Analyzing SARS-CoV-2 Sequence Patterns by Semantic Trajectories.

Since the beginning of the pandemic due to the SARS-CoV-2 emergence, several variants has been observed all over the world. One of the last known, Omicron, caused a large spread of the virus in few days, and several countries reached a record number of contaminations. Indeed, the mutation in the Spike region of the virus played an important role in altering its behavior. Therefore, it is important to understand the virus evolution by extracting and analyzing the virus structure of each variant. In this work we show how patterns sequence could be analyzed and extracted by means of semantic trajectories modeling. To do so, we designed a graph-based model in which the genome organization is handled using nodes and edges to represent respectively the nucleotides and sequence connection (point of interest and routes for trajectories). The modeling choices and pattern extraction from the graph allowed to retrieve a region where a mutation occurred in Omicron (NCBI version:OM011974.1).

OntoRepliCov: an Ontology-Based Approach for Modeling the SARS-CoV-2 Replication Process.

Understanding the replication machinery of viruses contributes to suggest and try effective antiviral strategies. Exhaustive knowledge about the proteins structure, their function, or their interaction is one of the preconditions for successfully modeling it. In this context, modeling methods based on a formal representation with a high semantic expressiveness would be relevant to extract proteins and their nucleotide or amino acid sequences as an element from the replication process. Consequently, our approach relies on the use of semantic technologies to design the SARS-CoV-2 replication machinery. This provides the ability to infer new knowledge related to each step of the virus replication. More specifically, we developed an ontology-based approach enriched with reasoning process of a complete replication machinery process for SARS-CoV-2. We present in this paper a partial overview of our ontology OntoRepliCov to describe one step of this process, namely, the continuous translation or protein synthesis, through classes, properties, axioms, and SWRL (Semantic Web Rule Language) rules.