The Divergent Pattern of SARS-CoV-2 Variant Predominance and Transmission Dynamics in the Brazilian Island of Ilhabela

Abstract

Our effort in SARS-CoV-2 genomic surveillance in Brazil has detected the Alpha Variant of Concern with a predominance higher than 75% in the population of Ilhabela island (São Paulo State) at a time when the Gamma VOC was already predominating the mainland raised concerns for closer surveillance on this island. Therefore, we intensified the surveillance for 24 weeks by generating data from 34% of local positive cases. Our data show that the patterns of VOC predominance dynamics and infection rates were in general distinct from the mainland. We report here the first known case of Alpha predominance in a Brazilian population, a delay greater than 3 months for the Gamma to dominate the previous variants compared to the mainland, and a faster dispersion rate of Gamma and Delta VOCs compared to the mainland. Phylogenetic analysis revealed the SARS-CoV-2 transmission dynamics in Ilhabela were characterized by multiple independent introduction events of Gamma and Delta, with a few events of Alpha introduction, two of them followed by community transmission. This study evidenced the peculiar behavior of SARS-CoV-2 variants in an isolated population and brought to light the importance of specific programs for SARS-CoV-2 genomic surveillance in isolated populations.

Keywords: Brazil; SARS-CoV-2; molecular epidemiology; variants of concern (VOC).

Figure 1

Comparison of the SARS-CoV-2 lineage predominance dynamics and record of new COVID-19 cases per 10 thousand inhabitants between São Paulo (SP) State (A), eastern SP (B) and Ilhabela island (C) from April to October 2021. The graph’s left axis indicates new cases per 10,000 inhabitants (purple line) and the right axis indicates the proportion of VOCs (Alpha VOC: blue area; Gamma VOC: light pink area; Delta VOC: yellow area; Other lineages: green area). The sampled areas are colored in light green in maps (A,B). The Ilhabela map (C) shows the protected forest area (dark green) and the unprotected area (yellow) with its denser urban spots (purple) (density map adapted from [21]).

Figure 2

Maximum Likelihood time-tree of SARS-CoV-2 genomes of Ilhabela (red tips) inferred to a dataset with reference Alpha, Gamma and Delta VOC genomes obtained in Brazil and worldwide, downloaded from GISAID. Bootstrap values are presented for major branches. (A). Full dataset phylogeny with VOC clusters highlighted: Delta (light yellow background), Gamma (light pink background) and Alpha (light blue background). (B). Zoom in the Alpha branch showing the two monophyletic clustering of Ilhabela samples and their defining mutations.