M. Chatzou, C. Magis, J. Chang, C. Kemena, G. Bussotti et al., Multiple sequence alignment modeling: methods and applications, Briefings in Bioinformatics, vol.17, issue.6, pp.1009-1023, 2015.

N. De-maio, Figure 1: Modes of transmission of viruses, emphasizing multi-system infections such as SARS-CoV, MERS-CoV, and SARS-COV-2 (modified from Otter et al. (2016)).

P. Di-tommaso, M. Chatzou, E. W. Floden, P. P. Barja, E. Palumbo et al., Nextflow enables reproducible computational workflows, Nature Biotechnology, vol.35, issue.4, pp.316-319, 2017.

R. Durbin, Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids, 1998.

D. Earl, N. Nguyen, G. Hickey, R. S. Harris, S. Fitzgerald et al., Alignathon: a competitive assessment of whole-genome alignment methods, Genome Research, vol.24, issue.12, pp.2077-2089, 2014.

K. Katoh and D. M. Standley, MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability, Molecular Biology and Evolution, vol.30, issue.4, pp.772-780, 2013.

F. Lemoine, D. Correia, V. Lefort, O. Doppelt-azeroual, F. Mareuil et al., NGPhylogeny.fr: new generation phylogenetic services for non-specialists, Nucleic Acids Research, vol.47, issue.W1, pp.W260-W265, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02341225

Y. Li, Similarities and Evolutionary Relationships of COVID-19 and Related Viruses, 2020.

M. Nute and T. Warnow, Scaling statistical multiple sequence alignment to large datasets, BMC Genomics, vol.17, issue.S10, p.764, 2016.

Y. Shu and J. Mccauley, GISAID: Global initiative on sharing all influenza data ? from vision to reality, Eurosurveillance, vol.22, issue.13, p.22, 2017.

T. Xiaolu, On the origin and continuing evolution of SARS-CoV-2, National Science Review, nwaa036, Bioinformatics, vol.32, issue.22, pp.3501-3503, 2016.

, Figure 5: Pan-genome (Core, accessory, and unique) analysis amongst 19 Betacoronavirus reference genomes (including one Pangolin CoV)., Figure 1. Visualization and Statistics Summary. Left: MSAviewer visualization of the Receptor Binding Domain (RBD) of the Spike gene, with reference genome (top)

, Table 2: Summary of genome sequences of SARS-CoV-2 strains isolated in Latin America and collected in GISAID database., with unique and new statistics with respect to the database as of