Supplementary Materials

Evolution and epidemic spread of SARS-CoV-2 in Brazil

Darlan S. Candido, Ingra M. Claro, Jaqueline G. de Jesus, William M. Souza, Filipe R. R. Moreira, Simon Dellicour, Thomas A. Mellan, Louis du Plessis, Rafael H. M. Pereira, Flavia C. S. Sales, Erika R. Manuli, Julien Thézé, Luiz Almeida, Mariane T. Menezes, Carolina M. Voloch, Marcilio J. Fumagalli, Thaís M. Coletti, Camila A. M. da Silva, Mariana S. Ramundo, Mariene R. Amorim, Henrique H. Hoeltgebaum, Swapnil Mishra, Mandev S. Gill, Luiz M. Carvalho, Lewis F. Buss, Carlos A. Prete Jr, Jordan Ashworth, Helder I. Nakaya, Pedro S. Peixoto, Oliver J. Brady, Samuel M. Nicholls, Amilcar Tanuri, Átila D. Rossi, Carlos K.V. Braga, Alexandra L. Gerber, Ana Paula de C. Guimarães, Nelson Gaburo Jr, Cecila Salete Alencar, Alessandro C. S. Ferreira, Cristiano X. Lima, José Eduardo Levi, Celso Granato, Giulia M. Ferreira, Ronaldo S. Francisco Jr, Fabiana Granja, Marcia T. Garcia, Maria Luiza Moretti, Mauricio W. Perroud Jr, Terezinha M. P. P. Castiñeiras, Carolina S. Lazari, Sarah C. Hill, Andreza Aruska de Souza Santos, Camila L. Simeoni, Julia Forato, Andrei C. Sposito, Angelica Z. Schreiber, Magnun N. N. Santos, Camila Zolini de Sá, Renan P. Souza, Luciana C. Resende-Moreira, Mauro M. Teixeira, Josy Hubner, Patricia A. F. Leme, Rennan G Moreira, Maurício L. Nogueira, Brazil-UK Centre for Arbovirus Discovery, Diagnosis, Genomics and Epidemiology (CADDE) Genomic Network, Neil M. Ferguson, Silvia F. Costa, José Luiz Proenca-Modena, Ana Tereza R. Vasconcelos, Samir Bhatt, Philippe Lemey, Chieh-Hsi Wu, Andrew Rambaut, Nick J. Loman, Renato S. Aguiar, Oliver G. Pybus, Ester C. Sabino, Nuno Rodrigues Faria

Materials/Methods, Supplementary Text, Tables, Figures, and/or References

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  • Materials and Methods
  • Figs. S1 to S7
  • Caption for Fig. S8
  • Figs. S9 to S15
  • Tables S1 to S3
  • Captions for Data S1 and Data S2
  • List of Members of the CADDE Genomic Network
  • References
Fig. S8
Detailed annotated maximum clade phylogenetic tree. Time-resolved maximum clade credibility phylogeny of 1,182 SARS-CoV-2 sequences, 490 from Brazil (red) and 692 from outside Brazil (blue). The largest Brazilian clusters are highlighted in grey (Clade 1, Clade 2 and Clade 3). States are defined by their 2-letter ISO 3166-1 codes. The MCC tree can be found at our Dryad repository (see Data Availability).
Data S1
Detailed metadata on all 1,182 sequences used in this study. File contains information on epidemiology, demography, location, diagnostics, sequencing statistics and evolution of 427 SARS-CoV-2 sequences generated in this study and 755 sequences downloaded from GISAID.
Data S2
Acknowledgment GISAID table. File contains Accession ID, collection date, originating and submitting lab and authors, from https://www.gisaid.org.
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