Abstract
BackgroundBrazil is the third country most affected by Coronavirus disease-2019 (COVID-19), but viral evolution in municipality resolution is still poorly understood in Brazil and it is crucial to understand the epidemiology of viral spread. We aimed to track molecular evolution and spread of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Esteio (Southern Brazil) using phylogenetics and phylodynamics inferences from 21 new genomes in global and regional context. Importantly, the case fatality rate (CFR) in Esteio (3.26%) is slightly higher compared to the Rio Grande do Sul (RS) state (2.56%) and the entire Brazil (2.74%).ResultsWe provided a comprehensive view of mutations from a representative sampling from May to October 2020, highlighting two frequent mutations in spike glycoprotein (D614G and V1176F), an emergent mutation (E484K) in spike Receptor Binding Domain (RBD) characteristic of the B.1.351 and P.1 lineages, and the adjacent replacement of 2 amino acids in Nucleocapsid phosphoprotein (R203K and G204R). E484K was found in two genomes from mid-October, which is the earliest description of this mutation in Southern Brazil. Lineages containing this substitution must be subject of intense surveillance due to its association with immune evasion. We also found two epidemiologically-related clusters, including one from patients of the same neighborhood. Phylogenetics and phylodynamics analysis demonstrates multiple introductions of the Brazilian most prevalent lineages (B.1.1.33 and B.1.1.248) and the establishment of Brazilian lineages ignited from the Southeast to other Brazilian regions.ConclusionsOur data show the value of correlating clinical, epidemiological and genomic information for the understanding of viral evolution and its spatial distribution over time. This is of paramount importance to better inform policy making strategies to fight COVID-19.
Highlights
Brazil is the third country most affected by Coronavirus disease-2019 (COVID-19), but viral evolution in municipality resolution is still poorly understood in Brazil and it is crucial to understand the epidemiology of viral spread
It was determined that: (i) B.1 and derived lineages were predominant at the beginning of the pandemic; (ii) > 100 independent international introductions occurred in the country; (iii) a significant movement of the virus among the Brazilian regions was observed after international travel restrictions; and (iv) non-pharmacological measures were able to reduce the reproduction number (R0) from > 4 to ≈1 [12]
In the present work, we accessed SARS-CoV-2 mutations, circulating lineages and phylogenetic patterns of SARS-CoV-2 from a time- and age-representative set of patients admitted in a municipal healthcare system from the Southern region of Brazil, the third country most affected by the Covid-19 pandemic
Summary
Brazil is the third country most affected by Coronavirus disease-2019 (COVID-19), but viral evolution in municipality resolution is still poorly understood in Brazil and it is crucial to understand the epidemiology of viral spread. Unprecedented international efforts of viral sequencing have allowed the submission of ~ 1.3 million genomes in the Global Initiative on Sharing All Influenza Data (GISAID) up to date [3], which are available for studies of genomic epidemiology to follow the evolutionary history and dynamics of SARSCoV-2 through space and time In this sense, some important studies were already conducted in highly-affected countries, including USA [4,5,6,7], Italy [8], Netherlands [9], Australia [10, 11], and Brazil [12,13,14]. It was determined that: (i) B.1 and derived lineages were predominant at the beginning of the pandemic; (ii) > 100 independent international introductions occurred in the country; (iii) a significant movement of the virus among the Brazilian regions was observed after international travel restrictions; and (iv) non-pharmacological measures were able to reduce the reproduction number (R0) from > 4 to ≈1 [12]
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