HIV-1 is remarkable for the diversity of strains comprising the HIV/AIDS pandemic. In the last decade, classification of viral variants as groups, subtypes, and circulating recombinant forms (CRF) and the observation of specific mutational patterns have become powerful tools for studying viral molecular dynamics. Monitoring the worldwide distribution of HIV-1 diversity has been used in both epidemiological surveillance programs and in reconstructing the history of regional epidemics. Specific patterns of virus spatial distribution also suggest differences in pathogenicity and transmissibility among the various subtypes. Molecular analyses of viral sequences allow estimating the rate of divergence among variants and the dynamic forces shaping the phylogenetic trees.

The emergence of SARS-CoV-2 variants, as observed with the D614G spike protein mutant and, more recently, with B.1.1.7 (501Y.V1), B.1.351 (501Y.V2) and B.1.1.28.1 (P.1) lineages, represent a continuous threat and might lead to strains of higher infectivity and/or virulence. We report on the occurrence of a SARS-CoV-2 haplotype with nine mutations including D614G/T307I double-mutation of the spike. This variant expanded and completely replaced previous lineages within a short period in the subantarctic Magallanes Region, southern Chile. The rapid lineage shift was accompanied by a significant increase of cases, resulting in one of the highest incidence rates worldwide. Comparative coarse-grained molecular dynamic simulations indicated that T307I and D614G belong to a previously unrecognized dynamic domain, interfering with the mobility of the receptor binding domain of the spike. The T307I mutation showed a synergistic effect with the D614G. Continuous surveillance of new mutations and molecular analyses of such variations are important tools to understand the molecular mechanisms defining infectivity and virulence of current and future SARS-CoV-2 strains.

ABStRACt. In spite of the remarkable diversity of HIV-1 env genes, several amino acids are extremely conserved, probably due to functional constraints. One example is the proline found at the second position of the GPGR motif. Several viruses, however, bear substitutions at this site, for instance, GWGR subtype B variant. GWGR viruses are described in Brazil since the beginning of the epidemics, but the extent of their dispersion or the geographical origin of the variant remains unknown. In the present study, phylogenetic trees were constructed in order to study the origin and spread of this variant. All GWGR sequences as well as a subset of subtype B sequences available were included in the analyses. Analyses of differential selection were also performed on GWGR and non-GWGR sequences in order to unveil evolutionary novelties due to the action of positive selection. Although the GWGR variant was found at least in 23 countries, its expansion probably has a single origin, and Brazil is the epicenter.

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