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Article ; Online: Global and regional dispersal patterns of hepatitis B virus genotype E from and in Africa

Luicer Anne Olubayo Ingasia / Evangelia Georgia Kostaki / Dimitrios Paraskevis / Anna Kramvis

PLoS ONE, Vol 15, Iss 10, p e

A full-genome molecular analysis.

2020 Volume 0240375

Abstract: Description of the spatial characteristics of viral dispersal is important in understanding the history of infections. Nine hepatitis B virus (HBV) genotypes (A-I), and a putative 10th genotype (J), with distinct geographical distribution, are recognized. ...

Abstract	Description of the spatial characteristics of viral dispersal is important in understanding the history of infections. Nine hepatitis B virus (HBV) genotypes (A-I), and a putative 10th genotype (J), with distinct geographical distribution, are recognized. In sub-Saharan Africa (sub)-genotypes A1, D3 and E circulate, with E predominating in western Africa (WA), where HBV is hyperendemic. The low genetic diversity of genotype E (HBV/E) suggests its recent emergence. Our aim was to study the dispersal of HBV/E using full-length, non-redundant and non-recombinant sequences available in public databases. HBV/E was confirmed, and the phylogeny reconstruction performed using maximum likelihood (ML) with bootstrapping. Phylogeographic analysis was conducted by reconstruction of ancestral states using the criterion of parsimony on the estimated ML phylogeny. 46.5% of HBV/E sequences were found within monophyletic clusters. Country-wise analysis revealed the existence of 50 regional clusters. Sequences from WA were located close to the root of the tree, indicating this region as the most probable origin of the HBV/E epidemic and expanded to other geographical regions, within and outside of Africa. A localized dispersal was observed with sequences from Nigeria and Guinea as compared to other WA countries. Based on the sequences available in the databases, the phylogenetic results suggest that European strains originated primarily from WA whereas a majority of American strains originated in Western Central Africa. The differences in regional dispersal patterns of HBV/E suggest limited cross-border transmissions because of restricted population movements.
Keywords	Medicine ; R ; Science ; Q
Subject code	570
Language	English
Publishing date	2020-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Temporal Dominance of B.1.1.7 over B.1.354 SARS-CoV-2 Variant

Evangelia Georgia Kostaki / Ioulia Tseti / Sotirios Tsiodras / George N. Pavlakis / Petros P. Sfikakis / Dimitrios Paraskevis

Life, Vol 11, Iss 375, p

A Hypothesis Based on Areas of Variant Co-Circulation

2021 Volume 375

Abstract: Some emergent SARS-CoV-2 variants raise concerns due to their altered biological properties. For both B.1.1.7 and B.1351 variants, named as variants of concern (VOC), increased transmissibility was reported, whereas B.1.351 was more resistant to multiple ...

Abstract	Some emergent SARS-CoV-2 variants raise concerns due to their altered biological properties. For both B.1.1.7 and B.1351 variants, named as variants of concern (VOC), increased transmissibility was reported, whereas B.1.351 was more resistant to multiple monoclonal antibodies (mAbs), as well as convalescent and vaccination sera. To test this hypothesis, we examined the proportion of VOC over time across different geographic areas where the two VOC, B.1.1.7 and B.1.351, co-circulate. Our comparative analysis was based on the number of SARS-CoV-2 sequences on GISAID database. We report that B.1.1.7 dominates over B.1.351 in geographic areas where both variants co-circulate and the B.1.1.7 was the first variant introduced in the population. The only areas where B.1.351 was detected at higher proportion were South Africa and Mayotte in Africa, where this strain was associated with increased community transmission before the detection of B.1.1.7. The dominance of B.1.1.7 over B.1.351 could be important since B.1.351 was more resistant to certain mAbs, as well as heterologous convalescent and vaccination sera, thus suggesting that it may be transmitted more effectively in people with pre-existing immunity to other VOC. This scenario would lessen the effectiveness of vaccine and urge the need to update them with new strains.
Keywords	SARS-CoV-2 ; variants ; co-circulation ; dominance ; vaccines ; Science ; Q
Language	English
Publishing date	2021-04-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Automated, phylogeny-based genotype delimitation of the Hepatitis Viruses HBV and HCV

Dora Serdari / Evangelia-Georgia Kostaki / Dimitrios Paraskevis / Alexandros Stamatakis / Paschalia Kapli

PeerJ, Vol 7, p e

2019 Volume 7754

Abstract: 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 ... ...

Abstract	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.
Keywords	Virus ; DNA-barcoding ; Species delimitation ; Phylogeny ; HBV ; HCV ; Medicine ; R ; Biology (General) ; QH301-705.5
Subject code	500
Language	English
Publishing date	2019-10-01T00:00:00Z
Publisher	PeerJ Inc.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Overview of HIV molecular epidemiology among people who inject drugs in Europe and Asia

Nikolopoulos, Georgios K / Dimitrios Paraskevis / Evangelia-Georgia Kostaki

Infection, genetics, and evolution. 2016 Dec., v. 46

2016

Abstract: 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 ...

Abstract	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.
Keywords	antiretroviral agents ; disease outbreaks ; drug abuse ; drugs ; evolution ; Human immunodeficiency virus ; molecular epidemiology ; people ; public health ; United Nations ; vaccine development ; virulence ; Afghanistan ; China ; Greece ; Malaysia ; Myanmar ; Portugal ; Romania ; Russia ; Spain ; Thailand ; Ukraine ; USSR
Language	English
Dates of publication	2016-12
Size	p. 256-268.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	2037068-4
ISSN	1567-1348
ISSN	1567-1348
DOI	10.1016/j.meegid.2016.06.017
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Unravelling the history of hepatitis B virus genotypes A and D infection using a full-genome phylogenetic and phylogeographic approach

Evangelia-Georgia Kostaki / Timokratis Karamitros / Garyfallia Stefanou / Ioannis Mamais / Konstantinos Angelis / Angelos Hatzakis / Anna Kramvis / Dimitrios Paraskevis

eLife, Vol

2018 Volume 7

Abstract: 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 ... ...

Abstract	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.
Keywords	hepatitis B virus ; phylogeny ; phylogeography ; global dispersal ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
Subject code	570
Language	English
Publishing date	2018-08-01T00:00:00Z
Publisher	eLife Sciences Publications Ltd
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: SARS-CoV-2 Molecular Transmission Clusters and Containment Measures in Ten European Regions During the First Pandemic Wave

Maria Bousali / Aristea Dimadi / Evangelia-Georgia Kostaki / Sotirios Tsiodras / Georgios K. Nikolopoulos / Dionyssios N. Sgouras / Gkikas Magiorkinis / George Papatheodoridis / Vasiliki Pogka / Giota Lourida / Aikaterini Argyraki / Emmanouil Angelakis / George Sourvinos / Apostolos Beloukas / Dimitrios Paraskevis / Timokratis Karamitros

Life, Vol 11, Iss 219, p

2021 Volume 219

Abstract: 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 ...

Abstract	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.
Keywords	SARS-CoV-2 ; COVID-19 ; pandemic ; transmission ; clusters ; phylodynamics ; Science ; Q
Language	English
Publishing date	2021-03-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: SARS-CoV-2 Infection Is Asymptomatic in Nearly Half of Adults with Robust Anti-Spike Protein Receptor-Binding Domain Antibody Response

Ourania E. Tsitsilonis / Dimitrios Paraskevis / Evi Lianidou / Evangelos Terpos / Athanasios Akalestos / Vassilios Pierros / Evangelia Georgia Kostaki / Efstathios Kastritis / Paraskevi Moutsatsou / Marianna Politou / Andreas Scorilas / Thomas Sphicopoulos / Nikolaos Thomaidis / Ioannis P. Trougakos / Athanassios Tsakris / Nikolaos Voulgaris / Christina C. Daskalaki / Zoi Evangelakou / Christina Fouki /

Despoina D. Gianniou / Sentiljana Gumeni / Ioannis V. Kostopoulos / Maria S. Manola / Nikolaos Orologas-Stavrou / Chrysanthi Panteli / Eleni-Dimitra Papanagnou / Pantelis Rousakis / Aimilia D. Sklirou / Stavroula Smilkou / Dimitra Stergiopoulou / Sotirios Tsiodras / Meletios-Athanasios Dimopoulos / Petros P. Sfikakis

Vaccines, Vol 9, Iss 3, p

2021 Volume 207

Abstract: Between June and November 2020, we assessed plasma antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid protein in 4996 participants (aged 18–82 years, 34.5% men) from the National and Kapodistrian University of ... ...

Abstract	Between June and November 2020, we assessed plasma antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid protein in 4996 participants (aged 18–82 years, 34.5% men) from the National and Kapodistrian University of Athens. The weighted overall prevalence was 1.6% and monthly prevalence correlated with viral RNA-confirmed SARS-CoV-2 infections in Greece, in the same period. Notably, 49% of seropositive cases reported no history of SARS-CoV-2 infection-related clinical symptoms and 33% were unsuspected of their previous infection. Additionally, levels of anti-SARS-CoV-2 antibodies against the spike-protein receptor-binding domain were similar between symptomatic and asymptomatic individuals, irrespective of age and gender. Using Food and Drug Administration Emergency Use Authorization-approved assays, these results support the need for such studies on pandemic evaluation and highlight the development of robust humoral immune responses even among asymptomatic individuals. The high percentage of unsuspected/asymptomatic active cases, which may contribute to community transmission for more days than that of cases who are aware and self-isolate, underscores the necessity of measures across the population for the efficient control of the pandemic.
Keywords	SARS-CoV-2 ; seroepidemiology ; asymptomatic ; unsuspected/asymptomatic ; antibodies ; Medicine ; R
Language	English
Publishing date	2021-03-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Seroprevalence of Antibodies against SARS-CoV-2 among the Personnel and Students of the National and Kapodistrian University of Athens, Greece

Ourania E. Tsitsilonis / Dimitrios Paraskevis / Evi Lianidou / Vassilios Pierros / Athanasios Akalestos / Efstathios Kastritis / Paraskevi Moutsatsou / Andreas Scorilas / Thomas Sphicopoulos / Evangelos Terpos / Nikolaos Thomaidis / Athanassios Tsakris / Nikolaos Voulgaris / Christina C. Daskalaki / Zoi Evangelakou / Christina Fouki / Despoina D. Gianniou / Sentiljana Gumeni / Evangelia-Georgia Kostaki /

Ioannis V. Kostopoulos / Maria S. Manola / Nikolaos Orologas-Stavrou / Chrysanthi Panteli / Eleni-Dimitra Papanagnou / Pantelis Rousakis / Aimilia D. Sklirou / Stavroula Smilkou / Dimitra Stergiopoulou / Ioannis P. Trougakos / Petros P. Sfikakis / Meletios-Athanasios Dimopoulos

Life, Vol 10, Iss 214, p

A Preliminary Report

2020 Volume 214

Abstract: 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 (ΝΚUA), especially its health-care/medical ... ...

Abstract	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 (ΝΚUA), 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.
Keywords	SARS-CoV-2 antibodies ; seroepidemiological study ; seroprevalence ; National and Kapodistrian University of Athens ; Science ; Q
Language	English
Publishing date	2020-09-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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