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1. Multiplex qPCR Discriminates Variants of Concern to Enhance Global Surveillance of SARS-CoV-2

Author

Vogels, Chantal B. F., primary, Breban, Mallery I., additional, Ott, Isabel M., additional, Alpert, Tara, additional, Petrone, Mary E., additional, Watkins, Anne E., additional, Kalinich, Chaney C., additional, Earnest, Rebecca, additional, Rothman, Jessica E., additional, de Jesus, Jaqueline Goes, additional, Claro, Ingra Morales, additional, Ferreira, Giulia Magalhães, additional, Crispim, Myuki A. E., additional, Singh, Lavanya, additional, Tegally, Houriiyah, additional, Anyaneji, Ugochukwu J., additional, Hodcroft, Emma B., additional, Mason, Christopher E., additional, Khullar, Gaurav, additional, Metti, Jessica, additional, Dudley, Joel T., additional, MacKay, Matthew J., additional, Nash, Megan, additional, Wang, Jianhui, additional, Liu, Chen, additional, Hui, Pei, additional, Murphy, Steven, additional, Neal, Caleb, additional, Laszlo, Eva, additional, Landry, Marie L., additional, Muyombwe, Anthony, additional, Downing, Randy, additional, Razeq, Jafar, additional, de Oliveira, Tulio, additional, Faria, Nuno R., additional, Sabino, Ester C., additional, Neher, Richard A., additional, Fauver, Joseph R., additional, and Grubaugh, Nathan D., additional

Published
2023
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2. An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar

Author

Grubaugh, Nathan D, Gangavarapu, Karthik, Quick, Joshua, Matteson, Nathaniel L, De Jesus, Jaqueline Goes, Main, Bradley J, Tan, Amanda L, Paul, Lauren M, Brackney, Doug E, Grewal, Saran, Gurfield, Nikos, Van Rompay, Koen KA, Isern, Sharon, Michael, Scott F, Coffey, Lark L, Loman, Nicholas J, and Andersen, Kristian G

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Emerging Infectious Diseases, Nanotechnology, West Nile Virus, Biodefense, Bioengineering, Infectious Diseases, Rare Diseases, Genetics, Vector-Borne Diseases, Infection, Good Health and Well Being, Genetic Variation, Genomics, Sequence Analysis, RNA, West Nile virus, Zika Virus, Viral sequencing, Amplicon sequencing, Intrahost evolution, Zika, West Nile, SNP calling, Environmental Sciences, Information and Computing Sciences, Bioinformatics
Abstract

How viruses evolve within hosts can dictate infection outcomes; however, reconstructing this process is challenging. We evaluate our multiplexed amplicon approach, PrimalSeq, to demonstrate how virus concentration, sequencing coverage, primer mismatches, and replicates influence the accuracy of measuring intrahost virus diversity. We develop an experimental protocol and computational tool, iVar, for using PrimalSeq to measure virus diversity using Illumina and compare the results to Oxford Nanopore sequencing. We demonstrate the utility of PrimalSeq by measuring Zika and West Nile virus diversity from varied sample types and show that the accumulation of genetic diversity is influenced by experimental and biological systems.

Published
2019

3. Nanopore native RNA sequencing of a human poly(A) transcriptome

Author

Workman, Rachael E, Tang, Alison D, Tang, Paul S, Jain, Miten, Tyson, John R, Razaghi, Roham, Zuzarte, Philip C, Gilpatrick, Timothy, Payne, Alexander, Quick, Joshua, Sadowski, Norah, Holmes, Nadine, de Jesus, Jaqueline Goes, Jones, Karen L, Soulette, Cameron M, Snutch, Terrance P, Loman, Nicholas, Paten, Benedict, Loose, Matthew, Simpson, Jared T, Olsen, Hugh E, Brooks, Angela N, Akeson, Mark, and Timp, Winston

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Nanotechnology, Human Genome, Bioengineering, Biotechnology, Cells, Cultured, Humans, Nanopore Sequencing, Poly A, Sequence Analysis, RNA, Transcriptome, Technology, Medical and Health Sciences, Developmental Biology, Biological sciences
Abstract

High-throughput complementary DNA sequencing technologies have advanced our understanding of transcriptome complexity and regulation. However, these methods lose information contained in biological RNA because the copied reads are often short and modifications are not retained. We address these limitations using a native poly(A) RNA sequencing strategy developed by Oxford Nanopore Technologies. Our study generated 9.9 million aligned sequence reads for the human cell line GM12878, using thirty MinION flow cells at six institutions. These native RNA reads had a median length of 771 bases, and a maximum aligned length of over 21,000 bases. Mitochondrial poly(A) reads provided an internal measure of read-length quality. We combined these long nanopore reads with higher accuracy short-reads and annotated GM12878 promoter regions to identify 33,984 plausible RNA isoforms. We describe strategies for assessing 3' poly(A) tail length, base modifications and transcript haplotypes.

Published
2019

5. Epidemiologic History and Genetic Diversity Origins of Chikungunya and Dengue Viruses, Paraguay

Author

Graf, Tiago, Vazquez, Cynthia, Giovanetti, Marta, de Bruycker-Nogueira, Fernanda, Fonseca, Vagner, Claro, Ingra Morales, de Jesus, Jaqueline Goes, Gomez, Andrea, Xavier, Joilson, de Mendonca, Marcos Cesar Lima, Villalba, Shirley, Torales, Juan, Gamarra, Maria Liz, Theze, Julien, de Filippis, Ana Maria Bispo, Azevedo, Vasco, de Oliveira, Tulio, Franco, Leticia, de Albuquerque, Carlos F. Campelo, Irala, Sandra, Holmes, Edward Charles, Rico, Jairo Andres Mendez, and Alcantara, Luiz Carlos, Jr.

Subjects
Chikungunya virus -- Natural history -- Distribution -- Genetic aspects, Biological diversity -- Research, Dengue viruses -- Natural history -- Distribution -- Genetic aspects, Virus research, Company distribution practices, Health
Abstract

Chikungunya virus (CHIKV), dengue virus (DENV), and Zika virus (ZIKV) are 3 of the most common arthropod-borne viruses (arboviruses) that infect humans. All are transmitted by the anthropophilic and urban-adapted [...]

Published
2021
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6. Phylogenetics, Epidemiology and Temporal Patterns of Dengue Virus in Araraquara, São Paulo State

Author

de Souza, Caio Santos, primary, Caleiro, Giovana Santos, additional, Claro, Ingra Morales, additional, de Jesus, Jaqueline Goes, additional, Coletti, Thaís Moura, additional, da Silva, Camila Alves Maia, additional, Costa, Ângela Aparecida, additional, Inenami, Marta, additional, Ribeiro, Andreia C., additional, Felix, Alvina Clara, additional, de Paula, Anderson Vicente, additional, Figueiredo, Walter M., additional, de Albuquerque Luna, Expedito José, additional, Sabino, Ester C., additional, and Romano, Camila M., additional

Published
2024
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8. Local Transmission of SARS-CoV-2 Lineage B.1.1.7, Brazil, December 2020

Author

Claro, Ingra Morales, Sales, Flavia Cristina da Silva, Ramundo, Mariana Severo, Candido, Darlan S., Silva, Camila A.M., de Jesus, Jaqueline Goes, Manuli, Erika R., de Oliveira, Cristina Mendes, Scarpelli, Luciano, Campana, Gustavo, Pybus, Oliver G., Sabino, Ester Cerdeira, Faria, Nuno Rodrigues, and Levi, Jose Eduardo

Subjects
Distribution, Case studies, Causes of, Company distribution practices, SARS-CoV-2 variants -- Distribution -- Case studies, Disease transmission -- Case studies, COVID-19 -- Distribution -- Causes of -- Case studies
Abstract

Genomic sequencing and analysis during the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic have led to identification of [approximately equals to] 800 distinct SARS-CoV-2 lineages worldwide. A new phylogenetic [...]

Published
2021
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9. Lessons from a Multilaboratorial Task Force for Diagnosis of a Fatal Toxoplasmosis Outbreak in Captive Primates in Brazil

Author

Schiffler, Francine Bittencourt, primary, Pereira, Asheley Henrique Barbosa, additional, Moreira, Silvia Bahadian, additional, Arruda, Igor Falco, additional, Moreira, Filipe Romero Rebello, additional, D’arc, Mirela, additional, Claro, Ingra Morales, additional, Pissinatti, Thalita de Abreu, additional, Cavalcante, Liliane Tavares de Faria, additional, Miranda, Thamiris dos Santos, additional, Cosentino, Matheus Augusto Calvano, additional, de Oliveira, Renata Carvalho, additional, Fernandes, Jorlan, additional, Assis, Matheus Ribeiro da Silva, additional, de Oliveira, Jonathan Gonçalves, additional, da Silva, Thayssa Alves Coelho, additional, Galliez, Rafael Mello, additional, Faffe, Debora Souza, additional, de Jesus, Jaqueline Goes, additional, Sobreira Bezerra da Silva, Marise, additional, Bezerra, Matheus Filgueira, additional, Ferreira Junior, Orlando da Costa, additional, Tanuri, Amilcar, additional, Castiñeiras, Terezinha Marta, additional, Aguiar, Renato Santana, additional, Faria, Nuno Rodrigues, additional, Almeida, Alzira Paiva de, additional, Pissinatti, Alcides, additional, Sabino, Ester Cerdeira, additional, Amendoeira, Maria Regina Reis, additional, de Lemos, Elba Regina Sampaio, additional, Ubiali, Daniel Guimarães, additional, and Santos, André F. A., additional

Published
2023
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10. Pan-genomics of virus and its applications

Author

Giovanetti, Marta, primary, Salgado, Alvaro, additional, de Souza Fonseca, Vagner, additional, Tosta, Fraga de Oliveira, additional, Xavier, Joilson, additional, de Jesus, Jaqueline Goes, additional, Iani, Felipe Campos Melo, additional, Adelino, Talita Emile Ribeiro, additional, Barreto, Fernanda Khouri, additional, Faria, Nuno Rodrigues, additional, de Oliveira, Tulio, additional, and Alcantara, Luiz Carlos Junior, additional

Published
2020
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11. Contributors

Author

Adelino, Talita Emile Ribeiro, primary, Ahmad, Jamil, additional, Ahmed, Shahbaz, additional, Alcantara, Luiz Carlos Junior, additional, Ali, Amjad, additional, Amir, Rabia, additional, Araujo, Fabricio, additional, Arveen, Muneeba, additional, Azevedo, Vasco, additional, Azhar, Jahanzaib, additional, Balbo, Luciana, additional, Bao, Li, additional, Barh, Debmalya, additional, Barreto, Fernanda Khouri, additional, Bhatti, Attya, additional, Burkovski, Andreas, additional, Chideroli, Roberta Torres, additional, Corredor, Mauricio, additional, da Costa Pinheiro, Kenny, additional, da Costa Silva, Artur Luiz, additional, Dar, Hamza Arshad, additional, de Castro Oliveira, Letícia, additional, de Castro Soares, Siomar, additional, de Jesus, Jaqueline Goes, additional, de Jesus Sousa, Thiago, additional, de Oliveira, Tulio, additional, de Oliveira Tosta, Stephane Fraga, additional, de Pádua Pereira, Ulisses, additional, de Souza Fonseca, Vagner, additional, Dhawan, Dipali, additional, Facimoto, César Toshio, additional, Faria, Nuno Rodrigues, additional, Fatima, Nosheen, additional, Figueiredo, Henrique César Pereira, additional, Giovanetti, Marta, additional, Góes-Neto, Aristóteles, additional, Gomide, Anne Cybelle Pinto, additional, Guimarães, Luis Carlos, additional, Hurtado, Raquel Enma, additional, Iani, Felipe Campos Melo, additional, Ibraim, Izabela Coimbra, additional, Imchen, Madangchanok, additional, Jaiswal, Arun Kumar, additional, Jamal, Syed Babar, additional, John, Peter, additional, Kato, Rodrigo Bentes, additional, Kaur, Jaspreet, additional, Kaur, Bineypreet, additional, Kumavath, Ranjith, additional, Liu, Xiaofeng, additional, Luan, Nguyen Thanh, additional, Maqsood, Wajahat, additional, da Silva, Wanderson Marques, additional, Minhas, Anupriya, additional, Munir, Faiza, additional, Muñoz-Gómez, Amalia, additional, Naz, Kanwal, additional, Naz, Anam, additional, Obaid, Ayesha, additional, Pantoja, Yan, additional, Ramos, Rommel, additional, Saba, Noor Ul, additional, Salgado, Alvaro, additional, Sangal, Vartul, additional, Sani, Qurat-ul-Ain, additional, Seyffert, Nubia, additional, Sheraz Shah, Faisal, additional, Shahid, Fatima, additional, Shehroz, Muhammad, additional, Siddiqa, Amnah, additional, Srivastava, Gyan P., additional, Tavares, Guilherme Campos, additional, Thi, Hai Ha Pham, additional, Tiwari, Sandeep, additional, Tiwary, Basant K., additional, Ullah, Nimat, additional, Vennapu, Ravali Krishna, additional, Xavier, Joilson, additional, Yadav, Neelam, additional, Yadav, Bhupendra N.S., additional, Yadav, Rajiv K., additional, Yadav, Dinesh K., additional, and Zaheer, Tahreem, additional

Published
2020
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12. SARS-CoV-2 Detection and Culture in Different Biological Specimens from Immunocompetent and Immunosuppressed COVID-19 Patients Infected with Two Different Viral Strains

Author

Mendes-Correa, Maria Cassia, primary, Salomão, Matias Chiarastelli, additional, Ghilardi, Fabio, additional, Tozetto-Mendoza, Tania Regina, additional, Santos Vilas Boas, Lucy, additional, De Paula, Anderson Vicente, additional, Paiao, Heuder Gustavo Oliveira, additional, Da Costa, Antonio Charlys, additional, Leal, Fabio Eudes, additional, Ferraz, Andrea de Barros Coscelli, additional, Salles, Flavia Cristina, additional, Claro, Ingra M., additional, Ferreira, Noely Evangelista, additional, Pereira, Geovana M., additional, Junior, Almir Ribeiro, additional, Freire, Wilton, additional, Espinoza, Evelyn Patricia Sánchez, additional, Manuli, Erika R., additional, Romano, Camila, additional, De Jesus, Jaqueline Goes, additional, Sabino, Ester Cerdeira, additional, and Witkin, Steven Sol, additional

Published
2023
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13. Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples

Author

Quick, Joshua, Grubaugh, Nathan D, Pullan, Steven T, Claro, Ingra M, Smith, Andrew D, Gangavarapu, Karthik, Oliveira, Glenn, Robles-Sikisaka, Refugio, Rogers, Thomas F, Beutler, Nathan A, Burton, Dennis R, Lewis-Ximenez, Lia Laura, de Jesus, Jaqueline Goes, Giovanetti, Marta, Hill, Sarah C, Black, Allison, Bedford, Trevor, Carroll, Miles W, Nunes, Marcio, Alcantara, Jr., Luiz Carlos, Sabino, Ester C, Baylis, Sally A, Faria, Nuno R, Loose, Matthew, Simpson, Jared T, Pybus, Oliver G, Andersen, Kristian G, and Loman, Nicholas J

Published
2017
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15. Author Correction: Nanopore native RNA sequencing of a human poly(A) transcriptome

Author

Workman, Rachael E., Tang, Alison D., Tang, Paul S., Jain, Miten, Tyson, John R., Razaghi, Roham, Zuzarte, Philip C., Gilpatrick, Timothy, Payne, Alexander, Quick, Joshua, Sadowski, Norah, Holmes, Nadine, de Jesus, Jaqueline Goes, Jones, Karen L., Soulette, Cameron M., Snutch, Terrance P., Loman, Nicholas, Paten, Benedict, Loose, Matthew, Simpson, Jared T., Olsen, Hugh E., Brooks, Angela N., Akeson, Mark, and Timp, Winston

Published
2020
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16. Performance of vaccination with CoronaVac in a cohort of healthcare workers (HCW) - preliminary report

Author

de Faria, Elizabeth, primary, Guedes, Ana Rubia, additional, Oliveira, Maura S., additional, de Godoy Moreira, Moacyr Vergara, additional, Maia, Fernando Liebhart, additional, dos Santos Barboza, Antonio, additional, Leme, Mariana Deckers, additional, Letaif, Leila S. Harima, additional, Miethke-Morais, Anna, additional, Bonfá, Eloisa, additional, Segurado, Aluisio C., additional, Tomazini, Francis M., additional, dos Santos, Alcir Alves, additional, Figueiredo, Pedro, additional, dos Santos Andrade, Pâmela, additional, de Oliveira, Franciane Mendes, additional, de Araújo Eliodoro, Raissa Heloisa, additional, de Jesus, Jaqueline Goes, additional, dos Santos Lazari, Carolina, additional, Sabino, Ester C., additional, Costa, Silvia F., additional, Pedroso de Lima, Antonio Carlos, additional, and Levin, Anna S., additional

Published
2021
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17. Chapter 11 - Pan-genomics of virus and its applications

Author

Giovanetti, Marta, Salgado, Alvaro, de Souza Fonseca, Vagner, Tosta, Fraga de Oliveira, Xavier, Joilson, de Jesus, Jaqueline Goes, Iani, Felipe Campos Melo, Adelino, Talita Emile Ribeiro, Barreto, Fernanda Khouri, Faria, Nuno Rodrigues, de Oliveira, Tulio, and Alcantara, Luiz Carlos Junior

Published
2020
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18. Prolonged presence of replication-competent SARS-CoV-2 in mildly symptomatic individuals: A Report of 2 Cases

Author

Mendes-Correa, Maria Cassia, primary, Leal, Fabio E., additional, Villas-Boas, Lucy S., additional, Witkin, Steven S., additional, de Paula, Anderson, additional, Tozetto-Mendonza, Tania Regina, additional, Ferreira, Noely Evangelista, additional, Curty, Gislaine, additional, de Carvalho, Pedro Santos, additional, Buss, Lewis F., additional, Costa, Silvia F., additional, da Cunha Carvalho, Flavia Mendes, additional, Kawakami, Joyce, additional, Taniwaki, Noemi Nosomi, additional, Paiao, Heuder, additional, da Silva Bizário, Joao Carlos, additional, de Jesus, Jaqueline Goes, additional, Sabino, Ester Cerdeira, additional, Romano, Camila Malta, additional, Zetone Grepan, Regina Maura, additional, and Sesso, Antonio, additional

Published
2020
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19. Genomic surveillance of Yellow fever virus epizootic in São Paulo, Brazil, 2016-2018

Author

Hill, Sarah Catherine, de Souza, Renato, Thézé, Julien, Claro, Ingra Morales, Aguiar, Renato Santana, Abade, Leandro, Santos, Fabiana Cristina Pereira Dos F.C.P., Cunha, Mariana Sequetin, Nogueira, Juliana Silva, Salles, Flavia F.C.S., Rocco, Iray Maria, Maeda, Adriana Yurika, Vasami, Fernanda Gisele Silva, du Plessis, Louis, Silveira, Paola Paz, de Jesus, Jaqueline Goes, Quick, Joshua, Fernandes, Natália N.C.C.A., Guerra, Juliana Mariotti, Réssio, Rodrigo Albergaria, Giovanetti, Marta, Alcantara, Luiz Carlos L.C.J., Cirqueira, Cinthya Dos Santos C.S., Díaz-Delgado, Josué, Macedo, Fernando Luiz Lima, Timenetsky, Maria Do Carmo Sampaio Tavares Timenetsky M.d.C.S.T., de Paula, Regiane, Spinola, Roberta, Telles de Deus, Juliana, Mucci, Luís Filipe, Tubaki, Rosa Maria, de Menezes, Regiane María Tironi, Ramos, Patrícia Locosque, de Abreu, André Luiz, Cruz, Laura Nogueira, Loman, Nick, Dellicour, Simon, Pybus, Oliver George, Sabino, Ester Cerdeira, Faria, Nuno Rodrigues, Hill, Sarah Catherine, de Souza, Renato, Thézé, Julien, Claro, Ingra Morales, Aguiar, Renato Santana, Abade, Leandro, Santos, Fabiana Cristina Pereira Dos F.C.P., Cunha, Mariana Sequetin, Nogueira, Juliana Silva, Salles, Flavia F.C.S., Rocco, Iray Maria, Maeda, Adriana Yurika, Vasami, Fernanda Gisele Silva, du Plessis, Louis, Silveira, Paola Paz, de Jesus, Jaqueline Goes, Quick, Joshua, Fernandes, Natália N.C.C.A., Guerra, Juliana Mariotti, Réssio, Rodrigo Albergaria, Giovanetti, Marta, Alcantara, Luiz Carlos L.C.J., Cirqueira, Cinthya Dos Santos C.S., Díaz-Delgado, Josué, Macedo, Fernando Luiz Lima, Timenetsky, Maria Do Carmo Sampaio Tavares Timenetsky M.d.C.S.T., de Paula, Regiane, Spinola, Roberta, Telles de Deus, Juliana, Mucci, Luís Filipe, Tubaki, Rosa Maria, de Menezes, Regiane María Tironi, Ramos, Patrícia Locosque, de Abreu, André Luiz, Cruz, Laura Nogueira, Loman, Nick, Dellicour, Simon, Pybus, Oliver George, Sabino, Ester Cerdeira, and Faria, Nuno Rodrigues

Abstract

São Paulo, a densely inhabited state in southeast Brazil that contains the fourth most populated city in the world, recently experienced its largest yellow fever virus (YFV) outbreak in decades. YFV does not normally circulate extensively in São Paulo, so most people were unvaccinated when the outbreak began. Surveillance in non-human primates (NHPs) is important for determining the magnitude and geographic extent of an epizootic, thereby helping to evaluate the risk of YFV spillover to humans. Data from infected NHPs can give more accurate insights into YFV spread than when using data from human cases alone. To contextualise human cases, identify epizootic foci and uncover the rate and direction of YFV spread in São Paulo, we generated and analysed virus genomic data and epizootic case data from NHPs in São Paulo. We report the occurrence of three spatiotemporally distinct phases of the outbreak in São Paulo prior to February 2018. We generated 51 new virus genomes from YFV positive cases identified in 23 different municipalities in São Paulo, mostly sampled from NHPs between October 2016 and January 2018. Although we observe substantial heterogeneity in lineage dispersal velocities between phylogenetic branches, continuous phylogeographic analyses of generated YFV genomes suggest that YFV lineages spread in São Paulo at a mean rate of approximately 1km per day during all phases of the outbreak. Viral lineages from the first epizootic phase in northern São Paulo subsequently dispersed towards the south of the state to cause the second and third epizootic phases there. This alters our understanding of how YFV was introduced into the densely populated south of São Paulo state. Our results shed light on the sylvatic transmission of YFV in highly fragmented forested regions in São Paulo state and highlight the importance of continued surveillance of zoonotic pathogens in sentinel species., SCOPUS: ar.j, info:eu-repo/semantics/published

Published
2020

20. Genomic, epidemiological and digital surveillance of Chikungunya virus in the Brazilian Amazon

Author

Naveca, Felipe Gomes, Claro, Ingra, Giovanetti, Marta, de Jesus, Jaqueline Goes, Xavier, Joilson, Iani, Felipe Campos de Melo, do Nascimento, Valdinete Alves, de Souza, Victor Costa, Silveira, Paola Paz, Lourenço, José, Santillana, Mauricio, Kraemer, Moritz U. G., Quick, Josh, Hill, Sarah C., Thézé, Julien, Carvalho, Rodrigo Dias de Oliveira, Azevedo, Vasco, Salles, Flavia Cristina da Silva, Nunes, Marcio Roberto Teixeira, Lemos, Poliana da Silva, Candido, Darlan da Silva, Pereira, Glauco de Carvalho, Oliveira, Marluce Aparecida Assunção, Meneses, Cátia Alexandra Ribeiro, Maito, Rodrigo Melo, Cunha, Claudeth Rocha Santa Brígida, Campos, Daniela Palha de Sousa, Castilho, Marcia da Costa, Siqueira, Thalita Caroline da Silva, Terra, Tiza Matos, de Albuquerque, Carlos F. Campelo, da Cruz, Laura Nogueira, de Abreu, André Luis, Martins, Divino Valerio, Simoes, Daniele Silva de Moraes Vanlume, de Aguiar, Renato Santana, Luz, Sérgio Luiz Bessa, Loman, Nicholas, Pybus, Oliver G., Sabino, Ester C., Okumoto, Osnei, Alcantara, Luiz Carlos Junior, Faria, Nuno Rodrigues, and University of Oxford [Oxford]

Subjects
RNA viruses, Viral Diseases, Epidemiology, [SDV]Life Sciences [q-bio], RC955-962, Filogeografia, Pathology and Laboratory Medicine, Geographical locations, Disease Outbreaks, Arctic medicine. Tropical medicine, Zoonoses, Medicine and Health Sciences, Public and Occupational Health, Genome Sequencing, Phylogeny, V?rus Chikungunya / gen?tica, Boa Vista (RR), Chikungunya Virus, virus diseases, Genomics, Infectious Diseases, Medical Microbiology, Viral Pathogens, Epidemiological Monitoring, Viruses, Public aspects of medicine, RA1-1270, Pathogens, Brazil, Research Article, Neglected Tropical Diseases, Alphaviruses, Genome, Viral, Research and Analysis Methods, Microbiology, Togaviruses, parasitic diseases, Genetics, Genoma Viral, Animals, Humans, Molecular Biology Techniques, Sequencing Techniques, Microbial Pathogens, Molecular Biology, Varia??o Gen?tica, Whole Genome Sequencing, Biology and life sciences, Organisms, Chikungunya Infection, Computational Biology, South America, Monitoramento Epidemiol?gico, Tropical Diseases, Genome Analysis, Genomic Libraries, Filogenia, Arbovirus / patogenicidade, Chikungunya Fever, People and places
Abstract

Background Since its first detection in the Caribbean in late 2013, chikungunya virus (CHIKV) has affected 51 countries in the Americas. The CHIKV epidemic in the Americas was caused by the CHIKV-Asian genotype. In August 2014, local transmission of the CHIKV-Asian genotype was detected in the Brazilian Amazon region. However, a distinct lineage, the CHIKV-East-Central-South-America (ECSA)-genotype, was detected nearly simultaneously in Feira de Santana, Bahia state, northeast Brazil. The genomic diversity and the dynamics of CHIKV in the Brazilian Amazon region remains poorly understood despite its importance to better understand the epidemiological spread and public health impact of CHIKV in the country. Methodology/Principal findings We report a large CHIKV outbreak (5,928 notified cases between August 2014 and August 2018) in Boa vista municipality, capital city of Roraima’s state, located in the Brazilian Amazon region. We generated 20 novel CHIKV-ECSA genomes from the Brazilian Amazon region using MinION portable genome sequencing. Phylogenetic analyses revealed that despite an early introduction of the Asian genotype in 2015 in Roraima, the large CHIKV outbreak in 2017 in Boa Vista was caused by an ECSA-lineage most likely introduced from northeastern Brazil. Epidemiological analyses suggest a basic reproductive number of R0 of 1.66, which translates in an estimated 39 (95% CI: 36 to 45) % of Roraima’s population infected with CHIKV-ECSA. Finally, we find a strong association between Google search activity and the local laboratory-confirmed CHIKV cases in Roraima. Conclusions/Significance This study highlights the potential of combining traditional surveillance with portable genome sequencing technologies and digital epidemiology to inform public health surveillance in the Amazon region. Our data reveal a large CHIKV-ECSA outbreak in Boa Vista, limited potential for future CHIKV outbreaks, and indicate a replacement of the Asian genotype by the ECSA genotype in the Amazon region., Author summary Until the end of 2017, Brazil notified the highest number of infections caused by chikungunya virus (CHIKV) in the Americas. We investigated a large CHIKV outbreak in Boa vista municipality in the Brazilian Amazon region. Rapid portable genome sequencing of 20 novel isolates and subsequent genetic analysis revealed that ECSA lineage was introduced from northeastern Brazil to Roraima around July 2016. Epidemiological analyses suggest a basic reproductive number of R0 of 1.66, which suggests that approximately 39% of Roraima’s population was infected with CHIKV-ECSA. Given the dominance of the CHIKV-Asian genotype in the Americas, our data highlights the rapid spread of a less understood and poorly characterized CHIKV-ECSA genotype in Brazil. Investigations on potential associations between public health impact of CHIKV and genetic diversity of circulating strains are warranted to better evaluate its impact in Brazil and beyond.

Published
2019
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21. Genomic detection of a virus lineage replacement event of dengue virus serotype 2 in Brazil, 2019

Author

de Jesus, Jaqueline Goes, primary, Dutra, Karina Rocha, additional, Sales, Flavia Cristina da Silva, additional, Claro, Ingra Morales, additional, Terzian, Ana Carolina, additional, Candido, Darlan da Silva, additional, Hill, Sarah C, additional, Thézé, Julien, additional, Torres, Celeste, additional, D’Agostini, Tatiana Lang, additional, Felix, Alvina Clara, additional, Reis, Andreia F Negri, additional, Alcantara, Luiz Carlos Junior, additional, de Abreu, André L, additional, Croda, Júlio HR, additional, de Oliveira, Wanderson K, additional, de Filipis, Ana Maria Bispo, additional, Camis, Maria do Carmo Rodrigues dos Santos, additional, Romano, Camila Malta, additional, Loman, Nick J, additional, Pybus, Oliver G, additional, Sabino, Ester Cerdeira, additional, Nogueira, Mauricio L, additional, and Faria, Nuno Rodrigues, additional

Published
2020
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22. Yellow Fever Virus Reemergence and Spread in Southeast Brazil, 2016–2019

Author

Giovanetti, Marta, primary, de Mendonça, Marcos Cesar Lima, additional, Fonseca, Vagner, additional, Mares-Guia, Maria Angélica, additional, Fabri, Allison, additional, Xavier, Joilson, additional, de Jesus, Jaqueline Goes, additional, Gräf, Tiago, additional, dos Santos Rodrigues, Cintia Damasceno, additional, dos Santos, Carolina Cardoso, additional, Sampaio, Simone Alves, additional, Chalhoub, Flavia Lowen Levy, additional, de Bruycker Nogueira, Fernanda, additional, Theze, Julien, additional, Romano, Alessandro Pecego Martins, additional, Ramos, Daniel Garkauskas, additional, de Abreu, Andre Luiz, additional, Oliveira, Wanderson Kleber, additional, do Carmo Said, Rodrigo Fabiano, additional, de Alburque, Carlos F. Campelo, additional, de Oliveira, Tulio, additional, Fernandes, Carlos Augusto, additional, Aguiar, Shirlei Ferreira, additional, Chieppe, Alexandre, additional, Sequeira, Patrícia Carvalho, additional, Faria, Nuno Rodrigues, additional, Cunha, Rivaldo Venâncio, additional, Alcantara, Luiz Carlos Junior, additional, and de Filippis, Ana Maria Bispo, additional

Published
2019
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23. Author Correction: Nanopore native RNA sequencing of a human poly(A) transcriptome

Author

Workman, Rachael E., primary, Tang, Alison D., additional, Tang, Paul S., additional, Jain, Miten, additional, Tyson, John R., additional, Razaghi, Roham, additional, Zuzarte, Philip C., additional, Gilpatrick, Timothy, additional, Payne, Alexander, additional, Quick, Joshua, additional, Sadowski, Norah, additional, Holmes, Nadine, additional, de Jesus, Jaqueline Goes, additional, Jones, Karen L., additional, Soulette, Cameron M., additional, Snutch, Terrance P., additional, Loman, Nicholas, additional, Paten, Benedict, additional, Loose, Matthew, additional, Simpson, Jared T., additional, Olsen, Hugh E., additional, Brooks, Angela N., additional, Akeson, Mark, additional, and Timp, Winston, additional

Published
2019
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24. A32 Genomic surveillance of Zika virus transmission in the Amazonas State, Brazil

Author

Giovanetti, Marta, primary, de Jesus, Jaqueline Goes, additional, Joshua, Quick, additional, Claro, Ingra Morales, additional, Junior, Joilson Xavier, additional, Hill, Sarah C, additional, Renato, Souza, additional, Paz, Paola, additional, Lourenco, Jose, additional, Dellicour, Simon, additional, Sabino, Esther, additional, Loman, Nicholas J, additional, Naveca, Felipe, additional, Pybus, Oliver G, additional, Faria, Nuno Rodrigues, additional, and Carlos Junior Alcantara, Luiz, additional

Published
2019
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25. Early identification of dengue virus lineage replacement in Brazil using portable genomic surveillance

Author

de Jesus, Jaqueline Goes, primary, Dutra, Karina Rocha, additional, da Silva Salles, Flavia Cristina, additional, Claro, Ingra Morales, additional, Terzian, Ana Carolina, additional, da Silva Candido, Darlan, additional, Hill, Sarah C., additional, Thézé, Julien, additional, D’Agostini, Tatiana Lang, additional, Felix, Alvina Clara, additional, Negri Reis, Andreia F., additional, Alcantara, Luiz Carlos Junior, additional, Abreu, André L., additional, Croda, Júlio H. R., additional, de Oliveira, Wanderson K., additional, de Filipis, Ana Maria Bispo, additional, dos Santos Camis, Maria do Carmo Rodrigues, additional, Romano, Camila Malta, additional, Loman, Nick J., additional, Pybus, Oliver G., additional, Sabino, Ester Cerdeira, additional, Nogueira, Mauricio L., additional, and Faria, Nuno Rodrigues, additional

Published
2019
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26. Yellow fever virus spread in Rio de Janeiro and Espírito Santo, 2016-2019: Phylodynamic assessment to improve intervention strategies

Author

Giovanetti, Marta, primary, de Mendonça, Marcos Cesar Lima, additional, Fonseca, Vagner, additional, Mares-Guia, Maria Angélica, additional, Fabri, Allison, additional, Xavier, Joilson, additional, de Jesus, Jaqueline Goes, additional, Gräf, Tiago, additional, dos Santos Rodrigues, Cintia Damasceno, additional, dos Santos, Carolina Cardoso, additional, Sampaio, Simone Alves, additional, Chalhoub, Flavia Lowen Levy, additional, de Bruycker Nogueira, Fernanda, additional, Theze, Julien, additional, Romano, Alessandro Pecego Martins, additional, Ramos, Daniel Garkauskas, additional, de Abreu, Andre Luiz, additional, Oliveira, Wanderson Kleber, additional, do Carmo Said, Rodrigo Fabiano, additional, de Alburque, Carlos F. Campelo, additional, de Oliveira, Tulio, additional, Fernandes, Carlos Augusto, additional, Aguiar, Shirlei Ferreira, additional, Chieppe, Alexandre, additional, Sequeira, Patrícia Carvalho, additional, Faria, Nuno Rodrigues, additional, Cunha, Rivaldo Venâncio, additional, Alcantara, Luiz Carlos Junior, additional, and de Filippis, Ana Maria Bispo, additional

Published
2019
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28. Lipidomic Analysis Reveals Serum Alteration of Plasmalogens in Patients Infected With ZIKA Virus

Author

Queiroz, Adriano, primary, Pinto, Isabella Fernanda Dantas, additional, Lima, Maricélia, additional, Giovanetti, Marta, additional, de Jesus, Jaqueline Goes, additional, Xavier, Joilson, additional, Barreto, Fernanda Khouri, additional, Canuto, Gisele André Baptista, additional, do Amaral, Helineide Ramos, additional, de Filippis, Ana Maria Bispo, additional, Mascarenhas, Denise Lima, additional, Falcão, Melissa Barreto, additional, Santos, Normeide Pedreira, additional, Azevedo, Vasco Ariston de Carvalho, additional, Yoshinaga, Marcos Yukio, additional, Miyamoto, Sayuri, additional, and Alcantara, Luiz Carlos Junior, additional

Published
2019
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29. Chikungunya virus outbreak in the Amazon region: replacement of the Asian genotype by an ECSA lineage

Author

Naveca, Felipe Gomes, primary, Claro, Ingra, additional, Giovanetti, Marta, additional, de Jesus, Jaqueline Goes, additional, Xavier, Joilson, additional, Iani, Felipe Campos de Melo, additional, do Nascimento, Valdinete Alves, additional, de Souza, Victor Costa, additional, Silveira, Paola Paz, additional, Lourenço, José, additional, Santillana, Mauricio, additional, Kraemer, Moritz U. G., additional, Quick, Josh, additional, Hill, Sarah C., additional, Theze, Julien, additional, Carvalho, Rodrigo Dias de Oliveira, additional, Azevedo, Vasco, additional, Sales, Flavia Cristina da Silva, additional, Nunes, Márcio Roberto Teixeira, additional, Lemos, Poliana da Silva, additional, Candido, Darlan da Silva, additional, Pereira, Glauco de Carvalho, additional, Oliveira, Marluce Aparecida Assunção, additional, Meneses, Catia Alexandra Ribeiro, additional, Maito, Rodrigo Melo, additional, Cunha, Claudeth Rocha Santa Brígida, additional, Campos, Daniela Palha de Sousa, additional, Castilho, Marcia da Costa, additional, Siqueira, Thalita Caroline da Silva, additional, Terra, Tiza Matos, additional, Albuquerque, Carlos F. Campelo de, additional, Cruz, Laura Nogueira da, additional, Abreu, André Luis de, additional, Martins, Divino Valerio, additional, Simoes, Daniele Silva de Moraes Vanlume, additional, Aguiar, Renato Santana, additional, Luz, Sergio Luiz Bessa, additional, Loman, Nicholas, additional, Pybus, Oliver G., additional, Sabino, Ester Cerdeira, additional, Okumoto, Osnei, additional, Alcantara, Luiz Carlos Junior, additional, and Faria, Nuno Rodrigues, additional

Published
2018
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30. An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar

Author

Grubaugh, Nathan D, primary, Gangavarapu, Karthik, additional, Quick, Joshua, additional, Matteson, Nathaniel L., additional, De Jesus, Jaqueline Goes, additional, Main, Bradley J, additional, Tan, Amanda L, additional, Paul, Lauren M, additional, Brackney, Doug E, additional, Grewal, Saran, additional, Gurfield, Nikos, additional, Van Rompay, Koen KA, additional, Isern, Sharon, additional, Michael, Scott F, additional, Coffey, Lark L, additional, Loman, Nicholas J, additional, and Andersen, Kristian G, additional

Published
2018
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31. Importation and early local transmission of COVID-19 in Brazil, 2020.

Author

de Jesus, Jaqueline Goes, Sacchi, Claudio, da Silva Candido, Darlan, Claro, Ingra Morales, Silva Sales, Flávia Cristina, Manuli, Erika Regina, Borges da Silva, Daniela Bernardes, de Paiva, Terezinha Maria, Benega Pinho, Margarete Aparecida, de Oliveira Santos, Katia Correa, Hill, Sarah Catherine, Aguiar, Renato Santana, Romero, Filipe, Pereira dos Santos, Fabiana Cristina, Gonçalves, Claudia Regina, do Carmo Timenetsky, Maria, Quick, Joshua, Rosa Croda, Julio Henrique, de Oliveira, Wanderson, and Rambaut, Andrew

Subjects
COVID-19, PUBLIC health surveillance, NUCLEOTIDE sequencing
Abstract

We conducted the genome sequencing and analysis of the first confirmed COVID-19 infections in Brazil. Rapid sequencing coupled with phylogenetic analyses in the context of travel history corroborate multiple independent importations from Italy and local spread during the initial stage of COVID-19 transmission in Brazil. [ABSTRACT FROM AUTHOR]

Published
2020
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32. Local Transmission of SARS-CoV-2 Lineage B.1.1.7, Brazil, December 2020.

Author

Morales Claro, Ingra, da Silva Sales, Flavia Cristina, Severo Ramundo, Mariana, Candido, Darlan S., Silva, Camila A. M., de Jesus, Jaqueline Goes, Manuli, Erika R., de Oliveira, Cristina Mendes, Scarpelli, Luciano, Campana, Gustavo, Pybus, Oliver G., Cerdeira Sabino, Ester, Rodrigues Faria, Nuno, Eduardo Levi, José, Claro, Ingra Morales, Ramundo, Mariana Severo, Sabino, Ester Cerdeira, Faria, Nuno Rodrigues, and Levi, José Eduardo

Subjects
SARS-CoV-2, COVID-19
Abstract

In December 2020, research surveillance detected the B.1.1.7 lineage of severe acute respiratory syndrome coronavirus 2 in São Paulo, Brazil. Rapid genomic sequencing and phylogenetic analysis revealed 2 distinct introductions of the lineage. One patient reported no international travel. There may be more infections with this lineage in Brazil than reported. [ABSTRACT FROM AUTHOR]

Published
2021
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33. PCR assay to enhance global surveillance for SARS-CoV-2 variants of concern.

Author

Vogels CBF, Breban MI, Alpert T, Petrone ME, Watkins AE, Ott IM, de Jesus JG, Claro IM, Ferreira GM, Crispim MAE, Singh L, Tegally H, Anyaneji UJ, Hodcroft EB, Mason CE, Khullar G, Metti J, Dudley JT, MacKay MJ, Nash M, Wang J, Liu C, Hui P, Murphy S, Neal C, Laszlo E, Landry ML, Muyombwe A, Downing R, Razeq J, de Oliveira T, Faria NR, Sabino EC, Neher RA, Fauver JR, and Grubaugh ND

Abstract

With the emergence of SARS-CoV-2 variants that may increase transmissibility and/or cause escape from immune responses 1-3 , there is an urgent need for the targeted surveillance of circulating lineages. It was found that the B.1.1.7 (also 501Y.V1) variant first detected in the UK 4,5 could be serendipitously detected by the ThermoFisher TaqPath COVID-19 PCR assay because a key deletion in these viruses, spike Δ69-70, would cause a "spike gene target failure" (SGTF) result. However, a SGTF result is not definitive for B.1.1.7, and this assay cannot detect other variants of concern that lack spike Δ69-70, such as B.1.351 (also 501Y.V2) detected in South Africa 6 and P.1 (also 501Y.V3) recently detected in Brazil 7 . We identified a deletion in the ORF1a gene (ORF1a Δ3675-3677) in all three variants, which has not yet been widely detected in other SARS-CoV-2 lineages. Using ORF1a Δ3675-3677 as the primary target and spike Δ69-70 to differentiate, we designed and validated an open source PCR assay to detect SARS-CoV-2 variants of concern 8 . Our assay can be rapidly deployed in laboratories around the world to enhance surveillance for the local emergence spread of B.1.1.7, B.1.351, and P.1.

Published
2021
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