COVID-19

The spread of the SARS-CoV-2 virus demanded an international research effort to face the all the forms of issues caused by the pandemic.

As part of this international research effort, each group of the PANGAIA network contributed with their knowledge and skills. This page provides a short summary of the main research activities related to COVID-19 and SARS-CoV-2. Please feel free to contact us for further information.

Evolutionary history of SARS-CoV-2

Leen Stougie (CWI and Vrije University, Amsterdam), together with colleagues of Delft University and Maastricht University, studied the applicability of existing phylogenetic network reconstruction algorithms to infer the evolutionary history of SARS-CoV-2. Their results partially corroborate existing theories about SARS-CoV-2 and partially produce new avenues for exploration regarding the location and significance of reticulate activity within the wider group of SARS-like viruses.

Contact: Leen Sougie <leen.stougie@cwi.nl>

Novel RNA virus discovery

Rayan Chikhi (Pasteur Institute) is part of a consortium aiming to re-analyzing existing public databases of nucleic acid sequences in order to identify potential novel RNA viruses. To this aim, they developed a cloud computing infrastructure, called Serratus, able to deal with multiple petabases corpora. With their research, they characterized novel viruses potentially related to coronaviruses and to hepatitis δ virus. A preprint describing the results is available at: https://www.biorxiv.org/content/10.1101/2020.08.07.241729v2

Contact: Rayan Chikhi <rayan.chikhi@pasteur.fr>

Viral genotyping and variant identification

The wide availability of genomic data of viral samples allowed their use in nearly-real time epidemiological studies. A fundamental task to this aim is the characterization of mutations of each viral sample (I.e., their genotype). Yuri Pirola, Marco Previtali and colleagues of the University of Milano-Biccoca developed a tool to genotype viral samples and to impute their lineages. The tool, called MALVIRUS, is focused on accuracy, simplicity, and computational efficiency. A preprint describing the tool is available at: https://www.biorxiv.org/content/10.1101/2020.05.05.076992v2

Contact: Yuri Pirola <yuri.pirola@unimib.it>

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