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Mayer ADM, Gröhs Ferrareze PA, de Oliveira LFV, Gregianini TS, Neves CLAM, Caldana GD, Kmetzsch L, Thompson CE. Genomic characterization and molecular evolution of SARS-CoV-2 in Rio Grande do Sul State, Brazil. Virology 2023; 582:1-11. [PMID: 36989935 PMCID: PMC10018445 DOI: 10.1016/j.virol.2023.03.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 03/08/2023] [Accepted: 03/10/2023] [Indexed: 03/18/2023]
Abstract
SARS-CoV-2 is the virus responsible for the COVID-19 and has afflicted the world since the end of 2019. Different lineages have been discovered and the Gamma lineage, which started the second wave of infections, was first described in Brazil, one of the most affected countries by pandemic. Therefore, this study analyzed SARS-CoV-2 sequenced genomes from Esteio city in Rio Grande do Sul, Southern Brazil. We also comparatively analyzed genomes of the two first years of the pandemic from Rio Grande do Sul state for understanding their genomic and evolutionary patterns. The phylogenomic analysis showed monophyletic groups for Alpha, Gamma, Delta and Omicron, as well as for other circulating lineages in the state. Molecular evolutionary analysis identified several sites under adaptive selection in membrane and nucleocapsid proteins which could be related to a prevalent stabilizing effect on membrane protein structure, as well as majoritarily destabilizing effects on C-terminal nucleocapsid domain.
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Affiliation(s)
- 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
| | - Patrícia Aline Gröhs Ferrareze
- Graduate Program in Health Sciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil
| | | | - Tatiana Schäffer Gregianini
- Laboratório Central de Saúde Pública do Centro Estadual de Vigilância em Saúde da Secretaria de Saúde do Estado do Rio Grande do Sul (LACEN/CEVS/SES-RS), 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
| | - 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), Porto Alegre, Brazil.
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Franceschi VB, Santos AS, Glaeser AB, Paiz JC, Caldana GD, Machado Lessa CL, de Menezes Mayer A, Küchle JG, Gazzola Zen PR, Vigo A, Winck AT, Rotta LN, Thompson CE. Population-based prevalence surveys during the Covid-19 pandemic: A systematic review. Rev Med Virol 2021; 31:e2200. [PMID: 34260777 PMCID: PMC7883186 DOI: 10.1002/rmv.2200] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 11/18/2020] [Accepted: 11/18/2020] [Indexed: 01/08/2023]
Abstract
Population-based prevalence surveys of Covid-19 contribute to establish the burden of infection, the role of asymptomatic and mild infections in transmission, and allow more precise decisions about reopen policies. We performed a systematic review to evaluate qualitative aspects of these studies, assessing their reliability and compiling practices that can influence the methodological quality. We searched MEDLINE, EMBASE, bioRxiv and medRxiv, and included cross-sectional studies using molecular and/or serological tests to estimate the prevalence of Covid-19 in the general population. Survey quality was assessed using the Joanna Briggs Institute Critical Appraisal Checklist for Prevalence Studies. A correspondence analysis correlated methodological parameters of each study to identify patterns related to higher, intermediate and lower risks of bias. The available data described 37 surveys from 19 countries. The majority were from Europe and America, used antibody testing, and reached highly heterogeneous sample sizes and prevalence estimates. Minority communities were disproportionately affected by Covid-19. Important risk of bias was detected in four domains: sample size, data analysis with sufficient coverage, measurements in standard way and response rate. The correspondence analysis showed few consistent patterns for high risk of bias. Intermediate risk of bias was related to American and European studies, municipal and regional initiatives, blood samples and prevalence >1%. Low risk of bias was related to Asian studies, nationwide initiatives, reverse-transcriptase polymerase chain reaction tests and prevalence <1%. We identified methodological standards applied worldwide in Covid-19 prevalence surveys, which may assist researchers with the planning, execution and reporting of future population-based surveys.
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Affiliation(s)
- Vinícius Bonetti Franceschi
- Graduate Program in Cell and Molecular Biology (PPGBCM)Center of BiotechnologyUniversidade Federal do Rio Grande do Sul (UFRGS)Porto AlegreRio Grande do SulBrazil
| | - Andressa Schneiders Santos
- Undergraduate Program in BiomedicineUniversidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA)Porto AlegreRio Grande do SulBrazil
| | - Andressa Barreto Glaeser
- Graduate Program in PathologyUniversidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA)Porto AlegreRio Grande do SulBrazil
| | - Janini Cristina Paiz
- Graduate Program in EpidemiologyUniversidade Federal do Rio Grande do Sul (UFRGS)Porto AlegreRio Grande do SulBrazil
| | - Gabriel Dickin Caldana
- Graduate Program in Health SciencesUniversidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA)Porto AlegreRio Grande do SulBrazil
| | - Carem Luana Machado Lessa
- Graduate Program in PathologyUniversidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA)Porto AlegreRio Grande do SulBrazil
| | - Amanda de Menezes Mayer
- Graduate Program in Cell and Molecular Biology (PPGBCM)Center of BiotechnologyUniversidade Federal do Rio Grande do Sul (UFRGS)Porto AlegreRio Grande do SulBrazil
| | - Julia Gonçalves Küchle
- Undergraduate Program in Biomedical InformaticsUniversidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA)Porto AlegreRio Grande do SulBrazil
| | - Paulo Ricardo Gazzola Zen
- Graduate Program in PathologyUniversidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA)Porto AlegreRio Grande do SulBrazil
- Department of Internal MedicineUniversidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA)Porto AlegreRio Grande do SulBrazil
| | - Alvaro Vigo
- Graduate Program in EpidemiologyUniversidade Federal do Rio Grande do Sul (UFRGS)Porto AlegreRio Grande do SulBrazil
- Department of StatisticsUniversidade Federal do Rio Grande do Sul (UFRGS)Porto AlegreRio Grande do SulBrazil
| | - Ana Trindade Winck
- Department of Exact and Social Applied SciencesUniversidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA)Porto AlegreRio Grande do SulBrazil
| | - Liane Nanci Rotta
- Graduate Program in Health SciencesUniversidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA)Porto AlegreRio Grande do SulBrazil
- Department of Diagnostic MethodsUniversidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA)Porto AlegreRio Grande do SulBrazil
| | - Claudia Elizabeth Thompson
- Graduate Program in Cell and Molecular Biology (PPGBCM)Center of BiotechnologyUniversidade Federal do Rio Grande do Sul (UFRGS)Porto AlegreRio Grande do SulBrazil
- Graduate Program in Health SciencesUniversidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA)Porto AlegreRio Grande do SulBrazil
- Department of PharmacosciencesUniversidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA)Porto AlegreRio Grande do SulBrazil
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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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