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Dr. Francesco Messina
Laboratory of Virology, National Institute for Infectious Diseases "L. Spallanzani", IRCCS, Rome Italy

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0 Bioinformatics
0 CoronaVirus
0 covid-19
0 SARS Virus
0 Host patogen interaction

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CoronaVirus

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Journal article
Published: 12 August 2021 in Cell Death & Disease
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In the last months, many studies have clearly described several mechanisms of SARS-CoV-2 infection at cell and tissue level, but the mechanisms of interaction between host and SARS-CoV-2, determining the grade of COVID-19 severity, are still unknown. We provide a network analysis on protein–protein interactions (PPI) between viral and host proteins to better identify host biological responses, induced by both whole proteome of SARS-CoV-2 and specific viral proteins. A host-virus interactome was inferred, applying an explorative algorithm (Random Walk with Restart, RWR) triggered by 28 proteins of SARS-CoV-2. The analysis of PPI allowed to estimate the distribution of SARS-CoV-2 proteins in the host cell. Interactome built around one single viral protein allowed to define a different response, underlining as ORF8 and ORF3a modulated cardiovascular diseases and pro-inflammatory pathways, respectively. Finally, the network-based approach highlighted a possible direct action of ORF3a and NS7b to enhancing Bradykinin Storm. This network-based representation of SARS-CoV-2 infection could be a framework for pathogenic evaluation of specific clinical outcomes. We identified possible host responses induced by specific proteins of SARS-CoV-2, underlining the important role of specific viral accessory proteins in pathogenic phenotypes of severe COVID-19 patients.

ACS Style

Francesco Messina; Emanuela Giombini; Chiara Montaldo; Ashish Arunkumar Sharma; Antonio Zoccoli; Rafick-Pierre Sekaly; Franco Locatelli; Alimuddin Zumla; Markus Maeurer; Maria R. Capobianchi; Francesco Nicola Lauria; Giuseppe Ippolito. Looking for pathways related to COVID-19: confirmation of pathogenic mechanisms by SARS-CoV-2–host interactome. Cell Death & Disease 2021, 12, 1 .

AMA Style

Francesco Messina, Emanuela Giombini, Chiara Montaldo, Ashish Arunkumar Sharma, Antonio Zoccoli, Rafick-Pierre Sekaly, Franco Locatelli, Alimuddin Zumla, Markus Maeurer, Maria R. Capobianchi, Francesco Nicola Lauria, Giuseppe Ippolito. Looking for pathways related to COVID-19: confirmation of pathogenic mechanisms by SARS-CoV-2–host interactome. Cell Death & Disease. 2021; 12 (8):1.

Chicago/Turabian Style

Francesco Messina; Emanuela Giombini; Chiara Montaldo; Ashish Arunkumar Sharma; Antonio Zoccoli; Rafick-Pierre Sekaly; Franco Locatelli; Alimuddin Zumla; Markus Maeurer; Maria R. Capobianchi; Francesco Nicola Lauria; Giuseppe Ippolito. 2021. "Looking for pathways related to COVID-19: confirmation of pathogenic mechanisms by SARS-CoV-2–host interactome." Cell Death & Disease 12, no. 8: 1.

Journal article
Published: 06 July 2021 in Viruses
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Complex systems are inherently multilevel and multiscale systems. The infectious disease system is considered a complex system resulting from the interaction between three sub-systems (host, pathogen, and environment) organized into a hierarchical structure, ranging from the cellular to the macro-ecosystem level, with multiscales. Therefore, to describe infectious disease phenomena that change through time and space and at different scales, we built a model framework where infectious disease must be considered the set of biological responses of human hosts to pathogens, with biological pathways shared with other pathologies in an ecological interaction context. In this paper, we aimed to design a framework for building a disease model for COVID-19 based on current literature evidence. The model was set up by identifying the molecular pathophysiology related to the COVID-19 phenotypes, collecting the mechanistic knowledge scattered across scientific literature and bioinformatic databases, and integrating it using a logical/conceptual model systems biology. The model framework building process began from the results of a domain-based literature review regarding a multiomics approach to COVID-19. This evidence allowed us to define a framework of COVID-19 conceptual model and to report all concepts in a multilevel and multiscale structure. The same interdisciplinary working groups that carried out the scoping review were involved. The conclusive result is a conceptual method to design multiscale models of infectious diseases. The methodology, applied in this paper, is a set of partially ordered research and development activities that result in a COVID-19 multiscale model.

ACS Style

Francesco Messina; Chiara Montaldo; Isabella Abbate; Manuela Antonioli; Veronica Bordoni; Giulia Matusali; Alessandra Sacchi; Emanuela Giombini; Gian Fimia; Mauro Piacentini; Maria Capobianchi; Francesco Lauria; Giuseppe Ippolito; on behalf of COVID-19 Scoping Review Working Group. Rationale and Criteria for a COVID-19 Model Framework. Viruses 2021, 13, 1309 .

AMA Style

Francesco Messina, Chiara Montaldo, Isabella Abbate, Manuela Antonioli, Veronica Bordoni, Giulia Matusali, Alessandra Sacchi, Emanuela Giombini, Gian Fimia, Mauro Piacentini, Maria Capobianchi, Francesco Lauria, Giuseppe Ippolito, on behalf of COVID-19 Scoping Review Working Group. Rationale and Criteria for a COVID-19 Model Framework. Viruses. 2021; 13 (7):1309.

Chicago/Turabian Style

Francesco Messina; Chiara Montaldo; Isabella Abbate; Manuela Antonioli; Veronica Bordoni; Giulia Matusali; Alessandra Sacchi; Emanuela Giombini; Gian Fimia; Mauro Piacentini; Maria Capobianchi; Francesco Lauria; Giuseppe Ippolito; on behalf of COVID-19 Scoping Review Working Group. 2021. "Rationale and Criteria for a COVID-19 Model Framework." Viruses 13, no. 7: 1309.

Preprint content
Published: 21 May 2021
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Early sequencing and quick analysis of SARS-CoV-2 genome are contributing to understand the dynamics of COVID19 epidemics and to countermeasures design at global level. Amplicon-based NGS methods are widely used to sequence the SARS-CoV-2 genome and to identify novel variants that are emerging in rapid succession, harboring multiple deletions and amino acid changing mutations. To facilitate the analysis of NGS sequencing data obtained from amplicon-based sequencing methods, here we propose an easy-to-use SARS-CoV-2 genome Assembler: the ESCA pipeline. Results showed that ESCA can perform high quality genome assembly from IonTor-rent and Illumina raw data, and help the user in easily correct low-coverage regions. Moreover, ESCA includes the possibility to compare assembled genomes of multi sample runs through an easy table format. Script and manuals are available on GitHub: https://github.com/cesaregruber/ESCA

ACS Style

Martina Rueca; Emanuela Giombini; Francesco Messina; Barbara Bartolini; Antonino Di Caro; Maria R. Capobianchi; Cesare E. M. Gruber. ESCA pipeline: Easy-to-use SARS-CoV-2 genome Assembler. 2021, 1 .

AMA Style

Martina Rueca, Emanuela Giombini, Francesco Messina, Barbara Bartolini, Antonino Di Caro, Maria R. Capobianchi, Cesare E. M. Gruber. ESCA pipeline: Easy-to-use SARS-CoV-2 genome Assembler. . 2021; ():1.

Chicago/Turabian Style

Martina Rueca; Emanuela Giombini; Francesco Messina; Barbara Bartolini; Antonino Di Caro; Maria R. Capobianchi; Cesare E. M. Gruber. 2021. "ESCA pipeline: Easy-to-use SARS-CoV-2 genome Assembler." , no. : 1.

Preprint content
Published: 30 November 2020
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A new SARS-CoV-2 clade (GV) characterized by S substitution A222V, first reported from Spain in March, is rapidly spreading across Europe. To establish the A222V variant involvement in the infection rise in Italy, all GISAID sequences from Italy and those from our Laboratory (Lazio) in the period June-October were analysed. A222V, first recognized in August, represents 11.2% of sequences in this period, reaching 100% of autochthonous sequences in October, supporting increased GV circulation in Italy.

ACS Style

Barbara Bartolini; Martina Rueca; Cesare Ernesto Maria Gruber; Francesco Messina; Emanuela Giombini; Giuseppe Ippolito; Maria Rosaria Capobianchi; Antonino Di Caro. The newly introduced SARS-CoV-2 variant A222V is rapidly spreading in Lazio region, Italy. 2020, 1 .

AMA Style

Barbara Bartolini, Martina Rueca, Cesare Ernesto Maria Gruber, Francesco Messina, Emanuela Giombini, Giuseppe Ippolito, Maria Rosaria Capobianchi, Antonino Di Caro. The newly introduced SARS-CoV-2 variant A222V is rapidly spreading in Lazio region, Italy. . 2020; ():1.

Chicago/Turabian Style

Barbara Bartolini; Martina Rueca; Cesare Ernesto Maria Gruber; Francesco Messina; Emanuela Giombini; Giuseppe Ippolito; Maria Rosaria Capobianchi; Antonino Di Caro. 2020. "The newly introduced SARS-CoV-2 variant A222V is rapidly spreading in Lazio region, Italy." , no. : 1.

Preprint content
Published: 03 November 2020
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In the last months, many studies have clearly described several mechanisms of SARS−CoV−2 infection at cell and tissue level. Host conditions and comorbidities were identified as risk factors for severe and fatal disease courses, but the mechanisms of interaction between host and SARS−CoV−2 determining the grade of COVID−19 severity, are still unknown. We provide a network analysis on protein−protein interactions (PPI) between viral and host proteins to better identify host biological responses, induced by both whole proteome of SARS−CoV−2 and specific viral proteins. A host−virus interactome was inferred on published PPI, using an explorative algorithm (Random Walk with Restart) triggered by all the 28 proteins of SARS−CoV−2, or each single viral protein one−by−one. The functional analysis for all proteins, linked to many aspects of COVID−19 pathogenesis, allows to identify the subcellular districts, where SARS−CoV−2 proteins seem to be distributed, while in each interactome built around one single viral protein, a different response was described, underlining as ORF8 and ORF3a modulated cardiovascular diseases and pro-inflammatory pathways, respectively. Finally, an explorative network-based approach was applied to Bradykinin Storm, highlighting a possible direct action of ORF3a and NS7b to enhancing this condition. This network-based model for SARS−CoV−2 infection could be a framework for pathogenic evaluation of specific clinical outcomes. We identified possible host responses induced by specific proteins of SARS−CoV−2, underlining the important role of specific viral accessory proteins in pathogenic phenotypes of severe COVID−19 patients.

ACS Style

Francesco Messina; Emanuela Giombini; Chiara Montaldo; Ashish Arunkumar Sharma; Mauro Piacentini; Antonio Zoccoli; Rafick Pierre Sekaly; Franco Locatelli; Alimuddin Zumla; Markus Maeurer; Maria Rosaria Capobianchi; Francesco Nicola Lauria; Giuseppe Ippolito. Looking for pathways related to COVID-19 phenotypes: Confirmation of pathogenic mechanisms by SARS-CoV-2 - Host interactome. 2020, 1 .

AMA Style

Francesco Messina, Emanuela Giombini, Chiara Montaldo, Ashish Arunkumar Sharma, Mauro Piacentini, Antonio Zoccoli, Rafick Pierre Sekaly, Franco Locatelli, Alimuddin Zumla, Markus Maeurer, Maria Rosaria Capobianchi, Francesco Nicola Lauria, Giuseppe Ippolito. Looking for pathways related to COVID-19 phenotypes: Confirmation of pathogenic mechanisms by SARS-CoV-2 - Host interactome. . 2020; ():1.

Chicago/Turabian Style

Francesco Messina; Emanuela Giombini; Chiara Montaldo; Ashish Arunkumar Sharma; Mauro Piacentini; Antonio Zoccoli; Rafick Pierre Sekaly; Franco Locatelli; Alimuddin Zumla; Markus Maeurer; Maria Rosaria Capobianchi; Francesco Nicola Lauria; Giuseppe Ippolito. 2020. "Looking for pathways related to COVID-19 phenotypes: Confirmation of pathogenic mechanisms by SARS-CoV-2 - Host interactome." , no. : 1.

Preprint content
Published: 28 October 2020
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We describe a large-scale community effort to build an open-access, interoperable, and computable repository of COVID-19 molecular mechanisms - the COVID-19 Disease Map. We discuss the tools, platforms, and guidelines necessary for the distributed development of its contents by a multi-faceted community of biocurators, domain experts, bioinformaticians, and computational biologists. We highlight the role of relevant databases and text mining approaches in enrichment and validation of the curated mechanisms. We describe the contents of the Map and their relevance to the molecular pathophysiology of COVID-19 and the analytical and computational modelling approaches that can be applied for mechanistic data interpretation and predictions. We conclude by demonstrating concrete applications of our work through several use cases and highlight new testable hypotheses.

ACS Style

Marek Ostaszewski; Anna Niarakis; Alexander Mazein; Inna Kuperstein; Robert Phair; Aurelio Orta-Resendiz; Vidisha Singh; Sara Sadat Aghamiri; Marcio Luis Acencio; Enrico Glaab; Andreas Ruepp; Gisela Fobo; Corinna Montrone; Barbara Brauner; Goar Frischman; Luis Cristóbal Monraz Gómez; Julia Somers; Matti Hoch; Shailendra Kumar Gupta; Julia Scheel; Hanna Borlinghaus; Tobias Czauderna; Falk Schreiber; Arnau Montagud; Miguel Ponce de Leon; Akira Funahashi; Yusuke Hiki; Noriko Hiroi; Takahiro G. Yamada; Andreas Dräger; Alina Renz; Muhammad Naveez; Zsolt Bocskei; Francesco Messina; Daniela Börnigen; Liam Fergusson; Marta Conti; Marius Rameil; Vanessa Nakonecnij; Jakob Vanhoefer; Leonard Schmiester; Muying Wang; Emily E. Ackerman; Jason Shoemaker; Jeremy Zucker; Kristie Oxford; Jeremy Teuton; Ebru Kocakaya; Gökçe Yağmur Summak; Kristina Hanspers; Martina Kutmon; Susan Coort; Lars Eijssen; Friederike Ehrhart; D. A. B. Rex; Denise Slenter; Marvin Martens; Robin Haw; Bijay Jassal; Lisa Matthews; Marija Orlic-Milacic; Andrea Senff Ribeiro; Karen Rothfels; Veronica Shamovsky; Ralf Stephan; Cristoffer Sevilla; Thawfeek Varusai; Jean-Marie Ravel; Rupsha Fraser; Vera Ortseifen; Silvia Marchesi; Piotr Gawron; Ewa Smula; Laurent Heirendt; Venkata Satagopam; Guanming Wu; Anders Riutta; Martin Golebiewski; Stuart Owen; Carole Goble; XiaoMing Hu; Rupert W. Overall; Dieter Maier; Angela Bauch; Benjamin M. Gyori; John A. Bachman; Carlos Vega; Valentin Grouès; Miguel Vazquez; Pablo Porras; Luana Licata; Marta Iannuccelli; Francesca Sacco; Anastasia Nesterova; Anton Yuryev; Anita de Waard; Denes Turei; Augustin Luna; Ozgun Babur; Sylvain Soliman; Alberto Valdeolivas; Marina Esteban- Medina; Maria Peña-Chilet; Tomáš Helikar; Bhanwar Lal Puniya; Dezso Modos; Agatha Treveil; Marton Olbei; Bertrand De Meulder; Aurélien Dugourd; Aurelien Naldi; Vincent Noel; Laurence Calzone; Chris Sander; Emek Demir; Tamas Korcsmaros; Tom C. Freeman; Franck Augé; Jacques S. Beckmann; Jan Hasenauer; Olaf Wolkenhauer; Egon L. Wilighagen; Alexander R. Pico; Chris T. Evelo; Marc E. Gillespie; Lincoln D. Stein; Henning Hermjakob; Peter D’Eustachio; Julio Saez-Rodriguez; Joaquin Dopazo; Alfonso Valencia; Hiroaki Kitano; Emmanuel Barillot; Charles Auffray; Rudi Balling; Reinhard Schneider; the COVID-19 Disease Map Community. COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms. 2020, 1 .

AMA Style

Marek Ostaszewski, Anna Niarakis, Alexander Mazein, Inna Kuperstein, Robert Phair, Aurelio Orta-Resendiz, Vidisha Singh, Sara Sadat Aghamiri, Marcio Luis Acencio, Enrico Glaab, Andreas Ruepp, Gisela Fobo, Corinna Montrone, Barbara Brauner, Goar Frischman, Luis Cristóbal Monraz Gómez, Julia Somers, Matti Hoch, Shailendra Kumar Gupta, Julia Scheel, Hanna Borlinghaus, Tobias Czauderna, Falk Schreiber, Arnau Montagud, Miguel Ponce de Leon, Akira Funahashi, Yusuke Hiki, Noriko Hiroi, Takahiro G. Yamada, Andreas Dräger, Alina Renz, Muhammad Naveez, Zsolt Bocskei, Francesco Messina, Daniela Börnigen, Liam Fergusson, Marta Conti, Marius Rameil, Vanessa Nakonecnij, Jakob Vanhoefer, Leonard Schmiester, Muying Wang, Emily E. Ackerman, Jason Shoemaker, Jeremy Zucker, Kristie Oxford, Jeremy Teuton, Ebru Kocakaya, Gökçe Yağmur Summak, Kristina Hanspers, Martina Kutmon, Susan Coort, Lars Eijssen, Friederike Ehrhart, D. A. B. Rex, Denise Slenter, Marvin Martens, Robin Haw, Bijay Jassal, Lisa Matthews, Marija Orlic-Milacic, Andrea Senff Ribeiro, Karen Rothfels, Veronica Shamovsky, Ralf Stephan, Cristoffer Sevilla, Thawfeek Varusai, Jean-Marie Ravel, Rupsha Fraser, Vera Ortseifen, Silvia Marchesi, Piotr Gawron, Ewa Smula, Laurent Heirendt, Venkata Satagopam, Guanming Wu, Anders Riutta, Martin Golebiewski, Stuart Owen, Carole Goble, XiaoMing Hu, Rupert W. Overall, Dieter Maier, Angela Bauch, Benjamin M. Gyori, John A. Bachman, Carlos Vega, Valentin Grouès, Miguel Vazquez, Pablo Porras, Luana Licata, Marta Iannuccelli, Francesca Sacco, Anastasia Nesterova, Anton Yuryev, Anita de Waard, Denes Turei, Augustin Luna, Ozgun Babur, Sylvain Soliman, Alberto Valdeolivas, Marina Esteban- Medina, Maria Peña-Chilet, Tomáš Helikar, Bhanwar Lal Puniya, Dezso Modos, Agatha Treveil, Marton Olbei, Bertrand De Meulder, Aurélien Dugourd, Aurelien Naldi, Vincent Noel, Laurence Calzone, Chris Sander, Emek Demir, Tamas Korcsmaros, Tom C. Freeman, Franck Augé, Jacques S. Beckmann, Jan Hasenauer, Olaf Wolkenhauer, Egon L. Wilighagen, Alexander R. Pico, Chris T. Evelo, Marc E. Gillespie, Lincoln D. Stein, Henning Hermjakob, Peter D’Eustachio, Julio Saez-Rodriguez, Joaquin Dopazo, Alfonso Valencia, Hiroaki Kitano, Emmanuel Barillot, Charles Auffray, Rudi Balling, Reinhard Schneider, the COVID-19 Disease Map Community. COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms. . 2020; ():1.

Chicago/Turabian Style

Marek Ostaszewski; Anna Niarakis; Alexander Mazein; Inna Kuperstein; Robert Phair; Aurelio Orta-Resendiz; Vidisha Singh; Sara Sadat Aghamiri; Marcio Luis Acencio; Enrico Glaab; Andreas Ruepp; Gisela Fobo; Corinna Montrone; Barbara Brauner; Goar Frischman; Luis Cristóbal Monraz Gómez; Julia Somers; Matti Hoch; Shailendra Kumar Gupta; Julia Scheel; Hanna Borlinghaus; Tobias Czauderna; Falk Schreiber; Arnau Montagud; Miguel Ponce de Leon; Akira Funahashi; Yusuke Hiki; Noriko Hiroi; Takahiro G. Yamada; Andreas Dräger; Alina Renz; Muhammad Naveez; Zsolt Bocskei; Francesco Messina; Daniela Börnigen; Liam Fergusson; Marta Conti; Marius Rameil; Vanessa Nakonecnij; Jakob Vanhoefer; Leonard Schmiester; Muying Wang; Emily E. Ackerman; Jason Shoemaker; Jeremy Zucker; Kristie Oxford; Jeremy Teuton; Ebru Kocakaya; Gökçe Yağmur Summak; Kristina Hanspers; Martina Kutmon; Susan Coort; Lars Eijssen; Friederike Ehrhart; D. A. B. Rex; Denise Slenter; Marvin Martens; Robin Haw; Bijay Jassal; Lisa Matthews; Marija Orlic-Milacic; Andrea Senff Ribeiro; Karen Rothfels; Veronica Shamovsky; Ralf Stephan; Cristoffer Sevilla; Thawfeek Varusai; Jean-Marie Ravel; Rupsha Fraser; Vera Ortseifen; Silvia Marchesi; Piotr Gawron; Ewa Smula; Laurent Heirendt; Venkata Satagopam; Guanming Wu; Anders Riutta; Martin Golebiewski; Stuart Owen; Carole Goble; XiaoMing Hu; Rupert W. Overall; Dieter Maier; Angela Bauch; Benjamin M. Gyori; John A. Bachman; Carlos Vega; Valentin Grouès; Miguel Vazquez; Pablo Porras; Luana Licata; Marta Iannuccelli; Francesca Sacco; Anastasia Nesterova; Anton Yuryev; Anita de Waard; Denes Turei; Augustin Luna; Ozgun Babur; Sylvain Soliman; Alberto Valdeolivas; Marina Esteban- Medina; Maria Peña-Chilet; Tomáš Helikar; Bhanwar Lal Puniya; Dezso Modos; Agatha Treveil; Marton Olbei; Bertrand De Meulder; Aurélien Dugourd; Aurelien Naldi; Vincent Noel; Laurence Calzone; Chris Sander; Emek Demir; Tamas Korcsmaros; Tom C. Freeman; Franck Augé; Jacques S. Beckmann; Jan Hasenauer; Olaf Wolkenhauer; Egon L. Wilighagen; Alexander R. Pico; Chris T. Evelo; Marc E. Gillespie; Lincoln D. Stein; Henning Hermjakob; Peter D’Eustachio; Julio Saez-Rodriguez; Joaquin Dopazo; Alfonso Valencia; Hiroaki Kitano; Emmanuel Barillot; Charles Auffray; Rudi Balling; Reinhard Schneider; the COVID-19 Disease Map Community. 2020. "COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms." , no. : 1.

Journal article
Published: 13 September 2020 in Viruses
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The Republic of Congo (RoC) declared a chikungunya (CHIK) outbreak on 9 February 2019. We conducted a ONE-Human-Animal HEALTH epidemiological, virological and entomological investigation. Methods: We collected national surveillance and epidemiological data. CHIK diagnosis was based on RT-PCR and CHIKV-specific antibodies. Full CHIKV genome sequences were obtained by Sanger and MinION approaches and Bayesian tree phylogenetic analysis was performed. Mosquito larvae and 215 adult mosquitoes were collected in different villages of Kouilou and Pointe-Noire districts and estimates of Aedes (Ae.) mosquitos’ CHIKV-infectious bites obtained. We found two new CHIKV sequences of the East/Central/South African (ECSA) lineage, clustering with the recent enzootic sub-clade 2, showing the A226V mutation. The RoC 2019 CHIKV strain has two novel mutations, E2-T126M and E2-H351N. Phylogenetic suggests a common origin from 2016 Angola strain, from which it diverged around 1989 (95% HPD 1985–1994). The infectious bite pattern was similar for 2017, 2018 and early 2019. One Ae. albopictus pool was RT-PCR positive. The 2019 RoC CHIKV strain seems to be recently introduced or be endemic in sylvatic cycle. Distinct from the contemporary Indian CHIKV isolates and in contrast to the original Central-African strains (transmitted by Ae. aegypti), it carries the A226V mutation, indicating an independent adaptive mutation in response to vector replacement (Ae. albopictus vs Ae. aegypti).

ACS Style

Francesco Vairo; Martin Aimè Coussoud-Mavoungou; Francine Ntoumi; Concetta Castilletti; Lambert Kitembo; Najmul Haider; Fabrizio Carletti; Francesca Colavita; Cesare Gruber; Marco Iannetta; Francesco Messina; Simone Lanini; Biez Ulrich Judicaël; Emanuela Giombini; Chiara Montaldo; Chantal Portella; Steve Diafouka-Diatela; Martina Rueca; Richard Kock; Barbara Bartolini; Leonard Mboera; Vincent Munster; Robert Fischer; Stephanie Seifert; César Muñoz-Fontela; Beatriz Escudero-Pérez; Sergio Gomez-Medina; Emily Nelson; Patrick Kjia Tungu; Emanuele Nicastri; Vincenzo Puro; Antonino Di Caro; Maria Capobianchi; Jacqueline Mikolo; Alimuddin Zumla; Giuseppe Ippolito; on behalf of the Pandora-ID-NET Consortium Chikungunya Outbreak Group Taskforce. Chikungunya Outbreak in the Republic of the Congo, 2019—Epidemiological, Virological and Entomological Findings of a South-North Multidisciplinary Taskforce Investigation. Viruses 2020, 12, 1020 .

AMA Style

Francesco Vairo, Martin Aimè Coussoud-Mavoungou, Francine Ntoumi, Concetta Castilletti, Lambert Kitembo, Najmul Haider, Fabrizio Carletti, Francesca Colavita, Cesare Gruber, Marco Iannetta, Francesco Messina, Simone Lanini, Biez Ulrich Judicaël, Emanuela Giombini, Chiara Montaldo, Chantal Portella, Steve Diafouka-Diatela, Martina Rueca, Richard Kock, Barbara Bartolini, Leonard Mboera, Vincent Munster, Robert Fischer, Stephanie Seifert, César Muñoz-Fontela, Beatriz Escudero-Pérez, Sergio Gomez-Medina, Emily Nelson, Patrick Kjia Tungu, Emanuele Nicastri, Vincenzo Puro, Antonino Di Caro, Maria Capobianchi, Jacqueline Mikolo, Alimuddin Zumla, Giuseppe Ippolito, on behalf of the Pandora-ID-NET Consortium Chikungunya Outbreak Group Taskforce. Chikungunya Outbreak in the Republic of the Congo, 2019—Epidemiological, Virological and Entomological Findings of a South-North Multidisciplinary Taskforce Investigation. Viruses. 2020; 12 (9):1020.

Chicago/Turabian Style

Francesco Vairo; Martin Aimè Coussoud-Mavoungou; Francine Ntoumi; Concetta Castilletti; Lambert Kitembo; Najmul Haider; Fabrizio Carletti; Francesca Colavita; Cesare Gruber; Marco Iannetta; Francesco Messina; Simone Lanini; Biez Ulrich Judicaël; Emanuela Giombini; Chiara Montaldo; Chantal Portella; Steve Diafouka-Diatela; Martina Rueca; Richard Kock; Barbara Bartolini; Leonard Mboera; Vincent Munster; Robert Fischer; Stephanie Seifert; César Muñoz-Fontela; Beatriz Escudero-Pérez; Sergio Gomez-Medina; Emily Nelson; Patrick Kjia Tungu; Emanuele Nicastri; Vincenzo Puro; Antonino Di Caro; Maria Capobianchi; Jacqueline Mikolo; Alimuddin Zumla; Giuseppe Ippolito; on behalf of the Pandora-ID-NET Consortium Chikungunya Outbreak Group Taskforce. 2020. "Chikungunya Outbreak in the Republic of the Congo, 2019—Epidemiological, Virological and Entomological Findings of a South-North Multidisciplinary Taskforce Investigation." Viruses 12, no. 9: 1020.

Journal article
Published: 26 August 2020 in Microorganisms
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We report whole-genome and intra-host variability of SARS-Cov-2 assessed by next generation sequencing (NGS) in upper (URT) and lower respiratory tract (LRT) from COVID-19 patients. The aim was to identify possible tissue-specific patterns and signatures of variant selection for each respiratory compartment. Six patients, admitted to the Intensive Care Unit, were included in the study. Thirteen URT and LRT were analyzed by NGS amplicon-based approach on Ion Torrent Platform. Bioinformatic analysis was performed using both realized in-house and supplied by ThermoFisher programs. Phylogenesis showed clade V clustering of the first patients diagnosed in Italy, and clade G for later strains. The presence of quasispecies was observed, with variants uniformly distributed along the genome and frequency of minority variants spanning from 1% to ~30%. For each patient, the patterns of variants in URT and LRT were profoundly different, indicating compartmentalized virus replication. No clear variant signature and no significant difference in nucleotide diversity between LRT and URT were observed. SARS-CoV-2 presents genetic heterogeneity and quasispecies compartmentalization in URT and LRT. Intra-patient diversity was low. The pattern of minority variants was highly heterogeneous and no specific district signature could be identified, nevertheless, analysis of samples, longitudinally collected in patients, supported quasispecies evolution.

ACS Style

Martina Rueca; Barbara Bartolini; Cesare Gruber; Antonio Piralla; Fausto Baldanti; Emanuela Giombini; Francesco Messina; Luisa Marchioni; Giuseppe Ippolito; Antonino Di Caro; Maria Capobianchi. Compartmentalized Replication of SARS-Cov-2 in Upper vs. Lower Respiratory Tract Assessed by Whole Genome Quasispecies Analysis. Microorganisms 2020, 8, 1302 .

AMA Style

Martina Rueca, Barbara Bartolini, Cesare Gruber, Antonio Piralla, Fausto Baldanti, Emanuela Giombini, Francesco Messina, Luisa Marchioni, Giuseppe Ippolito, Antonino Di Caro, Maria Capobianchi. Compartmentalized Replication of SARS-Cov-2 in Upper vs. Lower Respiratory Tract Assessed by Whole Genome Quasispecies Analysis. Microorganisms. 2020; 8 (9):1302.

Chicago/Turabian Style

Martina Rueca; Barbara Bartolini; Cesare Gruber; Antonio Piralla; Fausto Baldanti; Emanuela Giombini; Francesco Messina; Luisa Marchioni; Giuseppe Ippolito; Antonino Di Caro; Maria Capobianchi. 2020. "Compartmentalized Replication of SARS-Cov-2 in Upper vs. Lower Respiratory Tract Assessed by Whole Genome Quasispecies Analysis." Microorganisms 8, no. 9: 1302.

Author correction
Published: 17 July 2020 in Scientific Data
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An amendment to this paper has been published and can be accessed via a link at the top of the paper.

ACS Style

Marek Ostaszewski; Alexander Mazein; Marc E. Gillespie; Inna Kuperstein; Anna Niarakis; Henning Hermjakob; Alexander R. Pico; Egon L. Willighagen; Chris T. Evelo; Jan Hasenauer; Falk Schreiber; Andreas Dräger; Emek Demir; Olaf Wolkenhauer; Laura I. Furlong; Emmanuel Barillot; Joaquin Dopazo; Aurelio Orta-Resendiz; Francesco Messina; Alfonso Valencia; Akira Funahashi; Hiroaki Kitano; Charles Auffray; Rudi Balling; Reinhard Schneider. Author Correction: COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms. Scientific Data 2020, 7, 1 -1.

AMA Style

Marek Ostaszewski, Alexander Mazein, Marc E. Gillespie, Inna Kuperstein, Anna Niarakis, Henning Hermjakob, Alexander R. Pico, Egon L. Willighagen, Chris T. Evelo, Jan Hasenauer, Falk Schreiber, Andreas Dräger, Emek Demir, Olaf Wolkenhauer, Laura I. Furlong, Emmanuel Barillot, Joaquin Dopazo, Aurelio Orta-Resendiz, Francesco Messina, Alfonso Valencia, Akira Funahashi, Hiroaki Kitano, Charles Auffray, Rudi Balling, Reinhard Schneider. Author Correction: COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms. Scientific Data. 2020; 7 (1):1-1.

Chicago/Turabian Style

Marek Ostaszewski; Alexander Mazein; Marc E. Gillespie; Inna Kuperstein; Anna Niarakis; Henning Hermjakob; Alexander R. Pico; Egon L. Willighagen; Chris T. Evelo; Jan Hasenauer; Falk Schreiber; Andreas Dräger; Emek Demir; Olaf Wolkenhauer; Laura I. Furlong; Emmanuel Barillot; Joaquin Dopazo; Aurelio Orta-Resendiz; Francesco Messina; Alfonso Valencia; Akira Funahashi; Hiroaki Kitano; Charles Auffray; Rudi Balling; Reinhard Schneider. 2020. "Author Correction: COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms." Scientific Data 7, no. 1: 1-1.

Research article
Published: 29 May 2020 in PLOS ONE
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In Europe HAV infection occurs mainly among specific risk groups, such as consumers of specific food. Sexual transmission of HAV has been demonstrated, particularly among Men-Who-Have-Sex-With-Men (MSM), causing MSM-specific outbreaksin Europe. Here we report a molecular epidemiologic and phylodynamic analysis on HAV sequences in Lazio (central Italy)to identify genetic background and the phylogenetic relations, and test the HAV infection dynamics during a large outbreak through phylodynamic model.Among all HAV sequences found during 2013-2018 in Lazio, low genetic diversity was observed in HAV population in 2016 and 2017, along with high frequenciesVRD_521_2016and RIVM-HAV16-090, suggesting a large expansion event of viral population. The initial expansion of both VRD_521_2016 and RIVM-HAV16-090 clusters dated back to 2012 (95% HPD:2006-2015). During the2016-2017outbreak in Lazio region, the Re peaked around mid-2016, with a value of 1.73 (95% HPD: 1.03-2.37), consistent with incidence trend of AHA cases in Lazio between 2016 and mid-2017. This study showed the magnitude of HAV outbreak in Lazio during 2016-2017, demonstrating the epidemic continuity to MSM-specific outbreak in Europe. The HAV dataset is available on interactive phylodynamic platform https://nextstrain.org to real-time update of future outbreaks.

ACS Style

Claudia Minosse; Francesco Messina; Anna Rosa Garbuglia; Silvia Meschi; Paola Scognamiglio; Maria Rosaria Capobianchi; Giuseppe Ippolito; Simone Lanini. Origin of HAV strains responsible for 2016–2017 outbreak among MSM: Viral phylodynamics in Lazio region. PLOS ONE 2020, 15, e0234010 .

AMA Style

Claudia Minosse, Francesco Messina, Anna Rosa Garbuglia, Silvia Meschi, Paola Scognamiglio, Maria Rosaria Capobianchi, Giuseppe Ippolito, Simone Lanini. Origin of HAV strains responsible for 2016–2017 outbreak among MSM: Viral phylodynamics in Lazio region. PLOS ONE. 2020; 15 (5):e0234010.

Chicago/Turabian Style

Claudia Minosse; Francesco Messina; Anna Rosa Garbuglia; Silvia Meschi; Paola Scognamiglio; Maria Rosaria Capobianchi; Giuseppe Ippolito; Simone Lanini. 2020. "Origin of HAV strains responsible for 2016–2017 outbreak among MSM: Viral phylodynamics in Lazio region." PLOS ONE 15, no. 5: e0234010.

Preprint content
Published: 07 May 2020
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Background Epidemiological, virological and pathogenetic characteristics of SARS-CoV-2 infection are under evaluation. A better understanding of the pathophysiology associated with COVID-19 is crucial to improve treatment modalities and to develop effective prevention strategies. Transcriptomic and proteomic data on the host response against SARS-CoV-2 still have anecdotic character; currently available data from other coronavirus infections are therefore a key source of information. Methods We investigated selected molecular aspects of three human coronavirus (HCoV) infections, namely SARS-CoV, MERS-CoV and HCoV-229E, through a network based-approach. A functional analysis of HCoV-host interactome was carried out in order to provide a theoretic host-pathogen interaction model for HCoV infections and in order to translate the results in prediction for SARS-CoV-2 pathogenesis. The 3D model of S-glycoprotein of SARS-CoV-2 was compared to the structure of the corresponding SARS-CoV, HCoV-229E and MERS-CoV S-glycoprotein. SARS-CoV, MERS-CoV, HCoV-229E and the host interactome were inferred through published protein-protein interactions (PPI) as well as gene co-expression, triggered by HCoV S-glycoprotein in host cells. Results Although the amino acid sequences of the S-glycoprotein were found to be different between the various HCoV, the structures showed high similarity, but the best 3D structural overlap shared by SARS-CoV and SARS-CoV-2, consistent with the shared ACE2 predicted receptor. The host interactome, linked to the S-glycoprotein of SARS-CoV and MERS-CoV, mainly highlighted innate immunity pathway components, such as Toll Like receptors, cytokines and chemokines. Conclusions In this paper, we developed a network-based model with the aim to define molecular aspects of pathogenic phenotypes in HCoV infections. The resulting pattern may facilitate the process of structure-guided pharmaceutical and diagnostic research with the prospect to identify potential new biological targets.

ACS Style

Francesco Messina; Emanuela Giombini; Chiara Agrati; Francesco Vairo; Tommaso Ascoli Bartoli; Samir Al Moghazi; Mauro Piancentini; Franco Locatelli; Gary Kobinger; Markus Maeurer; Alimuddin Zumla; Maria R. Capobianchi; Francesco Nicola Lauria; Giuseppe Ippolito. COVID-19: Viral-host interactome analyzed by network based-approach model to study pathogenesis of SARS-CoV-2 infection. 2020, 1 .

AMA Style

Francesco Messina, Emanuela Giombini, Chiara Agrati, Francesco Vairo, Tommaso Ascoli Bartoli, Samir Al Moghazi, Mauro Piancentini, Franco Locatelli, Gary Kobinger, Markus Maeurer, Alimuddin Zumla, Maria R. Capobianchi, Francesco Nicola Lauria, Giuseppe Ippolito. COVID-19: Viral-host interactome analyzed by network based-approach model to study pathogenesis of SARS-CoV-2 infection. . 2020; ():1.

Chicago/Turabian Style

Francesco Messina; Emanuela Giombini; Chiara Agrati; Francesco Vairo; Tommaso Ascoli Bartoli; Samir Al Moghazi; Mauro Piancentini; Franco Locatelli; Gary Kobinger; Markus Maeurer; Alimuddin Zumla; Maria R. Capobianchi; Francesco Nicola Lauria; Giuseppe Ippolito. 2020. "COVID-19: Viral-host interactome analyzed by network based-approach model to study pathogenesis of SARS-CoV-2 infection." , no. : 1.

Comment
Published: 05 May 2020 in Scientific Data
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Researchers around the world join forces to reconstruct the molecular processes of the virus-host interactions aiming to combat the cause of the ongoing pandemic.

ACS Style

Marek Ostaszewski; Alexander Mazein; Marc E. Gillespie; Inna Kuperstein; Anna Niarakis; Henning Hermjakob; Alexander R. Pico; Egon L. Willighagen; Chris T. Evelo; Jan Hasenauer; Falk Schreiber; Andreas Dräger; Emek Demir; Olaf Wolkenhauer; Laura I. Furlong; Emmanuel Barillot; Joaquin Dopazo; Aurelio Orta-Resendiz; Francesco Messina; Alfonso Valencia; Akira Funahashi; Hiroaki Kitano; Charles Auffray; Rudi Balling; Reinhard Schneider. COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms. Scientific Data 2020, 7, 1 -4.

AMA Style

Marek Ostaszewski, Alexander Mazein, Marc E. Gillespie, Inna Kuperstein, Anna Niarakis, Henning Hermjakob, Alexander R. Pico, Egon L. Willighagen, Chris T. Evelo, Jan Hasenauer, Falk Schreiber, Andreas Dräger, Emek Demir, Olaf Wolkenhauer, Laura I. Furlong, Emmanuel Barillot, Joaquin Dopazo, Aurelio Orta-Resendiz, Francesco Messina, Alfonso Valencia, Akira Funahashi, Hiroaki Kitano, Charles Auffray, Rudi Balling, Reinhard Schneider. COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms. Scientific Data. 2020; 7 (1):1-4.

Chicago/Turabian Style

Marek Ostaszewski; Alexander Mazein; Marc E. Gillespie; Inna Kuperstein; Anna Niarakis; Henning Hermjakob; Alexander R. Pico; Egon L. Willighagen; Chris T. Evelo; Jan Hasenauer; Falk Schreiber; Andreas Dräger; Emek Demir; Olaf Wolkenhauer; Laura I. Furlong; Emmanuel Barillot; Joaquin Dopazo; Aurelio Orta-Resendiz; Francesco Messina; Alfonso Valencia; Akira Funahashi; Hiroaki Kitano; Charles Auffray; Rudi Balling; Reinhard Schneider. 2020. "COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms." Scientific Data 7, no. 1: 1-4.

Commentary
Published: 06 April 2020 in Journal of Medical Virology
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In the 5th February 2020 issue of Journal of Medical Virology a paper was published by Giovannetti et al., entitled “The first two cases of 2019‐nCoV in Italy: where they come from?”1. In this paper a phylogenetic and evolutionary analysis was applied to the virus identified in the first two subjects diagnosed in Italy with 2019‐nCoV infection, recently renamed SARS‐CoV‐22, two Chinese spouses arrived in Italy for tourism. The diagnosis was performed by the virology team under direction of Maria R. Capobianchi, at the National Institute of Infectious Diseases (INMI) in Rome, Italy, where the patients are currently hospitalized. This article is protected by copyright. All rights reserved.

ACS Style

Fabrizio Carletti; Eleonora Lalle; Francesco Messina; Giuseppe Ippolito; Maria R. Capobianchi. About the origin of the first two Sars‐CoV‐2 infections in Italy: Inference not supported by appropriate sequence analysis. Journal of Medical Virology 2020, 92, 1404 -1405.

AMA Style

Fabrizio Carletti, Eleonora Lalle, Francesco Messina, Giuseppe Ippolito, Maria R. Capobianchi. About the origin of the first two Sars‐CoV‐2 infections in Italy: Inference not supported by appropriate sequence analysis. Journal of Medical Virology. 2020; 92 (9):1404-1405.

Chicago/Turabian Style

Fabrizio Carletti; Eleonora Lalle; Francesco Messina; Giuseppe Ippolito; Maria R. Capobianchi. 2020. "About the origin of the first two Sars‐CoV‐2 infections in Italy: Inference not supported by appropriate sequence analysis." Journal of Medical Virology 92, no. 9: 1404-1405.

Journal article
Published: 29 October 2019 in mSystems
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The composition of the gut microbiome has been associated with various aspects of human health, but the mechanism of this interaction is still unclear. We utilized a cellular system to characterize the effect of the microbiome on human gene expression. We showed that some of these changes in expression may be mediated by changes in chromatin accessibility. Furthermore, we validate the role of a specific microbe and show that changes in its abundance can modify the host gene expression response. These results show an important role of gut microbiota in regulating host gene expression and suggest that manipulation of microbiome composition could be useful in future therapies.

ACS Style

Allison L. Richards; Amanda L. Muehlbauer; Adnan Alazizi; Michael B. Burns; Anthony Findley; Francesco Messina; Trevor J. Gould; Camilla Cascardo; Roger Pique-Regi; Ran Blekhman; Francesca Luca. Gut Microbiota Has a Widespread and Modifiable Effect on Host Gene Regulation. mSystems 2019, 4, e00323-18 .

AMA Style

Allison L. Richards, Amanda L. Muehlbauer, Adnan Alazizi, Michael B. Burns, Anthony Findley, Francesco Messina, Trevor J. Gould, Camilla Cascardo, Roger Pique-Regi, Ran Blekhman, Francesca Luca. Gut Microbiota Has a Widespread and Modifiable Effect on Host Gene Regulation. mSystems. 2019; 4 (5):e00323-18.

Chicago/Turabian Style

Allison L. Richards; Amanda L. Muehlbauer; Adnan Alazizi; Michael B. Burns; Anthony Findley; Francesco Messina; Trevor J. Gould; Camilla Cascardo; Roger Pique-Regi; Ran Blekhman; Francesca Luca. 2019. "Gut Microbiota Has a Widespread and Modifiable Effect on Host Gene Regulation." mSystems 4, no. 5: e00323-18.

Journal article
Published: 17 January 2019 in Eurosurveillance
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Blood donation screening for West Nile virus (WNV) was mandatory in the Lazio region in 2017 and 2018 (June-November) according to the national surveillance plan. In these years, all five donations reactive in WNV nucleic acid amplification tests harboured instead Usutu virus (USUV). Clade ‘Europe 2’ was identified in four blood donations and a 2018 mosquito pool. The cocirculation of WNV and USUV in Lazio warrants increased laboratory support and awareness of possible virus misidentification.

ACS Style

Fabrizio Carletti; Francesca Colavita; Francesca Rovida; Elena Percivalle; Fausto Baldanti; Ida Ricci; Claudio De Liberato; Francesca Rosone; Francesco Messina; Eleonora Lalle; Licia Bordi; Francesco Vairo; Maria Rosaria Capobianchi; Giuseppe Ippolito; Giuseppina Cappiello; Alberto Spanò; Silvia Meschi; Concetta Castilletti. Expanding Usutu virus circulation in Italy: detection in the Lazio region, central Italy, 2017 to 2018. Eurosurveillance 2019, 24, 1800649 .

AMA Style

Fabrizio Carletti, Francesca Colavita, Francesca Rovida, Elena Percivalle, Fausto Baldanti, Ida Ricci, Claudio De Liberato, Francesca Rosone, Francesco Messina, Eleonora Lalle, Licia Bordi, Francesco Vairo, Maria Rosaria Capobianchi, Giuseppe Ippolito, Giuseppina Cappiello, Alberto Spanò, Silvia Meschi, Concetta Castilletti. Expanding Usutu virus circulation in Italy: detection in the Lazio region, central Italy, 2017 to 2018. Eurosurveillance. 2019; 24 (3):1800649.

Chicago/Turabian Style

Fabrizio Carletti; Francesca Colavita; Francesca Rovida; Elena Percivalle; Fausto Baldanti; Ida Ricci; Claudio De Liberato; Francesca Rosone; Francesco Messina; Eleonora Lalle; Licia Bordi; Francesco Vairo; Maria Rosaria Capobianchi; Giuseppe Ippolito; Giuseppina Cappiello; Alberto Spanò; Silvia Meschi; Concetta Castilletti. 2019. "Expanding Usutu virus circulation in Italy: detection in the Lazio region, central Italy, 2017 to 2018." Eurosurveillance 24, no. 3: 1800649.

Original research article
Published: 12 August 2018 in American Journal of Human Biology
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Objectives This work aimed to describe the genetic landscape of the Balkan Peninsula, as revealed by STR markers commonly used in forensics and spatial methods specifically developed for genetic data. Methods We generated and analyzed 16 short tandem repeats (STRs) autosomal genotypes in 287 subjects from ten administrative/geographical regions of Eastern Europe (Romania and the Republic of Moldova). We report estimates of the allele frequencies in these sub‐populations, their fixation indexes, and use these results to complement previous spatial analyses of Southern Europe. Results In seven out of ten analyzed regional samples the heterozygosity, averaged across loci, was lower than expected. The average Fis was 0.011. Among the 16 loci, five returned a significant fixation index Fst. The composite Fst across the 16 loci, among the 10 regional samples, was 0.00417, a figure twice as large as that obtained with the same markers across the entire Northern Mediterranean. The first spatial principal component (sPC1) returned the picture of a Central‐European pattern of frequencies for the Carpathians, which extended to the Southern boundary of the Balkan Peninsula. However, the 8 alleles extracted by sPC1 returned a picture of a strong reduction of the migration rate in the Carpathian region, mostly between the inner locations. Conclusions Our results revealed an unexpected heterogeneity in the area. We believe that populations from some regions will require treatment as distinct entities when considered in forensic applications.

ACS Style

Alessandro Benvisto; Francesco Messina; Andrea Finocchio; Luis Popa; Mihaela Stefan; Gheorghe Stefanescu; Catalin Mironeanu; Andrea Novelletto; Cesare Rapone; Andrea Berti. A genetic portrait of the South-Eastern Carpathians based on autosomal short tandem repeats loci used in forensics. American Journal of Human Biology 2018, 30, e23139 .

AMA Style

Alessandro Benvisto, Francesco Messina, Andrea Finocchio, Luis Popa, Mihaela Stefan, Gheorghe Stefanescu, Catalin Mironeanu, Andrea Novelletto, Cesare Rapone, Andrea Berti. A genetic portrait of the South-Eastern Carpathians based on autosomal short tandem repeats loci used in forensics. American Journal of Human Biology. 2018; 30 (5):e23139.

Chicago/Turabian Style

Alessandro Benvisto; Francesco Messina; Andrea Finocchio; Luis Popa; Mihaela Stefan; Gheorghe Stefanescu; Catalin Mironeanu; Andrea Novelletto; Cesare Rapone; Andrea Berti. 2018. "A genetic portrait of the South-Eastern Carpathians based on autosomal short tandem repeats loci used in forensics." American Journal of Human Biology 30, no. 5: e23139.

Research article
Published: 18 July 2018 in PLOS ONE
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The human genetic diversity around the world was studied through several high variable genetic markers. In South America the demic consequences of admixture events between Native people, European colonists and African slaves have been displayed by uniparental markers variability. The mitochondrial DNA (mtDNA) has been the most widely used genetic marker for studying American mixed populations, although nuclear markers, such as microsatellite loci (STRs) commonly used in forensic science, showed to be genetically and geographically structured. In this work, we analyzed DNA from buccal swab samples of 296 individuals across Peru: 156 Native Amazons (Ashaninka, Cashibo and Shipibo from Ucayali, Huambiza from Loreto and Moche from Lambayeque) and 140 urban Peruvians from Lima and other 33 urban areas. The aim was to evaluate, through STRs and mtDNA variability, recent migrations in urban Peruvian populations and to gain more information about their continental ancestry. STR data highlighted that most individuals (67%) of the urban Peruvian sample have a strong similarity to the Amazon Native population, whereas 22% have similarity to African populations and only ~1% to European populations. Also the maternally-transmitted mtDNA confirmed the strong Native contribution (~90% of Native American haplogroups) and the lower frequencies of African (~6%) and European (~3%) haplogroups. This study provides a detailed description of the urban Peruvian genetic structure and proposes forensic STRs as a useful tool for studying recent migrations, especially when coupled with mtDNA.

ACS Style

Francesco Messina; Tullia Di Corcia; Michele Ragazzo; Cesar Sanchez Mellado; Irene Contini; Patrizia Malaspina; Bianca Maria Ciminelli; Olga Rickards; Carla Jodice. Signs of continental ancestry in urban populations of Peru through autosomal STR loci and mitochondrial DNA typing. PLOS ONE 2018, 13, e0200796 .

AMA Style

Francesco Messina, Tullia Di Corcia, Michele Ragazzo, Cesar Sanchez Mellado, Irene Contini, Patrizia Malaspina, Bianca Maria Ciminelli, Olga Rickards, Carla Jodice. Signs of continental ancestry in urban populations of Peru through autosomal STR loci and mitochondrial DNA typing. PLOS ONE. 2018; 13 (7):e0200796.

Chicago/Turabian Style

Francesco Messina; Tullia Di Corcia; Michele Ragazzo; Cesar Sanchez Mellado; Irene Contini; Patrizia Malaspina; Bianca Maria Ciminelli; Olga Rickards; Carla Jodice. 2018. "Signs of continental ancestry in urban populations of Peru through autosomal STR loci and mitochondrial DNA typing." PLOS ONE 13, no. 7: e0200796.

Journal article
Published: 10 May 2018 in Scientific Reports
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In order to improve the phylogeography of the male-specific genetic traces of Greek and Phoenician colonizations on the Northern coasts of the Mediterranean, we performed a geographically structured sampling of seven subclades of haplogroup J in Turkey, Greece and Italy. We resequenced 4.4 Mb of Y-chromosome in 58 subjects, obtaining 1079 high quality variants. We did not find a preferential coalescence of Turkish samples to ancestral nodes, contradicting the simplistic idea of a dispersal and radiation of Hg J as a whole from the Middle East. Upon calibration with an ancient Hg J chromosome, we confirmed that signs of Holocenic Hg J radiations are subtle and date mainly to the Bronze Age. We pinpointed seven variants which could potentially unveil star clusters of sequences, indicative of local expansions. By directly genotyping these variants in Hg J carriers and complementing with published resequenced chromosomes (893 subjects), we provide strong temporal and distributional evidence for markers of the Greek settlement of Magna Graecia (J2a-L397) and Phoenician migrations (rs760148062). Our work generated a minimal but robust list of evolutionarily stable markers to elucidate the demographic dynamics and spatial domains of male-mediated movements across and around the Mediterranean, in the last 6,000 years.

ACS Style

Andrea Finocchio; Beniamino Trombetta; Francesco Messina; Eugenia D’Atanasio; Nejat Akar; Aphrodite Loutradis; Emmanuel I. Michalodimitrakis; Fulvio Cruciani; Andrea Novelletto. A finely resolved phylogeny of Y chromosome Hg J illuminates the processes of Phoenician and Greek colonizations in the Mediterranean. Scientific Reports 2018, 8, 7465 .

AMA Style

Andrea Finocchio, Beniamino Trombetta, Francesco Messina, Eugenia D’Atanasio, Nejat Akar, Aphrodite Loutradis, Emmanuel I. Michalodimitrakis, Fulvio Cruciani, Andrea Novelletto. A finely resolved phylogeny of Y chromosome Hg J illuminates the processes of Phoenician and Greek colonizations in the Mediterranean. Scientific Reports. 2018; 8 (1):7465.

Chicago/Turabian Style

Andrea Finocchio; Beniamino Trombetta; Francesco Messina; Eugenia D’Atanasio; Nejat Akar; Aphrodite Loutradis; Emmanuel I. Michalodimitrakis; Fulvio Cruciani; Andrea Novelletto. 2018. "A finely resolved phylogeny of Y chromosome Hg J illuminates the processes of Phoenician and Greek colonizations in the Mediterranean." Scientific Reports 8, no. 1: 7465.

Journal article
Published: 02 January 2018 in Annals of Human Biology
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Tetranucleotide Short Tandem Repeats (STRs) for human identification and common use in forensic cases have recently been used to address the population genetics of the North-Eastern Mediterranean area. However, to gain confidence in the inferences made using STRs, this kind of analysis should be challenged with changes in three main aspects of the data, i.e. the sizes of the samples, their distance across space and the genetic background from which they are drawn. To test the resilience of the gradients previously detected in the North-Eastern Mediterranean to the enlargement of the surveyed area and population set, using revised data. STR genotype profiles were obtained from a publicly available database (PopAffilietor databank) and a dataset was assembled including >7000 subjects from the Arabian Peninsula to Scandinavia, genotyped at eight loci. Spatial principal component analysis (sPCA) was applied and the frequency maps of the nine alleles which contributed most strongly to sPC1 were examined in detail. By far the greatest part of diversity was summarised by a single spatial principal component (sPC1), oriented along a SouthEast-to-NorthWest axis. The alleles with the top 5% squared loadings were TH01(9.3), D19S433(14), TH01(6), D19S433(15.2), FGA(20), FGA(24), D3S1358(14), FGA(21) and D2S1338(19). These results confirm a clinal pattern over the whole range for at least four loci (TH01, D19S433, FGA, D3S1358). Four of the eight STR loci (or even alleles) considered here can reproducibly capture continental arrangements of diversity. This would, in principle, allow for the exploitation of forensic data to clarify important aspects in the formation of local gene pools.

ACS Style

Francesco Messina; Andrea Finocchio; Nejat Akar; Aphrodite Loutradis; Emmanuel I. Michalodimitrakis; Radim Brdicka; Carla Jodice; Andrea Novelletto. Enlarging the gene-geography of Europe and the Mediterranean area to STR loci of common forensic use: longitudinal and latitudinal frequency gradients. Annals of Human Biology 2018, 45, 77 -85.

AMA Style

Francesco Messina, Andrea Finocchio, Nejat Akar, Aphrodite Loutradis, Emmanuel I. Michalodimitrakis, Radim Brdicka, Carla Jodice, Andrea Novelletto. Enlarging the gene-geography of Europe and the Mediterranean area to STR loci of common forensic use: longitudinal and latitudinal frequency gradients. Annals of Human Biology. 2018; 45 (1):77-85.

Chicago/Turabian Style

Francesco Messina; Andrea Finocchio; Nejat Akar; Aphrodite Loutradis; Emmanuel I. Michalodimitrakis; Radim Brdicka; Carla Jodice; Andrea Novelletto. 2018. "Enlarging the gene-geography of Europe and the Mediterranean area to STR loci of common forensic use: longitudinal and latitudinal frequency gradients." Annals of Human Biology 45, no. 1: 77-85.

Comparative study
Published: 01 January 2018 in Human Immunology
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A geographical stratification of Killer Immunoglobulin-like Receptors (KIR) has been reported worldwide. We first analyzed the distribution of 15 KIR genes in a sample of 50 East-Sicilians (ES). We used a Principal Component Analysis (PCA) to compare the KIR genetic content among ES and 10 modern populations who are descendants of the ancient invaders of Sicily: Spanish, French, Norwegians, Swedes, Finns, Tunisians, Moroccans, Arabs, Greeks, Turks. We also included a sample of Sardinians, and Senegalese (as outlier group). Then, we also compared the HLA-A, HLA-B and HLA-C allelic frequencies among ES and the same populations investigated for KIR. As to HLA-A and HLA-B polymorphisms, ES are close to Greek population who invaded the island for long time until 827 CE; while HLA-C and KIR distribution in ES are close to Spanish population that invaded Sicily (and Sardinia) starting from 1283. As to KIR, ES are close to Spanish and Sardinians. The immunogenetic fingerprint of ES may be the finely balanced result of the invasions that overwhelmed Sicily over the centuries.

ACS Style

Cristina Capittini; Francesco Messina; Fabrizio Puglisi; Maria Azzaro; Sebastiana Toscano; Annalisa De Silvestri; Carmine Tinelli; Grazia Sortino. An historical approach to the genetic distribution of KIR and HLA ligands in Eastern Sicilians compared to modern descendants of their invaders. Human Immunology 2018, 79, 5 -12.

AMA Style

Cristina Capittini, Francesco Messina, Fabrizio Puglisi, Maria Azzaro, Sebastiana Toscano, Annalisa De Silvestri, Carmine Tinelli, Grazia Sortino. An historical approach to the genetic distribution of KIR and HLA ligands in Eastern Sicilians compared to modern descendants of their invaders. Human Immunology. 2018; 79 (1):5-12.

Chicago/Turabian Style

Cristina Capittini; Francesco Messina; Fabrizio Puglisi; Maria Azzaro; Sebastiana Toscano; Annalisa De Silvestri; Carmine Tinelli; Grazia Sortino. 2018. "An historical approach to the genetic distribution of KIR and HLA ligands in Eastern Sicilians compared to modern descendants of their invaders." Human Immunology 79, no. 1: 5-12.