Genomics and epidemiology of SARS-CoV-2 in Brazil
<p>As of the 24th January 2021, it is estimated that the coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to over 350 million reported cases and over 5.6 million deaths worldwide. Brazil has the third highest case...
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| Format: | Thesis |
| Language: | English |
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2022
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| _version_ | 1797111831726129152 |
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| author | da Silva Candido, D |
| author2 | R Faria, N |
| author_facet | R Faria, N da Silva Candido, D |
| author_sort | da Silva Candido, D |
| collection | OXFORD |
| description | <p>As of the 24th January 2021, it is estimated that the coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to over 350 million reported cases and over 5.6 million deaths worldwide. Brazil has the third highest case count, over 24 million, and the second highest death count, over 623,000. In this thesis, I apply genomic and epidemiological approaches to describe and understand SARS-CoV-2 importation, transmission, spread, evolution and response during the first year of the COVID-19 pandemic in Brazil.</p>
<p>Chapter 2 provides and overview of the early importation, spread and response. I start by identifying the probable air routes for SARS-CoV-2 importation into Brazil. I also provide a description of the first SARS-CoV-2 cases reported in Latin America, followed by epidemiological estimates of the basic reproduction number for the most affected Brazilian states. This chapter ends with a description of the implementation and easing of non-pharmaceutical interventions (NPIs) in 72.3% of the Brazilian municipalities.</p>
<p>In Chapter 3, I couple genomic insights obtained from a novel representative dataset of 427 SARS-CoV-2 genomes from Brazil with human mobility data to describe SARSCoV-2 importation and genomic diversity, reconstruct SARS-CoV-2 nationwide spatial spread and investigate the impact of NPIs implemented in Brazil.</p>
<p>Chapter 4 covers the application of genomic epidemiology approaches to the identification and description of new SARS-CoV-2 variants of concern (VOCs). I describe the first two cases of the Alpha VOC in Brazil and provide a genomic characterization of the first cases of the Gamma VOC in Manaus, north Brazil.</p>
<p>Finally, I apply epidemiological and genomic approaches to uncover the dynamics of hospital-associated transmission in the largest hospital complex in Latin America. Chapter 5 shows evidence for SARS-CoV-2 within-hospital transmission to be higher in non-COVID-19 hospitals.</p> |
| first_indexed | 2024-03-07T08:15:57Z |
| format | Thesis |
| id | oxford-uuid:a0dbebb2-109c-4a3a-a2af-90fd1e537194 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T08:15:57Z |
| publishDate | 2022 |
| record_format | dspace |
| spelling | oxford-uuid:a0dbebb2-109c-4a3a-a2af-90fd1e5371942024-01-03T12:00:53ZGenomics and epidemiology of SARS-CoV-2 in BrazilThesishttp://purl.org/coar/resource_type/c_db06uuid:a0dbebb2-109c-4a3a-a2af-90fd1e537194EpidemiologyGenomicsMolecular virologyCOVID-19 (Disease)Molecular epidemiologyGenomic epidemiologyEnglishHyrax Deposit2022da Silva Candido, DR Faria, NPybus, O<p>As of the 24th January 2021, it is estimated that the coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to over 350 million reported cases and over 5.6 million deaths worldwide. Brazil has the third highest case count, over 24 million, and the second highest death count, over 623,000. In this thesis, I apply genomic and epidemiological approaches to describe and understand SARS-CoV-2 importation, transmission, spread, evolution and response during the first year of the COVID-19 pandemic in Brazil.</p> <p>Chapter 2 provides and overview of the early importation, spread and response. I start by identifying the probable air routes for SARS-CoV-2 importation into Brazil. I also provide a description of the first SARS-CoV-2 cases reported in Latin America, followed by epidemiological estimates of the basic reproduction number for the most affected Brazilian states. This chapter ends with a description of the implementation and easing of non-pharmaceutical interventions (NPIs) in 72.3% of the Brazilian municipalities.</p> <p>In Chapter 3, I couple genomic insights obtained from a novel representative dataset of 427 SARS-CoV-2 genomes from Brazil with human mobility data to describe SARSCoV-2 importation and genomic diversity, reconstruct SARS-CoV-2 nationwide spatial spread and investigate the impact of NPIs implemented in Brazil.</p> <p>Chapter 4 covers the application of genomic epidemiology approaches to the identification and description of new SARS-CoV-2 variants of concern (VOCs). I describe the first two cases of the Alpha VOC in Brazil and provide a genomic characterization of the first cases of the Gamma VOC in Manaus, north Brazil.</p> <p>Finally, I apply epidemiological and genomic approaches to uncover the dynamics of hospital-associated transmission in the largest hospital complex in Latin America. Chapter 5 shows evidence for SARS-CoV-2 within-hospital transmission to be higher in non-COVID-19 hospitals.</p> |
| spellingShingle | Epidemiology Genomics Molecular virology COVID-19 (Disease) Molecular epidemiology Genomic epidemiology da Silva Candido, D Genomics and epidemiology of SARS-CoV-2 in Brazil |
| title | Genomics and epidemiology of SARS-CoV-2 in Brazil |
| title_full | Genomics and epidemiology of SARS-CoV-2 in Brazil |
| title_fullStr | Genomics and epidemiology of SARS-CoV-2 in Brazil |
| title_full_unstemmed | Genomics and epidemiology of SARS-CoV-2 in Brazil |
| title_short | Genomics and epidemiology of SARS-CoV-2 in Brazil |
| title_sort | genomics and epidemiology of sars cov 2 in brazil |
| topic | Epidemiology Genomics Molecular virology COVID-19 (Disease) Molecular epidemiology Genomic epidemiology |
| work_keys_str_mv | AT dasilvacandidod genomicsandepidemiologyofsarscov2inbrazil |