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Mental health-related stigma is poorly understood, and minimal research has focused on the experience of stigma from children’s perspectives. We sought to investigate whether children treated as inpatients and outpatients had different experiences of stigma over time and whether stigma is linked to global functioning cross-sectionally and longitudinally. Children, aged 8–12 years, receiving treatment within a national specialist mental health inpatient unit were matched for age, gender and diagnosis with children receiving outpatient treatment (N = 64). Validated measures of stigma, global functioning and symptom severity were collected at the start of treatment and upon discharge from the ward for inpatients, and a similar timeframe for their individually matched outpatients. Latent change score models and partial correlation coefficients were employed to test our hypotheses. No differences in most aspects of stigma between children treated as inpatients and outpatients were observed, except for personal rejection at baseline and self-stigma at follow-up favouring outpatients. A reduction in stigma was observed in societal devaluation, personal rejection and secrecy for inpatients, and self-stigma and secrecy for outpatients between the two assessments. Societal devaluation declined at a higher rate among inpatients compared to outpatients, albeit reductions in stigma were comparable for all remaining measures. No association was found between the change in stigma and change in global functioning. Future research may offer further insights into the development and maintenance of stigma and identify key targets for anti-stigma interventions to reduce its long-term impact. © 2021, The Author(s).

Numerous studies covering some aspects of SARS-CoV-2 data analyses are being published on a daily basis, including a regularly updated phylogeny on nextstrain.org. Here, we review the difficulties of inferring reliable phylogenies by example of a data snapshot comprising a quality-filtered subset of 8,736 out of all 16,453 virus sequences available on May 5, 2020 from gisaid.org. We find that it is difficult to infer a reliable phylogeny on these data due to the large number of sequences in conjunction with the low number of mutations. We further find that rooting the inferred phylogeny with some degree of confidence either via the bat and pangolin outgroups or by applying novel computational methods on the ingroup phylogeny does not appear to be credible. Finally, an automatic classification of the current sequences into subclasses using the mPTP tool for molecular species delimitation is also, as might be expected, not possible, as the sequences are too closely related. We conclude that, although the application of phylogenetic methods to disentangle the evolution and spread of COVID-19 provides some insight, results of phylogenetic analyses, in particular those conducted under the default settings of current phylogenetic inference tools, as well as downstream analyses on the inferred phylogenies, should be considered and interpreted with extreme caution. © 2020 The Author(s).

Background: The spatiotemporal profiling of molecular transmission clusters (MTCs) using viral genomic data can effectively identify transmission networks in order to inform public health actions targeting SARS‐CoV‐2 spread. Methods: We used whole genome SARS‐CoV‐2 sequences derived from ten European regions belonging to eight countries to perform phylogenetic and phylodynamic analysis. We developed dedicated bioinformatics pipelines to identify regional MTCs and to assess demographic factors potentially associated with their formation. Results: The total number and the scale of MTCs varied from small household clusters identified in all regions, to a super‐spreading event found in Uusimaa‐FI. Specific age groups were more likely to belong to MTCs in different regions. The clustered sequences referring to the age groups 50–100 years old (y.o.) were increased in all regions two weeks after the establishment of the lockdown, while those referring to the age group 0–19 y.o. decreased only in those regions where schools’ closure was combined with a lockdown. Conclusions: The spatiotemporal profiling of the SARS‐CoV‐2 MTCs can be a useful tool to monitor the effectiveness of the interventions and to reveal cryptic transmissions that have not been identified through contact tracing. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.

Due to early implementation of public health measures, Greece had low number of SARS-CoV-2 infections and COVID-19 severe incidents in hospitalized patients. The National and Kapodistrian University of Athens (NKUA), especially its health-care/medical personnel, has been actively involved in the first line of state responses to COVID-19. To estimate the prevalence of antibodies (Igs) against SARS-CoV-2 among NKUA members, we designed a five consecutive monthly serosurvey among randomly selected NKUA consenting volunteers. Here, we present the results from the first 2500 plasma samples collected during June–July 2020. Twenty-five donors were tested positive for anti-SARS-CoV-2 Igs; thus, the overall seroprevalence was 1.00%. The weighted overall seroprevalence was 0.93% (95% CI: 0.27, 2.09) and varied between males [1.05% (95% CI: 0.18, 2.92)] and females [0.84% (95% CI: 0.13, 2.49)], age-groups and different categories (higher in participants from the School of Health Sciences and in scientific affiliates/faculty members/laboratory assistants), but no statistical differences were detected. Although focused on the specific population of NKUA members, our study shows that the prevalence of anti-SARS-CoV-2 Igs for the period June–July 2020 remained low and provides knowledge of public health importance for the NKUA members. Given that approximately one in three infections was asymptomatic, continuous monitoring of the progression of the pandemic by assessing Ig seroprevalence is needed. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.

Background and Aim: The circulating recombinant form 02_AG (CRF02_AG) is the predominant clade among the human immunodeficiency virus type-1 (HIV-1) non-Bs with a prevalence of 5.97% (95% Confidence Interval-CI: 5.41-6.57%) across Spain. Our aim was to estimate the levels of regional clustering for CRF02_AG and the spatiotemporal characteristics of the largest CRF02_AG subepidemic in Spain. Methods: We studied 396 CRF02_AG sequences obtained from HIV-1 diagnosed patients during 2000-2014 from 10 autonomous communities of Spain. Phylogenetic analysis was performed on the 391 CRF02_AG sequences along with all globally sampled CRF02_AG sequences (N = 3,302) as references. Phylodynamic and phylogeographic analysis was performed to the largest CRF02_AG monophyletic cluster by a Bayesian method in BEAST v1.8.0 and by reconstructing ancestral states using the criterion of parsimony in Mesquite v3.4, respectively. Results: The HIV-1 CRF02_AG prevalence differed across Spanish autonomous communities we sampled from (p < 0.001). Phylogenetic analysis revealed that 52.7% of the CRF02_AG sequences formed 56 monophyletic clusters, with a range of 2-79 sequences. The CRF02_AG regional dispersal differed across Spain (p = 0.003), as suggested by monophyletic clustering. For the largest monophyletic cluster (subepidemic) (N = 79), 49.4% of the clustered sequences originated from Madrid, while most sequences (51.9%) had been obtained from men having sex with men (MSM). Molecular clock analysis suggested that the origin (tMRCA) of the CRF02_AG subepidemic was in 2002 (median estimate; 95% Highest Posterior Density-HPD interval: 1999-2004). Additionally, we found significant clustering within the CRF02_AG subepidemic according to the ethnic origin. Conclusion: CRF02_AG has been introduced as a result of multiple introductions in Spain, following regional dispersal in several cases. We showed that CRF02_AG transmissions were mostly due to regional dispersal in Spain. The hot-spot for the largest CRF02_AG regional subepidemic in Spain was in Madrid associated with MSM transmission risk group. The existence of subepidemics suggest that several spillovers occurred from Madrid to other areas. CRF02_AG sequences from Hispanics were clustered in a separate subclade suggesting no linkage between the local and Hispanic subepidemics. © 2019 Kostaki, Flampouris, Karamitros, Chueca, Alvarez, Casas, Alejos, Hatzakis, Garcia, Paraskevis and CoRIS. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

Background. The classification of hepatitis viruses still predominantly relies on ad hoc criteria, i.e., phenotypic traits and arbitrary genetic distance thresholds. Given the subjectivity of such practices coupled with the constant sequencing of samples and discovery of new strains, this manual approach to virus classification becomes cumbersome and impossible to generalize. Methods. Using two well-studied hepatitis virus datasets, HBV and HCV, we assess if computational methods for molecular species delimitation that are typically applied to barcoding biodiversity studies can also be successfully deployed for hepatitis virus classification. For comparison, we also used ABGD, a tool that in contrast to other distance methods attempts to automatically identify the barcoding gap using pairwise genetic distances for a set of aligned input sequences. Results-Discussion. We found that the mPTP species delimitation tool identified even without adapting its default parameters taxonomic clusters that either correspond to the currently acknowledged genotypes or to known subdivision of genotypes (subtypes or subgenotypes). In the cases where the delimited cluster corresponded to subtype or subgenotype, there were previous concerns that their status may be underestimated. The clusters obtained from the ABGD analysis differed depending on the parameters used. However, under certain values the results were very similar to the taxonomy and mPTP which indicates the usefulness of distance based methods in virus taxonomy under appropriate parameter settings. The overlap of predicted clusters with taxonomically acknowledged genotypes implies that virus classification can be successfully automated. © Copyright 2019 Serdari et al.

A growing body of evidence suggests that network-based interventions to reduce HIV transmission and/or improve HIV-related health outcomes have an important place in public health efforts to move towards 90–90–90 goals. However, the social processes involved in network-based recruitment may pose a risk to participants of increasing HIV-related stigma if network recruitment causes HIV status to be assumed, inferred, or disclosed. On the other hand, the social processes involved in network-based recruitment to HIV testing may also encourage HIV-related social support. Yet despite the relevance of these processes to both network-based interventions and to other more common interventions (e.g., partner services), there is a dearth of literature that directly examines them among participants of such interventions. Furthermore, both HIV-related stigma and social support may influence participants’ willingness and ability to recruit their network members to the study. This paper examines (1) the extent to which stigma and support were experienced by participants in the Transmission Reduction Intervention Project (TRIP), a risk network-tracing intervention aimed at locating recently HIV-infected and/or undiagnosed HIV-infected people and linking them to care in Athens, Greece; Odessa, Ukraine; and Chicago, Illinois; and (2) whether stigma and support predicted participant engagement in the intervention. Overall, experiences of stigma were infrequent and experiences of support frequent, with significant variation between study sites. Experiences and perceptions of HIV-related stigma did not change significantly between baseline and six-month follow-up for the full TRIP sample, and significantly decreased during the course of the study at the Chicago site. Experiences of HIV-related support significantly increased among recently-HIV-infected participants at all sites, and among all participants at the Odessa site. Both stigma and support were found to predict participants’ recruitment of network members to the study at the Athens site, and to predict participants’ interviewer-rated enthusiasm for naming and recruiting their network members at both the Athens and Odessa sites. These findings suggest that network-based interventions like TRIP which aim to reduce HIV transmission likely do not increase stigma-related risks to participants, and may even encourage increased social support among network members. However, the present study is limited by its associational design and by some variation in implementation by study site. Future research should directly assess contextual differences to improve understanding of the implications of site-level variation in stigma and support for the implementation of network-based interventions, given the finding that these constructs predict participants’ recruitment of network members and engagement in the intervention, and thereby could limit network-based interventions’ abilities to reach those most in need of HIV testing and care. © 2019, Springer Science+Business Media, LLC, part of Springer Nature.

A molecular epidemiology study of HIV-1 infection was conducted in one hundred diagnosed and untreated HIV-1-infected patients in Cyprus between 2010 and 2012, representing 65.4% of all the reported HIV-1 infections in Cyprus in this three-year period, using a previously defined enrolment strategy. Eighty-two patients were newly diagnosed (genotypic drug resistance testing within six months from diagnosis), and eighteen patients were HIV-1 diagnosed for a longer period or the diagnosis date was unknown. Phylogenetic trees of the pol sequences obtained in this study with reference sequences indicated that subtypes B and A1 were the most common subtypes present and accounted for 41.0 and 19.0% respectively, followed by subtype C (7.0%), F1 (8.0%), CRF02_AG (4.0%), A2 (2.0%), other circulating recombinant forms (CRFs) (7.0%) and unknown recombinant forms (URFs) (12%). Most of the newly-diagnosed study subjects were Cypriots (63%), males (78%) with median age 39 (Interquartile Range, IQR 33–48) reporting having sex with other men (MSM) (51%). A high rate of clustered transmission of subtype B drug-sensitive strains to reverse transcriptase and protease inhibitors was observed among MSM, twenty-eight out of forty-one MSM study subjects (68.0%) infected were implicated in five transmission clusters, two of which are sub-subtype A1 and three of which are subtype B strains. The two largest MSM subtype B clusters included nine and eight Cypriot men, respectively, living in all major cities in Cyprus. There were only three newly diagnosed patients with transmitted drug resistant HIV-1 strains, one study subject from the United Kingdom infected with subtype B strain and one from Romania with sub-subtype A2 strain, both with PI drug resistance mutation M46L and one from Greece with sub-subtype A1 with nonnucleoside reverse transcriptase inhibitors (NNRTI) drug resistance mutation K103N. © 2018 Kostrikis et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Background: TRIP (Transmission Reduction Intervention Project) was a network-based, contact tracing approach to locate and link to care, mostly people who inject drugs (PWID) with recent HIV infection.Objective: We investigated whether sequences from HIV-infected participants with high viral load cluster together more frequently than what is expected by chance. Methods: Paired end reads were generated for 104 samples using Illumina MiSeq next-generation sequencing. Results: 63 sequences belonged to previously identified local transmission networks of PWID (LTNs) of an HIV outbreak in Athens, Greece. For two HIV-RNA cut-offs (105 and 106 IU/mL), HIV transmissions were more likely between PWID with similar levels of HIV-RNA (p106 IU/mL were clustered in 5 pairs. For 4 of these clusters (80%), there was in each one of them at least one sequence from a recently HIV-infected PWID. Conclusion: We showed that transmissions are more likely among PWID with high viremia. © 2018 Bentham Science Publishers.

Eastern European countries, including Russia, Ukraine, and other former Soviet Union (FSU) countries, have experienced a human immunodeficiency virus (HIV) epidemic spreading mostly among people who inject drugs (PWID). We aimed to investigate the origin and the dispersal patterns of HIV-1 CRF02-AG in Russia and other FSU countries. We studied 136 CRF02-AG sequences originating from Russia, and FSU countries along with a globally sampled dataset of 3,580 CRF02-AG sequences. Maximum-likelihood phylogeny reconstruction with bootstrap evaluation was conducted in RAxML. Bayesian phylogeographic analysis was performed in BEAST v1.8 using the discrete trait model. We found that all CRF02-AG sequences from Russia and other FSU countries formed a single monophyletic cluster within CRF02-AG radiation. The Russian/FSU clade was classified as CRF63-02A1. Sequences from the FSU countries clustered further within distinct subclades (two from Russia, three from Uzbekistan, and one Kazakhstan) according to the geographic origin of sampling. Molecular clock analysis revealed that the time to the most recent common ancestor (t MRCA ) of the CRF63-02A1 epidemic was in 1996 [95% higher posterior density (95% HPD): 1992-1999], while for the two Russian subclades, t MRCA was estimated in 2003 (95% HPD: 2001-2004) and in 2007 (95% HPD: 2005-2008). Phylogeographic analysis suggested that the potential origin of the epidemic was in Uzbekistan. Early dispersal of CRF63-02A1 occurred in Kazakhstan and Uzbekistan and thereafter the epidemic spread to Russia. Notably, spillover transmissions to Russia kept occurring from both countries. Previous studies have shown that Russia and Ukraine have provided the source for the PWID-driven, HIV-1 subtype-A epidemic, spreading across the FSU countries (A FSU ). In great contrast, CRF63-02A1 established an epidemic in central Asia (Uzbekistan and Kazakhstan), from where it subsequently disseminated to Russia. Our study suggests that cross-border transmissions among PWID occur bidirectionally between Russian and other FSU populations. These results are of public health importance and suggest that prevention actions have to be reinforced in this area to assist the management of high-risk practices. © Copyright 2018, Mary Ann Liebert, Inc. 2018.

Hepatitis B virus (HBV) infection constitutes a global public health problem. In order to establish how HBV was disseminated across different geographic regions, we estimated the levels of regional clustering for genotypes D and A. We used 916 HBV-D and 493 HBV-A full-length sequences to reconstruct their global phylogeny. Phylogeographic analysis was conducted by the reconstruction of ancestral states using the criterion of parsimony. The putative origin of genotype D was in North Africa/Middle East. HBV-D sequences form low levels of regional clustering for the Middle East and Southern Europe. In contrast, HBV-A sequences form two major clusters, the first including sequences mostly from sub-Saharan Africa, and the second including sequences mostly from Western and Central Europe. Conclusion: We observed considerable differences in the global dissemination patterns of HBV-D and HBV-A and different levels of monophyletic clustering in relation to the regions of prevalence of each genotype. © Kostaki et al.

New diagnoses of HIV-1 infection among people who inject drugs (PWID) rocketed in Athens, Greece between 2011 and 2014 (HIV-1 outbreak). Our aim was to identify, during that period, potential cross-group transmissions between the within-Greece PWID and other risk or national groups using molecular methods. Sequences from 33 PWID were outside the PWID-outbreak networks in Greece (PWID-imported transmissions). Phylogenetic analyses on 28 of these sequences (subtypes A and B) showed that 11 subtype B infections originated from Greece, whereas 8 and 7 subtype A strains were from former Soviet Union countries (AFSU) and Greece, respectively. The putative source in half of the PWID-imported transmissions with Greek origin was an individual who acquired HIV via sexual contact. During four years of an HIV-1 outbreak among PWID in Athens, Greece, 33 individuals in this group (4.6% of all diagnoses with phylogenetic analyses) are likely to represent infections, sexually or injection-acquired, outside the within-Greece-PWID-outbreak networks. Combined molecular and traditional HIV surveillance to monitor introductions of new strains, and interventions that aim at reducing the rate of both injection and sexual risky practices are needed during drug injection-related HIV outbreaks. © 2018 Elsevier B.V.

Background. The Transmission Reduction Intervention Project (TRIP) is a network-based intervention that aims at decreasing human immunodeficiency virus type 1 (HIV-1) spread. We herein explore associations between transmission links as estimated by phylogenetic analyses, and social network-based ties among persons who inject drugs (PWID) recruited in TRIP. Methods. Phylogenetic trees were inferred from HIV-1 sequences of TRIP participants. Highly supported phylogenetic clusters (transmission clusters) were those fulfilling 3 different phylogenetic confidence criteria. Social network-based ties (injecting or sexual partners, same venue engagement) were determined based on personal interviews, recruitment links, and field observation. Results. TRIP recruited 356 individuals (90.2% PWID) including HIV-negative controls; recently HIV-infected seeds; longterm HIV-infected seeds; and their social network members. Of the 150 HIV-infected participants, 118 (78.7%) were phylogenetically analyzed. Phylogenetic analyses suggested the existence of 13 transmission clusters with 32 sequences. Seven of these clusters included 14 individuals (14/32 [43.8%]) who also had social ties with at least 1 member of their cluster. This proportion was significantly higher than what was expected by chance. Conclusions. Molecular methods can identify HIV-infected people socially linked with another person in about half of the phylogenetic clusters. This could help public health efforts to locate individuals in networks with high transmission rates. © The Author(s) 2018.

Hepatitis B virus (HBV) infection, a global public health problem can be asymptomatic, acute or chronic and can lead to serious consequences of infection, including cirrhosis, and hepatocellular carcinoma. HBV, a partially double stranded DNA virus, belongs to the family Hepadnaviridae, and replicates via reverse transcription of an RNA intermediate. This reverse transcription is catalyzed by a virus-encoded polymerase that lacks proof reading ability, which leads to sequence heterogeneity. HBV is classified into nine genotypes and at least 35 subgenotypes, which may be characterized by distinct geographical distributions. This HBV diversification and distinct geographical distribution has been proposed to be the result of the co-expansion of HBV with modern humans, after their out-of-Africa migration. HBeAg is a non-particulate protein of HBV that has immunomodulatory properties as a tolerogen that allows the virus to establish HBV infection in vivo. During the natural course of infection, there is seroconversion from a HBeAg-positive phase to a HBeAg-negative, anti-HBe-positive phase. During this seroconversion, there is loss of tolerance to infection and immune escape-HBeAg-negative mutants can be selected in response to the host immune response. The different genotypes and, in some cases, subgenotypes develop different mutations that can affect HBeAg expression at the transcriptional, translational and post-translational levels. The ability to develop mutations, affecting HBeAg expression, can influence the length of the HBeAg-positive phase, which is important in determining both the mode of transmission and the clinical course of HBV infection. Thus, the different genotypes/subgenotypes have evolved in such a way that they exhibit different modes of transmission and clinical manifestation of infection. Loss of HBeAg may be a sign of short-sighted evolution because there is loss of tolerogenic ability of HBeAg and HBeAgnegative virions are less transmissible. Depending on their ability to lead to HBeAg seroconversion, the genotype/subgenotypes exhibit varying degrees of short-sighted evolution. The "arms race" between HBV and the immune response to HBeAg is multifaceted and its elucidation intricate, with transmissibility and persistence being important for the survival of the virus. We attempt to shed some light on this complex interplay between host and virus. © 2018 Frontiers Media S.A. All rights reserved.

Purpose: This paper presents an overview of different kinds of risk and social network methods and the kinds of research questions each can address. Recent Findings: It also reviews what network research has discovered about how network characteristics are associated with HIV and other infections, risk behaviors, preventive behaviors, and care, and discusses some ways in which network-based public health interventions have been conducted. Summary: Based on this, risk and social network research and interventions seem both feasible and valuable for addressing the many public health and social problems raised by the widespread use of opioids in the US South. © 2018, Springer Science+Business Media, LLC, part of Springer Nature.

As part of a network study of HIV infection among people who inject drugs (PWID) and their contacts, we discovered a connected subcomponent of 29 uninfected PWID. In the context of a just-declining large epidemic outbreak, this raised a question: What explains the existence of large pockets of uninfected people? Possible explanations include "firewall effects" (Friedman et al., 2000; Dombrowski et al., 2017) wherein the only HIV+ people that the uninfected take risks with have low viral loads; "bottleneck effects" wherein few network paths into the pocket of non-infection exist; low levels of risk behavior; and an impending outbreak. We considered each of these. Participants provided information on their enhanced sexual and injection networks and assisted us in recruiting network members. The largest connected component had 241 members. Data on risk behaviors in the last 6 months were collected at the individual level. Recent infection was determined by LAg (SediaTM Biosciences Corporation), data on recent seronegative tests, and viral load. HIV RNA was quantified using Artus HI Virus-1 RG RT-PCR (Qiagen). The 29 members of the connected subcomponent of uninfected participants were connected (network distance = 1) to 17 recently-infected and 24 long-term infected participants. Fourteen (48%) of these 29 uninfected were classified as "extremely high risk" because they self-reported syringe sharing and had at least one injection partner with viral load > 100,000 copies/mL who also reported syringe sharing. Seventeen of the 29 uninfected were re-interviewed after 6 months, but none had seroconverted. These findings show the power of network research in discovering infection patterns that standard individual-level studies cannot. Theoretical development and exploratory network research studies may be needed to understand these findings and deepen our understanding of how HIV does and does not spread through communities. Finally, the methods developed here provide practical tools to study "bottleneck" and "firewall" network hypotheses in practice. © 2018 Williams, Kostaki, Pavlitina, Paraskevis, Hatzakis, Schneider, Smyrnov, Hadjikou, Nikolopoulos, Psichogiou and Friedman.

The presence of human immunodeficiency virus type 1 (HIV-1) drug resistance among drug-naïve patients remains stable, although the proportion of patients with virological failure to therapy is decreasing. The dynamics of transmitted resistance among drug-naïve patients remains largely unknown. The prevalence of non-nucleoside reverse transcriptase inhibitors (NNRTI) resistance was 16.9% among treatment-naïve individuals in Greece. We aimed to investigate the transmission dynamics and the effective reproductive number (Re) of the locally transmitted NNRTI resistance. We analyzed sequences with dominant NNRTI resistance mutations (E138A and K103N) found within monophyletic clusters (local transmission networks (LTNs)) from patients in Greece. For the K103N LTN, the Re was >1 between 2008 and the first half of 2013. For all E138A LTNs, the Re was >1 between 1998 and 2015, except the most recent one (E138A_4), where the Re was >1 between 2006 and 2011 and approximately equal to 1 thereafter. K103N and E138A_4 showed similar characteristics with a more recent origin, higher Re during the first years of the sub-epidemics, and a declining trend in the number of transmissions during the last two years. In the remaining LTNs the epidemic was still expanding. Our study highlights the added value of molecular epidemiology to public health. © 2017 by the authors. Licensee MDPI, Basel, Switzerland.

Background: New diagnoses of HIV-1 infection among people who inject drugs (PWID) increased significantly during 2011 in Athens. Objective: Our aim was to investigate the patterns of HIV epidemic spread among PWID and to estimate the transmission dynamics for the major local transmission networks (LTNs). Methods: We analyzed sequences from 2,274 HIV-infected subjects sampled in Greece during 01/01/2011-31/10/2014. Of specimens in our sample, 874 sequences were isolated from HIV-infected PWID. Phylodynamic analysis was performed using birth-death serial skyline models. Results: Phylogenetic analysis revealed that the majority of sequences from PWID (N=746, 85.4%) fell within four LTNs: CRF14_BG (N=456, 58.3%), CRF35_AD (N=149, 19.1%), subtype B (N=118, 15.1%) and A1 (N=59, 7.5%). In addition to PWID, we also found that sequences from 36 non-PWID belonged to the LTNs corresponding to cross-group transmissions. Based on the estimated plots of the effective reproductive number (R e ) over time, subtype A1 and CRF35_AD LTNs showed a sharp increase before and during 2011 (maximum value of R e =3.0 and R e =4.6, respectively). For subtype B and CRF14_BG LTNs, the R e was increasing until the end of 2012 (maximum value of R e =3.2 and R e =3.0, respectively). Conclusion: HIV transmissions within subtype A1 and CRF35_AD LTNs increased sharply during the early stage of the outbreak, in contrast to subtype B and CRF14_BG. A significant reduction in the number of infections was estimated on all transmission networks from the beginning of 2013 onwards. Prevention measures that took place in the Athens metropolitan area at the end of 2012 including also the ARISTOTLE program may explain this decrease. © 2017 Bentham Science Publishers.

Background. High numbers of human immunodeficiency virus type 1 (HIV-1) infections among people who inject drugs (PWID) have been diagnosed in Athens, Greece, since 2011. We aimed to trace the geographic origin of HIV-1 infection for migrants who inject drugs and to investigate whether transmissions occur more frequently among migrants than among Greek nationals. Methods. Multiple cross-sectional studies were pooled to assemble all persons diagnosed with HIV-1 in Greece between 1 January 2011 and 31 October 2014. Phylogenetic analyses used maximum likelihood estimation. The hypothesis of ethnic compartmentalization was tested by reconstructing ancestral states of characters at the tips using the criterion of parsimony over a set of bootstrap trees. Results. Of 2274 persons, 38.4% were PWID. Phylogenetic analyses showed the existence of 4 major PWID-specific local transmission networks (LTNs): CRF14-BG (437 [58.6%]), CRF35-AD (139 [18.6%]), subtype B (116 [15.6%]), and subtype A (54 [7.2%]). Of 184 non-Greek PWID, 78.3% had been infected within the PWID-LTNs. For 173 (94.3%), the origin of their infection was assumed to be in Greece (postmigration). For PWID infected within LTNs, transmissions for subtype A and CRF14-BG occurred more frequently among migrants than would be expected by chance (phyloethnic study). Conclusions. Our analysis showed that the majority of infections among migrants occurred postmigration. The existence of significant transmission networking among migrants highlights that this population is a priority for HIV prevention. As molecular analysis can estimate the probable country of HIV infection, it can help to inform the design of public health strategies. © 2017 The Author. Published by Oxford University Press for the Infectious Diseases Society of America.

Background The prevalence of HIV-1 drug resistance among treatment-naïve patients ranges between 8.3% and 15% in Europe and North America. Previous studies showed that subtypes A and B were the most prevalent in the Greek HIV-1 epidemic. Our aim was to estimate the prevalence of resistance among drug naïve patients in Greece and to investigate the levels of transmission networking among those carrying resistant strains. Methods HIV-1 sequences were determined from 3428 drug naïve HIV-1 patients, in Greece sampled during 01/01/2003–30/6/2015. Transmission clusters were estimated by means of phylogenetic analysis including as references sequences from patients failing antiretroviral treatment in Greece and sequences sampled globally. Results The proportion of sequences with SDRMs was 5.98% (n = 205). The most prevalent SDRMs were found for NNRTIs (3.76%), followed by N(t)RTIs (2.28%) and PIs (1.02%). The resistance prevalence was 22.2% based on all mutations associated with resistance estimated using the HIVdb resistance interpretation algorithm. Resistance to NNRTIs was the most common (16.9%) followed by PIs (4.9%) and N(t)RTIs (2.8%). The most frequently observed NNRTI resistant mutations were E138A (7.7%), E138Q (4.0%), K103N (2.3%) and V179D (1.3%). The majority of subtype A sequences (89.7%; 245 out of 273) with the dominant NNRTI resistance mutations (E138A, K103N, E138Q, V179D) were found to belong to monophyletic clusters suggesting regional dispersal. For subtype B, 68.1% (139 out of 204) of resistant strains (E138A, K103N, E138Q V179D) belonged to clusters. For N(t)RTI-resistance, evidence for regional dispersal was found for 27.3% and 21.6% of subtype A and B sequences, respectively. Conclusions The TDR rate based on the prevalence of SDRM is lower than the average rate in Europe. However, the prevalence of NNRTI resistance estimated using the HIVdb approach, is high in Greece and it is mostly due to onward transmissions among drug-naïve patients. © 2017 Elsevier B.V.

HIV strains continuously evolve, tend to recombine, and new circulating variants are being discovered. Novel strains complicate efforts to develop a vaccine against HIV and may exhibit higher transmission efficiency and virulence, and elevated resistance to antiretroviral agents. The United Nations Joint Programme on HIV/AIDS (UNAIDS) set an ambitious goal to end HIV as a public health threat by 2030 through comprehensive strategies that include epidemiological input as the first step of the process. In this context, molecular epidemiology becomes invaluable as it captures trends in HIV evolution rates that shape epidemiological pictures across several geographical areas. This review briefly summarizes the molecular epidemiology of HIV among people who inject drugs (PWID) in Europe and Asia. Following high transmission rates of subtype G and CRF14_BG among PWID in Portugal and Spain, two European countries, Greece and Romania, experienced recent HIV outbreaks in PWID that consisted of multiple transmission clusters including subtypes B, A, F1, and recombinants CRF14_BG and CRF35_AD. The latter was first identified in Afghanistan. Russia, Ukraine, and other Former Soviet Union (FSU) states are still facing the devastating effects of epidemics in PWID produced by AFSU (also known as IDU-A), BFSU (known as IDU-B), and CRF03_AB. In Asia, CRF01_AE and subtype B (Western B and Thai B) travelled from PWID in Thailand to neighboring countries. Recombination hotspots in South China, Northern Myanmar, and Malaysia have been generating several intersubtype and inter-CRF recombinants (e.g. CRF07_BC, CRF08_BC, CRF33_01B etc.), increasing the complexity of HIV molecular patterns. © 2016 Elsevier B.V.

Human Immunodeficiency Virus type 1 (HIV-1) is characterised by vast genetic diversity. Globally circulating HIV-1 viruses are classified into distinct phylogenetic strains (subtypes, sub-subtypes) and several recombinant forms. Here we describe the characteristics and evolution of European HIV-1 epidemic over time through a review of published literature and updated queries of existing HIV-1 sequence databases. HIV-1 in Western and Central Europe was introduced in the early-1980s in the form of subtype B, which is still the predominant clade. However, in Eastern Europe (Former Soviet Union (FSU) countries and Russia) the predominant strain, introduced into Ukraine in the mid-1990s, is subtype A (AFSU) with transmission mostly occurring in People Who Inject Drugs (PWID). In recent years, the epidemic is evolving towards a complex tapestry with an increase in the prevalence of non-B subtypes and recombinants in Western and Central Europe. Non-B epidemics are mainly associated with immigrants, heterosexuals and females but more recently, non-B clades have also spread amongst groups where non-B strains were previously absent - non-immigrant European populations and amongst men having sex with men (MSM). In some countries, non-B clades have spread amongst the native population, for example subtype G in Portugal and subtype A in Greece, Albania and Cyprus. Romania provides a unique case where sub-subtype F1 has predominated throughout the epidemic. In contrast, HIV-1 epidemic in FSU countries remains more homogeneous with AFSU clade predominating in all countries. The differences between the evolution of the Western epidemic and the Eastern epidemic may be attributable to differences in transmission risk behaviours, lifestyle and the patterns of human mobility. The study of HIV-1 epidemic diversity provides a useful tool by which we can understand the history of the pandemic in addition to allowing us to monitor the spread and growth of the epidemic over time. © 2016 Elsevier B.V.

The evolution of hepatitis B virus (HBV), particularly its origins and evolutionary timescale, has been the subject of debate. Three major scenarios have been proposed, variously placing the origin of HBV in humans and great apes from some million years to only a few thousand years ago (ka). To compare these scenarios, we analyzed 105 full-length HBV genome sequences from all major genotypes sampled globally. We found a high correlation between the demographic histories of HBV and humans, as well as coincidence in the times of origin of specific subgenotypes with human migrations giving rise to their host indigenous populations. Together with phylogenetic evidence, this suggests that HBV has co-expanded with modern humans. Based on the co-expansion, we conducted a Bayesian dating analysis to estimate a precise evolutionary timescale for HBV. Five calibrations were used at the origins of F/H genotypes, D4, C3 and B6 from respective indigenous populations in the Pacific and Arctic and A5 from Haiti. The estimated time for the origin of HBV was 34.1ka (95% highest posterior density interval 27.6-41.3ka), coinciding with the dispersal of modern non-African humans. Our study, the first to use full-length HBV sequences, places a precise timescale on the HBV epidemic and also shows that the "branching paradox" of the more divergent genotypes F/H from Amerindians is due to an accelerated substitution rate, probably driven by positive selection. This may explain previously observed differences in the natural history of HBV between genotypes F1 and A2, B1, and D. © 2015 Elsevier Inc.

This study investigated selected structural correlates of fencing performance. 33 elite fencers were tested on (a) selected anthropometric, flexibility, and strength-power related parameters, and (b) specific lower extremity functional fencing tests. Multiple regression showed that drop jump and thigh cross-sectional area were best predictors of lunge time and distance of squat jump on the shuttle test. When the two performance variables were expressed per Lean Body Mass, lunge time was significantly predicted only by the performance on the arm-driven counter-movement jump, while time on the shuttle test was best predicted by three noncollinear significant predictors: squat jump performance, thigh circumference, and percent body fat. Lunge time and time on the shuttle test were predicted by explosive power, while none of the nontrainable anthropometric measures or years of training seemed to be important in performance of fencing-related skills. © Perceptual and Motor Skills 2010.

Background Adequate identification and testing of people at risk for HIV is fundamental for the HIV care continuum. A key strategy to improve timely testing is HIV indicator condition (IC) guided testing. Aim To evaluate the uptake of HIV testing recommendations in HIV IC-specific guidelines in European countries. Methods Between 2019 and 2021, European HIV experts reviewed guideline databases to identify all national guidelines of 62 HIV ICs. The proportion of HIV IC guidelines recommending HIV testing was reported, stratified by subgroup (HIV IC, country, eastern/western Europe, achievement of 90–90–90 goals and medical specialty). Results Of 30 invited European countries, 15 participated. A total of 791 HIV IC guidelines were identified: median 47 (IQR: 38–68) per country. Association with HIV was reported in 69% (545/791) of the guidelines, and 46% (366/791) recommended HIV testing, while 42% (101/242) of the AIDS-defining conditions recommended HIV testing. HIV testing recommendations were observed more frequently in guidelines in eastern (53%) than western (42%) European countries and in countries yet to achieve the 90–90–90 goals (52%) compared to those that had (38%). The medical specialties internal medicine, neurology/neurosurgery, ophthalmology, pulmonology and gynaecology/obstetrics had an HIV testing recommendation uptake below the 46% average. None of the 62 HIV ICs, countries or medical specialties had 100% accurate testing recommendation coverage in all their available HIV IC guidelines. Conclusion Fewer than half the HIV IC guidelines recommended HIV testing. This signals an insufficient adoption of this recommendation in non-HIV specialty guidelines across Europe.