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2. The Omicron Lineages BA.1 and BA.2 (Betacoronavirus SARS-CoV-2) Have Repeatedly Entered Brazil through a Single Dispersal Hub

Author

Lamarca, Alessandra P., primary, Souza, Ueric José Borges de, additional, Moreira, Filipe Romero Rebello, additional, Almeida, Luiz G. P. de, additional, Menezes, Mariane Talon de, additional, Souza, Adrieli Barboza de, additional, Ferreira, Alessandro Clayton de Souza, additional, Gerber, Alexandra L., additional, Lima, Aline B. de, additional, Guimarães, Ana Paula de C., additional, Cavalcanti, Andréa Cony, additional, Silva, Aryel B. Paz e, additional, Lima, Bruna Israel, additional, Lobato, Cirley, additional, Silva, Cristiane Gomes Da, additional, Mendonça, Cristiane P. T. B., additional, Queiroz, Daniel Costa, additional, Zauli, Danielle Alves Gomes, additional, Menezes, Diego, additional, Possebon, Fábio Sossai, additional, Cardoso, Franciano Dias Pereira, additional, Malta, Frederico Scott Varella, additional, Braga-Paz, Isabela, additional, Silva, Joice do Prado, additional, Ferreira, Jorge Gomes Goulart, additional, Galvão, Jucimária Dantas, additional, Souza, Leandro Magalhães de, additional, Ferreira, Leonardo, additional, Possuelo, Lia Gonçalves, additional, Cavalcante, Liliane Tavares de Faria, additional, Alvim, Luige B., additional, Souza, Luiz Fellype Alves de, additional, Santos, Luiza C. G. de Araújo E, additional, Dias, Rillery Calixto, additional, Souza, Rutilene Barbosa, additional, Castro, Thaís Regina y, additional, Valim, Andréia Rosane de Moura, additional, Campos, Fabrício Souza, additional, Araujo, João Pessoa, additional, Trindade, Priscila de Arruda, additional, Aguiar, Renato S., additional, Michael Delai, Robson, additional, and Vasconcelos, Ana Tereza R de, additional

Published
2023
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3. The Role of Lebanon in the COVID-19 Butterfly Effect: The B.1.398 Example

Author

Nour, Dalal, primary, Rafei, Rayane, additional, Lamarca, Alessandra P., additional, de Almeida, Luiz G. P., additional, Osman, Marwan, additional, Ismail, Mohamad Bachar, additional, Mallat, Hassan, additional, Berry, Atika, additional, Burfin, Gwendolyne, additional, Semanas, Quentin, additional, Josset, Laurence, additional, Hassan, Hamad, additional, Dabboussi, Fouad, additional, Lina, Bruno, additional, Colson, Philippe, additional, Vasconcelos, Ana Tereza R., additional, and Hamze, Monzer, additional

Published
2022
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4. Emergence of Within-Host SARS-CoV-2 Recombinant Genome After Coinfection by Gamma and Delta Variants: A Case Report

Author

Francisco Junior, Ronaldo da Silva, primary, Almeida, Luiz G. P. de, additional, Lamarca, Alessandra P., additional, Cavalcante, Liliane, additional, Martins, Yasmmin, additional, Gerber, Alexandra L., additional, Guimarães, Ana Paula de C., additional, Salviano, Ricardo Barbosa, additional, dos Santos, Fernanda Leitão, additional, de Oliveira, Thiago Henrique, additional, de Souza, Isabelle Vasconcellos, additional, de Carvalho, Erika Martins, additional, Ribeiro, Mario Sergio, additional, Carvalho, Silvia, additional, da Silva, Flávio Dias, additional, Garcia, Marcio Henrique de Oliveira, additional, de Souza, Leandro Magalhães, additional, da Silva, Cristiane Gomes, additional, Ribeiro, Caio Luiz Pereira, additional, Cavalcanti, Andréa Cony, additional, de Mello, Claudia Maria Braga, additional, Tanuri, Amilcar, additional, and Vasconcelos, Ana Tereza R., additional

Published
2022
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6. Genomic Surveillance Tracks the First Community Outbreak of the SARS-CoV-2 Delta (B.1.617.2) Variant in Brazil

Author

Lamarca, Alessandra P., primary, de Almeida, Luiz G. P., additional, da Silva Francisco, Ronaldo, additional, Cavalcante, Liliane, additional, Machado, Douglas Terra, additional, Brustolini, Otávio, additional, Gerber, Alexandra L., additional, Guimarães, Ana Paula de C., additional, Policarpo, Cintia, additional, Oliveira, Gleidson da Silva de, additional, Boullosa, Lidia Theodoro, additional, Souza, Isabelle Vasconcellos de, additional, Carvalho, Erika Martins de, additional, Ribeiro, Mario Sergio, additional, Carvalho, Silvia, additional, Silva, Flávio Dias da, additional, Garcia, Marcio Henrique de Oliveira, additional, Souza, Leandro Magalhães de, additional, Silva, Cristiane Gomes Da, additional, Ribeiro, Caio Luiz Pereira, additional, Cavalcanti, Andréa Cony, additional, Mello, Claudia Maria Braga de, additional, Tanuri, Amilcar, additional, and Vasconcelos, Ana Tereza R., additional

Published
2022
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7. Phylodynamic analysis of SARS-CoV-2 spread in Rio de Janeiro, Brazil, highlights how metropolitan areas act as dispersal hubs for new variants.

Author

Lamarca, Alessandra P, primary, Almeida, Luiz G P de, additional, Francisco Junior, Ronaldo da Silva, additional, Cavalcante, Liliane, additional, Brustolini, Otavio, additional, Gerber, Alexandra L, additional, Guimaraes, Ana Paula de C, additional, Oliveira, Thiago Henrique de, additional, Nascimento, Erica Ramos dos Santos, additional, Policarpo, Cintia, additional, Souza, Isabelle Vasconcellos de, additional, Carvalho, Erika Martins de, additional, Ribeiro, Mario Sergio, additional, Carvalho, Silvia, additional, Silva, Flavio Dias da, additional, Garcia, Marcio Henrique de Oliveira, additional, Souza, Leandro Magalhaes de, additional, Silva, Cristiane Gomes da, additional, Ribeiro, Caio Luiz Pereira, additional, Cavalcanti, Andrea Cony, additional, Mello, Claudia Maria Braga de, additional, Tanuri, Amilcar, additional, and Vasconcelos, Ana Tereza R, additional

Published
2022
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8. Emergence of within-host SARS-CoV-2 recombinant genome after coinfection by Gamma and Delta variants

Author

Junior, Ronaldo da Silva Francisco, primary, de Almeida, Luiz G P, additional, Lamarca, Alessandra P, additional, Cavalcante, Liliane, additional, Martins, Yasmmin, additional, Gerber, Alexandra L, additional, Guimarães, Ana Paula de C, additional, Salviano, Ricardo Barbosa, additional, Santos, Fernanda Leitão dos, additional, de Oliveira, Thiago Henrique, additional, de Souza, Isabelle Vasconcellos, additional, de Carvalho, Erika Martins, additional, Ribeiro, Mario Sergio, additional, Carvalho, Silvia, additional, Silva, Flávio Dias da, additional, Garcia, Marcio Henrique de Oliveira, additional, de Souza, Leandro Magalhães, additional, Silva, Cristiane Gomes Da, additional, Ribeiro, Caio Luiz Pereira, additional, Cavalcanti, Andréa Cony, additional, de Mello, Claudia Maria Braga, additional, Tanuri, Amilcar, additional, and Vasconcelos, Ana Tereza R, additional

Published
2021
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9. Genomic surveillance of SARS-CoV-2 tracks early interstate transmission of P.1 lineage and diversification within P.2 clade in Brazil

Author

Lamarca, Alessandra P., primary, de Almeida, Luiz G. P., additional, Francisco, Ronaldo da Silva, additional, Lima, Lucymara Fassarella Agnez, additional, Scortecci, Kátia Castanho, additional, Perez, Vinícius Pietta, additional, Brustolini, Otavio J., additional, Sousa, Eduardo Sérgio Soares, additional, Secco, Danielle Angst, additional, Santos, Angela Maria Guimarães, additional, Albuquerque, George Rego, additional, Mariano, Ana Paula Melo, additional, Maciel, Bianca Mendes, additional, Gerber, Alexandra L., additional, Guimarães, Ana Paula de C., additional, Nascimento, Paulo Ricardo, additional, Neto, Francisco Paulo Freire, additional, Gadelha, Sandra Rocha, additional, Porto, Luís Cristóvão, additional, Campana, Eloiza Helena, additional, Jeronimo, Selma Maria Bezerra, additional, and Vasconcelos, Ana Tereza R., additional

Published
2021
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10. Turnover of SARS-CoV-2 Lineages Shaped the Pandemic and Enabled the Emergence of New Variants in the State of Rio de Janeiro, Brazil

Author

Francisco Junior, Ronaldo da Silva, primary, Lamarca, Alessandra P, additional, de Almeida, Luiz G P, additional, Cavalcante, Liliane, additional, Machado, Douglas Terra, additional, Martins, Yasmmin, additional, Brustolini, Otávio, additional, Gerber, Alexandra L, additional, Guimarães, Ana Paula de C, additional, Gonçalves, Reinaldo Bellini, additional, Alves, Cassia, additional, Mariani, Diana, additional, Cruz, Thais Felix, additional, de Souza, Isabelle Vasconcellos, additional, de Carvalho, Erika Martins, additional, Ribeiro, Mario Sergio, additional, Carvalho, Silvia, additional, da Silva, Flávio Dias, additional, Garcia, Márcio Henrique de Oliveira, additional, de Souza, Leandro Magalhães, additional, da Silva, Cristiane Gomes, additional, Ribeiro, Caio Luiz Pereira, additional, Cavalcanti, Andréa Cony, additional, de Mello, Claudia Maria Braga, additional, Struchiner, Cláudio J., additional, Tanuri, Amilcar, additional, and de Vasconcelos, Ana Tereza R, additional

Published
2021
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11. Pervasive transmission of E484K and emergence of VUI-NP13L with evidence of SARS-CoV-2 co-infection events by two different lineages in Rio Grande do Sul, Brazil

Author

Francisco Jr, Ronaldo da Silva, primary, Benites, L. Felipe, additional, Lamarca, Alessandra P., additional, de Almeida, Luiz G.P., additional, Hansen, Alana Witt, additional, Gularte, Juliana Schons, additional, Demoliner, Meriane, additional, Gerber, Alexandra L., additional, de C Guimarães, Ana Paula, additional, Antunes, Ana Karolina Eisen, additional, Heldt, Fagner Henrique, additional, Mallmann, Larissa, additional, Hermann, Bruna, additional, Ziulkoski, Ana Luiza, additional, Goes, Vyctoria, additional, Schallenberger, Karoline, additional, Fillipi, Micheli, additional, Pereira, Francini, additional, Weber, Matheus Nunes, additional, de Almeida, Paula Rodrigues, additional, Fleck, Juliane Deise, additional, Vasconcelos, Ana Tereza R., additional, and Spilki, Fernando Rosado, additional

Published
2021
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12. Genomic surveillance of SARS-CoV-2 tracks early interstate transmission of P.1 lineage and diversification within P.2 clade in Brazil

Author

Lamarca, Alessandra P, primary, de Almeida, Luiz G P, additional, Francisco, Ronaldo da Silva, additional, Lima, Lucymara Fassarella Agnez, additional, Scortecci, Kátia Castanho, additional, Perez, Vinícius Pietta, additional, Brustolini, Otavio J., additional, Sousa, Eduardo Sérgio Soares, additional, Secco, Danielle Angst, additional, Santos, Angela Maria Guimarães, additional, Albuquerque, George Rego, additional, Mariano, Ana Paula Melo, additional, Maciel, Bianca Mendes, additional, Gerber, Alexandra L, additional, Guimarães, Ana Paula de C, additional, Nascimento, Paulo Ricardo, additional, Neto, Francisco Paulo Freire, additional, Gadelha, Sandra Rocha, additional, Porto, Luís Cristóvão, additional, Campana, Eloiza Helena, additional, Jeronimo, Selma Maria Bezerra, additional, and Vasconcelos, Ana Tereza R, additional

Published
2021
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13. Pervasive transmission of E484K and emergence of VUI-NP13L with evidence of SARS-CoV-2 co-infection events by two different lineages in Rio Grande do Sul, Brazil

Author

da Silva Francisco, Ronaldo, primary, Benites, L. Felipe, additional, Lamarca, Alessandra P, additional, de Almeida, Luiz G P, additional, Hansen, Alana Witt, additional, Gularte, Juliana Schons, additional, Demoliner, Meriane, additional, Gerber, Alexandra L, additional, de C Guimarães, Ana Paula, additional, Antunes, Ana Karolina Eisen, additional, Heldt, Fagner Henrique, additional, Mallmann, Larissa, additional, Hermann, Bruna, additional, Ziulkoski, Ana Luiza, additional, Goes, Vyctoria, additional, Schallenberger, Karoline, additional, Fillipi, Micheli, additional, Pereira, Francini, additional, Weber, Matheus Nunes, additional, de Almeida, Paula Rodrigues, additional, Fleck, Juliane Deise, additional, Vasconcelos, Ana Tereza R, additional, and Spilki, Fernando Rosado, additional

Published
2021
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14. Transcriptome of the Southern Muriqui Brachyteles arachnoides (Primates:Platyrrhini), a Critically Endangered New World Monkey: Evidence of Adaptive Evolution

Author

Moreira, Daniel A., primary, Lamarca, Alessandra P., additional, Soares, Rafael Ferreira, additional, Coelho, Ana M. A., additional, Furtado, Carolina, additional, Scherer, Nicole M., additional, Moreira, Miguel A. M., additional, Seuánez, Hector N., additional, and Boroni, Mariana, additional

Published
2020
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16. Fast speciations and slow genes: uncovering the root of living canids.

Author

Lamarca, Alessandra P and Schrago, Carlos G

Subjects
*FOXES, *GENES, *CANIDAE, *GENOMES, *RADIATION, *MITOCHONDRIAL DNA abnormalities
Abstract

Despite ongoing efforts relying on computationally intensive tree-building methods and large datasets, the deeper phylogenetic relationships between living canid genera remain controversial. We demonstrate that this issue arises fundamentally from the uncertainty of root placement as a consequence of the short length of the branch connecting the major canid clades, which probably resulted from a fast radiation during the early diversification of extant Canidae. Using both nuclear and mitochondrial genes, we investigate the position of the canid root and its consistency by using three rooting methods. We find that mitochondrial genomes consistently retrieve a root node separating the tribe Canini from the remaining canids, whereas nuclear data mostly recover a root that places the Urocyon foxes as the sister lineage of living canids. We demonstrate that, to resolve the canid root, the nuclear segments sequenced so far are significantly less informative than mitochondrial genomes. We also propose that short intervals between speciations obscure the place of the true root, because methods are susceptible to stochastic error in the presence of short internal branches near the root. [ABSTRACT FROM AUTHOR]

Published
2020
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17. Turnover of SARS-CoV-2 Lineages Shaped the Pandemic and Enabled the Emergence of New Variants in the State of Rio de Janeiro, Brazil.

Author

da Silva Francisco Junior, Ronaldo, Lamarca, Alessandra P, de Almeida, Luiz G P, Cavalcante, Liliane, Machado, Douglas Terra, Martins, Yasmmin, Brustolini, Otávio, Gerber, Alexandra L, de C Guimarães, Ana Paula, Gonçalves, Reinaldo Bellini, Alves, Cassia, Mariani, Diana, Cruz, Thais Felix, de Souza, Isabelle Vasconcellos, de Carvalho, Erika Martins, Ribeiro, Mario Sergio, Carvalho, Silvia, da Silva, Flávio Dias, de Oliveira Garcia, Márcio Henrique, and de Souza, Leandro Magalhães

Subjects
*SARS-CoV-2, *COVID-19 pandemic, *PANDEMICS, *GENOMICS, *COVID-19
Abstract

In the present study, we provide a retrospective genomic epidemiology analysis of the SARS-CoV-2 pandemic in the state of Rio de Janeiro, Brazil. We gathered publicly available data from GISAID and sequenced 1927 new genomes sampled periodically from March 2021 to June 2021 from 91 out of the 92 cities of the state. Our results showed that the pandemic was characterized by three different phases driven by a successive replacement of lineages. Interestingly, we noticed that viral supercarriers accounted for the overwhelming majority of the circulating virus (>90%) among symptomatic individuals in the state. Moreover, SARS-CoV-2 genomic surveillance also revealed the emergence and spread of two new variants (P.5 and P.1.2), firstly reported in this study. Our findings provided important lessons learned from the different epidemiological aspects of the SARS-CoV-2 dynamic in Rio de Janeiro. Altogether, this might have a strong potential to shape future decisions aiming to improve public health management and understanding mechanisms underlying virus dispersion. [ABSTRACT FROM AUTHOR]

Published
2021
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