Genomic and phylogenetic characterisation of an imported case of SARS-CoV-2 in Amazonas State, Brazil

Abstract

A new coronavirus [severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)] is currently causing a life-threatening pandemic. In this study, we report the complete genome sequencing and genetic characterisation of a SARS-CoV-2 detected in Manaus, Amazonas, Brazil, and the protocol we designed to generate high-quality SARS-CoV-2 full genome data. The isolate was obtained from an asymptomatic carrier returning from Madrid, Spain. Nucleotide sequence analysis showed a total of nine mutations in comparison with the original human case in Wuhan, China, and support this case as belonging to the recently proposed lineage A.2. Phylogeographic analysis further confirmed the likely European origin of this case. To our knowledge, this is the first SARS-CoV-2 genome obtained from the North Brazilian Region. We believe that the information generated in this study may contribute to the ongoing efforts toward the SARS-CoV-2 emergence.

Fig. 1:. maximum-likelihood (ML) phylogeny of subsampled severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes. (A) ML tree rooted on the branch separating lineages A and B sequences colored following the legend. (B) A close view of the lineage A highlighting the A.2 lineage (light blue box) that comprises the BR_AM_ILMD_20140001 strain (indicated with an arrow). The nodes representing the most recent common ancestor (MRCA) of the lineage A.2 is indicated with a red diamond. In both trees, tips representing the Spanish strains inside lineage A.2 are coloured red and the scale bar represents nucleotide substitutions per site.

Fig. 2:. phylogeography of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage A. (A) Temporal signal analysis correlating the sampling date of each sequence and its genetic distance from the root of a maximum likelihood phylogeny. (B) Time-scaled Bayesian phylogeographic maximum clade credibility (MCC) tree of the SARS-CoV-2 complete coding sequences (CDS) classified as lineage A. The branch’s colors represent the most probable location of their descendent nodes (diamonds) as indicated at the legend. Branch support are indicated only at key nodes posterior (PP) and posterior state probability (PSP). The lineage A.2 is highlighted with a light blue box. All horizontal branch lengths are drawn to a scale of years.