Viral Infections and Schizophrenia: A Comprehensive Review.

Schizophrenia is a complex mental disorder with multiple genetic and environmental factors contributing to its pathogenesis. Viral infections have been suggested to be one of the environmental factors associated with the development of this disorder. We comprehensively review all relevant published literature focusing on the relationship between schizophrenia and various viral infections, such as influenza virus, herpes virus 1 and 2 (HSV-1 and HSV-2), cytomegalovirus (CMV), Epstein-Barr virus (EBV), retrovirus, coronavirus, and Borna virus. These viruses may interfere with the normal maturation of the brain directly or through immune-induced mediators, such as cytokines, leading to the onset of schizophrenia. Changes in the expression of critical genes and elevated levels of inflammatory cytokines have been linked to virally-induced infections and relevant immune activities in schizophrenia. Future research is necessary to understand this relationship better and provide insight into the molecular mechanisms underlying the pathophysiology of schizophrenia.

Antimicrobial Resistance, FlaA Sequencing, and Phylogenetic Analysis of Campylobacter Isolates from Broiler Chicken Flocks in Greece.

Human campylobacteriosis caused by thermophilic Campylobacter species is the most commonly reported foodborne zoonosis. Consumption of contaminated poultry meat is regarded as the main source of human infection. This study was undertaken to determine the antimicrobial susceptibility and the molecular epidemiology of 205 Campylobacter isolates derived from Greek flocks slaughtered in three different slaughterhouses over a 14-month period. A total of 98.5% of the isolates were resistant to at least one antimicrobial agent. In terms of multidrug resistance, 11.7% of isolates were resistant to three or more groups of antimicrobials. Extremely high resistance to fluoroquinolones (89%), very high resistance to tetracycline (69%), and low resistance to macrolides (7%) were detected. FlaA sequencing was performed for the subtyping of 64 C. jejuni and 58 C. coli isolates. No prevalence of a specific flaA type was observed, indicating the genetic diversity of the isolates, while some flaA types were found to share similar antimicrobial resistance patterns. Phylogenetic trees were constructed using the neighbor-joining method. Seven clusters of the C. jejuni phylogenetic tree and three clusters of the C. coli tree were considered significant with bootstrap values >75%. Some isolates clustered together were originated from the same or adjacent farms, indicating transmission via personnel or shared equipment. These results are important and help further the understanding of the molecular epidemiology and antimicrobial resistance of Campylobacter spp. derived from poultry in Greece.

Ugo Cerletti (1877-1963): An Early Italian Father of Electroshock and a Pioneer in Many Other Ways.

This article provides a biographical review of the life and the professional achievements of the Italian doctor Ugo Cerletti and an introduction on electroshock. Throughout his medical career, he travelled and studied in many countries all over the world. Building upon his systematic and comprehensive analysis of mental diseases, Cerletti introduced electroshock, which, at his time, was a novel therapeutic method. The main beneficial feature of electroshock was that it ameliorated refractory mental illnesses such as depression, mania, and schizophrenia. Additionally, Cerletti filmed the first scientific movie on electroshock. Furthermore, Cerletti left great lessons in the area of dementia, by proving the interaction between spirochaetes and progressive paralysis and exploring the causes of inflammation in the syphilitic brain. Cerletti was the first to announce the theory of acroagonines. Cerletti also made early discoveries on perivascular corpuscles, a discovery of such importance that the perivascular corpuscles are named corpuscles of Cerletti. Outside of the medical realm, Cerletti invented a new type of gun, and produced an early medical documentary. Cerletti received many national and international distinctions and awards. He died in 1963 at the age of 86.

Prevalence of and Risk Factors for Campylobacter spp. Colonization of Broiler Chicken Flocks in Greece.

The prevalence and risk factors for Campylobacter spp. colonization of broiler flocks and broiler carcass contamination in Greek slaughterhouses were investigated. Over a 14-month period, a pool of 10 ceca and 5 neck skin samples from chicken carcasses were collected from each of 142 batches of broiler flocks slaughtered in 3 different slaughterhouses. Information on potential risk factors for Campylobacter infection in broilers was collected by an on-farm interview and linked according to the Campylobacter contamination status of broiler flocks and differences in farm characteristics and management practices identified from questionnaires. Campylobacter spp. was isolated from 73.94% and 70.42% of ceca (95% CI 65.92-80.94) and carcasses (95% CI 62.19-77.78), respectively. A significant correlation (p < 0.001) between the presence of Campylobacter spp. in broiler ceca and contamination of carcasses was found, suggesting the spread of the microorganism on the skin of carcasses during the slaughtering procedure. A multiple logistic regression showed the disinfection of the poultry house being conducted by unskilled personnel (odds ratio [OR] » = 3.983) as a significant risk factor (p < 0.05) and the use of straw litter as bedding material (OR » = 0.170) and closure of windows during the intervals of production cycles (OR » = 0.396) as significant protective factors (p < 0.05) for broiler flock contamination. These results are important and help further the understanding of the epidemiology of Campylobacter spp. derived from poultry in Greece.

Prevalence and clinical implications of respiratory viruses in stable chronic obstructive pulmonary disease (COPD) and exacerbations: a systematic review and meta-analysis protocol.

INTRODUCTION: Both stable chronic obstructive pulmonary disease (COPD) and acute exacerbations represent leading causes of death, disability and healthcare expenditure. They are complex, heterogeneous and their mechanisms are poorly understood. The role of respiratory viruses has been studied extensively but is still not adequately addressed clinically. Through a rigorous evidence update, we aim to define the prevalence and clinical burden of the different respiratory viruses in stable COPD and exacerbations, and to investigate whether viral load of usual respiratory viruses could be used for diagnosis of exacerbations triggered by viruses, which are currently not diagnosed or treated aetiologically. METHODS AND ANALYSIS: Based on a prospectively registered protocol, we will systematically review the literature using standard methods recommended by the Cochrane Collaboration and the Grading of Recommendations Assessment, Development and Evaluation working group. We will search Medline/PubMed, Excerpta Medica dataBASE (EMBASE), the Cochrane Library, the WHO's Clinical Trials Registry and the proceedings of relevant international conferences on 2 March 2020. We will evaluate: (A) the prevalence of respiratory viruses in stable COPD and exacerbations, (B) differences in the viral loads of respiratory viruses in stable COPD vs exacerbations, to explore whether the viral load of prevalent respiratory viruses could be used as a diagnostic biomarker for exacerbations triggered by viruses and (C) the association between the presence of respiratory viruses and clinical outcomes in stable COPD and in exacerbations. ETHICS AND DISSEMINATION: Ethics approval is not required since no primary data will be collected. Our findings will be presented in national and international scientific conferences and will be published in peer reviewed journals. Respiratory viruses currently represent a lost opportunity to improve the outcomes of both stable COPD and exacerbations. Our work aspires to 'demystify' the prevalence and clinical burden of viruses in stable COPD and exacerbations and to promote clinical and translational research. PROSPERO REGISTRATION NUMBER: CRD42019147658.

Options and Limitations in Clinical Investigation of Bacterial Biofilms.

Bacteria can form single- and multispecies biofilms exhibiting diverse features based upon the microbial composition of their community and microenvironment. The study of bacterial biofilm development has received great interest in the past 20 years and is motivated by the elegant complexity characteristic of these multicellular communities and their role in infectious diseases. Biofilms can thrive on virtually any surface and can be beneficial or detrimental based upon the community's interplay and the surface. Advances in the understanding of structural and functional variations and the roles that biofilms play in disease and host-pathogen interactions have been addressed through comprehensive literature searches. In this review article, a synopsis of the methodological landscape of biofilm analysis is provided, including an evaluation of the current trends in methodological research. We deem this worthwhile because a keyword-oriented bibliographical search reveals that less than 5% of the biofilm literature is devoted to methodology. In this report, we (i) summarize current methodologies for biofilm characterization, monitoring, and quantification; (ii) discuss advances in the discovery of effective imaging and sensing tools and modalities; (iii) provide an overview of tailored animal models that assess features of biofilm infections; and (iv) make recommendations defining the most appropriate methodological tools for clinical settings.

Detecting the Diversity of Mycoplasma and Ureaplasma Endosymbionts Hosted by Trichomonas vaginalis Isolates.

Objectives: The symbiosis of Trichomonas vaginalis and Mycoplasma hominis is the first described association between two obligate human parasites. Trichomonas is the niche and the vector for the transmission of M. hominis infection. This clinically significant symbiosis may affect T. vaginalis virulence and susceptibility to treatment. The aims of this study were to investigate the intracellularly present Mycoplasma and Ureaplasma species in T. vaginalis strains isolated from the vaginal discharge of infected women as well as to trace the diversity pattern among the species detected in the isolated strains. Methods: Hundred pure T. vaginalis cultures were isolated from ~7,500 patient specimens presented with clinical purulent vaginitis. PCR and sequencing for Mycoplasma/Ureaplasma spp. were performed in DNA extracted from the pure cultures. In addition, vaginal discharge samples were cultured for the presence of M. hominis and U. urealyticum. Phylogenetic analysis assisted the identification of interspecies relationships between the Mycoplasma and Ureaplasma isolates. Results: Fifty four percentage of T. vaginalis isolates were harboring Mycoplasma spp. Phylogenetic analysis revealed three distinct clusters, two with already characterized M. hominis and Ureaplasma spp. (37% of total Mycoplasma spp.), whereas one group formed a distinct cluster matched with the newly identified species Candidatus Mycoplasma girerdii (59.3%) and one or more unknown Mycoplasma spp. (3.7%). Conclusions:T. vaginalis strains associated with vaginal infection might host intracellular mycoplasmas or ureaplasmas. Intracellular Mollicutes that remain undetected in the extracellular environment when conventional diagnostic methods are implemented may comprise either novel species, such as Candidatus M. giredii, or unknown species with yet unexplored clinical significance.

The fascinating story of urine examination: From uroscopy to the era of microscopy and beyond.

The purpose of this study was to present the evolution of ideas on the examination of urine from antiquity till our days. A thorough study of texts, medical books from antiquity till twentieth century along with a thorough review of the available literature in PubMed was conducted. The first observation on urine examination can be traced back to the Babylonian and Sumerian texts. Almost all physicians in antiquity including Hippocrates referred to the value of urine examination in the diagnosis and prognosis of diseases. The construction of first compound microscope lead to the examination of urine sediment and the development of Urine Cytology which was revolutionized during the twentieth century with the studies of important cytologists such as George Papanicolaou, Geoffrey Krabbe, and Leopold Koss. The introduction of molecular tests in the diagnosis of urothelial cancer inaugurated a new era in the study of urine cytology. The history of urine examination spans a period of 6,000 years. The application of microscope in the examination of urine sediment during the nineteenth century established urine analysis as an important diagnostic tool in clinical practice.

Therapeutic options and emerging alternatives for multidrug resistant staphylococcal infections.

Methicillin-resistant Staphylococcus aureus (MRSA) remains the single biggest challenge in infectious disease in the civilized world. Moreover, vancomycin resistance is also spreading, leading to fears of untreatable infections as were common in ancient times. Molecular microbiology and bioinformatics have revealed many of the mechanisms involved in resistance development. Mobile genetic elements, up-regulated virulence factors and multi-drug efflux pumps have been implicated. A range of approved antibiotics from the glycopeptide, lipopeptide, pleuromutilin, macrolide, oxazolidinone, lincosamide, aminoglycoside, tetracycline, steptogramin, and cephalosporin classes has been employed to treat MRSA infections. The upcoming pipeline of drugs for MRSA includes some new compounds from the above classes, together with fluoroquinolones, antibacterial peptide mimetics, aminomethylciclines, porphyrins, peptide deformylase inhibitors, oxadiazoles, and diaminopyrimidines. A range of non-drug alternative approaches has emerged for MRSA treatment. Bacteriophage-therapy including purified lysins has made a comeback after being discovered in the 1930s. Quorum-sensing inhibitors are under investigation. Small molecule inhibitors of multi-drug efflux pumps may potentiate existing antibiotics. The relative failure of staphylococcal vaccines is being revisited by efforts with multi-valent vaccines and improved adjuvants. Photodynamic therapy uses non-toxic photosensitizers and harmless visible light to produce reactive oxygen species that can nonspecifically destroy bacteria while preserving host cells. Preparation of nanoparticles can kill bacteria themselves, as well as improve the delivery of anti-bacterial drugs. Anti-MRSA drug discovery remains an exciting field with great promise for the future.

Patterns of drug resistance among newly diagnosed HIV-1 infected patients in Greece during the last decade: the crucial role of transmission networks.

INTRODUCTION: The prevalence of drug resistance is approximately 10% in Europe and North America among newly infected patients. We aim to investigate the temporal patterns of resistance among drug naive HIV-infected individuals in Greece and also to determine transmission networking among those with resistant strains. MATERIALS AND METHODS: Protease (PR) and partial reverse transcriptase (RT) sequences were determined from 2499 newly diagnosed HIV-1 patients, in Greece, during 2003-2013. Genotypic drug resistance was estimated using the HIVdb: Genotypic Resistance Interpretation Algorithm. We identified transmission clusters of resistant strains on the basis of a large collection of HIV-1 sequences from 4024 seropositives in Greece. Phylodynamic analysis was performed using a Bayesian method. RESULTS: We estimated drug resistance levels among naïve patients on the basis of all resistance mutations in PR and partial RT. The overall prevalence of resistance was 19.6% (490/2499). Resistance to NNRTIs was the most common (397/2499, 15.9%) followed by PIs (116/2499, 4.6%) and NRTIs (79/2499, 3.2%). We found a significant trend for decreasing resistance to NRTIs over time (6.7%-1.6%). There was no time trend for the overall PI and NNRTI resistance. The most frequently observed major resistant sites in PR were V82 (2.0%) and L90 (1.8%). In RT, we found E138 (58.6%), K103 (13.1%), V179 (8.4%) and T215 (7.1%), M41 (4.7%) associated with resistance to NNRTIs and NRTIs, respectively. The prevalence of K103N and E138Q were significantly increased during 2003-2013. Crucially, we found that both K103N, E138Q are associated with transmission networking within men having sex with men (MSM) and intravenous drug user (IDU) local networks. The K103N network included seropositives across Greece, while the latter only from the recent IDU outbreak in Athens metropolitan area (1). Phylodynamic analyses revealed that the exponential growth for K103N network started in 2009 (Figure 1) and for the E138Q in 2010. CONCLUSIONS: The overall resistance has been stable in Greece over time; however, specific NNRTI resistance patterns are increasing. Notably, they are associated with local transmission networking, thus suggesting that this is the cause for the increased patterns of NNRTI resistance and not multiple transmissions of resistant strains from different sources among treated individuals. Our study highlights the advance of molecular epidemiology for understanding the dynamics of resistance.

50 years after the death of George Nicholas Papanicolaou (1883-1962): evaluation of his scientific work.

The purpose of this review article is to summarise the scientific work of George Nicholas Papanicolaou, one of the most eminent figures in the 20th century history of clinical cytology and medicine. Fifty years after his death, his work still remains invaluable, from the early steps in biology and zoology to the application of the Pap test as the most important advancement in the prevention of cervical cancer. The publication of his Atlas was the first important step for the foundation of a new branch in medicine, that of exfoliative cytology. His contribution to cytology undoubtedly earned him the title of the "father of exfoliative cytology" and saved the lives of many women worldwide.

Highights in the history of epilepsy: the last 200 years.

The purpose of this study was to present the evolution of views on epilepsy as a disease and symptom during the 19th and the 20th century. A thorough study of texts, medical books, and reports along with a review of the available literature in PubMed was undertaken. The 19th century is marked by the works of the French medical school and of John Hughlings Jackson who set the research on epilepsy on a solid scientific basis. During the 20th century, the invention of EEG, the advance in neurosurgery, the discovery of antiepileptic drugs, and the delineation of underlying pathophysiological mechanisms, were the most significant advances in the field of research in epilepsy. Among the most prestigious physicians connected with epilepsy one can pinpoint the work of Henry Gastaut, Wilder Penfield, and Herbert Jasper. The most recent advances in the field of epilepsy include the development of advanced imaging techniques, the development of microsurgery, and the research on the connection between genetic factors and epileptic seizures.

Persistence of frequently transmitted drug-resistant HIV-1 variants can be explained by high viral replication capacity.

BACKGROUND: In approximately 10% of newly diagnosed individuals in Europe, HIV-1 variants harboring transmitted drug resistance mutations (TDRM) are detected. For some TDRM it has been shown that they revert to wild type while other mutations persist in the absence of therapy. To understand the mechanisms explaining persistence we investigated the in vivo evolution of frequently transmitted HIV-1 variants and their impact on in vitro replicative capacity. RESULTS: We selected 31 individuals infected with HIV-1 harboring frequently observed TDRM such as M41L or K103N in reverse transcriptase (RT) or M46L in protease. In all these samples, polymorphisms at non-TDRM positions were present at baseline (median protease: 5, RT: 6). Extensive analysis of viral evolution of protease and RT demonstrated that the majority of TDRM (51/55) persisted for at least a year and even up to eight years in the plasma. During follow-up only limited selection of additional polymorphisms was observed (median: 1).To investigate the impact of frequently observed TDRM on the replication capacity, mutant viruses were constructed with the most frequently encountered TDRM as site-directed mutants in the genetic background of the lab strain HXB2. In addition, viruses containing patient-derived protease or RT harboring similar TDRM were made. The replicative capacity of all viral variants was determined by infecting peripheral blood mononuclear cells and subsequently monitoring virus replication. The majority of site-directed mutations (M46I/M46L in protease and M41L, M41L + T215Y and K103N in RT) decreased viral replicative capacity; only protease mutation L90M did not hamper viral replication. Interestingly, most patient-derived viruses had a higher in vitro replicative capacity than the corresponding site-directed mutant viruses. CONCLUSIONS: We demonstrate limited in vivo evolution of protease and RT harbouring frequently observed TDRM in the plasma. This is in line with the high in vitro replication capacity of patient-derived viruses harbouring TDRM compared to site-directed mutant viruses harbouring TDRM. As site-directed mutant viruses have a lower replication capacity than the patient-derived viruses with similar mutational patterns, we propose that (baseline) polymorphisms function as compensatory mutations improving viral replication capacity.

Multilocus sequence typing (and phylogenetic analysis) of Campylobacter jejuni and Campylobacter coli strains isolated from clinical cases in Greece.

BACKGROUND: The molecular epidemiology of C. jejuni and C. coli clinical strains isolated from children with gastroenteritis, was investigated using the multilocus sequence typing method (MLST). This analysis establishes for the first time in Greece and constitutes an important tool for the epidemiological surveillance and control of Campylobacter infection in our country. METHODS: The MLST genotypes were compared with those gained by other typing methods (HS-typing, PFGE and FlaA typing) and were also phylogenetically analyzed, in order to uncover genetic relationships. RESULTS: Among 68 C. jejuni strains, 41 different MLST-Sequence Types (MLST-STs) were found. Fifty six strains or 34 MLST-STs could be sorted into 15 different MLST-Sequence Type Complexes (MLST-STCs), while twelve strains or seven MLST-STs did not match any of the MLST-STCs of the database. Twenty C. coli strains belonged to 14 different MLST-STs. Eleven MLST-STs were classified in the same MLST-STC (828), and three were unclassifiable. There was no significant association between the MLST-STs and the results of the other typing methods.Phylogenetic analysis revealed that some strains, classified to the species of C. jejuni, formed a separate, phylogenetically distinct group. In eight strains some alleles belonging to the taxonomic cluster of C. jejuni, were also detected in C. coli and vice versa, a phenomenon caused by the genetic mosaic encountered inside the genus Campylobacter. CONCLUSIONS: The MLST-ST determination proved to be a very useful tool for the typing as well as the identification of Campylobacter on the species level.

First report of a phylogenetic analysis of an autochthonous Plasmodium vivax strain isolated from a malaria case in East Attica, Greece.

Malaria has become an emerging infection in Greece, which is the doorstep to Europe for thousands of immigrants. With increasing immigration, cases with evidence of domestic transmission (autochthonous) are being reported. In the present study, an isolate of Plasmodium vivax from an autochthonous clinical case was subjected to phylogenetic analysis of the genes encoding the merozoite surface protein 1 (MSP-1) and the circumsporozoite protein (CSP). In the MSP region, the strain was related with strains from Brazil, South Korea, Turkey and Thailand, whereas in the CSP region, with strains from Brazil, Colombia and New Guinea. The present study establishes for the first time in Greece the basis for the creation of a database comprising genotypic and phylogenetic characteristics of Plasmodium spp.

Integrating phylodynamics and epidemiology to estimate transmission diversity in viral epidemics.

The epidemiology of chronic viral infections, such as those caused by Hepatitis C Virus (HCV) and Human Immunodeficiency Virus (HIV), is affected by the risk group structure of the infected population. Risk groups are defined by each of their members having acquired infection through a specific behavior. However, risk group definitions say little about the transmission potential of each infected individual. Variation in the number of secondary infections is extremely difficult to estimate for HCV and HIV but crucial in the design of efficient control interventions. Here we describe a novel method that combines epidemiological and population genetic approaches to estimate the variation in transmissibility of rapidly-evolving viral epidemics. We evaluate this method using a nationwide HCV epidemic and for the first time co-estimate viral generation times and superspreading events from a combination of molecular and epidemiological data. We anticipate that this integrated approach will form the basis of powerful tools for describing the transmission dynamics of chronic viral diseases, and for evaluating control strategies directed against them.

Milestones in the history of research on cardiac energy metabolism.

The present study summarizes the history of research on cardiac metabolism from antiquity till the 21st century. It describes important landmarks regarding the discovery of oxygen and of the 3 steps of cellular respiration, as well as major research on cardiac energy metabolism. For this purpose, we conducted a thorough search of original manuscripts, books, and contemporary reviews published in PubMed. The first views and concepts about the heart's function appear in Greek philosophic manuscripts of 2500 years ago. According to Aristotle, the heart is responsible for heat production, which is essential for life. The understanding of cardiac metabolism awaited new discoveries. The discovery of oxygen during the 18th century, along with the idea of energy conservation, or what is now known as one of the first versions of the first law of thermodynamics, played an important role in initiating the study of energy metabolism in general and heart metabolism later. The discovery of glycolysis, of the Krebs cycle, and of adenosine triphosphate offered a better understanding of cellular respiration, necessary for later research. Indeed, many researchers dedicated their studies to energy metabolism, but Richard John Bing, the renowned German research cardiologist, is the one who guided the exploration of cardiac metabolism, and he is therefore considered to be the father of cardiac energy metabolism. Since then, encouraging new research has been taking place, offering important clinical applications for heart patients.

Dating the origin and dispersal of hepatitis B virus infection in humans and primates.

UNLABELLED: The origin of hepatitis B virus (HBV) infection in humans and other primates remains largely unresolved. Understanding the origin of HBV is crucial because it provides a framework for studying the burden, and subsequently the evolution, of HBV pathogenicity with respect to changes in human population size and life expectancy. To investigate this controversy we examined the relationship between HBV phylogeny and genetic diversity of modern humans, investigated the timescale of global HBV dispersal, and tested the hypothesis of HBV-human co-divergence. We find that the global distribution of HBV genotypes and subgenotypes are consistent with the major prehistoric modern human migrations. We calibrate the HBV molecular clock using the divergence times of different indigenous human populations based on archaeological and genetic evidence and show that HBV jumped into humans around 33,600 years ago; 95% higher posterior density (HPD): 22,000-47,100 years ago (estimated substitution rate: 2.2 × 10(-6) ; 95% HPD: 1.5-3.0 × 10(-6) substitutions/site/year). This coincides with the origin of modern non-African humans. Crucially, the most pronounced increase in the HBV pandemic correlates with the global population increase over the last 5,000 years. We also show that the non-human HBV clades in orangutans and gibbons resulted from cross-species transmission events from humans that occurred no earlier than 6,100 years ago. CONCLUSION: Our study provides, for the first time, an estimated timescale for the HBV epidemic that closely coincides with dates of human dispersals, supporting the hypothesis that HBV has been co-expanding and co-migrating with human populations for the last 40,000 years. (HEPATOLOGY 2013).

A brief chronicle of cytology: from Janssen to Papanicolaou and beyond.

The aim of our study was to outline and present the major hallmarks in the history of clinical cytology. For this purpose, an extensive research in modern literature and the PubMed database was undertaken. Furthermore, we studied original papers and books of the pioneers in cytopathology. The development of the first microscope by Hans and Sacharias Janssen is a hallmark in biological sciences, since the study of microcosmos was made feasible. From the discovery of single cells by Robert Hooke and the cell theory by Schleiden and Schwann till the establishment of exfoliative cytology by George Papanicolaou and the invention of fine-needle aspiration biopsy technique by Martin and Ellis, there is a three-century continuum of important discoveries and research. Today, flow cytometry and the introduction of molecular techniques have revolutionized medicine and are expected to change the face of cytology in the near future.

Assessment of phylogenetic sensitivity for reconstructing HIV-1 epidemiological relationships.

Phylogenetic analysis has been extensively used as a tool for the reconstruction of epidemiological relations for research or for forensic purposes. It was our objective to assess the sensitivity of different phylogenetic methods and various phylogenetic programs to reconstruct epidemiological links among HIV-1 infected patients that is the probability to reveal a true transmission relationship. Multiple datasets (90) were prepared consisting of HIV-1 sequences in protease (PR) and partial reverse transcriptase (RT) sampled from patients with documented epidemiological relationship (target population), and from unrelated individuals (control population) belonging to the same HIV-1 subtype as the target population. Each dataset varied regarding the number, the geographic origin and the transmission risk groups of the sequences among the control population. Phylogenetic trees were inferred by neighbor-joining (NJ), maximum likelihood heuristics (hML) and Bayesian methods. All clusters of sequences belonging to the target population were correctly reconstructed by NJ and Bayesian methods receiving high bootstrap and posterior probability (PP) support, respectively. On the other hand, TreePuzzle failed to reconstruct or provide significant support for several clusters; high puzzling step support was associated with the inclusion of control sequences from the same geographic area as the target population. In contrary, all clusters were correctly reconstructed by hML as implemented in PhyML 3.0 receiving high bootstrap support. We report that under the conditions of our study, hML using PhyML, NJ and Bayesian methods were the most sensitive for the reconstruction of epidemiological links mostly from sexually infected individuals.