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Franceschi VB, Caldana GD, Perin C, Horn A, Peter C, Cybis GB, Ferrareze PAG, Rotta LN, Cadegiani FA, Zimerman RA, Thompson CE. Predominance of the SARS-CoV-2 Lineage P.1 and Its Sublineage P.1.2 in Patients from the Metropolitan Region of Porto Alegre, Southern Brazil in March 2021. Pathogens 2021; 10:988. [PMID: 34451453 PMCID: PMC8402156 DOI: 10.3390/pathogens10080988] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/28/2021] [Accepted: 07/29/2021] [Indexed: 12/02/2022] Open
Abstract
Almost a year after the COVID-19 pandemic had begun, new lineages (B.1.1.7, B.1.351, P.1, and B.1.617.2) associated with enhanced transmissibility, immunity evasion, and mortality were identified in the United Kingdom, South Africa, and Brazil. The previous most prevalent lineages in the state of Rio Grande do Sul (RS, Southern Brazil), B.1.1.28 and B.1.1.33, were rapidly replaced by P.1 and P.2, two B.1.1.28-derived lineages harboring the E484K mutation. To perform a genomic characterization from the metropolitan region of Porto Alegre, we sequenced viral samples to: (i) identify the prevalence of SARS-CoV-2 lineages in the region, the state, and bordering countries/regions; (ii) characterize the mutation spectra; (iii) hypothesize viral dispersal routes by using phylogenetic and phylogeographic approaches. We found that 96.4% of the samples belonged to the P.1 lineage and approximately 20% of them were assigned as the novel P.1.2, a P.1-derived sublineage harboring signature substitutions recently described in other Brazilian states and foreign countries. Moreover, sequences from this study were allocated in distinct branches of the P.1 phylogeny, suggesting multiple introductions in RS and placing this state as a potential diffusion core of P.1-derived clades and the emergence of P.1.2. It is uncertain whether the emergence of P.1.2 and other P.1 clades is related to clinical or epidemiological consequences. However, the clear signs of molecular diversity from the recently introduced P.1 warrant further genomic surveillance.
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Affiliation(s)
- Vinícius Bonetti Franceschi
- Graduate Program in Cell and Molecular Biology (PPGBCM), Center of Biotechnology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 91501-970, RS, Brazil;
| | - Gabriel Dickin Caldana
- Graduate Program in Health Sciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre 90050-170, RS, Brazil; (G.D.C.); (P.A.G.F.); (L.N.R.)
| | - Christiano Perin
- Department of Infection Control and Prevention, Hospital da Brigada Militar, Porto Alegre 91900-590, RS, Brazil; (C.P.); (A.H.)
| | - Alexandre Horn
- Department of Infection Control and Prevention, Hospital da Brigada Militar, Porto Alegre 91900-590, RS, Brazil; (C.P.); (A.H.)
| | - Camila Peter
- Laboratório Exame, Novo Hamburgo 93510-250, RS, Brazil;
| | - Gabriela Bettella Cybis
- Department of Statistics, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, RS, Brazil;
| | - Patrícia Aline Gröhs Ferrareze
- Graduate Program in Health Sciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre 90050-170, RS, Brazil; (G.D.C.); (P.A.G.F.); (L.N.R.)
| | - Liane Nanci Rotta
- Graduate Program in Health Sciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre 90050-170, RS, Brazil; (G.D.C.); (P.A.G.F.); (L.N.R.)
| | | | - Ricardo Ariel Zimerman
- Department of Infection Control and Prevention, Hospital da Brigada Militar, Porto Alegre 91900-590, RS, Brazil; (C.P.); (A.H.)
| | - Claudia Elizabeth Thompson
- Graduate Program in Cell and Molecular Biology (PPGBCM), Center of Biotechnology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 91501-970, RS, Brazil;
- Graduate Program in Health Sciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre 90050-170, RS, Brazil; (G.D.C.); (P.A.G.F.); (L.N.R.)
- Department of Pharmacosciences, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre 90050-170, RS, Brazil
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Franceschi VB, Ferrareze PAG, Zimerman RA, Cybis GB, Thompson CE. Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021. Virus Res 2021; 304:198532. [PMID: 34363852 PMCID: PMC8654641 DOI: 10.1016/j.virusres.2021.198532] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/21/2021] [Accepted: 07/29/2021] [Indexed: 12/21/2022]
Abstract
The COVID-19 pandemic has already reached more than 110 million people and is associated with 2.5 million deaths worldwide. Brazil is the third worst-hit country, with approximately 10.2 million cases and 250 thousand deaths. International efforts have been established to share information about Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemiology and evolution to support the development of effective strategies for public health and disease management. We aimed to analyze the high-quality genome sequences from Brazil from February 2020-2021 to identify mutation hotspots, geographical and temporal distribution of SARS-CoV-2 lineages by using phylogenetics and phylodynamics analyses. We describe heterogeneous sequencing efforts, the progression of the different lineages along time, evaluating mutational spectra and frequency oscillations derived from the prevalence of specific lineages across different Brazilian regions. We found at least seven major (1–7) and two minor clades related to the six most prevalent lineages in the country and described its spatial distribution and dynamics. The emergence and recent frequency shift of lineages (P.1 and P.2) carrying mutations of concern in the spike protein (e. g., E484K, N501Y) draws attention due to their association with immune evasion and enhanced receptor binding affinity. Improvements in genomic surveillance are of paramount importance and should be extended in Brazil to better inform policy makers about better decisions to fight the COVID-19 pandemic.
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Affiliation(s)
- Vinícius Bonetti Franceschi
- Graduate Program in Cell and Molecular Biology (PPGBCM), Center of Biotechnology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Patrícia Aline Gröhs Ferrareze
- Graduate Program in Health Sciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil
| | - Ricardo Ariel Zimerman
- Department of Infection Control and Prevention, Hospital da Brigada Militar, Porto Alegre, RS, Brazil
| | - Gabriela Bettella Cybis
- Department of Statistics, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Claudia Elizabeth Thompson
- Graduate Program in Cell and Molecular Biology (PPGBCM), Center of Biotechnology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil; Graduate Program in Health Sciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil; Department of Pharmacosciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), 245/200C Sarmento Leite St, Porto Alegre, RS 90050-170, Brazil.
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Franceschi VB, Caldana GD, de Menezes Mayer A, Cybis GB, Neves CAM, Ferrareze PAG, Demoliner M, de Almeida PR, Gularte JS, Hansen AW, Weber MN, Fleck JD, Zimerman RA, Kmetzsch L, Spilki FR, Thompson CE. Genomic epidemiology of SARS-CoV-2 in Esteio, Rio Grande do Sul, Brazil. BMC Genomics 2021; 22:371. [PMID: 34016042 PMCID: PMC8136996 DOI: 10.1186/s12864-021-07708-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 05/11/2021] [Indexed: 02/07/2023] Open
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.
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Affiliation(s)
- Vinícius Bonetti Franceschi
- Center of Biotechnology, Graduate Program in Cell and Molecular Biology (PPGBCM), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Gabriel Dickin Caldana
- Graduate Program in Health Sciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil
| | - Amanda de Menezes Mayer
- Center of Biotechnology, Graduate Program in Cell and Molecular Biology (PPGBCM), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Gabriela Bettella Cybis
- Department of Statistics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Carla Andretta Moreira Neves
- Graduate Program in Health Sciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil
| | - Patrícia Aline Gröhs Ferrareze
- Graduate Program in Health Sciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil
| | - Meriane Demoliner
- Molecular Microbiology Laboratory, Universidade Feevale, Novo Hamburgo, RS, Brazil
| | | | | | - Alana Witt Hansen
- Molecular Microbiology Laboratory, Universidade Feevale, Novo Hamburgo, RS, Brazil
| | - Matheus Nunes Weber
- Molecular Microbiology Laboratory, Universidade Feevale, Novo Hamburgo, RS, Brazil
| | - Juliane Deise Fleck
- Molecular Microbiology Laboratory, Universidade Feevale, Novo Hamburgo, RS, Brazil
| | | | - Lívia Kmetzsch
- Center of Biotechnology, Graduate Program in Cell and Molecular Biology (PPGBCM), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | | | - Claudia Elizabeth Thompson
- Center of Biotechnology, Graduate Program in Cell and Molecular Biology (PPGBCM), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil. .,Graduate Program in Health Sciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil. .,Department of Pharmacosciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), 245/200C Sarmento Leite St, Porto Alegre, RS, 90050-170, Brazil.
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Valk M, Cybis GB. U-Statistical Inference for Hierarchical Clustering. J Comput Graph Stat 2020. [DOI: 10.1080/10618600.2020.1796398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Marcio Valk
- Department of Statistics, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
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