz sezone 2012/2013, pokazala je da su u na&scaron;oj sredini, bili prisutni virusi iz dve različite genogrupe, 6C i 7, dok su naredne sezone svi analizirani virusi pripadali genogrupi 6B. Virusi iz na&scaron;e sredine bili su filogenetski srodni A(H1N1)pdm09 virusima iz drugih evropskih zemalja. Svi ispitani A(H3N2) virusi iz sezone 2012/2013 i2013/2014, pripadali su genetičkoj grupi&nbsp; 3C.3.Filogenetski su bili srodni sa virusima iz drugih gografskih regiona Evrope.</p><p>Svih 20 izolata influenca A(H1N1)pdm09 podtipa i 23 A(H3N2) podtipa pokazali su normalnu inhibiciju aktivnosti neuraminidaze pod dejstvom oseltamivira.ekvenciranje neuraminidaza gena jednog A(H3N2) virusa, koji je imao 8 puta redukovanu inhibiciju aktivnosti neuraminidaze oseltamivirom, ukazalo jena prisustvo retke mutacije Q391H, povezane sa rezistencijom na inhibitore neuraminidaze.</p><p>Rezultati ovog rada ukazali su na značaj influenca A virusa kao etiolo&scaron;kih uzročnika akutnih respiratornih obolenja u na&scaron;oj sredini, naročito za osobe sa hroničnim bolestima koje su pod povećanim rizikom od razvoja te&scaron;kih oblika gripa. U ovom istraživanju stečena su i saznanja koja imaju praktičnu primenu u postupku antigenske karakterizacije influenca A virusa, koja je jedna od ključnih faza u procesu pripreme vakcine protiv gripa. Značajna antigenska razlika A(H3N2) virusa koji su cirkulisali u sezonama 2012/2013 i 2013/2014 u odnosu na viruse koji su bili u sastavu vakcina u datim sezonama, ukazala je na neophodnost unapređenja proizvodnje vakcine protiv gripa. Dobijeni su i prvipodaci orezistenciji na antivirotik oseltamivir, kao i o filogenetskim odnosima i genetičkim grupama virusa koji su&nbsp; cirkulisali u na&scaron;oj sredini.</p> / <p>In this study we investigated the representation, antigenic and genetic properties, and sensitivity to antiviral drug oseltamivir of influenza A viruses. The study was conducted&nbsp; during 4 consecutiveseasons 2010/2011 - 2013/2014, and included 887 nasal and throat swabs taken from patients with influenza-like symptoms from South&nbsp; Backa district. All samples were tested for influenza A(H1N1)pdm09, A(H3N2), A(H1N1), A(H5), A(H7) and influenza B viruses, by real-time RT-PCR. Isolation on MDCK cell culture was performed with positive samples from seasons 2012/2013 and 2013/2014, and virus isolates were tested for ability&nbsp; to agglutinate guinea pig, chicken and human red blood cells in reaction of virus hemagglutination. Antigenic properties of isolates with hemagglutination titre &ge;40, were investigated using reaction&nbsp; of hemagglutination inhibition. Genetic characterization was performed by sequencing of neuraminidase and hemagglutination genes of representative isolates from seasons 2012/2013 and 2013/2014. Testing for sensitivity to oseltamivir was done with chemiluminescent neuraminidase inhibition assay.</p><p>Total of 46,3% (411/887) of samples were influenza positive, out of which 73% (300/411) were influenza A positive and 27% (111/4111, p&lt;0,0001) were influenza&nbsp; B positive. Influenza A(H1N1)pdm09 subtype was detected in 48% (144/300), and A(H3N2) subtype in 52% (156/300) of influenza A positive samples. The highest proportion of influenza A positive samples wasfound in age group 5-14&nbsp; years (48,2%,&nbsp; 77/160) and among patients with uncomplicated influenza (43,7%, 153/350).</p><p>Influenza A(H1N1)pdm09 subtype predominated in age group 15-29 years (66%, 31/47, p=0,0400) and 30-64 years (55,9%,71/127, p=0,0215), in patients with severe acute respiratory illness (63,5%, 80/126, p&lt;0,0001), in fatal cases (100%, 9/9, p=0,0039), and among patients with underlying chronic diseases and conditions (68,8%,84/122, p&lt;0,0001).</p><p>Influenza A(H3N2) subtype predominated in age group &le;4 years (72,2%, 13/18, p=0,0381) and 5-14 years (75,3%,58/77, p&lt;0,0001), in patients with mild form of influenza (69,3%,106/153, p&lt;0,0001), and in group of patients without chronic diseases and conditions (66,3%,60/478, p&lt;0,0001).</p><p>The most significant risk factors for severe influenza were: the presence of underlying diseases and conditions and age &ge;15 years. Patients with chronic illnesses and conditions had 34 times higher and patients &ge;15 years of age 10 times higher risk from severe influenza.</p><p>Isolation rate of influenza A viruses in MDCK cell cultures was 34,3% (70/204). For samples with real time RT-PCR Ct values &lt;30 isolation rate was 80,5% (62/77), for samples with Ct values 30-34 it was 8,7% (8/92), while isolation of viruses from samples with Ct values &gt;34 was not successful. In the reaction of virus hemagglutination, the best results were achieved with guinea pig red blood cells which agglutinated in titre &ge;40, 56% (14/25) of influenza A(H1N1)pdm09 viruses and&nbsp; 62,5% (15/24) of A(H3N2) viruses. With human erythrocytes, good titre gave 16% (4/25) of influenza A(H1N1)pdm09 and 8,3% (2/24)of A(H3N2) viruses and with chicken erythrocytes 8% (2/25) A(H1N1)pdm09 viruses and none of the A(H3N2) viruses.</p><p>Results of the antigenic characterization of 23 influenza A(H1N1)pdm09 viruses, showed that they were antigenically similarto referent, vaccine virus A/California/7/2009. On the contrary, only 1 out of 7 influenza A(H3N2) viruses from season 2012/2013,was antigenically similar to A/Victoria/361/2011 vaccine virus, and only 2 out of 20 from season 2013/2014 were antigenically similar to A/Texas/50/2012&nbsp; vaccine virus.</p><p>Filogenetic analysis of hemagglutinin genes indicated co-circulation of 2 distinct genetic groups, 6C and 7, of A(H1N1)pdm09 viruses during the season 2012/2013, while during the season 2013/2014 all tested viruses were from genetic group 6B. Influenza A(H1N1)pdm09 viruses from our region, were closely related to viruses from other European countries. All influenza A(H3N2) viruses from season 2012/2013 and 2013/2014 belonged to genetic clade 3C.3 and were closely related to viruses from different European countries.</p><p>Total of 20 A(H1N1)pdm09 isolates and 23 A(H3N2) isolates were tested for sensitivity to oseltamivir, and all of them showed normal inhibition of neuraminidase activity with oseltamivir. Sequencing of&nbsp; neuraminidase gene of one A(H3N2) virus with 8-fold reduced inhibition by oseltamivir, revealed rare mutation Q391H associated with antiviral resistance.</p><p>Results of this study indicate the significance of influenza A viruses as etiological factors of acute respiratory diseases in our area, especially for persons with chronic medical conditions who are at higher risk for severe influenza. Data gathered during&nbsp;the process of virus isolation and investigation of hemagglutination abilities of&nbsp; isolated viruses, have practical application in antigenic testing of influenza A viruses which is one of the key points of process of anti-flu vaccine production. Significant &nbsp;antigenic difference between influenza A(H3N2) viruses from seasons 2012/2013 and&nbsp; 2013/2014 and vaccine viruses, emphasis the importance of vaccine production improvement. During this study, the first data about antiviral resistance, filogenetic relationships and genetic groups of influenza viruses from our region, were obtained.</p>

Objetivos: Avaliar a imunogenicidade e segurança da vacina anti-influenza A/H1N1 2009 em pacientes com dermatomiosite juvenil (DMJ) comparados com controles saudáveis e a possível associação entre taxas de soroconversão com dados demográficos, enzimas musculares, escores da DMJ, linfopenia e tratamento nos pacientes com DMJ atendidos em dois serviços de Reumatologia Pediátrica. Métodos: Trinta pacientes com DMJ entre 9 e 21 anos e 81 controles saudáveis foram imunizados com a vacina anti-influenza A H1N1/2009 sem adjuvante. Todos foram avaliados pré e 21 dias após a vacinação. As taxas de soroproteção e soroconversão, a média geométrica dos títulos de anticorpos (MGT) e o fator de aumento (FA) na MGT foram calculados. Foram analisados os eventos adversos (EAs), assim como: enzimas musculares, instrumentos de força muscular, presença de linfopenia e tratamento atual da DMJ. Resultados: Pacientes com DMJ e controles foram comparáveis em relação à mediana de idade atual [15,5 (9- 21) vs. 15 (9-21) anos, p=0,511] e frequência do sexo feminino (63% vs. 51%, p=0,286). A mediana do tempo de duração da DMJ foi de 5,5 (2-17) anos. Após a imunização, as taxas de soroconversão foram significantemente menores em pacientes com DMJ comparados com controles saudáveis (86,7% vs. 97,5%, p=0,044), enquanto soroproteção (p=0,121), MGT (p=0,992) e FA na MGT (p=0,827) foram semelhantes entre os grupos. As avaliações clínicas e laboratoriais na DMJ mostraram que as medianas dos escores de avaliação da atividade doença e enzimas musculares permaneceram estáveis no período do estudo (p > 0,05). Uma alta frequência de curso clínico crônico da doença foi observada em pacientes que não apresentaram soroconversão em comparação aos pacientes soroconvertidos (100% vs. 27%, p=0,012). Em relação à influência do tratamento, baixas taxas de soroconversão foram observadas em pacientes em uso de metotrexate (100% vs. 38%, p=0,036) e associação de prednisona, metotrexate e ciclosporina (50% vs. 4%, p=0,039). EAs locais e/ou sistêmicos foram leves e similares entre pacientes e controles (p > 0,05). Conclusão: Este foi o primeiro estudo que avaliou a vacina anti-influenza A H1N1/2009 na DMJ, identificando que o curso crônico da doença e a terapia imunossupressora são fatores que podem prejudicar a resposta humoral nos pacientes. Uma única dose da vacina foi soroprotetora nos pacientes avaliados, sem evidências de efeitos deletérios na atividade da doença / Objectives: To assess the immunogenicity and safety of influenza A H1N1/2009 vaccine in juvenile dermatomyositis (JDM) patients compared to age-matched controls and the possible association of seroconversion rates whith demographic, muscle enzymes, JDM scores, lymphopenia and treatment in JDM patients routinely followed at two Pediatric Rheumatology Units. Methods: Thirty JDM patients between 9 and 21 years old and 81 healthy age-matched controls were vaccinated with non-adjuvanted influenza A H1N1/2009 vaccine. All participants were evaluated pre- and 21 days postvaccination. Seroconversion and seroprotection rates, geometric mean titres (GMT) and factor increase (FI) in GMT were assessed. Adverse events, as well as muscle enzymes, JDM scores, lymphopenia and current treatment in JDM were also evaluated. Results: JDM patients and healthy controls had similar median of current age [15.5 (9-21) vs. 15 (9-21) years, p=0.511] and frequencies of female gender (63% vs. 51%, p=0.286). The median disease duration of JDM was 5.5 (2-17) years. After immunization, seroconversion rate was significantly lower in JDM patients compared to age-matched controls (86.7 vs. 97.5%, p=0.044), whereas seroprotection (p=0.121), GMT (p=0.992) and FI in GMT (p=0.827) were similar in both groups. Clinical and laboratorial evaluations revealed that JDM scores and muscle enzymes remained stable throughout the study (p > 0.05). A higher frequency of chronic course was observed in non-seroconvert compared to seroconverted (100% vs. 27%, p=0.012). Regarding treatment, a lower rate of seroconversion was observed in patients treated with methotrexate (100% vs. 38%, p=0.036) and in those with a combination of prednisone, methotrexate and cyclosporine (50% vs. 4%, p=0.039). Local and systemic adverse events were mild and similar in JDM patients and controls (p > 0.05). Conclusions: This was the first study that evaluated the influenza A H1N1/2009 vaccine in JDM, identified that chronic course and immunosuppressive therapy were factors hampering immune response in patients. A single dose of non-adjuvanted influenza A/H1N1 2009 vaccine was seroprotective in assessed patients with no evident deleterious effect in disease itself