Phylogenetic analysis of SARS-CoV-2: strengths, limitations and over-interpretations

The Institut Pasteur's bioinformatics research teams have been closely involved in the response to COVID-19, working to analyze the sequencing data produced worldwide. On January 29, 2020, the Institut Pasteur, which is responsible for monitoring respiratory viruses in France, was the first in Europe to sequence the whole genome of the coronavirus known as SARS-CoV-2. Since then, it has sequenced more than 200 genomes. The results are used in phylogeographic and phylodynamic research (respectively tracing the geographical spread of the virus and using phylogenetics to determine the dynamics of the outbreak). A phylogenetic analysis conducted by the Institut Pasteur on around a hundred genomes from samples collected from patients in France between January 24 and March 24, 2020 revealed several early introductions of SARS-CoV-2 without local transmission, emphasizing the efficacy of the measures taken to prevent the spread of the virus from symptomatic cases. Given the scale of the pandemic, it is important to remain cautious in the race for knowledge when it comes to the possible over-interpretation of scientific results.

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