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Projetos de Pesquisa
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LIM/46 - Laboratório de Parasitologia Médica, Hospital das Clínicas, Faculdade de Medicina
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- Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil(2021) FARIA, Nuno R.; MELLAN, Thomas A.; WHITTAKER, Charles; CLARO, Ingra M.; CANDIDO, Darlan da S.; MISHRA, Swapnil; CRISPIM, Myuki A. E.; SALES, Flavia C.; HAWRYLUK, Iwona; MCCRONE, John T.; HULSWIT, Ruben J. G.; FRANCO, Lucas A. M.; RAMUNDO, Mariana S.; JESUS, Jaqueline G. de; ANDRADE, Pamela S.; COLETTI, Thais M.; FERREIRA, Giulia M.; SILVA, Camila A. M.; MANULI, Erika R.; PEREIRA, Rafael H. M.; PEIXOTO, Pedro S.; KRAEMER, Moritz U.; GABURO JR., Nelson; CAMILO, Cecilia da C.; HOELTGEBAUM, Henrique; SOUZA, William M.; ROCHA, Esmenia C.; SOUZA, Leandro M. de; PINHO, Mariana C. de; ARAUJO, Leonardo J. T.; V, Frederico S. Malta; LIMA, Aline B. de; SILVA, Joice do P.; ZAULI, Danielle A. G.; FERREIRA, Alessandro C. de S.; SCHNEKENBERG, Ricardo P.; LAYDON, Daniel J.; WALKER, Patrick G. T.; SCHLUETER, Hannah M.; SANTOS, Ana L. P. dos; VIDAL, Maria S.; CARO, Valentina S. Del; FILHO, Rosinaldo M. F.; SANTOS, Helem M. dos; AGUIAR, Renato S.; PROENCA-MODENA, Jose L. P.; NELSON, Bruce; HAY, James A.; MONOD, Melodie; MISCOURIDOU, Xenia; COUPLAND, Helen; SONABEND, Raphael; VOLLMER, Michaela; GANDY, Axel; PRETE JR., Carlos A.; NASCIMENTO, Vitor H.; SUCHARD, Marc A.; BOWDEN, Thomas A.; POND, Sergei L. K.; WU, Chieh-Hsi; RATMANN, Oliver; FERGUSON, Neil M.; DYE, Christopher; LOMAN, Nick J.; LEMEY, Philippe; RAMBAUT, Andrew; FRAIJI, Nelson A.; CARVALHO, Maria do P. S. S.; PYBUS, Oliver G.; FLAXMAN, Seth; BHATT, Samir; SABINO, Ester C.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.
- Genomic Surveillance of Yellow Fever Virus Epizootic in Sao Paulo, Brazil, 2016-2018(2020) HILL, Sarah C.; SOUZA, Renato de; THEZE, Julien; CLARO, Ingra; AGUIAR, Renato S.; ABADE, Leandro; SANTOS, Fabiana C. P.; CUNHA, Mariana S.; NOGUEIRA, Juliana S.; SALLES, Flavia C. S.; ROCCO, Iray M.; MAEDA, Adriana Y.; VASAMI, Fernanda G. S.; PLESSIS, Louis du; SILVEIRA, Paola P.; JESUS, Jaqueline G. de; QUICK, Joshua; FERNANDES, Natalia C. C. A.; GUERRA, Juliana M.; RESSIO, Rodrigo A.; GIOVANETTI, Marta; ALCANTARA, Luiz C. J.; CIRQUEIRA, Cinthya S.; DIAZ-DELGADO, Josue; MACEDO, Fernando L. L.; TIMENETSKY, Maria do Carmo S. T.; PAULA, Regiane de; SPINOLA, Roberta; DEUS, Juliana Telles de; MUCCI, Luis F.; TUBAKI, Rosa Maria; MENEZES, Regiane M. T. de; RAMOS, Patricia L.; ABREU, Andre L. de; CRUZ, Laura N.; LOMAN, Nick; DELLICOUR, Simon; PYBUS, Oliver G.; SABINO, Ester C.; FARIA, Nuno R.Sao 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 Sao 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 spill over 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 Sao Paulo, we generated and analysed virus genomic data and epizootic case data from NHP in Sao Paulo. We report the occurrence of three spatiotemporally distinct phases of the outbreak in Sao Paulo prior to February 2018. We generated 51 new virus genomes from YFV positive cases identified in 23 different municipalities in Sao 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 Sao 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 Sao 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 Sao Paulo state. Our results shed light on the sylvatic transmission of YFV in highly fragmented forested regions in Sao Paulo state and highlight the importance of continued surveillance of zoonotic pathogens in sentinel species.
- Evolution and epidemic spread of SARS-CoV-2 in Brazil(2020) CANDIDO, Darlan S.; CLARO, Ingra M.; JESUS, Jaqueline G. de; SOUZA, William M.; MOREIRA, Filipe R. R.; DELLICOUR, Simon; MELLAN, Thomas A.; PLESSIS, Louis du; PEREIRA, Rafael H. M.; SALES, Flavia C. S.; MANULI, Erika R.; THEZE, Julien; ALMEIDA, Luiz; MENEZES, Mariane T.; VOLOCH, Carolina M.; FUMAGALLI, Marcilio J.; COLETTI, Thais M.; SILVA, Camila A. M.; RAMUNDO, Mariana S.; AMORIM, Mariene R.; HOELTGEBAUM, Henrique H.; MISHRA, Swapnil; GILL, Mandev S.; CARVALHO, Luiz M.; BUSS, Lewis F.; JR, Carlos A. Prete; ASHWORTH, Jordan; I, Helder Nakaya; PEIXOTO, Pedro S.; BRADY, Oliver J.; NICHOLLS, Samuel M.; TANURI, Amilcar; ROSSI, Atila D.; V, Carlos K. Braga; GERBER, Alexandra L.; GUIMARAES, Ana Paula de C.; JR, Nelson Gaburo; ALENCAR, Cecila Salete; FERREIRA, Alessandro C. S.; LIMA, Cristiano X.; LEVI, Jose Eduardo; GRANATO, Celso; FERREIRA, Giulia M.; JR, Ronaldo S. Francisco; GRANJA, Fabiana; GARCIA, Marcia T.; MORETTI, Maria Luiza; JR, Mauricio W. Perroud; CASTINEIRAS, Terezinha M. P. P.; LAZARI, Carolina S.; HILL, Sarah C.; SANTOS, Andreza Aruska de Souza; SIMEONI, Camila L.; FORATO, Julia; SPOSITO, Andrei C.; SCHREIBER, Angelica Z.; SANTOS, Magnun N. N.; SA, Camila Zolini de; SOUZA, Renan P.; RESENDE-MOREIRA, Luciana C.; TEIXEIRA, Mauro M.; HUBNER, Josy; LEME, Patricia A. F.; MOREIRA, Rennan G.; NOGUEIRA, Mauricio L.; FERGUSON, Neil M.; COSTA, Silvia F.; PROENCA-MODENA, Jose Luiz; VASCONCELOS, Ana Tereza R.; BHATT, Samir; LEMEY, Philippe; WU, Chieh-Hsi; RAMBAUT, Andrew; LOMAN, Nick J.; AGUIAR, Renato S.; PYBUS, Oliver G.; SABINO, Ester C.; FARIA, Nuno RodriguesBrazil currently has one of the fastest-growing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemics in the world. Because of limited available data, assessments of the impact of nonpharmaceutical interventions (NPIs) on this virus spread remain challenging. Using a mobility-driven transmission model, we show that NPIs reduced the reproduction number from >3 to 1 to 1.6 in Sao Paulo and Rio de Janeiro. Sequencing of 427 new genomes and analysis of a geographically representative genomic dataset identified >100 international virus introductions in Brazil. We estimate that most (76%) of the Brazilian strains fell in three clades that were introduced from Europe between 22 February and 11 March 2020. During the early epidemic phase, we found that SARS-CoV-2 spread mostly locally and within state borders. After this period, despite sharp decreases in air travel, we estimated multiple exportations from large urban centers that coincided with a 25% increase in average traveled distances in national flights. This study sheds new light on the epidemic transmission and evolutionary trajectories of SARS-CoV-2 lineages in Brazil and provides evidence that current interventions remain insufficient to keep virus transmission under control in this country.