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Volume 27, Number 5—May 2021
Research

Genetic Evidence and Host Immune Response in Persons Reinfected with SARS-CoV-2, Brazil

Natalia Fintelman-Rodrigues, Aline P.D. da Silva, Monique Cristina dos Santos, Felipe B. Saraiva, Marcelo A. Ferreira, João Gesto, Danielle A.S. Rodrigues, André M. Vale, Isaclaudia G. de Azevedo, Vinícius C. Soares, Hui Jiang, Hongdong Tan, Diogo A. Tschoeke, Carolina Q. Sacramento, Fernando A. Bozza, Carlos M. Morel, Patrícia T. Bozza, and Thiago Moreno L. SouzaComments to Author 
Author affiliations: Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil (N. Fintelman-Rodrigues, A.P.D. da Silva, M.C. dos Santos, F.B. Saraiva, M.A. Ferreira, J. Gesto, I.G. de Azevedo, V.C. Soares, C.Q. Sacramento, F.A. Bozza, C.M. Morel, P.T. Bozza, T.M.L. Souza); Universidade Federal do Rio de Janeiro, Rio de Janeiro (D.A.S. Rodrigues, A.M. Vale, V.C. Soares, D.A. Tschoeke); MGI Tech Co., Ltd., Shenzhen, China (H. Jiang, H. Tan); D’Or Institute for Research and Education (F.A. Bozza)

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Figure 2

Phylogenetic analysis of severe acute respiratory syndrome coronavirus 2 genomes from reinfected patients, Brazil, 2020. Representative genomes deposited in GISAID (Appendix Table 1, Figure 3) were compared with sequences from virus genomes found in the respiratory samples from the first infection of patients B and C, and the second infection of patients A–D. A condensed phylogenetic tree rooted by reference genome Wuhan-Hu-1 (EPI_ISL_402125) was created with 1,000 bootstraps. Initial trees for the heuristic search were obtained automatically by applying neighbor-joining and BioNJ algorithms to a matrix of pairwise distances estimated using the Jukes-Cantor model (24), and then selecting the topology with a superior log-likelihood value. The tree with the highest log likelihood (−46487.36) is shown. The final dataset included a total of 29,920 positions. Evolutionary analyses were conducted in MEGA version 7.0 (22,23). Evolutionary history was inferred using the maximum-likelihood method and Jukes-Cantor model. Brown represents the emerging clade 19A, orange the clade 20A, and blue the clade 20B. Scale bar indicates substitutions per site. hCoV, human coronavirus.

Figure 2. Phylogenetic analysis of severe acute respiratory syndrome coronavirus 2 genomes from reinfected patients, Brazil, 2020. Representative genomes deposited in GISAID (Appendix Table 1, Figure 3) were compared with sequences from virus genomes found in the respiratory samples from the first infection of patients B and C, and the second infection of patients A–D. A condensed phylogenetic tree rooted by reference genome Wuhan-Hu-1 (EPI_ISL_402125) was created with 1,000 bootstraps. Initial trees for the heuristic search were obtained automatically by applying neighbor-joining and BioNJ algorithms to a matrix of pairwise distances estimated using the Jukes-Cantor model (24), and then selecting the topology with a superior log-likelihood value. The tree with the highest log likelihood (−46487.36) is shown. The final dataset included a total of 29,920 positions. Evolutionary analyses were conducted in MEGA version 7.0 (22,23). Evolutionary history was inferred using the maximum-likelihood method and Jukes-Cantor model. Brown represents the emerging clade 19A, orange the clade 20A, and blue the clade 20B. Scale bar indicates substitutions per site. hCoV, human coronavirus.

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Page updated: April 20, 2021
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