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Characterization, genomics and diagnostic of viruses with importance for public health in Brazil by high throughput sequencing

Grant number: 17/13981-0
Support Opportunities:Scholarships in Brazil - Post-Doctoral
Effective date (Start): December 01, 2017
Effective date (End): October 27, 2021
Field of knowledge:Biological Sciences - Microbiology - Biology and Physiology of Microorganisms
Principal Investigator:Luiz Tadeu Moraes Figueiredo
Grantee:William Marciel de Souza
Host Institution: Faculdade de Medicina de Ribeirão Preto (FMRP). Universidade de São Paulo (USP). Ribeirão Preto , SP, Brazil
Associated research grant:14/02438-6 - Studies with Bunyaviridae that produce human disease, AP.TEM
Associated scholarship(s):19/24251-9 - Multi-omic approaches for the study of Chikungunya disease, BE.EP.PD

Abstract

High throughput sequencing (HTS) allowed important advances in the identification and characterization of viruses, without requirement the viral isolation or propagation in cell culture system. In recent year, the costs these methods have been drastically reduced, making that use this method increasingly in studies of viruses with importance in human public health, including zoonotic viruses. Therefore, exploring this methodology, we will characterize ~40 new viruses from bats, rodents, opossums and ticks from different regions of Brazil. To this end, we will perform the genomic characterization, taxonomy, evolution and molecular epidemiology, as well as try viral isolation. In the second part of this project, we will use HTS based on MinION platform to perform diagnostic and sequencing in a single step. Therefore, we will develop panels for arbovirus that cause human diseases and for viruses that affect immunosuppressed patients or infection in the central nervous system. Our diagnostic approaches with MinION sequencing may be implemented in the clinical routine, patented and made available in commercial diagnostic kits. (AU)

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Scientific publications (35)
(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)
TEIXEIRA NUNES, MARCIO ROBERTO; DE SOUZA, WILLIAM MARCIEL; SAVJI, NAZIR; FIGUEIREDO, MARIO LUIS; CARDOSO, JEDSON FERREIRA; DA SILVA, SANDRO PATROCA; DA SILVA DE LIMA, CLAYTON PEREIRA; VASCONCELOS, HELENA BALDEZ; RODRIGUES, SUELI GUERREIRO; LIPKIN, W. IAN; et al. Oropouche orthobunyavirus: Genetic characterization of full-length genomes and development of molecular methods to discriminate natural reassortments. INFECTION GENETICS AND EVOLUTION, v. 68, p. 16-22, . (12/24150-9, 17/13981-0, 15/05778-5)
DE SOUZA, WILLIAM MARCIEL; ROMEIRO, MARILIA FARIGNOLI; SABINO-SANTOS, JR., GILBERTO; MOTTA MAIA, FELIPE GONCALVES; FUMAGALLI, MARCILIO JORGE; MODHA, SEJAL; TEIXEIRA NUNES, MARCIO ROBERTO; MURCIA, PABLO RAMIRO; MORAES FIGUEIREDO, LUIZ TADEU. Novel orthohepeviruses in wild rodents from Sao Paulo State, Brazil. VIROLOGY, v. 519, p. 12-16, . (16/02568-2, 12/24150-9, 17/13981-0, 16/01414-1, 14/20851-8, 15/05778-5, 13/14929-1, 11/06810-9, 08/06411-4, 11/22663-6)
FUMAGALLI, MARCILIO JORGE; DE SOUZA, WILLIAM MARCIEL; ALVES ESPOSITO, DANILLO LUCAS; SILVA, ANGELICA; ROMEIRO, MARILIA FARIGNOLI; MARTINEZ, EDSON ZANGIACOMI; LOPES DA FONSECA, BENEDITO ANTONIO; MORAES FIGUEIREDO, LUIZ TADEU. Enzyme-linked immunosorbent assay using recombinant envelope protein 2 antigen for diagnosis of Chikungunya virus. VIROLOGY JOURNAL, v. 15, . (16/01414-1, 14/02438-6, 12/24150-9, 17/13981-0, 14/20851-8)
DENNIS, TRISTAN P. W.; FLYNN, PETER J.; DE SOUZA, WILLIAM MARCIEL; SINGER, JOSHUA B.; MOREAU, CORRIE S.; WILSON, SAM J.; GIFFORD, ROBERT J.. Insights into Circovirus Host Range from the Genomic Fossil Record. Journal of Virology, v. 92, n. 16, . (17/13981-0, 15/05778-5, 12/24150-9)
DE SOUZA, WILLIAM MARCIE; FUMAGALLI, MARCILIO JORGE; TORRES CARRASCO, ADRIANO DE OLIVEIRA; ROMEIRO, MARILIA FARIGNOLI; MODHA, SEJAL; SEKI, MEIRE CHRISTINA; GHELLER, JANAINA MENEGAZZO; DAFFRE, SIRLEI; TEIXEIRA NUNES, MARCIO ROBERTO; MURCIA, PABLO RAMIRO; et al. Viral diversity of Rhipicephalus microplus parasitizing cattle in southern Brazil. SCIENTIFIC REPORTS, v. 8, . (16/01414-1, 14/02438-6, 15/05778-5, 13/14929-1, 12/24150-9, 17/13981-0, 14/20851-8)
DE SOUZA, WILLIAM MARCIEL; FUMAGALLI, MARCILIO JORGE; CARRERA, JEAN PAUL; DE ARAUJO, JANSEN; CARDOSO, JEDSON FERREIRA; DE CARVALHO, CRISTIANO; DURIGON, EDISON LUIZ; QUEIROZ, LUZIA HELENA; FARIA, NUNO RODRIGUES; MURCIA, PABLO R.; et al. Paramyxoviruses from neotropical bats suggest a novel genus and nephrotropism. INFECTION GENETICS AND EVOLUTION, v. 95, . (15/05778-5, 19/24251-9, 13/14929-1, 18/09383-3, 17/13981-0, 18/14389-0)
ROMANO, CAMILA MALTA; FELIX, ALVINA CLARA; DE PAULA, ANDERSON VICENTE; DE JESUS, JAQUELINE GOES; ANDRADE, PAMELA S.; CANDIDO, DARLAN; DE OLIVEIRA, FRANCIANE M.; RIBEIRO, ANDREIA C.; DA SILVA, FRANCINI C.; INEMAMI, MARTA; et al. SARS-CoV-2 reinfection caused by the P.1 lineage in Araraquara city, Sao Paulo State, Brazil. Revista do Instituto de Medicina Tropical de São Paulo, v. 63, . (17/13981-0, 19/03859-9, 19/24251-9, 18/14389-0)
DE SOUZA SANTOS, ANDREZA ARUSKA; CANDIDO, DARLAN DA SILVA; DE SOUZA, WILLIAM MARCIEL; BUSS, LEWIS; LI, SABRINA L.; PEREIRA, RAFAEL H. M.; WU, CHIEH-HSI; SABINO, ESTER C.; FARIA, NUNO R.. Dataset on SARS-CoV-2 non-pharmaceutical interventions in Brazilian municipalities. SCIENTIFIC DATA, v. 8, n. 1, . (17/13981-0, 19/24251-9, 18/14389-0)
DE SOUZA, WILLIAM MARCIEL; BUSS, LEWIS FLETCHER; CANDIDO, DARLAN DA SILVA; CARRERA, JEAN-PAUL; LI, SABRINA; ZAREBSKI, ALEXANDER E.; PEREIRA, RAFAEL HENRIQUE MORAES; PRETE, JR., CARLOS A.; DE SOUZA-SANTOS, ANDREZA ARUSKA; PARAG, KRIS V.; et al. Epidemiological and clinical characteristics of the COVID-19 epidemic in Brazil. NATURE HUMAN BEHAVIOUR, v. 4, n. 8, . (17/13981-0, 19/24251-9, 18/12579-7, 18/14389-0)
FUMAGALLI, MARCILIO JORGE; DE SOUZA, WILLIAM MARCIEL; DE ARAUJO, JANSEN; MODHA, SEJAL; QUEIROZ, LUZIA HELENA; DURIGON, EDISON LUIZ; MURCIA, PABLO RAMIRO; MORAES FIGUEIREDO, LUIZ TADEU. Krykfeie dicistrovirus: A novel dicistrovirus in velvety free-tailed bats from Brazil. INFECTION GENETICS AND EVOLUTION, v. 75, . (12/24150-9, 17/13981-0, 16/01414-1, 13/14929-1, 14/20851-8, 15/05778-5)
HUGHES, HOLLY R.; ADKINS, SCOTT; ALKHOVSKIY, SERGEY; BEER, MARTIN; BLAIR, CAROL; CALISHER, CHARLES H.; DREBOT, MIKE; LAMBERT, AMY J.; DE SOUZA, WILLIAM MARCIEL; MARKLEWITZ, MARCO; et al. ICTV Virus Taxonomy Profile: Peribunyaviridae. JOURNAL OF GENERAL VIROLOGY, v. 101, n. 1, p. 1-2, . (17/13981-0)
TAURO, LAURA B.; DE SOUZA, WILLIAM MARCIEL; ELISA RIVAROLA, MARIA; DE OLIVEIRA, RODRIGO; KONIGHEIM, BRENDA; SILVA, SANDRO PATROCA; LIMA, CLAYTON; OLIVEIRA, LAYANNA; VASCONCELOS, JANAINA M.; CARDOSO, JEDSON FERREIRA; et al. Genomic characterization of orthobunyavirus of veterinary importance in America. INFECTION GENETICS AND EVOLUTION, v. 73, p. 205-209, . (17/13981-0)
COSTA BARREIRA, LUZIA APARECIDA; SCHEUCHER, PRISCILA SANTOS; ROMEIRO, MARILIA FARIGNOLI; LA SERRA, LEONARDO; BADRA, SORAYA JABUR; DE SOUZA, WILLIAM MARCIEL; MORAES FIGUEIREDO, LUIZ TADEU. Evaluating the use of fluorescence-based flow cytometry assay for dengue diagnosis using peripheral blood mononuclear cells. Revista da Sociedade Brasileira de Medicina Tropical, v. 51, n. 2, p. 168-173, . (17/13981-0, 12/24150-9, 14/02438-6, 14/20851-8)
FERNANDEZ, DIANA; DE SOUZA, WILLIAM MARCIEL; SILVAS, JESUS A.; DEARDORFF, ELEANOR R.; WIDEN, STEVEN G.; ESTRADA-FRANCO, JOSE G.; WEAVER, SCOTT C.; NUNES, MARCIO; AGUILAR, PATRICIA V.. Barrita Virus, a Novel Virus of the Patois Serogroup (Genus Orthobunyavirus; Family Peribunyaviridae). American Journal of Tropical Medicine and Hygiene, v. 103, n. 1, p. 3-pg., . (17/13981-0)
FUMAGALLI, MARCILIO JORGE; DE SOUZA, WILLIAM MARCIEL; DE CASTRO-JORGE, LUIZA ANTUNES; HOMEM DE CARVALHO, RENAN VILLANOVA; CASTRO, ITALO DE ARAUJO; NOGUEIRA DE ALMEIDA, LUIZ GUSTAVO; CONSONNI, SILVIO ROBERTO; ZAMBONI, DARIO SIMOES; MORAES FIGUEIREDO, LUIZ TADEU. Chikungunya Virus Exposure Partially Cross-Protects against Mayaro Virus Infection in Mice. Journal of Virology, v. 95, n. 23, . (19/27333-6, 17/13981-0, 18/09383-3)
DE SOUZA, WILLIAM M.; MURARO, STEFANIE P.; SOUZA, GABRIELA F.; AMORIM, MARIENE R.; SESTI-COSTA, RENATA; MOFATTO, LUCIANA S.; FORATO, JULIA; BARBOSA, PRISCILLA P.; TOLEDO-TEIXEIRA, DANIEL A.; BISPO-DOS-SANTOS, KARINA; et al. lusters of SARS-CoV-2 Lineage B.1.1.7 Infection after Vaccination with Adenovirus-Vectored and Inactivated Vaccine. Viruses-Basel, v. 13, n. 11, . (16/00194-8, 18/14389-0, 18/13645-3, 17/26908-0, 20/02159-0, 17/13981-0, 19/09704-7, 18/10224-7, 19/24251-9, 20/04558-0)
CANDIDO, DARLAN S.; CLARO, INGRA M.; DE JESUS, JAQUELINE G.; SOUZA, WILLIAM M.; MOREIRA, FILIPE R. R.; DELLICOUR, SIMON; MELLAN, THOMAS A.; DU PLESSIS, LOUIS; PEREIRA, RAFAEL H. M.; SALES, FLAVIA C. S.; et al. Evolution and epidemic spread of SARS-CoV-2 in Brazil. Science, v. 369, n. 6508, SI, p. 1255+, . (20/04558-0, 16/00194-8, 19/21301-5, 18/14389-0, 18/14933-2, 17/13981-0, 20/04836-0, 18/25468-9, 16/18445-7, 18/09383-3, 18/17176-8, 19/12000-1, 19/07544-2, 19/24251-9)
DE SOUZA, WILLIAM MARCIEL; FUMAGALLI, MARCILIO JORGE; SABINO-SANTOS, JR., GILBERTO; MOTTA MAIA, FELIPE GONCALVES; MODHA, SEJAL; TEIXEIRA NUNES, MARCIO ROBERTO; MURCIA, PABLO RAMIRO; MORAES FIGUEIREDO, LUIZ TADEU. A Novel Hepacivirus in Wild Rodents from South America. Viruses-Basel, v. 11, n. 3, . (12/24150-9, 17/13981-0, 16/01414-1, 13/14929-1, 16/02568-2, 11/06810-9, 08/06411-4, 11/22663-6, 15/05778-5)
FUMAGALLI, MARCILIO JORGE; DE SOUZA, WILLIAM MARCIEL; ROMEIRO, MARILIA FARIGNOLI; DE SOUZA COSTA, MICHELL CHARLES; SLHESSARENKO, RENATA DEZENGRINI; MORAES FIGUEIREDO, LUIZ TADEU. Development of an Enzyme-Linked Immunosorbent Assay To Detect Antibodies Targeting Recombinant Envelope Protein 2 of Mayaro Virus. Journal of Clinical Microbiology, v. 57, n. 5, . (14/20851-8, 17/13981-0, 16/01414-1, 12/24150-9, 14/02438-6)
PENZES, JUDIT J.; DE SOUZA, WILLIAM MARCIEL; AGBANDJE-MCKENNA, MAVIS; GIFFORD, ROBERT J.. An Ancient Lineage of Highly Divergent Parvoviruses Infects both Vertebrate and Invertebrate Hosts. Viruses-Basel, v. 11, n. 6, . (17/13981-0)
DE MELO JUNIOR, ARISTIDES BEZERRA; DE SOUZA, WILLIAM MARCIEL; ACRANI, GUSTAVO OLSZANSKI; CARVALHO, VALERIA LIMA; ROMEIRO, MARILIA FARIGNOLI; TOLARDO, ALINE LAVADO; DA SILVA, SANDRO PATROCA; CARDOSO, JEDSON FERREIRA; CHIANG, JANNIFER DE OLIVEIRA; DA SILVA GONCALVES VIANEZ JUNIOR, JOAO LIDIO; et al. Genomic characterization and evolution of Tacaiuma orthobunyavirus (Peribunyaviridae family) isolated in Brazil. INFECTION GENETICS AND EVOLUTION, v. 60, p. 71-76, . (16/17457-1, 14/20851-8, 17/13981-0, 12/24150-9, 14/02438-6)
DENNIS, TRISTAN P. W.; DE SOUZA, WILLIAM MARCIEL; MARSILE-MEDUN, SOLEDAD; SINGER, JOSHUA B.; WILSON, SAM J.; GIFFORD, ROBERT J.. The evolution, distribution and diversity of endogenous circoviral elements in vertebrate genomes. VIRUS RESEARCH, v. 262, n. SI, p. 15-23, . (17/13981-0)
LEE, QUINTIN; PADULA, MATTHEW P.; PINELLO, NATALIA; WILLIAMS, SIMON H.; O'ROURKE, MATTHEW B.; FUMAGALLI, MARCILIO JORGE; ORKIN, JOSEPH D.; SONG, RENHUA; SHABAN, BABAK; BRENNER, ORI; et al. Murine and related chapparvoviruses are nephro-tropic and produce novel accessory proteins in infected kidneys. PLOS PATHOGENS, v. 16, n. 1, . (17/13981-0, 18/09383-3)
ABUDUREXITI, ABULIKEMU; ADKINS, SCOTT; ALIOTO, DANIELA; ALKHOVSKY, SERGEY V.; AVSIC-ZUPANC, TATJANA; BALLINGER, MATTHEW J.; BENTE, DENNIS A.; BEER, MARTIN; BERGERON, ERIC; BLAIR, CAROL D.; et al. Taxonomy of the order Bunyavirales: update 2019. ARCHIVES OF VIROLOGY, v. 164, n. 7, p. 1949-1965, . (17/13981-0)
AGUILAR, PATRICIA V.; DE SOUZA, WILLIAM MARCIEL; SILVAS, JESUS A.; WOOD, THOMAS; WIDEN, STEVEN; FUMAGALLI, MARCILIO JORGE; TEIXEIRA NUNES, MARCIO ROBERTO. Genetic Characterization of the Patois Serogroup (Genus Orthobunyavirus; Family Peribunyaviridae) and Evidence That Estero Real Virus is a Member of the Genus Orthonairovirus. American Journal of Tropical Medicine and Hygiene, v. 99, n. 2, p. 451-457, . (17/13981-0, 16/01414-1, 12/24150-9)
MOTTA MAIA, FELIPE GONCALVES; DE SOUZA, WILLIAM MARCIEL; SABINO-SANTOS, JR., GILBERTO; FUMAGALLI, MARCILIO JORGE; MODHA, SEJAL; MURCIA, PABLO RAMIRO; MORAES FIGUEIREDO, LUIZ TADEU. A novel polyomavirus in sigmodontine rodents from So Paulo State, Brazil. ARCHIVES OF VIROLOGY, v. 163, n. 10, p. 2913-2915, . (12/24150-9, 17/13981-0, 16/01414-1, 13/14929-1, 16/02568-2, 11/06810-9, 08/06411-4, 11/22663-6, 15/05778-5)
DE SOUZA, WILLIAM MARCIEL; FUMAGALLI, MARCILIO JORGE; DE ARAUJO, JANSEN; OMETTO, TATIANA; MODHA, SEJAL; THOMAZELLI, LUCIANO MATSUMIYA; DURIGON, EDISON LUIS; MURCIA, PABLO RAMIRO; MORAES FIGUEIREDO, LUIZ TADEU. Discovery of novel astrovirus and calicivirus identified in ruddy turnstones in Brazil. SCIENTIFIC REPORTS, v. 9, . (11/13821-7, 12/24150-9, 17/13981-0, 16/01414-1, 15/05778-5, 18/09383-3, 13/05485-2, 13/14929-1, 09/05994-9)
SILVA DE LIMA, SHIRLENE TELMOS; DE SOUZA, WILLIAM MARCIEL; CAVALCANTE, JOHN WASHINGTON; CANDIDO, DARLAN DA SILVA; FUMAGALLI, MARCILIO JORGE; CARRERA, JEAN-PAUL; SIMOES MELLO, LEDA MARIA; DE CARVALHO ARAUJO, FERNANDA MONTENEGRO; CAVALCANTE RAMALHO, IZABEL LETICIA; DE ALMEIDA BARRETO, FRANCISCA KALLINE; et al. Fatal Outcome of Chikungunya Virus Infection in Brazil. Clinical Infectious Diseases, v. 73, n. 7, p. E2436-E2443, . (18/00837-1, 17/13981-0, 18/09383-3, 19/24251-9)
AMORIM, MARIENE R.; SOUZA, WILLIAM M.; BARROS, JR., ANTONIO C. G.; TOLEDO-TEIXEIRA, DANIEL A.; BISPO-DOS-SANTOS, KARINA; SIMEONI, CAMILA L.; PARISE, PIERINA L.; VIEIRA, ALINE; FORATO, JULIA; CLARO, INGRA M.; et al. Respiratory Viral Shedding in Healthcare Workers Reinfected with SARS-CoV-2, Brazil, 2020. Emerging Infectious Diseases, v. 27, n. 6, p. 1737-1740, . (20/04558-0, 16/00194-8, 20/02448-2, 18/14389-0, 17/13981-0, 17/26908-0, 19/24251-9, 20/02159-0)
DE SOUZA, WILLIAM MARCIEL; FUMAGALLI, MARCILIO JORGE; MARTIN, MATHEUS CAVALHEIRO; DE ARAUJO, JANSEN; ORSI, MARIA ANGELA; SANFILIPPO, LUIZ FRANCISCO; MODHA, SEJAL; DURIGON, EDISON LUIZ; PROENCA-MODENA, JOSE LUIZ; ARNS, CLARICE WEIS; et al. Pingu virus: A new picornavirus in penguins from Antarctica. VIRUS EVOLUTION, v. 5, n. 2, . (17/13981-0, 12/24150-9, 16/01414-1, 13/14929-1, 14/20851-8, 15/05778-5)
LI, SABRINA L.; PEREIRA, RAFAEL H. M.; PRETE JR, CARLOS A.; ZAREBSKI, ALEXANDER E.; EMANUEL, LUCAS; ALVES, PEDRO J. H.; PEIXOTO, PEDRO S.; BRAGA, CARLOS K., V; DE SOUZA SANTOS, ANDREZA ARUSKA; DE SOUZA, WILLIAM M.; et al. Higher risk of death from COVID-19 in low-income and non-White populations of SAo Paulo, Brazil. BMJ GLOBAL HEALTH, v. 6, n. 4, p. 11-pg., . (19/21858-0, 19/24251-9, 18/14389-0, 17/13981-0)
IANI, FELIPE C. M.; GIOVANETTI, MARTA; FONSECA, VAGNER; SOUZA, WILLIAM M.; ADELINO, TALITA E. R.; XAVIER, JOILSON; JESUS, JAQUELINE G.; PEREIRA, MAIRA A.; SILVA, MARCOS V. F.; COSTA, ALANA V. B.; et al. Epidemiology and evolution of Zika virus in Minas Gerais, Southeast Brazil. INFECTION GENETICS AND EVOLUTION, v. 91, . (18/14389-0, 17/13981-0, 18/17176-8, 19/12000-1, 19/24251-9)
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.; et al. Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil. Science, v. 372, n. 6544, p. 815+, . (20/04558-0, 19/21568-1, 19/21301-5, 18/14389-0, 17/13981-0, 20/04272-9, 18/25468-9, 16/18445-7, 19/21858-0, 18/17176-8, 19/12000-1, 19/07544-2, 18/12579-7, 19/24251-9)
DE SOUZA, WILLIAM MARCIEL; DENNIS, TRISTAN; FUMAGALLI, MARCILIO JORGE; ARAUJO, JANSEN; SABINO-SANTOS, JR., GILBERTO; MOTTA MAIA, FELIPE GONCALVES; ACRANI, GUSTAVO OLSZANSKI; TORRES CARRASCO, ADRIANO DE OLIVEIRA; ROMEIRO, MARILIA FARIGNOLI; MODHA, SEJAL; et al. Novel Parvoviruses from Wild and Domestic Animals in Brazil Provide New Insights into Parvovirus Distribution and Diversity. Viruses-Basel, v. 10, n. 4, . (11/13821-7, 16/02568-2, 12/24150-9, 17/13981-0, 16/01414-1, 14/20851-8, 15/05778-5, 13/14929-1, 09/05994-9, 11/06810-9, 08/06411-4, 11/22663-6)
DENNIS, TRISTAN P. W.; DE SOUZA, WILLIAM MARCIEL; MARSILE-MEDUN, SOLEDAD; SINGER, JOSHUA B.; WILSON, SAM J.; GIFFORD, ROBERT J.. The evolution, distribution and diversity of endogenous circoviral elements in vertebrate genomes. VIRUS RESEARCH, v. 262, p. 9-pg., . (17/13981-0)

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