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Evolution and epidemic spread of SARS-CoV-2 in Brazil

Our take —

This phylogenetic study analyzed SARS-CoV-2 sequences isolated from individuals across Brazil. The study investigated how SARS-CoV-2 became established in Brazil, and determined the impact of social and physical distancing measures on the spread of the virus. Specifically, the researchers showed that there were multiple international introductions into Brazil, but that relaxation of distancing measures led to increased spread within the country. Internationally connected cities in Brazil played an important role in the local and inter-state spread of SARS-CoV-2 and its subsequent establishment in the country.

Study design

Modeling/Simulation, Other

Study population and setting

The purpose of the study was to investigate how SARS-CoV-2 became established in Brazil and to quantify the impact of non-pharmaceutical interventions (NPIs) on virus spatiotemporal spread. Authors generated 427 new SARS-CoV-2 genomes from Brazilian samples collected between March 5 and April 30, 2020 from 85 municipalities spanning all regions of Brazil and analyzed these data in conjunction with 63 additional previously published sequences from Brazil. Authors used a continuous phylogeographic model to infer the origins of each phylogenetic node and human mobility data to estimate daily changes in R (effective reproductive number).

Summary of Main Findings

The study showed that NPIs reduced R from >3 to close to 1 in São Paulo and Rio de Janeiro during the start of the epidemic, but the increased mobility after this initial decline led to a rising R in Sao Paulo. Genome analysis showed that 99% of the Brazilian sequences belonged to SARS-CoV-2 lineage B, with only 5 strains belonging to lineage A. Within the dominant B lineage, the authors found that sequences from Brazil fell into three primary clusters. Analysis of these three clades indicated that community-driven transmission was already established in Brazil by early March, 2020, and international travel restrictions initiated after this period may have had limited impact. Further phylogeographic analysis revealed there were at least 102 international introductions of SARS-CoV-2 into Brazil, primarily into internationally well-connected states such as São Paulo (36% of all imports), Minas Gerais (24%), Ceará (10%) and Rio de Janeiro (8%). Overall, the authors found that SARS-CoV-2 spread was initially driven by local and within-state movement, but was later characterized by long-distance movement, though within-state virus movement was always more frequent than between-state movement.

Study Strengths

A key strength of this study is that the genomic data is representative of the distribution of cases in Brazil. Furthermore, the methodology is clear and well presented, and the results of this study revealed the importance of customizing diagnostic assays with specificity for locally circulating strains.

Limitations

There is limited description of the 24% Brazilian sequences that did not fall in the three main clades.

Value added

The COVID-19 epidemic in Brazil is currently among the largest in the world, and this paper explains how it grew to that level. The paper demonstrates the role that introductions from other countries had in fueling the spread of the virus and examines the relative contributions of within- and between-state travel. The authors also describe how social and physical distancing measures initially curbed spread of the virus before their relaxation led to increased transmission and details the different SARS-CoV-2 lineages and clades that are spreading in the region, which may have an impact on the diagnostic tests used locally.

This review was posted on: 2 October 2020