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High level HIV-1 DNA concentrations in brain tissues differentiate patients with post-HAART AIDS dementia complex or cardiovascular disease from those with AIDS

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Science China(Life Sciences) 2009年第7期52卷 651-656页

作者： GALLIGAN Derek C. LAMERS Susanna L. YU Stephanie SHAGRUN Lamia salemi marco MCGRATH Michael S. Department of Laboratory Medicine Positive Health Program University of CaliforniaSan Francisco California 94110 USA Gene Johnson Inc. St.Augustine Florida32080USA Pathologica Inc. Burlingame California 94010 USA Department of Pathology Immunology and Laboratory Medicine University of FloridaGainesville Florida 32610 USA

Highly active antiretroviral treatment(HAART) has had a significant impact on survival of individuals with acquired immunodeficiency syndrome(AIDS);however,with the longer life-span of patients with AIDS,there is increasing prevalence of AIDS dementia complex(ADC) and other non-AIDS-defining illness,and cardiovascular diseases(CVD) are also *** influence of these varied disease processes on HIV-1 DNA concentration in brain tissues has not been thoroughly assessed in the post-HAART *** purpose of the current study is to clarify the impacts of ADC and other complications of HIV disease on the viral load in the brains in AIDS patients with *** examined autopsy specimens from the brains of thirteen patients who died from complications of AIDS with quantitative polymerase chain reaction(QPCR).All but one patient had received HAART prior to death since *** patients died with severe CVD,multiple cerebrovascular atherosclerosis(CVA) throughout the brain and five patients died with *** patients had no ADC/CVA.A QPCR was used to measure the presence of HIV-1 DNA in six brain tissues(meninges,frontal grey matter,frontal white matter,temporal subcortex,cerebellum and basal ganglia).In the post-HARRT era,for non-ADC/CVA patients,HIV-1 DNA concentration in brain tissues was statistically higher than that in patients with *** a new finding,two patients who suffered from severe CVD,especially CVA,also had high concentrations of HIV-1 in brain compartments not showing ADC related *** our knowledge,this is the first report of a relationship between the CVA and HIV-1 viral burden in *** current observations suggest that HAART-resistant HIV reservoirs may survive within ADC lesions of the brain as well as the macrophage rich atherosclerosis,which needs to be confirmed by more AIDS cases with CVA.

关键词： HIV-1 AIDS dementia complex quantitative PCR DNA cardiovascular disease cerebrovascular atherosclerosis

Phylogeny of Murray Valley encephalitis virus in Australia and Papua New Guinea

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Asian Pacific Journal of Tropical Medicine 2016年第4期9卷 376-380页

作者： Eleonora Cella Ivan Gabrielli Gianguglielmo Zehender Marta Giovanetti Alessandra Lo Presti Alessia Lai Giordano Dicuonzo Silvia Angeletti marco salemi Massimo Ciccozzi Department of Infectious Parasitic and Immunomediated DiseasesNational Institute of Health Department of Public Health and Infectious Diseases.Sapienza University of Rome University of Rome 'La Sapienza' L.Sacco Department of Biomedical and Clinical Sciences University of Milan University of Rome 'Tor Vergata' Clinical Pathology and Microbiology Laboratory University Hospital Campus Bio-Medico of Rome Department of Pathology and Laboratory Medicine.University of Florida University Hospital Campus Bio-Medico

Objective:To study the genetic diversity of Murray Valley encephalitis virus(MVEV) in Australia and Papua New ***:MVEV envelope gene sequences were aligned using Clustal X and manual editing was performed with *** v.3.7 was used to select the simplest evolutionary model that adequately fitted the sequence *** likelihood analysis was performed using *** phylogenetic signal of the dataset wa.s investigated by the likelihood mapping *** Bayesian phylogenetic tree was built using ***:The phylogenetic trees showed two main *** clade Ⅰincluding eight strains isolated from West *** clade Ⅱ was characterized by at least four epidemic entries,three of which localized in Northern West Australia and one in Papua New *** estimated mean evolutionary rate value of the MVEV envelope gene wa.s0.407 × 10^(-3) substitution/site/year(95%HPD:0.623 × 10~4-0.780× 10^(-3)).Population dynamics defines a relative constant population until the year *** a reduction occurred,probably due to a ***:This study has been useful in supporting the probable connection between climate changes and viral evolution also by the vector point of view:multidisciplinary monitoring studies are important to prevent new viral epidemics inside and outside new endemic areas.

关键词： Murray Valley encephalitis virus Phylogeny Evolution

Mayaro virus infection, the next epidemic wave after Zika?Evolutionary and structural analysis

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Asian Pacific Journal of Tropical Medicine 2018年第3期11卷 194-201页

作者： Eleonora Cella Marta Giovanetti Teresa Milano Marta Fogolari Francesco Garilli Ivailo Alexiev Riccardo Bazzardi marco salemi Luiz Carlos Junior Alcantara Silvia Angeletti Stefano Pascarella Massimo Ciccozzi Public Health and Infectious Diseases Sapienza University Unit of Clinical Laboratory Science University Campus Bio-Medico of Rome Fundao Oswaldo Cruz University of Rome"Tor Vergata" Dipartimento di Scienze Biochimiche"A.Rossi Fanelli" Universita La Sapienza Department of Medicine University Campus Bio-Medico of Rome National Reference Laboratory of HIV National Center of Infectious and Parasitic Diseases Department of Food Hygiene Experimental Zooprophylactic Institute of Sardinia Emerging Pathogens Institute Unirersity of Florida

Objective: To evaluate the evolution of the pathogen Mayaro virus, causing Mayaro fever(a mosquito-borne disease) and to perform selective pressure analysis and homology ***: Nine different datasets were built, one for each protein(from protein C to non-structural protein 4) and the last one for the complete genome. Selective pressure and homology modelling analyses were applied. Results: Two main clades(A and B) were pointed in the maximum likelihood tree. The clade A included five Brazilian sequences sampled from 1955 to 2015. The Brazilian sequence sampled in 2014 significantly clustered with the Haitian sequence sampled in 2015. The clade B included the remaining 27 sequences sampled in the Central and Southern America from 1957 to 2013. Selective pressure analysis revealed several sites under episodic diversifying selection in envelope surface glycoprotein El, non-structural protein 1 and nonstructural protein 3 with a posterior probability P≤0.01. Homology modelling showed different sites modified by selective pressure and some protein-protein interaction sites at high interaction propensity. Conclusion: Maximum likelihood analysis confirmed the Mayaro virus previous circulation in Haiti and the successful spread to the Caribbean and USA. Selective pressure analysis revealed a strong presence of negatively selected sites, suggesting a probable purging of deleterious polymorphisms in functional genes. Homology model showed the position 31, under selective pressure, located in the edge of the ADP-ribose binding site predicting to possess a high potential of protein-protein interaction and suggesting the possible chance for a protective vaccine,thus preventing Mayaro virus urbanization as with Chikungunya virus.

关键词： Mayaro virus Proteins Evolutionary analysis

脑组织中高浓度的HIV-1DNA水平将HAART后AIDS痴呆综合征或心血管病的AIDS人与普通AIDS人区别开

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中国科学（C辑） 2009年第7期39卷 662-668页

作者：赵丽 Derek C.GALLIGAN Susanna L.LAMERS YU Stephanie Lamia SHAGRUN marco salemi Michael S.MCGRATH 山东大学公共卫生学院病毒学检验室 Department of Laboratory Medicine Positive Health ProgramUniversity of CaliforniaSan FranciscoCalifornia94110USA Gene Johnson Inc. St.AugustineFlorida32080USA Pathologica Inc. BurlingameCalifornia94010USA Department of Pathology Immunology and Laboratory MedicineUniversity of FloridaGainesvilleFlorida32610USA

高效抗逆转录病毒治疗(highly active antiretroviral treatment,HAART)在延长获得性免疫缺陷综合征(acquired immunodeficiency syndrome,AIDS)患者的生存方面具有重要作用,然而随着HIV感染者寿命的延长,AIDS痴呆综合征(AIDS dementiacomplex,ADC),其他非AIDS相关疾病,心血管病(cardiovascular disease,CVD)也比较常见.这些各种疾病对脑组织中HIV-1DNA的影响在HAART后还未完全搞清楚.本文的研究目的是澄清HAART后ADC以及其他HIV感染的并发症对AIDS病人脑组织中病毒载量的影响.本实验用定量PCR研究了13例AIDS病人脑组织尸检标本,这些病人死于AIDS并发症,除1例病人外,其他12例病人均从1995年开始接受HAART治疗,直到死亡.2例死于严重的CVD,脑组织中广泛的动脉粥样硬化(cerebrovascular atherosclerosis,CVA).5例AIDS病人死于ADC,6例AIDS人既无ADC,也无CVA.用定量PCR检测了病人脑组织6个部位(脑膜、前叶灰质、前叶白质、颞叶皮层下部、小脑和基底节)HIV-1DNA的含量并对其进行了比较.HAART后,与非ADC/CVA的AIDS病人相比,ADC的AIDS病人脑组织中HIV-1DNA含量明显升高.一个新的发现是,2例患有CVD,特别是CVA的病人,脑组织中,也同样检出高浓度的HIV-1DNA,这些病人并没有ADC的症状,这是首次报道CVA与脑组织中HIV-1病毒载量有关.研究表明,HAATR抗性的HIV病毒储存库可能存在于ACD患者脑组织的损伤部位及富含巨噬细胞的动脉粥样硬化斑块中,仍需要大量的CVA病例研究来证实后者.

关键词：人类免疫缺陷病毒-1型 AIDS痴呆综合征定量PCR DNA 心血管病脑血管动脉粥样硬化

The global spread of Middle East respiratory syndrome:an analysis fusing traditional epidemiological tracing and molecular phylodynamics

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Global Health Research and Policy 2016年第1期1卷 116-129页

作者： Jae Min Eleonora Cella Massimo Ciccozzi Antonello Pelosi marco salemi Mattia Prosperi Department of Epidemiology College of Public Health&Health Professions and College of MedicineUniversity of Florida2004 Mowry RdGainesvilleFL 32610-0231USA Department of Infectious Parasitic and Immune-mediated DiseasesNational Institute of HealthViale Regina Elena29900161 RomeItaly Department of Public Health and Infectious Diseases Sapienza University of RomePiazzale Aldo Moro500185 RomeItaly Department of Pathology Immunology and Laboratory MedicineEmerging Pathogens InstituteUniversity of Florida2055 Mowry RdGainesvilleFL 32611USA Department of Clinical Pathology and Microbiology Laboratory University of Biomedical CampusVia Alvaro del Portillo21RomeItaly

Background: Since its discovery in 2012, over 1700 confirmed cases of Middle East Respiratory Syndrome (MERS)have been documented worldwide and more than a third of those cases have died. While the greatest number ofcases has occurred in Saudi Arabia, the recent export of MERS-coronavirus (MERS-CoV) to Republic of Korea showedthat a pandemic is a possibility that cannot be ignored. Due to the deficit of knowledge in transmissionmethodology, targeted treatment and possible vaccines, understanding this virus should be a priority. Our aim wasto combine epidemiological data from literature with genetic information from viruses sequenced around theworld to present a phylodynamic picture of MERS spread molecular level to global ***: We performed a qualitative meta-analysis of all laboratory confirmed cases worldwide to date based onliterature, with emphasis on international transmission and healthcare associated infections. In parallel, we usedpublicly available MERS-CoV genomes from GenBank to create a phylogeographic tree, detailing geospatial timelineof viral ***: Several healthcare associated outbreaks starting with the retrospectively identified hospital outbreak inJordan to the most recent outbreak in Riyadh, Saudi Arabia have occurred. MERS has also crossed many oceans,entering multiple nations in eight waves between 2012 and 2015. In this paper, the spatiotemporal history of MERScases, as documented epidemiologically, was examined by Bayesian phylogenetic analysis. Distribution ofsequences into geographic clusters and interleaving of MERS-CoV sequences from camels among those isolatedfrom humans indicated that multiple zoonotic introductions occurred in endemic nations. We also report asummary of basic reproduction numbers for MERS-CoV in humans and ***: Together, these analyses can help us identify factors associated with viral evolution and spread as wellas establish efficacy of infection control measures. The results are es

关键词： Middle East Respiratory Syndrome Coronavirus Epidemiology Phylodynamics

Phylodynamic applications in 21^(st)century global infectious disease research

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Global Health Research and Policy 2017年第1期2卷 244-253页

作者： Brittany D Rife Carla Mavian Xinguang Chen Massimo Ciccozzi marco salemi Jae Min Mattia CF Prosperi Emerging Pathogens Institute and Department of Pathology Immunology and Laboratory MedicineUniversity of FloridaGainesvilleFLUSA Department of Epidemiology University of FloridaGainesvilleFLUSA Department of Infectious Parasitic and Immune-Mediated DiseasesIstituto Superiore di SanitàRomeItaly Unit of Clinical Pathology and Microbiology University Campus Biomedico of RomeRomeItaly

Background:Phylodynamics,the study of the interaction between epidemiological and pathogen evolutionary processes within and among populations,was originally defined in the context of rapidly evolving viruses and used to characterize transmission *** concept of phylodynamics has evolved since the early 21^(st)century,extending its reach to slower-evolving pathogens,including bacteria and fungi,and to the identification of influential factors in disease spread and pathogen population ***:The phylodynamic approach has now become a fundamental building block for the development of comparative phylogenetic tools capable of incorporating epidemiological surveillance data with molecular sequences into a single statistical *** innovative tools have greatly enhanced scientific investigations of the temporal and geographical origins,evolutionary history,and ecological risk factors associated with the growth and spread of viruses such as human immunodeficiency virus(HIV),Zika,and dengue and bacteria such as Methicillin-resistant Staphylococcus ***:Capitalizing on an extensive review of the literature,we discuss the evolution of the field of infectious disease epidemiology and recent accomplishments,highlighting the advancements in phylodynamics,as well as the challenges and limitations currently facing researchers studying emerging pathogen epidemics across the globe.

关键词： Molecular epidemiology Phylodynamics Phylogeography Comparative phylogenetics HIV Zika Dengue WGS MRSA