PhD Projects » ESR 1: Deciphering the RNA genome packaging code of influenza A viruses

Gabriel Lovate

I am Gabriel Lovate and I come from Brazil. I studied Pharmacy and Biochemistry as a bachelor, and then obtained a master in Biochemistry, at the University of São Paulo, Brazil. As an undergraduate student, I was involved in the field of Synthetic Biology, working on the development of bacterial-based biosensors. During my master’s studies I tried to better understand how antibiotic resistance is distributed in clinical settings, employing functional genomic characterization of bacterial pathogens.

During this training period, I was deeply interested in using computational tools to describe and understand biology. Following this drive, in February 2021, I joined the Friedrich Schiller University in Jena, Germany, to develop methods and tools for the analysis of RNA structure in viruses. Under the supervision of Prof. Dr. Marz, I am decided to embark on the challenge of deciphering the RNA genome packaging code of influenza A viruses.

I am always chaotically reading 3 or more books at the same time, always some kind of Sci-Fi/dystopia, biography, or science outreach. Another pleasure for me is going on hikes and camping.


Field:
Bioinformatics
Host institution:
Friedrich Schiller University Jena (FSU), Germany
Local supervisor:
Prof. Dr. Manja Marz (FSU Jena)
Local co-supervisor:
Prof. Dr. Andreas Henke (Jena University Hospital)
Project partner:
Rithu Paul Stansilaus (ESR 2)
Work packages:
WP 1.4 Virus regulation
WP 2.1 Microevolution: Virus quasispecies
WP 2.2 Macroevolution: Natural selection of viruses

Manja Marz
Andreas Henke

Project description

Currently, bioinformatical tools are not specifically designed for viruses. However, viruses bring unique features, which require specific bioinformatical tools to trace virus-host interaction. For example, the number of sequences in a quasispecies is massively high due to their high mutation rate, but only a few interact again with the host cells. Some viruses, such as IAV or as used by AG, are segmented RNA viruses, which urgently require tools with specific features: RNA viruses should include standardised secondary structure predictions, leading to RNA-RNA interaction prediction necessary for the packaging of segmented RNA viruses.

Therefore the precise aims of this project are

  • Development of a bioinformatical tool to predict RNA-RNA interactions as packaging signal for segmented viruses, such as IAV. The tool will also consider the 3D arrangement of the RNA molecules being essential to understand the nature of packaged viruses.
  • Development of a virus-specific full genome multiple sequence alignment algorithm to track the quasispecies. We will combine this tool with secondary structure information being available from literature and ESR 2 to build more accurate alignments.
  • Establishment of RNA-RNA interaction sets and more importantly non-interaction sets. The result will be used by ESR 2 to explore the reassortment space of IAVs. This understanding is essential for a prediction of future Flu outbreaks.
  • Application of the tool for at least 30 different viruses in other projects in VIROINF.
  • Publications

Journal Articles

Hufsky, Franziska; Abecasis, Ana B.; Babaian, Artem; Beck, Sebastian; Brierley, Liam; Dellicour, Simon; Eggeling, Christian; Elena, Santiago F.; Gieraths, Udo; Ha, Anh D.; Harvey, Will; Jones, Terry C.; Lamkiewicz, Kevin; Lovate, Gabriel Lencioni; Lücking, Dominik; Machyna, Martin; Nishimura, Luca; Nocke, Maximilian K.; Renard, Bernard Y.; Sakaguchi, Shoichi; Sakellaridi, Lygeri; Spangenberg, Jannes; Tarradas-Alemany, Maria; Triebel, Sandra; Vakulenko, Yulia; Wijesekara, Yasas; González-Candelas, Fernando; Krautwurst, Sarah; Pérez-Cataluña, Alba; Randazzo, Walter; Sánchez, Gloria; Marz, Manja

The International Virus Bioinformatics Meeting 2023. Journal Article

In: Viruses, vol. 15, iss. 10, pp. 2031, 2023.

Abstract | Links | BibTeX

Jakob, Celia; Lovate, Gabriel Lencioni; Desirò, Daniel; Gießler, Lara; Smyth, Redmond P.; Marquet, Roland; Lamkiewicz, Kevin; Marz, Manja; Schwemmle, Martin; Bolte, Hardin

Sequential disruption of SPLASH-identified vRNA–vRNA interactions challenges their role in influenza A virus genome packaging Journal Article

In: Nucleic Acids Research, vol. 51, iss. 12, pp. 6479-6494, 2023.

Abstract | Links | BibTeX

Presentations

Lovate, Gabriel Lencioni

Using high-throughput analysis to understand RNA-RNA interactions of Influenza Presentation

Talk at DiagnosTech Lecture, 29.04.2022.

Abstract | Links | BibTeX

Lovate, Gabriel Lencioni

RNAswarm: A pipeline for differential RNA-RNA Interaction probing Presentation

Oral poster at 31st Annual Meeting of the Society for Virology 2022, Munich, Germany, 30.03.2022.

BibTeX

Lovate, Gabriel Lencioni

Reproducible RNA-RNA interaction probing for RNA proximity ligation data with RNAswarm Presentation

Poster at International Virus Bioinformatics Meeting 2022, 24.03.2022, (Best Poster Award).

Links | BibTeX