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1. Molecular Epidemiology of Mayaro Virus among Febrile Patients, Roraima State, Brazil, 2018-2021

Author

Forato, Julia, Meira, Cassio A., Claro, Ingra M., Amorim, Mariene R., de Souza, Gabriela F., Muraro, Stefanie P., Toledo- Teixeira, Daniel A., Dias, Miguel F., Meneses, Catia A.R., Angerami, Rodrigo N., Lalwani, Pritesh, Weaver, Scott C., Sabino, Ester C., Faria, Nuno R., de Souza, William M., Granja, Fabiana, and Proenca-Modena, Jose Luiz

Subjects
Roraima, Brazil -- Health aspects, Fever -- Statistics -- Causes of, RNA virus infections -- Statistics -- Causes of -- Complications and side effects, Hyperthermia -- Statistics -- Causes of, Health
Abstract

Mayaro virus (MAYV) is an endemic and neglected mosquitoborne alphavirus that causes acute and chronic debilitating arthritogenic disease in Latin America and the Caribbean (1). MAYV infection can cause fever, [...]

Published
2024
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2. Human movement and environmental barriers shape the emergence of dengue

Author

Harish, Vinyas, Colón-González, Felipe J., Moreira, Filipe R. R., Gibb, Rory, Kraemer, Moritz U. G., Davis, Megan, Reiner, Jr., Robert C., Pigott, David M., Perkins, T. Alex, Weiss, Daniel J., Bogoch, Isaac I., Vazquez-Prokopec, Gonzalo, Saide, Pablo Manrique, Barbosa, Gerson L., Sabino, Ester C., Khan, Kamran, Faria, Nuno R., Hay, Simon I., Correa-Morales, Fabián, Chiaravalloti-Neto, Francisco, and Brady, Oliver J.

Published
2024
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4. Context-specific emergence and growth of the SARS-CoV-2 Delta variant

Author

McCrone, John T, Hill, Verity, Bajaj, Sumali, Pena, Rosario Evans, Lambert, Ben C, Inward, Rhys, Bhatt, Samir, Volz, Erik, Ruis, Christopher, Dellicour, Simon, Baele, Guy, Zarebski, Alexander E, Sadilek, Adam, Wu, Neo, Schneider, Aaron, Ji, Xiang, Raghwani, Jayna, Jackson, Ben, Colquhoun, Rachel, O’Toole, Áine, Peacock, Thomas P, Twohig, Kate, Thelwall, Simon, Dabrera, Gavin, Myers, Richard, Faria, Nuno R, Huber, Carmen, Bogoch, Isaac I, Khan, Kamran, du Plessis, Louis, Barrett, Jeffrey C, Aanensen, David M, Barclay, Wendy S, Chand, Meera, Connor, Thomas, Loman, Nicholas J, Suchard, Marc A, Pybus, Oliver G, Rambaut, Andrew, and Kraemer, Moritz UG

Subjects
Emerging Infectious Diseases, Infectious Diseases, Good Health and Well Being, COVID-19, Cities, Contact Tracing, England, Genome, Viral, Humans, Quarantine, SARS-CoV-2, Travel, COVID-19 Genomics UK (COG-UK) Consortium, General Science & Technology
Abstract

The SARS-CoV-2 Delta (Pango lineage B.1.617.2) variant of concern spread globally, causing resurgences of COVID-19 worldwide1,2. The emergence of the Delta variant in the UK occurred on the background of a heterogeneous landscape of immunity and relaxation of non-pharmaceutical interventions. Here we analyse 52,992 SARS-CoV-2 genomes from England together with 93,649 genomes from the rest of the world to reconstruct the emergence of Delta and quantify its introduction to and regional dissemination across England in the context of changing travel and social restrictions. Using analysis of human movement, contact tracing and virus genomic data, we find that the geographic focus of the expansion of Delta shifted from India to a more global pattern in early May 2021. In England, Delta lineages were introduced more than 1,000 times and spread nationally as non-pharmaceutical interventions were relaxed. We find that hotel quarantine for travellers reduced onward transmission from importations; however, the transmission chains that later dominated the Delta wave in England were seeded before travel restrictions were introduced. Increasing inter-regional travel within England drove the nationwide dissemination of Delta, with some cities receiving more than 2,000 observable lineage introductions from elsewhere. Subsequently, increased levels of local population mixing-and not the number of importations-were associated with the faster relative spread of Delta. The invasion dynamics of Delta depended on spatial heterogeneity in contact patterns, and our findings will inform optimal spatial interventions to reduce the transmission of current and future variants of concern, such as Omicron (Pango lineage B.1.1.529).

Published
2022

5. Pathophysiology of chikungunya virus infection associated with fatal outcomes

Author

de Souza, William M., Fumagalli, Marcilio J., de Lima, Shirlene T.S., Parise, Pierina L., Carvalho, Deyse C.M., Hernandez, Cristian, de Jesus, Ronaldo, Delafiori, Jeany, Candido, Darlan S., Carregari, Victor C., Muraro, Stefanie P., Souza, Gabriela F., Simões Mello, Leda M., Claro, Ingra M., Díaz, Yamilka, Kato, Rodrigo B., Trentin, Lucas N., Costa, Clauber H.S., Maximo, Ana Carolina B.M., Cavalcante, Karene F., Fiuza, Tayna S., Viana, Vânia A.F., Melo, Maria Elisabeth L., Ferraz, Clarissa P.M., Silva, Débora B., Duarte, Larissa M.F., Barbosa, Priscilla P., Amorim, Mariene R., Judice, Carla C., Toledo-Teixeira, Daniel A., Ramundo, Mariana S., Aguilar, Patricia V., Araújo, Emerson L.L., Costa, Fabio T.M., Cerqueira-Silva, Thiago, Khouri, Ricardo, Boaventura, Viviane S., Figueiredo, Luiz Tadeu M., Fang, Rong, Moreno, Brechla, López-Vergès, Sandra, Mello, Liana Perdigão, Skaf, Munir S., Catharino, Rodrigo R., Granja, Fabiana, Martins-de-Souza, Daniel, Plante, Jessica A., Plante, Kenneth S., Sabino, Ester C., Diamond, Michael S., Eugenin, Eliseo, Proença-Módena, José Luiz, Faria, Nuno R., and Weaver, Scott C.

Published
2024
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6. Global disparities in SARS-CoV-2 genomic surveillance

Author

Brito, Anderson F, Semenova, Elizaveta, Dudas, Gytis, Hassler, Gabriel W, Kalinich, Chaney C, Kraemer, Moritz UG, Ho, Joses, Tegally, Houriiyah, Githinji, George, Agoti, Charles N, Matkin, Lucy E, Whittaker, Charles, Howden, Benjamin P, Sintchenko, Vitali, Zuckerman, Neta S, Mor, Orna, Blankenship, Heather M, de Oliveira, Tulio, Lin, Raymond TP, Siqueira, Marilda Mendonça, Resende, Paola Cristina, Vasconcelos, Ana Tereza R, Spilki, Fernando R, Aguiar, Renato Santana, Alexiev, Ivailo, Ivanov, Ivan N, Philipova, Ivva, Carrington, Christine VF, Sahadeo, Nikita SD, Branda, Ben, Gurry, Céline, Maurer-Stroh, Sebastian, Naidoo, Dhamari, von Eije, Karin J, Perkins, Mark D, van Kerkhove, Maria, Hill, Sarah C, Sabino, Ester C, Pybus, Oliver G, Dye, Christopher, Bhatt, Samir, Flaxman, Seth, Suchard, Marc A, Grubaugh, Nathan D, Baele, Guy, and Faria, Nuno R

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Health Sciences, Prevention, Human Genome, Biodefense, Vaccine Related, Immunization, Emerging Infectious Diseases, Genetics, Infection, Good Health and Well Being, Humans, SARS-CoV-2, Genome, Viral, COVID-19, Pandemics, Genomics, Bulgarian SARS-CoV-2 sequencing group, Communicable Diseases Genomics Network, COVID-19 Impact Project, Danish Covid-19 Genome Consortium, Fiocruz COVID-19 Genomic Surveillance Network, GISAID core curation team, Network for Genomic Surveillance in South Africa, Swiss SARS-CoV-2 Sequencing Consortium
Abstract

Genomic sequencing is essential to track the evolution and spread of SARS-CoV-2, optimize molecular tests, treatments, vaccines, and guide public health responses. To investigate the global SARS-CoV-2 genomic surveillance, we used sequences shared via GISAID to estimate the impact of sequencing intensity and turnaround times on variant detection in 189 countries. In the first two years of the pandemic, 78% of high-income countries sequenced >0.5% of their COVID-19 cases, while 42% of low- and middle-income countries reached that mark. Around 25% of the genomes from high income countries were submitted within 21 days, a pattern observed in 5% of the genomes from low- and middle-income countries. We found that sequencing around 0.5% of the cases, with a turnaround time

Published
2022

7. 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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8. Chikungunya: a decade of burden in the Americas

Author

de Souza, William M., Ribeiro, Guilherme S., de Lima, Shirlene T.S., de Jesus, Ronaldo, Moreira, Filipe R.R., Whittaker, Charles, Sallum, Maria Anice M., Carrington, Christine V.F., Sabino, Ester C., Kitron, Uriel, Faria, Nuno R., and Weaver, Scott C.

Published
2024
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9. Relax, keep walking—a practical guide to continuous phylogeographic inference with BEAST

Author

Dellicour, Simon, Gill, Mandev S, Faria, Nuno R, Rambaut, Andrew, Pybus, Oliver G, Suchard, Marc A, and Lemey, Philippe

Subjects
Bayes Theorem, Biological Evolution, Phylogeography, Software, relaxed random walk, continuous phylogeography, viruses, BEAST, Biochemistry and Cell Biology, Evolutionary Biology, Genetics
Abstract

Spatially explicit phylogeographic analyses can be performed with an inference framework that employs relaxed random walks to reconstruct phylogenetic dispersal histories in continuous space. This core model was first implemented 10 years ago and has opened up new opportunities in the field of phylodynamics, allowing researchers to map and analyze the spatial dissemination of rapidly evolving pathogens. We here provide a detailed and step-by-step guide on how to set up, run, and interpret continuous phylogeographic analyses using the programs BEAUti, BEAST, Tracer, and TreeAnnotator.

Published
2021

10. Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil

Author

Faria, Nuno R, Mellan, Thomas A, Whittaker, Charles, Claro, Ingra M, Candido, Darlan da S, Mishra, Swapnil, Crispim, Myuki AE, Sales, Flavia CS, Hawryluk, Iwona, McCrone, John T, Hulswit, Ruben JG, Franco, Lucas AM, Ramundo, Mariana S, de Jesus, Jaqueline G, Andrade, Pamela S, Coletti, Thais M, Ferreira, Giulia M, Silva, Camila AM, Manuli, Erika R, Pereira, Rafael HM, Peixoto, Pedro S, Kraemer, Moritz UG, Gaburo, Nelson, Camilo, Cecilia da C, Hoeltgebaum, Henrique, Souza, William M, Rocha, Esmenia C, de Souza, Leandro M, de Pinho, Mariana C, Araujo, Leonardo JT, Malta, Frederico SV, de Lima, Aline B, Silva, Joice do P, Zauli, Danielle AG, Ferreira, Alessandro C de S, Schnekenberg, Ricardo P, Laydon, Daniel J, Walker, Patrick GT, Schlüter, Hannah M, Dos Santos, Ana LP, Vidal, Maria S, Del Caro, Valentina S, Filho, Rosinaldo MF, Dos Santos, Helem M, Aguiar, Renato S, Proença-Modena, José L, Nelson, Bruce, Hay, James A, Monod, Mélodie, Miscouridou, Xenia, Coupland, Helen, Sonabend, Raphael, Vollmer, Michaela, Gandy, Axel, Prete, Carlos A, Nascimento, Vitor H, Suchard, Marc A, Bowden, Thomas A, Pond, Sergei LK, Wu, Chieh-Hsi, Ratmann, Oliver, Ferguson, Neil M, Dye, Christopher, Loman, Nick J, Lemey, Philippe, Rambaut, Andrew, Fraiji, Nelson A, Carvalho, Maria do PSS, Pybus, Oliver G, Flaxman, Seth, Bhatt, Samir, and Sabino, Ester C

Subjects
Human Genome, Immunization, Pneumonia & Influenza, Lung, Prevention, Genetics, Vaccine Related, Biotechnology, Pneumonia, Emerging Infectious Diseases, Biodefense, Infectious Diseases, Infection, Good Health and Well Being, Angiotensin-Converting Enzyme 2, Brazil, COVID-19, Communicable Diseases, Emerging, Epidemiological Monitoring, Genome, Viral, Genomics, Humans, Models, Theoretical, Molecular Epidemiology, Mutation, Protein Binding, SARS-CoV-2, Spike Glycoprotein, Coronavirus, Viral Load, General Science & Technology
Abstract

Cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in Manaus, Brazil, resurged in late 2020 despite previously high levels of infection. Genome sequencing of viruses sampled in Manaus between November 2020 and January 2021 revealed the emergence and circulation of a novel SARS-CoV-2 variant of concern. Lineage P.1 acquired 17 mutations, including a trio in the spike protein (K417T, E484K, and N501Y) associated with increased binding to the human ACE2 (angiotensin-converting enzyme 2) receptor. Molecular clock analysis shows that P.1 emergence occurred around mid-November 2020 and was preceded by a period of faster molecular evolution. Using a two-category dynamical model that integrates genomic and mortality data, we estimate that P.1 may be 1.7- to 2.4-fold more transmissible and that previous (non-P.1) infection provides 54 to 79% of the protection against infection with P.1 that it provides against non-P.1 lineages. Enhanced global genomic surveillance of variants of concern, which may exhibit increased transmissibility and/or immune evasion, is critical to accelerate pandemic responsiveness.

Published
2021

11. Dispersal patterns and influence of air travel during the global expansion of SARS-CoV-2 variants of concern

Author

Tegally, Houriiyah, Wilkinson, Eduan, Tsui, Joseph L.- H., Moir, Monika, Martin, Darren, Brito, Anderson Fernandes, Giovanetti, Marta, Khan, Kamran, Huber, Carmen, Bogoch, Isaac I., San, James Emmanuel, Poongavanan, Jenicca, Xavier, Joicymara S., Candido, Darlan da S., Romero, Filipe, Baxter, Cheryl, Pybus, Oliver G., Lessells, Richard J., Faria, Nuno R., Kraemer, Moritz U.G., and de Oliveira, Tulio

Published
2023
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12. Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California.

Author

Deng, Xianding, Gu, Wei, Federman, Scot, du Plessis, Louis, Pybus, Oliver G, Faria, Nuno R, Wang, Candace, Yu, Guixia, Bushnell, Brian, Pan, Chao-Yang, Guevara, Hugo, Sotomayor-Gonzalez, Alicia, Zorn, Kelsey, Gopez, Allan, Servellita, Venice, Hsu, Elaine, Miller, Steve, Bedford, Trevor, Greninger, Alexander L, Roychoudhury, Pavitra, Starita, Lea M, Famulare, Michael, Chu, Helen Y, Shendure, Jay, Jerome, Keith R, Anderson, Catie, Gangavarapu, Karthik, Zeller, Mark, Spencer, Emily, Andersen, Kristian G, MacCannell, Duncan, Paden, Clinton R, Li, Yan, Zhang, Jing, Tong, Suxiang, Armstrong, Gregory, Morrow, Scott, Willis, Matthew, Matyas, Bela T, Mase, Sundari, Kasirye, Olivia, Park, Maggie, Masinde, Godfred, Chan, Curtis, Yu, Alexander T, Chai, Shua J, Villarino, Elsa, Bonin, Brandon, Wadford, Debra A, and Chiu, Charles Y

Subjects
General Science & Technology
Abstract

The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread globally, with >365,000 cases in California as of 17 July 2020. We investigated the genomic epidemiology of SARS-CoV-2 in Northern California from late January to mid-March 2020, using samples from 36 patients spanning nine counties and the Grand Princess cruise ship. Phylogenetic analyses revealed the cryptic introduction of at least seven different SARS-CoV-2 lineages into California, including epidemic WA1 strains associated with Washington state, with lack of a predominant lineage and limited transmission among communities. Lineages associated with outbreak clusters in two counties were defined by a single base substitution in the viral genome. These findings support contact tracing, social distancing, and travel restrictions to contain the spread of SARS-CoV-2 in California and other states.

Published
2020

13. Metagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillance.

Author

Deng, Xianding, Achari, Asmeeta, Federman, Scot, Yu, Guixia, Somasekar, Sneha, Bártolo, Inês, Yagi, Shigeo, Mbala-Kingebeni, Placide, Kapetshi, Jimmy, Ahuka-Mundeke, Steve, Muyembe-Tamfum, Jean-Jacques, Ahmed, Asim A, Ganesh, Vijay, Tamhankar, Manasi, Patterson, Jean L, Ndembi, Nicaise, Mbanya, Dora, Kaptue, Lazare, McArthur, Carole, Muñoz-Medina, José E, Gonzalez-Bonilla, Cesar R, López, Susana, Arias, Carlos F, Arevalo, Shaun, Miller, Steve, Stone, Mars, Busch, Michael, Hsieh, Kristina, Messenger, Sharon, Wadford, Debra A, Rodgers, Mary, Cloherty, Gavin, Faria, Nuno R, Thézé, Julien, Pybus, Oliver G, Neto, Zoraima, Morais, Joana, Taveira, Nuno, R Hackett, John, and Chiu, Charles Y

Subjects
Humans, Viruses, Dengue Virus, Chikungunya virus, Virus Diseases, Dengue, Yellow Fever, Hemorrhagic Fever, Ebola, DNA, Viral, RNA, Viral, Polymerase Chain Reaction, Computational Biology, Genome, Viral, Ebolavirus, Metagenome, Metagenomics, High-Throughput Nucleotide Sequencing, Zika Virus, Zika Virus Infection, Microbiology, Medical Microbiology
Abstract

Metagenomic next-generation sequencing (mNGS), the shotgun sequencing of RNA and DNA from clinical samples, has proved useful for broad-spectrum pathogen detection and the genomic surveillance of viral outbreaks. An additional target enrichment step is generally needed for high-sensitivity pathogen identification in low-titre infections, yet available methods using PCR or capture probes can be limited by high cost, narrow scope of detection, lengthy protocols and/or cross-contamination. Here, we developed metagenomic sequencing with spiked primer enrichment (MSSPE), a method for enriching targeted RNA viral sequences while simultaneously retaining metagenomic sensitivity for other pathogens. We evaluated MSSPE for 14 different viruses, yielding a median tenfold enrichment and mean 47% (±16%) increase in the breadth of genome coverage over mNGS alone. Virus detection using MSSPE arboviral or haemorrhagic fever viral panels was comparable in sensitivity to specific PCR, demonstrating 95% accuracy for the detection of Zika, Ebola, dengue, chikungunya and yellow fever viruses in plasma samples from infected patients. Notably, sequences from re-emerging and/or co-infecting viruses that have not been specifically targeted a priori, including Powassan and Usutu, were successfully enriched using MSSPE. MSSPE is simple, low cost, fast and deployable on either benchtop or portable nanopore sequencers, making this method directly applicable for diagnostic laboratory and field use.

Published
2020

14. Author Correction: Metagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillance

Author

Deng, Xianding, Achari, Asmeeta, Federman, Scot, Yu, Guixia, Somasekar, Sneha, Bártolo, Inês, Yagi, Shigeo, Mbala-Kingebeni, Placide, Kapetshi, Jimmy, Ahuka-Mundeke, Steve, Muyembe-Tamfum, Jean-Jacques, Ahmed, Asim A, Ganesh, Vijay, Tamhankar, Manasi, Patterson, Jean L, Ndembi, Nicaise, Mbanya, Dora, Kaptue, Lazare, McArthur, Carole, Muñoz-Medina, José E, Gonzalez-Bonilla, Cesar R, López, Susana, Arias, Carlos F, Arevalo, Shaun, Miller, Steve, Stone, Mars, Busch, Michael, Hsieh, Kristina, Messenger, Sharon, Wadford, Debra A, Rodgers, Mary, Cloherty, Gavin, Faria, Nuno R, Thézé, Julien, Pybus, Oliver G, Neto, Zoraima, Morais, Joana, Taveira, Nuno, Hackett, John R, and Chiu, Charles Y

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Good Health and Well Being, Microbiology, Medical Microbiology
Abstract

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Published
2020

15. Distinct rates and patterns of spread of the major HIV-1 subtypes in Central and East Africa.

Author

Faria, Nuno R, Vidal, Nicole, Lourenco, José, Raghwani, Jayna, Sigaloff, Kim CE, Tatem, Andy J, van de Vijver, David AM, Pineda-Peña, Andrea-Clemencia, Rose, Rebecca, Wallis, Carole L, Ahuka-Mundeke, Steve, Muyembe-Tamfum, Jean-Jacques, Muwonga, Jérémie, Suchard, Marc A, Rinke de Wit, Tobias F, Hamers, Raph L, Ndembi, Nicaise, Baele, Guy, Peeters, Martine, Pybus, Oliver G, Lemey, Philippe, and Dellicour, Simon

Subjects
Humans, HIV-1, HIV Infections, Africa, Central, Africa, Eastern, Africa, Central, Eastern, Virology, Microbiology, Immunology, Medical Microbiology
Abstract

Since the ignition of the HIV-1 group M pandemic in the beginning of the 20th century, group M lineages have spread heterogeneously throughout the world. Subtype C spread rapidly through sub-Saharan Africa and is currently the dominant HIV lineage worldwide. Yet the epidemiological and evolutionary circumstances that contributed to its epidemiological expansion remain poorly understood. Here, we analyse 346 novel pol sequences from the DRC to compare the evolutionary dynamics of the main HIV-1 lineages, subtypes A1, C and D. Our results place the origins of subtype C in the 1950s in Mbuji-Mayi, the mining city of southern DRC, while subtypes A1 and D emerged in the capital city of Kinshasa, and subtypes H and J in the less accessible port city of Matadi. Following a 15-year period of local transmission in southern DRC, we find that subtype C spread at least three-fold faster than other subtypes circulating in Central and East Africa. In conclusion, our results shed light on the origins of HIV-1 main lineages and suggest that socio-historical rather than evolutionary factors may have determined the epidemiological fate of subtype C in sub-Saharan Africa.

Published
2019

16. Spatial and temporal fluctuations in COVID-19 fatality rates in Brazilian hospitals

Author

Brizzi, Andrea, Whittaker, Charles, Servo, Luciana M. S., Hawryluk, Iwona, Prete, Jr, Carlos A., de Souza, William M., Aguiar, Renato S., Araujo, Leonardo J. T., Bastos, Leonardo S., Blenkinsop, Alexandra, Buss, Lewis F., Candido, Darlan, Castro, Marcia C., Costa, Silvia F., Croda, Julio, de Souza Santos, Andreza Aruska, Dye, Christopher, Flaxman, Seth, Fonseca, Paula L. C., Geddes, Victor E. V., Gutierrez, Bernardo, Lemey, Philippe, Levin, Anna S., Mellan, Thomas, Bonfim, Diego M., Miscouridou, Xenia, Mishra, Swapnil, Monod, Mélodie, Moreira, Filipe R. R., Nelson, Bruce, Pereira, Rafael H. M., Ranzani, Otavio, Schnekenberg, Ricardo P., Semenova, Elizaveta, Sonabend, Raphael, Souza, Renan P., Xi, Xiaoyue, Sabino, Ester C., Faria, Nuno R., Bhatt, Samir, and Ratmann, Oliver

Published
2022
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17. Publisher Correction: Past and future spread of the arbovirus vectors Aedes aegypti and Aedes albopictus

Author

Kraemer, Moritz UG, Reiner, Robert C, Brady, Oliver J, Messina, Jane P, Gilbert, Marius, Pigott, David M, Yi, Dingdong, Johnson, Kimberly, Earl, Lucas, Marczak, Laurie B, Shirude, Shreya, Weaver, Nicole Davis, Bisanzio, Donal, Perkins, T Alex, Lai, Shengjie, Lu, Xin, Jones, Peter, Coelho, Giovanini E, Carvalho, Roberta G, Van Bortel, Wim, Marsboom, Cedric, Hendrickx, Guy, Schaffner, Francis, Moore, Chester G, Nax, Heinrich H, Bengtsson, Linus, Wetter, Erik, Tatem, Andrew J, Brownstein, John S, Smith, David L, Lambrechts, Louis, Cauchemez, Simon, Linard, Catherine, Faria, Nuno R, Pybus, Oliver G, Scott, Thomas W, Liu, Qiyong, Yu, Hongjie, Wint, GR William, Hay, Simon I, and Golding, Nick

Subjects
Microbiology, Biological Sciences, Prevention, Good Health and Well Being, Medical Microbiology
Abstract

In the version of this Article originally published, the affiliation for author Catherine Linard was incorrectly stated as '6Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK'. The correct affiliation is '9Spatial Epidemiology Lab (SpELL), Universite Libre de Bruxelles, Brussels, Belgium'. The affiliation for author Hongjie Yu was also incorrectly stated as '11Department of Statistics, Harvard University, Cambridge, MA, USA'. The correct affiliation is '15School of Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China'. This has now been amended in all versions of the Article.

Published
2019

18. Past and future spread of the arbovirus vectors Aedes aegypti and Aedes albopictus

Author

Kraemer, Moritz UG, Reiner, Robert C, Brady, Oliver J, Messina, Jane P, Gilbert, Marius, Pigott, David M, Yi, Dingdong, Johnson, Kimberly, Earl, Lucas, Marczak, Laurie B, Shirude, Shreya, Davis Weaver, Nicole, Bisanzio, Donal, Perkins, T Alex, Lai, Shengjie, Lu, Xin, Jones, Peter, Coelho, Giovanini E, Carvalho, Roberta G, Van Bortel, Wim, Marsboom, Cedric, Hendrickx, Guy, Schaffner, Francis, Moore, Chester G, Nax, Heinrich H, Bengtsson, Linus, Wetter, Erik, Tatem, Andrew J, Brownstein, John S, Smith, David L, Lambrechts, Louis, Cauchemez, Simon, Linard, Catherine, Faria, Nuno R, Pybus, Oliver G, Scott, Thomas W, Liu, Qiyong, Yu, Hongjie, Wint, GR William, Hay, Simon I, and Golding, Nick

Subjects
Microbiology, Biological Sciences, Rare Diseases, Vaccine Related, Prevention, Infectious Diseases, Emerging Infectious Diseases, Biodefense, Vector-Borne Diseases, Infection, Good Health and Well Being, Aedes, Animals, Arbovirus Infections, Arboviruses, Female, Humans, Mosquito Vectors, Medical Microbiology
Abstract

The global population at risk from mosquito-borne diseases-including dengue, yellow fever, chikungunya and Zika-is expanding in concert with changes in the distribution of two key vectors: Aedes aegypti and Aedes albopictus. The distribution of these species is largely driven by both human movement and the presence of suitable climate. Using statistical mapping techniques, we show that human movement patterns explain the spread of both species in Europe and the United States following their introduction. We find that the spread of Ae. aegypti is characterized by long distance importations, while Ae. albopictus has expanded more along the fringes of its distribution. We describe these processes and predict the future distributions of both species in response to accelerating urbanization, connectivity and climate change. Global surveillance and control efforts that aim to mitigate the spread of chikungunya, dengue, yellow fever and Zika viruses must consider the so far unabated spread of these mosquitos. Our maps and predictions offer an opportunity to strategically target surveillance and control programmes and thereby augment efforts to reduce arbovirus burden in human populations globally.

Published
2019

20. Epidemiology of COVID-19 after Emergence of SARS-CoV-2 Gamma Variant, Brazilian Amazon, 2020-2021

Author

Nicolete, Vanessa C., Rodrigues, Priscila T., Fernandes, Anderson R.J., Corder, Rodrigo M., Tonini, Juliana, Buss, Lewis F., Sales, Flavia C., Faria, Nuno R., Sabino, Ester C., Castro, Marcia C., and Ferreira, Marcelo U.

Subjects
Amazonas, Brazil -- Health aspects, Company distribution practices, Health
Abstract

The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Gamma (P.1) variant emerged in November 2020 and drove the second wave of coronavirus disease (COVID-19) in Brazil. Emergence of this [...]

Published
2022
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21. Reinfection by the SARS-CoV-2 Gamma variant in blood donors in Manaus, Brazil

Author

Prete, Jr, Carlos A., Buss, Lewis F., Buccheri, Renata, Abrahim, Claudia M. M., Salomon, Tassila, Crispim, Myuki A. E., Oikawa, Marcio K., Grebe, Eduard, da Costa, Allyson G., Fraiji, Nelson A., do P. S. S. Carvalho, Maria, Whittaker, Charles, Alexander, Neal, Faria, Nuno R., Dye, Christopher, Nascimento, Vítor H., Busch, Michael P., and Sabino, Ester Cerdeira

Published
2022
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24. Phylodynamic assessment of intervention strategies for the West African Ebola virus outbreak.

Author

Dellicour, Simon, Baele, Guy, Dudas, Gytis, Faria, Nuno R, Pybus, Oliver G, Suchard, Marc A, Rambaut, Andrew, and Lemey, Philippe

Subjects
Humans, Hemorrhagic Fever, Ebola, Disease Outbreaks, Phylogeny, Genome, Viral, Geography, Time Factors, Africa, Western, Ebolavirus, Africa, Western, Genome, Viral, Hemorrhagic Fever, Ebola
Abstract

Genetic analyses have provided important insights into Ebola virus spread during the recent West African outbreak, but their implications for specific intervention scenarios remain unclear. Here, we address this issue using a collection of phylodynamic approaches. We show that long-distance dispersal events were not crucial for epidemic expansion and that preventing viral lineage movement to any given administrative area would, in most cases, have had little impact. However, major urban areas were critical in attracting and disseminating the virus: preventing viral lineage movement to all three capitals simultaneously would have contained epidemic size to one-third. We also show that announcements of border closures were followed by a significant but transient effect on international virus dispersal. By quantifying the hypothetical impact of different intervention strategies, as well as the impact of barriers on dispersal frequency, our study illustrates how phylodynamic analyses can help to address specific epidemiological and outbreak control questions.

Published
2018

25. Clinical and epidemiological characteristics of Madariaga and Venezuelan equine encephalitis virus infection

Author

Rivera, Luis Felipe, primary, Lezcano-Coba, Carlos, additional, Galue, Josefrancisco, additional, Rodriguez, Xacdiel, additional, Juarez, Yelissa, additional, de Souza, William M, additional, Capitan-Barrios, Zeuz, additional, Valderrama, Anayansi, additional, Abrego, Leyda, additional, Cedeno, Hector, additional, Jackman, Carmela, additional, Waggoner, Jesse, additional, Aguilar, Patricia V., additional, Guzman, Hilda, additional, Weaver, Scott, additional, Tesh, Robert B., additional, Lopez-Verges, Sandra L, additional, Donnelly, Christl A., additional, Estofolete, Cassia F., additional, Faria, Nuno R., additional, Vasilakis, Nikos, additional, Vittor, Amy Y., additional, Smith, Darci R., additional, and Carrera, Jean-Paul, additional

Published
2024
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26. Tracking arboviruses, their transmission vectors and potential hosts by nanopore sequencing of mosquitoes

Author

Mirza, Jeremy D., primary, de Oliveira Guimarães, Lilian, additional, Wilkinson, Sam, additional, Rocha, Esmenia C., additional, Bertanhe, Mayara, additional, Helfstein, Vanessa Christe, additional, de-Deus, Juliana Telles, additional, Claro, Ingra M., additional, Cumley, Nicola, additional, Quick, Joshua, additional, Faria, Nuno R., additional, Sabino, Ester C., additional, Kirchgatter, Karin, additional, and Loman, Nicholas J., additional

Published
2024
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27. Neutralisation of SARS-CoV-2 lineage P.1 by antibodies elicited through natural SARS-CoV-2 infection or vaccination with an inactivated SARS-CoV-2 vaccine: an immunological study

Author

Souza, William M, Amorim, Mariene R, Sesti-Costa, Renata, Coimbra, Lais D, Brunetti, Natalia S, Toledo-Teixeira, Daniel A, de Souza, Gabriela F, Muraro, Stefanie P, Parise, Pierina L, Barbosa, Priscilla P, Bispo-dos-Santos, Karina, Mofatto, Luciana S, Simeoni, Camila L, Claro, Ingra M, Duarte, Adriana S S, Coletti, Thais M, Zangirolami, Audrey B, Costa-Lima, Carolina, Gomes, Arilson B S P, Buscaratti, Lucas I, Sales, Flavia C, Costa, Vitor A, Franco, Lucas A M, Candido, Darlan S, Pybus, Oliver G, de Jesus, Jaqueline G, Silva, Camila A M, Ramundo, Mariana S, Ferreira, Giulia M, Pinho, Mariana C, Souza, Leandro M, Rocha, Esmenia C, Andrade, Pamela S, Crispim, Myuki A E, Maktura, Grazielle C, Manuli, Erika R, Santos, Magnun N N, Camilo, Cecilia C, Angerami, Rodrigo N, Moretti, Maria L, Spilki, Fernando R, Arns, Clarice W, Addas-Carvalho, Marcelo, Benites, Bruno D, Vinolo, Marco A R, Mori, Marcelo A S, Gaburo, Nelson, Dye, Christopher, Marques-Souza, Henrique, Marques, Rafael E, Farias, Alessandro S, Diamond, Michael S, Faria, Nuno R, Sabino, Ester C, Granja, Fabiana, and Proença-Módena, Jose Luiz

Published
2021
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28. Respiratory Viral Shedding in Healthcare Workers Reinfected with SARS-CoV-2, Brazil, 2020

Author

Amorim, Mariene R., Souza, William M., Barros, Antonio C.G., Jr., Toledo-Teixeira, Daniel A., Bispo-dos-Santos, Karina, Simeoni, Camila L., Parise, Pierina L., Vieira, Aline, Forato, Julia, Claro, Ingra M., Mofatto, Luciana S., Barbosa, Priscila P., Brunetti, Natalia S., Franca, Emerson S.S., Pedroso, Gisele A., Carvalho, Barbara F.N., Zaccariotto, Tania R., Krywacz, Kamila C.S., Vieira, Andre S., Mori, Marcelo A., Farias, Alessandro S., Pavan, Maria H.P., Bachur, Luis Felipe, Cardoso, Luis G.O., Spilki, Fernando R., Sabino, Ester C., Faria, Nuno R., Santos, Magnun N.N., Angerami, Rodrigo, Leme, Patricia A.F., Schreiber, Angelica, Moretti, Maria L., Granja, Fabiana, and Proenca-Modena, Jose Luiz

Subjects
Diseases -- Relapse, Respiratory tract infections -- Diagnosis -- Development and progression, Medical personnel -- Case studies -- Health aspects, Health
Abstract

Coronavirus disease (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which emerged in Wuhan, China, in late 2019. As of April 8, 2021, COVID-19 has affected >132 [...]

Published
2021
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29. Virus genomes reveal factors that spread and sustained the Ebola epidemic

Author

Dudas, Gytis, Carvalho, Luiz Max, Bedford, Trevor, Tatem, Andrew J, Baele, Guy, Faria, Nuno R, Park, Daniel J, Ladner, Jason T, Arias, Armando, Asogun, Danny, Bielejec, Filip, Caddy, Sarah L, Cotten, Matthew, D’Ambrozio, Jonathan, Dellicour, Simon, Di Caro, Antonino, Diclaro, Joseph W, Duraffour, Sophie, Elmore, Michael J, Fakoli, Lawrence S, Faye, Ousmane, Gilbert, Merle L, Gevao, Sahr M, Gire, Stephen, Gladden-Young, Adrianne, Gnirke, Andreas, Goba, Augustine, Grant, Donald S, Haagmans, Bart L, Hiscox, Julian A, Jah, Umaru, Kugelman, Jeffrey R, Liu, Di, Lu, Jia, Malboeuf, Christine M, Mate, Suzanne, Matthews, David A, Matranga, Christian B, Meredith, Luke W, Qu, James, Quick, Joshua, Pas, Suzan D, Phan, My VT, Pollakis, Georgios, Reusken, Chantal B, Sanchez-Lockhart, Mariano, Schaffner, Stephen F, Schieffelin, John S, Sealfon, Rachel S, Simon-Loriere, Etienne, Smits, Saskia L, Stoecker, Kilian, Thorne, Lucy, Tobin, Ekaete Alice, Vandi, Mohamed A, Watson, Simon J, West, Kendra, Whitmer, Shannon, Wiley, Michael R, Winnicki, Sarah M, Wohl, Shirlee, Wölfel, Roman, Yozwiak, Nathan L, Andersen, Kristian G, Blyden, Sylvia O, Bolay, Fatorma, Carroll, Miles W, Dahn, Bernice, Diallo, Boubacar, Formenty, Pierre, Fraser, Christophe, Gao, George F, Garry, Robert F, Goodfellow, Ian, Günther, Stephan, Happi, Christian T, Holmes, Edward C, Kargbo, Brima, Keïta, Sakoba, Kellam, Paul, Koopmans, Marion PG, Kuhn, Jens H, Loman, Nicholas J, Magassouba, N’Faly, Naidoo, Dhamari, Nichol, Stuart T, Nyenswah, Tolbert, Palacios, Gustavo, Pybus, Oliver G, Sabeti, Pardis C, Sall, Amadou, Ströher, Ute, Wurie, Isatta, Suchard, Marc A, Lemey, Philippe, and Rambaut, Andrew

Subjects
Infectious Diseases, Emerging Infectious Diseases, Biodefense, Vaccine Related, Prevention, Infection, Good Health and Well Being, Climate, Disease Outbreaks, Ebolavirus, Genome, Viral, Geography, Hemorrhagic Fever, Ebola, Humans, Internationality, Linear Models, Molecular Epidemiology, Phylogeny, Travel, General Science & Technology
Abstract

The 2013-2016 West African epidemic caused by the Ebola virus was of unprecedented magnitude, duration and impact. Here we reconstruct the dispersal, proliferation and decline of Ebola virus throughout the region by analysing 1,610 Ebola virus genomes, which represent over 5% of the known cases. We test the association of geography, climate and demography with viral movement among administrative regions, inferring a classic 'gravity' model, with intense dispersal between larger and closer populations. Despite attenuation of international dispersal after border closures, cross-border transmission had already sown the seeds for an international epidemic, rendering these measures ineffective at curbing the epidemic. We address why the epidemic did not spread into neighbouring countries, showing that these countries were susceptible to substantial outbreaks but at lower risk of introductions. Finally, we reveal that this large epidemic was a heterogeneous and spatially dissociated collection of transmission clusters of varying size, duration and connectivity. These insights will help to inform interventions in future epidemics.

Published
2017

30. Real-time RT-PCR for Venezuelan equine encephalitis complex, Madariaga, and Eastern equine encephalitis viruses: application in human and mosquito public health surveillance in Panama

Author

Carrera, Jean-Paul, primary, Araúz, Dimelza, additional, Rojas, Alejandra, additional, Cardozo, Fátima, additional, Stittleburg, Victoria, additional, Morales Claro, Ingra, additional, Galue, Josefrancisco, additional, Lezcano-Coba, Carlos, additional, Romero Rebello Moreira, Filipe, additional, -Rivera, Luis Felipe, additional, Chen-Germán, Maria, additional, Moreno, Brechla, additional, Capitan-Barrios, Zeuz, additional, López-Vergès, Sandra, additional, Pascale, Juan Miguel, additional, Sabino, Ester C., additional, Valderrama, Anayansi, additional, Hanley, Kathryn A., additional, Donnelly, Christl A., additional, Vasilakis, Nikos, additional, Faria, Nuno R., additional, and Waggoner, Jesse J., additional

Published
2023
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31. Main autopsy findings of visceral involvement by fatal mpox in patients with AIDS: necrotising nodular pneumonia, nodular ulcerative colitis, and diffuse vasculopathy

Author

Duarte-Neto, Amaro Nunes, primary, Gonçalves, Ana Maria, additional, Eliodoro, Raissa Heloisa de Araujo, additional, Martins, Wilker Dias, additional, Claro, Ingra Morales, additional, Valença, Ian Nunes, additional, Paes, Vitor Ribeiro, additional, Teixeira, Ralcyon, additional, Sztajnbok, Jaques, additional, França e Silva, Ivan Leonardo Avelino, additional, Leite, Luiz Antônio Ferreira, additional, Malaque, Ceila Maria Sant'Ana, additional, Borges, Luciana Marques Sansão, additional, Gonzalez, Mario Peribanez, additional, Barra, Luiz Alberto Costa, additional, Junior, Luiz Carlos Pereira, additional, Mello, Claudia Figueiredo, additional, Queiroz, Wladimir, additional, Atomya, Angela Naomi, additional, Fernezlian, Sandra de Morais, additional, Alves, Venâncio Avancini Ferreira, additional, Leite, Katia Ramos Moreira, additional, Ferreira, Cristiane Rubia, additional, Saldiva, Paulo Hilário Nascimento, additional, Mauad, Thais, additional, da Silva, Luiz Fernando Ferraz, additional, Faria, Nuno R, additional, Mendes Corrêa, Maria Cássia Jacinto, additional, Sabino, Ester Cerdeira, additional, Sotto, Mirian Nacagami, additional, and Dolhnikoff, Marisa, additional

Published
2023
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34. Emergence of the Asian lineage of Zika virus in Angola: an outbreak investigation

Author

Hill, Sarah C, Vasconcelos, Jocelyne, Neto, Zoraima, Jandondo, Domingos, Zé-Zé, Líbia, Aguiar, Renato Santana, Xavier, Joilson, Thézé, Julien, Mirandela, Marinela, Micolo Cândido, Ana Luísa, Vaz, Filipa, Sebastião, Cruz dos Santos, Wu, Chieh-Hsi, Kraemer, Moritz U G, Melo, Adriana, Schamber-Reis, Bruno L F, de Azevedo, Girlene S, Tanuri, Amilcar, Higa, Luiza M, Clemente, Carina, da Silva, Sara Pereira, da Silva Candido, Darlan, Claro, Ingra M, Quibuco, Domingos, Domingos, Cristóvão, Pocongo, Bárbara, Watts, Alexander G, Khan, Kamran, Alcantara, Luiz Carlos Junior, Sabino, Ester C, Lackritz, Eve, Pybus, Oliver G, Alves, Maria-João, Afonso, Joana, and Faria, Nuno R

Published
2019
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35. Author Correction: Spatial and temporal fluctuations in COVID-19 fatality rates in Brazilian hospitals

Author

Brizzi, Andrea, Whittaker, Charles, Servo, Luciana M. S., Hawryluk, Iwona, Prete, Jr, Carlos A., de Souza, William M., Aguiar, Renato S., Araujo, Leonardo J. T., Bastos, Leonardo S., Blenkinsop, Alexandra, Buss, Lewis F., Candido, Darlan, Castro, Marcia C., Costa, Silvia F., Croda, Julio, de Souza Santos, Andreza Aruska, Dye, Christopher, Flaxman, Seth, Fonseca, Paula L. C., Geddes, Victor E. V., Gutierrez, Bernardo, Lemey, Philippe, Levin, Anna S., Mellan, Thomas, Bonfim, Diego M., Miscouridou, Xenia, Mishra, Swapnil, Monod, Mélodie, Moreira, Filipe R. R., Nelson, Bruce, Pereira, Rafael H. M., Ranzani, Otavio, Schnekenberg, Ricardo P., Semenova, Elizaveta, Sonabend, Raphael, Souza, Renan P., Xi, Xiaoyue, Sabino, Ester C., Faria, Nuno R., Bhatt, Samir, and Ratmann, Oliver

Published
2022
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36. Longitudinal Genetic Characterization Reveals That Cell Proliferation Maintains a Persistent HIV Type 1 DNA Pool During Effective HIV Therapy

Author

von Stockenstrom, Susanne, Odevall, Lina, Lee, Eunok, Sinclair, Elizabeth, Bacchetti, Peter, Killian, Maudi, Epling, Lorrie, Shao, Wei, Hoh, Rebecca, Ho, Terence, Faria, Nuno R, Lemey, Philippe, Albert, Jan, Hunt, Peter, Loeb, Lisa, Pilcher, Christopher, Poole, Lauren, Hatano, Hiroyu, Somsouk, Ma, Douek, Daniel, Boritz, Eli, Deeks, Steven G, Hecht, Frederick M, and Palmer, Sarah

Subjects
Medical Microbiology, Biomedical and Clinical Sciences, Immunology, HIV/AIDS, Clinical Trials and Supportive Activities, Immunization, Sexually Transmitted Infections, Clinical Research, Genetics, Vaccine Related, Infectious Diseases, 2.1 Biological and endogenous factors, Aetiology, 2.2 Factors relating to the physical environment, Infection, Anti-HIV Agents, Cell Proliferation, DNA, Viral, HIV Infections, HIV-1, Humans, Longitudinal Studies, Lymph Nodes, Phylogeny, T-Lymphocyte Subsets, HIV-1 persistence, HIV-1 reservoir, memory T cells, Biological Sciences, Medical and Health Sciences, Microbiology, Biological sciences, Biomedical and clinical sciences, Health sciences
Abstract

BackgroundThe stability of the human immunodeficiency virus type 1 (HIV-1) reservoir and the contribution of cellular proliferation to the maintenance of the reservoir during treatment are uncertain. Therefore, we conducted a longitudinal analysis of HIV-1 in T-cell subsets in different tissue compartments from subjects receiving effective antiretroviral therapy (ART).MethodsUsing single-proviral sequencing, we isolated intracellular HIV-1 genomes derived from defined subsets of CD4(+) T cells from peripheral blood, gut-associated lymphoid tissue and lymph node tissue specimens from 8 subjects with virologic suppression during long-term ART at 2 time points (time points 1 and 2) separated by 7-9 months.ResultsDNA integrant frequencies were stable over time (

Published
2015

37. HIV epidemiology. The early spread and epidemic ignition of HIV-1 in human populations.

Author

Faria, Nuno R, Rambaut, Andrew, Suchard, Marc A, Baele, Guy, Bedford, Trevor, Ward, Melissa J, Tatem, Andrew J, Sousa, João D, Arinaminpathy, Nimalan, Pépin, Jacques, Posada, David, Peeters, Martine, Pybus, Oliver G, and Lemey, Philippe

Subjects
Humans, HIV-1, Communicable Diseases, Emerging, Acquired Immunodeficiency Syndrome, Population Dynamics, Evolution, Molecular, Phylogeny, Recombination, Genetic, Urbanization, History, 20th Century, History, 21st Century, Democratic Republic of the Congo, Pandemics, Communicable Diseases, Emerging, Evolution, Molecular, Recombination, Genetic, History, 20th Century, 21st Century, General Science & Technology
Abstract

Thirty years after the discovery of HIV-1, the early transmission, dissemination, and establishment of the virus in human populations remain unclear. Using statistical approaches applied to HIV-1 sequence data from central Africa, we show that from the 1920s Kinshasa (in what is now the Democratic Republic of Congo) was the focus of early transmission and the source of pre-1960 pandemic viruses elsewhere. Location and dating estimates were validated using the earliest HIV-1 archival sample, also from Kinshasa. The epidemic histories of HIV-1 group M and nonpandemic group O were similar until ~1960, after which group M underwent an epidemiological transition and outpaced regional population growth. Our results reconstruct the early dynamics of HIV-1 and emphasize the role of social changes and transport networks in the establishment of this virus in human populations.

Published
2014

38. The seasonal flight of influenza: a unified framework for spatiotemporal hypothesis testing

Author

Lemey, Philippe, Rambaut, Andrew, Bedford, Trevor, Faria, Nuno R., Bielejec, Filip, Baele, Guy, Russell, Colin A., Smith, Derek J., Pybus, Oliver G., Brockmann, Dirk, and Suchard, Marc A.

Subjects
Quantitative Biology - Populations and Evolution
Abstract

Global mobility flow data are at the heart of spatial epidemiological models used to predict infectious disease behavior but this wealth of data on human mobility has been largely neglected by reconstructions of pathogen evolutionary dynamics using viral genetic data. Although stochastic models of viral evolution may potentially be informed by such data, a major challenge lies in deciding which mobility processes are critical and to what extent they contribute to shaping contemporaneous distributions of pathogen diversity. Here, we develop a framework to integrate predictors of viral diffusion with phylogeographic inference and estimate human influenza H3N2 migration history while simultaneously testing and quantifying the factors that underly it. We provide evidence for air travel governing the global dynamics of human influenza whereas other processes act at a more local scale., Comment: 16 pages, 4 figures, 3 tables

Published
2012

39. Correction: Implementation of Genomic Surveillance of SARS-CoV-2 in the Caribbean: Lessons learned for sustainability in resource-limited settings

Author

Sahadeo, Nikita S. D., primary, Nicholls, Soren, additional, Moreira, Filipe R. R., additional, O’Toole, Áine, additional, Ramkissoon, Vernie, additional, Whittaker, Charles, additional, Hill, Verity, additional, McCrone, John T., additional, Mohammed, Nicholas, additional, Ramjag, Anushka, additional, Jordan, Arianne Brown, additional, Hill, Sarah C., additional, Singh, Risha, additional, Nathaniel-Girdharrie, Sue-Min, additional, Hinds, Avery, additional, Ramkissoon, Nuala, additional, Parag, Kris V., additional, Nandram, Naresh, additional, Parasram, Roshan, additional, Khan-Mohammed, Zobida, additional, Edghill, Lisa, additional, Indar, Lisa, additional, Andrewin, Aisha, additional, Sealey-Thomas, Rhonda, additional, McMillan, Pearl, additional, Oyinloye, Ayoola, additional, George, Kenneth, additional, Potter, Irad, additional, Lee, John, additional, Johnson, David, additional, Charles, Shawn, additional, Singh, Narine, additional, Bisesor-McKenzie, Jacquiline, additional, Laws, Hazel, additional, Belmar-George, Sharon, additional, Keizer-Beache, Simone, additional, Greenaway-Duberry, Sharra, additional, Ashwood, Nadia, additional, Foster, Jerome E., additional, Georges, Karla, additional, Naidu, Rahul, additional, Ivey, Marsha, additional, Giddings, Stanley, additional, Haraksingh, Rajini, additional, Ramsubhag, Adesh, additional, Jayaraman, Jayaraj, additional, Chinnadurai, Chinnaraja, additional, Oura, Christopher, additional, Pybus, Oliver G., additional, St. John, Joy, additional, Gonzalez-Escobar, Gabriel, additional, Faria, Nuno R., additional, and Carrington, Christine V. F., additional

Published
2023
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40. Convergent trends and spatiotemporal patterns of Aedes-borne arboviruses in Mexico and Central America

Author

Gutierrez, Bernardo, primary, da Silva Candido, Darlan, additional, Bajaj, Sumali, additional, Rodriguez Maldonado, Abril Paulina, additional, Ayala, Fabiola Garces, additional, Rodriguez, María de la Luz Torre, additional, Rodriguez, Adnan Araiza, additional, Arámbula, Claudia Wong, additional, González, Ernesto Ramírez, additional, Martínez, Irma López, additional, Díaz-Quiñónez, José Alberto, additional, Pichardo, Mauricio Vázquez, additional, Hill, Sarah C., additional, Thézé, Julien, additional, Faria, Nuno R., additional, Pybus, Oliver G., additional, Preciado-Llanes, Lorena, additional, Reyes-Sandoval, Arturo, additional, Kraemer, Moritz U. G., additional, and Escalera-Zamudio, Marina, additional

Published
2023
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41. Madariaga and Venezuelan equine encephalitis virus seroprevalence in rodent enzootic hosts in Eastern and Western Panama

Author

Carrera, Jean Paul, primary, Galue, Josefrancisco, additional, de Souza, William M., additional, Lezcano-Coba, Carlos A, additional, Torres-Cosme, Rolando, additional, Cumbrera, Alberto, additional, Vasilakis, Nikos, additional, Tesh, Robert B., additional, Guzman, Hilda, additional, Weaver, Scott, additional, Vittor, Amy Y., additional, Samudio, Rafael, additional, Pascale, Juan Miguel, additional, Valderrama, Anayansi, additional, Caceres-Carrera, Lorenzo, additional, Donnelly, Christl A, additional, and Faria, Nuno R., additional

Published
2023
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43. The HIV-1 reservoir in eight patients on long-term suppressive antiretroviral therapy is stable with few genetic changes over time

Author

Josefsson, Lina, von Stockenstrom, Susanne, Faria, Nuno R, Sinclair, Elizabeth, Bacchetti, Peter, Killian, Maudi, Epling, Lorrie, Tan, Alice, Ho, Terence, Lemey, Philippe, Shao, Wei, Hunt, Peter W, Somsouk, Ma, Wylie, Will, Douek, Daniel C, Loeb, Lisa, Custer, Jeff, Hoh, Rebecca, Poole, Lauren, Deeks, Steven G, Hecht, Frederick, and Palmer, Sarah

Subjects
Medical Microbiology, Biomedical and Clinical Sciences, Immunology, Genetics, HIV/AIDS, Clinical Research, Sexually Transmitted Infections, Infectious Diseases, Aetiology, 2.1 Biological and endogenous factors, Infection, Anti-Retroviral Agents, CD4 Lymphocyte Count, CD4-Positive T-Lymphocytes, Carrier State, DNA, Viral, Female, Genome, Viral, HIV Infections, HIV-1, Humans, Immunologic Memory, Lymphoid Tissue, Male, Mutation, Phylogeny, Time Factors
Abstract

The source and dynamics of persistent HIV-1 during long-term combinational antiretroviral therapy (cART) are critical to understanding the barriers to curing HIV-1 infection. To address this issue, we isolated and genetically characterized HIV-1 DNA from naïve and memory T cells from peripheral blood and gut-associated lymphoid tissue (GALT) from eight patients after 4-12 y of suppressive cART. Our detailed analysis of these eight patients indicates that persistent HIV-1 in peripheral blood and GALT is found primarily in memory CD4(+) T cells [CD45RO(+)/CD27((+/-))]. The HIV-1 infection frequency of CD4(+) T cells from peripheral blood and GALT was higher in patients who initiated treatment during chronic compared with acute/early infection, indicating that early initiation of therapy results in lower HIV-1 reservoir size in blood and gut. Phylogenetic analysis revealed an HIV-1 genetic change between RNA sequences isolated before initiation of cART and intracellular HIV-1 sequences from the T-cell subsets after 4-12 y of suppressive cART in four of the eight patients. However, evolutionary rate analyses estimated no greater than three nucleotide substitutions per gene region analyzed during all of the 4-12 y of suppressive therapy. We also identified a clearly replication-incompetent viral sequence in multiple memory T cells in one patient, strongly supporting asynchronous cell replication of a cell containing integrated HIV-1 DNA as the source. This study indicates that persistence of a remarkably stable population of infected memory cells will be the primary barrier to a cure, and, with little evidence of viral replication, this population could be maintained by homeostatic cell proliferation or other processes.

Published
2013

44. Early Genomic Detection of Cosmopolitan Genotype of Dengue Virus Serotype 2, Angola, 2018

Author

Hill, Sarah C., de Vasconcelos, Jocelyne Neto, Granja, Bernardo Gutierrez, Theze, Julien, Jandondo, Domingos, Neto, Zoraima, Mirandela, Marinela, Sebastiao, Cruz dos Santos, Candido, Ana Luisa Micolo, Clemente, Carina, da Silva, Sara Pereira, de Oliveira, Tulio, Pybus, Oliver G., Faria, Nuno R., and Afonso, Joana Morais

Subjects
DNA sequencing -- Health aspects, Infection -- Genetic aspects -- Health aspects, Genomics -- Health aspects, Dengue virus -- Health aspects, Mosquitoes, Genomes, Travelers, Medical tests, Biodiversity, Health
Abstract

In Africa, the prevalence of disease caused by Aedes mosquito-borne virus infections might be similar to that in the Americas (1,2). However, the transmission and genetic diversity of arthropodborne viruses [...]

Published
2019
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45. Spatiotemporal dynamics and recurrence of chikungunya virus in Brazil: an epidemiological study

Author

de Souza, William M, primary, de Lima, Shirlene T S, additional, Simões Mello, Leda M, additional, Candido, Darlan S, additional, Buss, Lewis, additional, Whittaker, Charles, additional, Claro, Ingra M, additional, Chandradeva, Nilani, additional, Granja, Fabiana, additional, de Jesus, Ronaldo, additional, Lemos, Poliana S, additional, Toledo-Teixeira, Daniel A, additional, Barbosa, Priscilla P, additional, Firmino, Antonio Carlos L, additional, Amorim, Mariene R, additional, Duarte, Larissa M F, additional, Pessoa, Ivan B, additional, Forato, Julia, additional, Vasconcelos, Irihane L, additional, Maximo, Ana Carolina B M, additional, Araújo, Emerson L L, additional, Perdigão Mello, Liana, additional, Sabino, Ester C, additional, Proença-Módena, José Luiz, additional, Faria, Nuno R, additional, and Weaver, Scott C, additional

Published
2023
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46. Spread of yellow fever virus outbreak in Angola and the Democratic Republic of the Congo 2015–16: a modelling study

Author

Kraemer, Moritz U G, Faria, Nuno R, Reiner, Robert C, Jr, Golding, Nick, Nikolay, Birgit, Stasse, Stephanie, Johansson, Michael A, Salje, Henrik, Faye, Ousmane, Wint, G R William, Niedrig, Matthias, Shearer, Freya M, Hill, Sarah C, Thompson, Robin N, Bisanzio, Donal, Taveira, Nuno, Nax, Heinrich H, Pradelski, Bary S R, Nsoesie, Elaine O, Murphy, Nicholas R, Bogoch, Isaac I, Khan, Kamran, Brownstein, John S, Tatem, Andrew J, de Oliveira, Tulio, Smith, David L, Sall, Amadou A, Pybus, Oliver G, Hay, Simon I, and Cauchemez, Simon

Published
2017
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47. Convergent trends and spatiotemporal patterns of arboviruses in Mexico and Central America

Author

Gutierrez, Bernardo, primary, Candido, Darlan da Silva, additional, Bajaj, Sumali, additional, Rodriguez Maldonado, Abril Paulina, additional, Ayala, Fabiola Garces, additional, Torre Rodriguez, María de la Luz, additional, Araiza Rodriguez, Adnan, additional, Wong Arámbula, Claudia, additional, Ramírez González, Ernesto, additional, Martínez, Irma López, additional, Díaz-Quiñónez, José Alberto, additional, Pichardo, Mauricio Vázquez, additional, Hill, Sarah C., additional, Thézé, Julien, additional, Faria, Nuno R., additional, Pybus, Oliver G., additional, Preciado-Llanes, Lorena, additional, Reyes-Sandoval, Arturo, additional, Kraemer, Moritz U.G., additional, and Escalera-Zamudio, Marina, additional

Published
2023
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48. Implementation of genomic surveillance of SARS-CoV-2 in the Caribbean: Lessons learned for sustainability in resource-limited settings

Author

Sahadeo, Nikita S. D., primary, Nicholls, Soren, additional, Moreira, Filipe R. R., additional, O’Toole, Áine, additional, Ramkissoon, Vernie, additional, Whittaker, Charles, additional, Hill, Verity, additional, McCrone, John T., additional, Mohammed, Nicholas, additional, Ramjag, Anushka, additional, Brown Jordan, Arianne, additional, Hill, Sarah C., additional, Singh, Risha, additional, Nathaniel-Girdharrie, Sue-Min, additional, Hinds, Avery, additional, Ramkissoon, Nuala, additional, Parag, Kris V., additional, Nandram, Naresh, additional, Parasram, Roshan, additional, Khan-Mohammed, Zobida, additional, Edghill, Lisa, additional, Indar, Lisa, additional, Andrewin, Aisha, additional, Sealey-Thomas, Rhonda, additional, McMillan, Pearl, additional, Oyinloye, Ayoola, additional, George, Kenneth, additional, Potter, Irad, additional, Lee, John, additional, Johnson, David, additional, Charles, Shawn, additional, Singh, Narine, additional, Bisesor-McKenzie, Jacquiline, additional, Laws, Hazel, additional, Belmar-George, Sharon, additional, Keizer-Beache, Simone, additional, Greenaway-Duberry, Sharra, additional, Ashwood, Nadia, additional, Foster, Jerome E., additional, Georges, Karla, additional, Naidu, Rahul, additional, Ivey, Marsha, additional, Giddings, Stanley, additional, Haraksingh, Rajini, additional, Ramsubhag, Adesh, additional, Jayaraman, Jayaraj, additional, Chinnadurai, Chinnaraja, additional, Oura, Christopher, additional, Pybus, Oliver G., additional, St. John, Joy, additional, Gonzalez-Escobar, Gabriel, additional, Faria, Nuno R., additional, and Carrington, Christine V. F., additional

Published
2023
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49. Dynamics of Early Establishment of SARS-CoV-2 VOC Omicron Lineages in Minas Gerais, Brazil

Author

de Menezes, Mariane Talon, primary, Moreira, Filipe Romero Rebello, additional, Whittaker, Charles, additional, Santos, Franciele Martins, additional, Queiroz, Daniel Costa, additional, Geddes, Victor, additional, Fonseca, Paula Luize Camargos, additional, de Jesus, Jaqueline Góes, additional, Mendes-Oliveira, Franciane, additional, Reis-Souza, Valquíria, additional, Santos, Bibiana, additional, Zauli, Danielle Alves Gomes, additional, de Lima, Aline Brito, additional, de Brito Mendonça, Cristiane, additional, Alvim, Luige Biciati, additional, do Prado Silva, Joice, additional, Malta, Frederico Scott Varella, additional, de Souza Ferreira, Alessandro Clayton, additional, Faria, Nuno R., additional, Sabino, Ester Cerdeira, additional, and Aguiar, Renato Santana, additional

Published
2023
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50. The Evolution and Transmission of Epidemic GII.17 Noroviruses

Author

Lu, Jing, Fang, Lin, Zheng, Huanying, Lao, Jiaqian, Yang, Fen, Sun, Limei, Xiao, Jianpeng, Lin, Jinyan, Song, Tie, Ni, Tao, Raghwani, Jayna, Ke, Changwen, Faria, Nuno R., Bowden, Thomas A., Pybus, Oliver G., and Li, Hui

Published
2016

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