tetano
Editor, Senior Moderator
BMC Genomics
. 2021 May 20;22(1):371.
doi: 10.1186/s12864-021-07708-w.
Genomic epidemiology of SARS-CoV-2 in Esteio, Rio Grande do Sul, Brazil
Vin?cius Bonetti Franceschi[SUP] 1 [/SUP], Gabriel Dickin Caldana[SUP] 2 [/SUP], Amanda de Menezes Mayer[SUP] 1 [/SUP], Gabriela Bettella Cybis[SUP] 3 [/SUP], Carla Andretta Moreira Neves[SUP] 2 [/SUP], Patr?cia Aline Gr?hs Ferrareze[SUP] 2 [/SUP], Meriane Demoliner[SUP] 4 [/SUP], Paula Rodrigues de Almeida[SUP] 4 [/SUP], Juliana Schons Gularte[SUP] 4 [/SUP], Alana Witt Hansen[SUP] 4 [/SUP], Matheus Nunes Weber[SUP] 4 [/SUP], Juliane Deise Fleck[SUP] 4 [/SUP], Ricardo Ariel Zimerman[SUP] 5 [/SUP], L?via Kmetzsch[SUP] 1 [/SUP], Fernando Rosado Spilki[SUP] 4 [/SUP], Claudia Elizabeth Thompson[SUP] 6 7 8 [/SUP]
Affiliations
Abstract
Background: 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. 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%).
Results: We 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.
Conclusions: Our 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.
Keywords: COVID-19; Infectious diseases; Molecular epidemiology; Sequencing; Severe acute respiratory syndrome coronavirus 2.
. 2021 May 20;22(1):371.
doi: 10.1186/s12864-021-07708-w.
Genomic epidemiology of SARS-CoV-2 in Esteio, Rio Grande do Sul, Brazil
Vin?cius Bonetti Franceschi[SUP] 1 [/SUP], Gabriel Dickin Caldana[SUP] 2 [/SUP], Amanda de Menezes Mayer[SUP] 1 [/SUP], Gabriela Bettella Cybis[SUP] 3 [/SUP], Carla Andretta Moreira Neves[SUP] 2 [/SUP], Patr?cia Aline Gr?hs Ferrareze[SUP] 2 [/SUP], Meriane Demoliner[SUP] 4 [/SUP], Paula Rodrigues de Almeida[SUP] 4 [/SUP], Juliana Schons Gularte[SUP] 4 [/SUP], Alana Witt Hansen[SUP] 4 [/SUP], Matheus Nunes Weber[SUP] 4 [/SUP], Juliane Deise Fleck[SUP] 4 [/SUP], Ricardo Ariel Zimerman[SUP] 5 [/SUP], L?via Kmetzsch[SUP] 1 [/SUP], Fernando Rosado Spilki[SUP] 4 [/SUP], Claudia Elizabeth Thompson[SUP] 6 7 8 [/SUP]
Affiliations
- PMID: 34016042
- DOI: 10.1186/s12864-021-07708-w
Abstract
Background: 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. 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%).
Results: We 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.
Conclusions: Our 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.
Keywords: COVID-19; Infectious diseases; Molecular epidemiology; Sequencing; Severe acute respiratory syndrome coronavirus 2.