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de Souza CS, Caleiro GS, Claro IM, de Jesus JG, Coletti TM, da Silva CAM, Costa ÂA, Inenami M, Ribeiro AC, Felix AC, de Paula AV, Figueiredo WM, de Albuquerque Luna EJ, Sabino EC, Romano CM. Phylogenetics, Epidemiology and Temporal Patterns of Dengue Virus in Araraquara, São Paulo State. Viruses 2024; 16:274. [PMID: 38400049 PMCID: PMC10892747 DOI: 10.3390/v16020274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 01/16/2024] [Accepted: 01/18/2024] [Indexed: 02/25/2024] Open
Abstract
Dengue virus (DENV) is a prominent arbovirus with global spread, causing approximately 390 million infections each year. In Brazil, yearly epidemics follow a well-documented pattern of serotype replacement every three to four years on average. Araraquara, located in the state of São Paulo, has faced significant impacts from DENV epidemics since the emergence of DENV-1 in 2010. The municipality then transitioned from low to moderate endemicity in less than 10 years. Yet, there remains an insufficient understanding of virus circulation dynamics, particularly concerning DENV-1, in the region, as well as the genetic characteristics of the virus. To address this, we sequenced 37 complete or partial DENV-1 genomes sampled from 2015 to 2022 in Araraquara. Then, using also Brazilian and worldwide DENV-1 sequences we reconstructed the evolutionary history of DENV-1 in Araraquara and estimated the time to the most recent common ancestor (tMRCA) for serotype 1, for genotype V and its main lineages. Within the last ten years, there have been at least three introductions of genotype V in Araraquara, distributed in two main lineages (L Ia and L Ib, and L II). The tMRCA for the first sampled lineage (2015/2016 epidemics) was approximately 15 years ago (in 2008). Crucially, our analysis challenges existing assumptions regarding the emergence time of the DENV-1 genotypes, suggesting that genotype V might have diverged more recently than previously described. The presence of the two lineages of genotype V in the municipality might have contributed to the extended persistence of DENV-1 in the region.
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Affiliation(s)
- Caio Santos de Souza
- Laboratório de Virologia, Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (C.S.d.S.); (G.S.C.); (A.C.F.); (A.V.d.P.)
| | - Giovana Santos Caleiro
- Laboratório de Virologia, Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (C.S.d.S.); (G.S.C.); (A.C.F.); (A.V.d.P.)
- Laboratório de Virologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo 05403-000, SP, Brazil
| | - Ingra Morales Claro
- Laboratório de Parasitologia, Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (I.M.C.); (J.G.d.J.); (T.M.C.); (C.A.M.d.S.); (E.C.S.)
- MRC Center for Global Infectious Disease Analysis, Imperial College London, London SW7 2AZ, UK
| | - Jaqueline Goes de Jesus
- Laboratório de Parasitologia, Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (I.M.C.); (J.G.d.J.); (T.M.C.); (C.A.M.d.S.); (E.C.S.)
- Instituto Oswaldo Cruz, Salvador 21040-900, BA, Brazil
| | - Thaís Moura Coletti
- Laboratório de Parasitologia, Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (I.M.C.); (J.G.d.J.); (T.M.C.); (C.A.M.d.S.); (E.C.S.)
| | - Camila Alves Maia da Silva
- Laboratório de Parasitologia, Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (I.M.C.); (J.G.d.J.); (T.M.C.); (C.A.M.d.S.); (E.C.S.)
| | - Ângela Aparecida Costa
- Serviço Especial de Saúde de Araraquara-SESA, Faculdade de Saúde Pública da USP, São Paulo 01246-904, SP, Brazil; (Â.A.C.); (M.I.); (A.C.R.); (W.M.F.)
| | - Marta Inenami
- Serviço Especial de Saúde de Araraquara-SESA, Faculdade de Saúde Pública da USP, São Paulo 01246-904, SP, Brazil; (Â.A.C.); (M.I.); (A.C.R.); (W.M.F.)
| | - Andreia C. Ribeiro
- Serviço Especial de Saúde de Araraquara-SESA, Faculdade de Saúde Pública da USP, São Paulo 01246-904, SP, Brazil; (Â.A.C.); (M.I.); (A.C.R.); (W.M.F.)
| | - Alvina Clara Felix
- Laboratório de Virologia, Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (C.S.d.S.); (G.S.C.); (A.C.F.); (A.V.d.P.)
| | - Anderson Vicente de Paula
- Laboratório de Virologia, Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (C.S.d.S.); (G.S.C.); (A.C.F.); (A.V.d.P.)
| | - Walter M. Figueiredo
- Serviço Especial de Saúde de Araraquara-SESA, Faculdade de Saúde Pública da USP, São Paulo 01246-904, SP, Brazil; (Â.A.C.); (M.I.); (A.C.R.); (W.M.F.)
| | - Expedito José de Albuquerque Luna
- Departamento de Medicina Preventiva/Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, SP, Brazil;
| | - Ester C. Sabino
- Laboratório de Parasitologia, Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (I.M.C.); (J.G.d.J.); (T.M.C.); (C.A.M.d.S.); (E.C.S.)
| | - Camila M. Romano
- Laboratório de Virologia, Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (C.S.d.S.); (G.S.C.); (A.C.F.); (A.V.d.P.)
- Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (HCFMUSP), São Paulo 05403-010, SP, Brazil
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2
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de Sousa FTG, Warnes CM, Manuli ER, Ng A, D’Elia Zanella LGFAB, Ho YL, Bhat S, Romano CM, Beatty PR, Biering SB, Kallas EG, Sabino EC, Harris E. Yellow fever disease severity and endothelial dysfunction are associated with elevated serum levels of viral NS1 protein and syndecan-1. medRxiv 2023:2023.06.29.23292053. [PMID: 37425955 PMCID: PMC10327263 DOI: 10.1101/2023.06.29.23292053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Yellow fever virus (YFV) infections can cause severe disease manifestations, including hepatic injury, endothelial damage, coagulopathy, hemorrhage, systemic organ failure, and shock, and are associated with high mortality in humans. While nonstructural protein 1 (NS1) of the related dengue virus is implicated in contributing to vascular leak, little is known about the role of YFV NS1 in severe YF and mechanisms of vascular dysfunction in YFV infections. Here, using serum samples from qRT-PCR-confirmed YF patients with severe (n=39) or non-severe (n=18) disease in a well-defined hospital cohort in Brazil, plus samples from healthy uninfected controls (n=11), we investigated factors associated with disease severity. We developed a quantitative YFV NS1 capture ELISA and found significantly increased levels of NS1, as well as syndecan-1, a marker of vascular leak, in serum from severe YF as compared to non-severe YF or control groups. We also showed that hyperpermeability of endothelial cell monolayers treated with serum from severe YF patients was significantly higher compared to non-severe YF and control groups as measured by transendothelial electrical resistance (TEER). Further, we demonstrated that YFV NS1 induces shedding of syndecan-1 from the surface of human endothelial cells. Notably, YFV NS1 serum levels significantly correlated with syndecan-1 serum levels and TEER values. Syndecan-1 levels also significantly correlated with clinical laboratory parameters of disease severity, viral load, hospitalization, and death. In summary, this study points to a role for secreted NS1 in YF disease severity and provides evidence for endothelial dysfunction as a mechanism of YF pathogenesis in humans.
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Affiliation(s)
- Francielle T. G. de Sousa
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
- Departamento de Doenças Infecciosas e Parasitárias, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, 05403000, Brazil
| | - Colin M. Warnes
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Erika R. Manuli
- Departamento de Doenças Infecciosas e Parasitárias, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, 05403000, Brazil
- Laboratório de Investigação Médica, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (HCFMUSP), São Paulo-SP, 05403000, Brazil
| | - Arash Ng
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Luiz G. F. A. B. D’Elia Zanella
- Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (HCFMUSP), São Paulo-SP, 05403000, Brazil
- Instituto de Infectologia Emílio Ribas, São Paulo-SP, 01246-900, Brazil
| | - Yeh-Li Ho
- Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (HCFMUSP), São Paulo-SP, 05403000, Brazil
| | - Samhita Bhat
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Camila M. Romano
- Departamento de Doenças Infecciosas e Parasitárias, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, 05403000, Brazil
- Laboratório de Investigação Médica, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (HCFMUSP), São Paulo-SP, 05403000, Brazil
| | - P. Robert Beatty
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Scott B. Biering
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Esper G. Kallas
- Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (HCFMUSP), São Paulo-SP, 05403000, Brazil
| | - Ester C. Sabino
- Departamento de Doenças Infecciosas e Parasitárias, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, 05403000, Brazil
- Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (HCFMUSP), São Paulo-SP, 05403000, Brazil
| | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
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3
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Mendes-Correa MC, Salomão MC, Ghilardi F, Tozetto-Mendoza TR, Santos Villas-Boas L, de Paula AV, Paiao HGO, da Costa AC, Leal FE, Ferraz ADBC, Sales FCS, Claro IM, Ferreira NE, Pereira GM, da Silva AR, Freire W, Espinoza EPS, Manuli ER, Romano CM, de Jesus JG, Sabino EC, Witkin SS. SARS-CoV-2 Detection and Culture in Different Biological Specimens from Immunocompetent and Immunosuppressed COVID-19 Patients Infected with Two Different Viral Strains. Viruses 2023; 15:1270. [PMID: 37376568 DOI: 10.3390/v15061270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 04/26/2023] [Accepted: 04/27/2023] [Indexed: 06/29/2023] Open
Abstract
Introduction-The dynamics of SARS-CoV-2 shedding and replication in humans remain incompletely understood. Methods-We analyzed SARS-CoV-2 shedding from multiple sites in individuals with an acute COVID-19 infection by weekly sampling for five weeks in 98 immunocompetent and 25 immunosuppressed individuals. Samples and culture supernatants were tested via RT-PCR for SARS-CoV-2 to determine viral clearance rates and in vitro replication. Results-A total of 2447 clinical specimens were evaluated, including 557 nasopharyngeal swabs, 527 saliva samples, 464 urine specimens, 437 anal swabs and 462 blood samples. The SARS-CoV-2 genome sequences at each site were classified as belonging to the B.1.128 (ancestral strain) or Gamma lineage. SARS-CoV-2 detection was highest in nasopharyngeal swabs regardless of the virus strain involved or the immune status of infected individuals. The duration of viral shedding varied between clinical specimens and individual patients. Prolonged shedding of potentially infectious virus varied from 10 days up to 191 days, and primarily occurred in immunosuppressed individuals. Virus was isolated in culture from 18 nasal swab or saliva samples collected 10 or more days after onset of disease. Conclusions-Our findings indicate that persistent SARS-CoV-2 shedding may occur in both competent or immunosuppressed individuals, at multiple clinical sites and in a minority of subjects is capable of in vitro replication.
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Affiliation(s)
- Maria Cássia Mendes-Correa
- Departamento de Molestias Infecciosas e Parasitarias, Aculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas Carvalho de Aguiar, n. 470, São Paulo 05403-000, Brazil
- Hospital das Clínicas, Faculdade de Medicina, Universidade de Sao Paulo, São Paulo 05403-010, Brazil
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Matias Chiarastelli Salomão
- Departamento de Molestias Infecciosas e Parasitarias, Aculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas Carvalho de Aguiar, n. 470, São Paulo 05403-000, Brazil
- Hospital das Clínicas, Faculdade de Medicina, Universidade de Sao Paulo, São Paulo 05403-010, Brazil
- Rua Peixoto Gomide, 645, Sao Paulo 01409-002, Brazil
| | - Fábio Ghilardi
- Departamento de Molestias Infecciosas e Parasitarias, Aculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas Carvalho de Aguiar, n. 470, São Paulo 05403-000, Brazil
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Tania Regina Tozetto-Mendoza
- Departamento de Molestias Infecciosas e Parasitarias, Aculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas Carvalho de Aguiar, n. 470, São Paulo 05403-000, Brazil
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Lucy Santos Villas-Boas
- Departamento de Molestias Infecciosas e Parasitarias, Aculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas Carvalho de Aguiar, n. 470, São Paulo 05403-000, Brazil
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Anderson Vicente de Paula
- Departamento de Molestias Infecciosas e Parasitarias, Aculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas Carvalho de Aguiar, n. 470, São Paulo 05403-000, Brazil
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Heuder Gustavo Oliveira Paiao
- Departamento de Molestias Infecciosas e Parasitarias, Aculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas Carvalho de Aguiar, n. 470, São Paulo 05403-000, Brazil
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Antonio Charlys da Costa
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Fábio E Leal
- Faculdade de Medicina da, Universidade Municipal de Sao Caetano do Sul, São Paulo 09521-160, Brazil
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro 20230-130, Brazil
| | | | - Flavia C S Sales
- Departamento de Molestias Infecciosas e Parasitarias, Aculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas Carvalho de Aguiar, n. 470, São Paulo 05403-000, Brazil
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Ingra M Claro
- Departamento de Molestias Infecciosas e Parasitarias, Aculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas Carvalho de Aguiar, n. 470, São Paulo 05403-000, Brazil
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Noely E Ferreira
- Departamento de Molestias Infecciosas e Parasitarias, Aculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas Carvalho de Aguiar, n. 470, São Paulo 05403-000, Brazil
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Geovana M Pereira
- Departamento de Molestias Infecciosas e Parasitarias, Aculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas Carvalho de Aguiar, n. 470, São Paulo 05403-000, Brazil
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Almir Ribeiro da Silva
- Departamento de Molestias Infecciosas e Parasitarias, Aculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas Carvalho de Aguiar, n. 470, São Paulo 05403-000, Brazil
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Wilton Freire
- Departamento de Molestias Infecciosas e Parasitarias, Aculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas Carvalho de Aguiar, n. 470, São Paulo 05403-000, Brazil
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Evelyn Patricia Sánchez Espinoza
- Departamento de Molestias Infecciosas e Parasitarias, Aculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas Carvalho de Aguiar, n. 470, São Paulo 05403-000, Brazil
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Erika R Manuli
- Departamento de Molestias Infecciosas e Parasitarias, Aculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas Carvalho de Aguiar, n. 470, São Paulo 05403-000, Brazil
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
- Faculdade de Medicina da, Universidade Municipal de Sao Caetano do Sul, São Paulo 09521-160, Brazil
| | - Camila M Romano
- Hospital das Clínicas, Faculdade de Medicina, Universidade de Sao Paulo, São Paulo 05403-010, Brazil
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Jaqueline G de Jesus
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Ester C Sabino
- Departamento de Molestias Infecciosas e Parasitarias, Aculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas Carvalho de Aguiar, n. 470, São Paulo 05403-000, Brazil
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
- Faculdade de Medicina da, Universidade Municipal de Sao Caetano do Sul, São Paulo 09521-160, Brazil
| | - Steven S Witkin
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY 10065, USA
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4
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Nastri AC, Duarte-Neto AN, Casadio LVB, Souza WMD, Claro IM, Manuli ER, Selegatto G, Salomão MC, Fialkovitz G, Taborda M, Almeida BLD, Magri MC, Guedes AR, Perdigão Neto LV, Sataki FM, Guimarães T, Mendes-Correa MC, Tozetto-Mendoza TR, Fumagalli MJ, Ho YL, Maia da Silva CA, Coletti TM, Goes de Jesus J, Romano CM, Hill SC, Pybus O, Rebello Pinho JR, Ledesma FL, Casal YR, Kanamura CT, Tadeu de Araújo LJ, Ferreira CSDS, Guerra JM, Figueiredo LTM, Dolhnikoff M, Faria NR, Sabino EC, Alves VAF, Levin AS. Understanding Sabiá virus infections (Brazilian mammarenavirus). Travel Med Infect Dis 2022; 48:102351. [PMID: 35537676 DOI: 10.1016/j.tmaid.2022.102351] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/27/2022] [Accepted: 04/28/2022] [Indexed: 02/09/2023]
Abstract
BACKGROUND Only two naturally occurring human Sabiá virus (SABV) infections have been reported, and those occurred over 20 years ago. METHODS We diagnosed two new cases of SABV infection using metagenomics in patients thought to have severe yellow fever and described new features of histopathological findings. RESULTS We characterized clinical manifestations, histopathology and analyzed possible nosocomial transmission. Patients presented with hepatitis, bleeding, neurological alterations and died. We traced twenty-nine hospital contacts and evaluated them clinically and by RT-PCR and neutralizing antibodies. Autopsies uncovered unique features on electron microscopy, such as hepatocyte "pinewood knot" lesions. Although previous reports with similar New-World arenavirus had nosocomial transmission, our data did not find any case in contact tracing. CONCLUSIONS Although an apparent by rare, Brazilian mammarenavirus infection is an etiology for acute hemorrhagic fever syndrome. The two fatal cases had peculiar histopathological findings not previously described. The virological diagnosis was possible only by contemporary techniques such as metagenomic assays. We found no subsequent infections when we used serological and molecular tests to evaluate close contacts.
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Affiliation(s)
- Ana Catharina Nastri
- Division of Infectious Diseases, Hospital das Clínicas, Faculdade de Medicina, Universidade de Sao Paulo, Brazil.
| | - Amaro Nunes Duarte-Neto
- Department of Pathology, Faculdade de Medicina, Universidade de Sao Paulo, Brazil; Núcleo de Anatomia Patológica, Instituto Adolfo Lutz, Sao Paulo, Brazil.
| | - Luciana Vilas Boas Casadio
- Division of Infectious Diseases, Hospital das Clínicas, Faculdade de Medicina, Universidade de Sao Paulo, Brazil.
| | - William Marciel de Souza
- World Reference Center for Emerging Viruses and Arboviruses and Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston, Galveston, TX, USA.
| | - Ingra M Claro
- Department of Infectious Diseases, Faculdade de Medicina, Universidade de Sao Paulo, Brazil; Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de Sao Paulo, Brazil.
| | - Erika R Manuli
- Department of Infectious Diseases, Faculdade de Medicina, Universidade de Sao Paulo, Brazil; Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de Sao Paulo, Brazil.
| | - Gloria Selegatto
- Division of Infectious Diseases, Hospital das Clínicas, Faculdade de Medicina, Universidade de Sao Paulo, Brazil.
| | - Matias C Salomão
- Infection Control Department, Hospital das Clínicas, Faculdade de Medicina, Universidade de Sao Paulo, Brazil.
| | - Gabriel Fialkovitz
- Division of Infectious Diseases, Hospital das Clínicas, Faculdade de Medicina, Universidade de Sao Paulo, Brazil.
| | - Mariane Taborda
- Division of Infectious Diseases, Hospital das Clínicas, Faculdade de Medicina, Universidade de Sao Paulo, Brazil.
| | - Bianca Leal de Almeida
- Division of Infectious Diseases, Hospital das Clínicas, Faculdade de Medicina, Universidade de Sao Paulo, Brazil; Infection Control Department, Hospital das Clínicas, Faculdade de Medicina, Universidade de Sao Paulo, Brazil.
| | - Marcello C Magri
- Division of Infectious Diseases, Hospital das Clínicas, Faculdade de Medicina, Universidade de Sao Paulo, Brazil.
| | - Ana Rúbia Guedes
- Infection Control Department, Hospital das Clínicas, Faculdade de Medicina, Universidade de Sao Paulo, Brazil.
| | - Lauro Vieira Perdigão Neto
- Infection Control Department, Hospital das Clínicas, Faculdade de Medicina, Universidade de Sao Paulo, Brazil.
| | - Fatima Mitie Sataki
- Division of Infectious Diseases, Hospital das Clínicas, Faculdade de Medicina, Universidade de Sao Paulo, Brazil.
| | - Thais Guimarães
- Infection Control Department, Hospital das Clínicas, Faculdade de Medicina, Universidade de Sao Paulo, Brazil.
| | - Maria Cassia Mendes-Correa
- Department of Infectious Diseases, Faculdade de Medicina, Universidade de Sao Paulo, Brazil; Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de Sao Paulo, Brazil.
| | | | - Marcilio Jorge Fumagalli
- Centro de Pesquisa em Virologia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil.
| | - Yeh-Li Ho
- Division of Infectious Diseases, Hospital das Clínicas, Faculdade de Medicina, Universidade de Sao Paulo, Brazil.
| | - Camila Alves Maia da Silva
- Department of Infectious Diseases, Faculdade de Medicina, Universidade de Sao Paulo, Brazil; Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de Sao Paulo, Brazil.
| | - Thaís M Coletti
- Department of Infectious Diseases, Faculdade de Medicina, Universidade de Sao Paulo, Brazil; Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de Sao Paulo, Brazil.
| | - Jaqueline Goes de Jesus
- Department of Infectious Diseases, Faculdade de Medicina, Universidade de Sao Paulo, Brazil; Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de Sao Paulo, Brazil.
| | - Camila M Romano
- Department of Infectious Diseases, Faculdade de Medicina, Universidade de Sao Paulo, Brazil; Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de Sao Paulo, Brazil.
| | - Sarah C Hill
- Department of Zoology, University of Oxford, United Kingdom Department of Pathobiology and Population Sciences, The Royal Veterinary College, United Kingdom; Department of Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, United Kingdom.
| | - Oliver Pybus
- Department of Zoology, University of Oxford, United Kingdom.
| | - João Renato Rebello Pinho
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de Sao Paulo, Brazil; Hospital Israelita Albert Einstein, São Paulo, SP, Brazil.
| | | | - Yuri R Casal
- Department of Pathology, Faculdade de Medicina, Universidade de Sao Paulo, Brazil.
| | | | | | | | | | - Luiz Tadeu Moraes Figueiredo
- Centro de Pesquisa em Virologia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil.
| | - Marisa Dolhnikoff
- Department of Pathology, Faculdade de Medicina, Universidade de Sao Paulo, Brazil.
| | - Nuno R Faria
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de Sao Paulo, Brazil; Department of Zoology, University of Oxford, United Kingdom; MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, United Kingdom.
| | - Ester C Sabino
- Department of Infectious Diseases, Faculdade de Medicina, Universidade de Sao Paulo, Brazil; Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de Sao Paulo, Brazil.
| | | | - Anna S Levin
- Division of Infectious Diseases, Hospital das Clínicas, Faculdade de Medicina, Universidade de Sao Paulo, Brazil; Department of Infectious Diseases, Faculdade de Medicina, Universidade de Sao Paulo, Brazil; Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de Sao Paulo, Brazil; Infection Control Department, Hospital das Clínicas, Faculdade de Medicina, Universidade de Sao Paulo, Brazil.
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5
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Sousa FTGD, Biering SB, Patel TS, Blanc SF, Camelini CM, Venzke D, Nunes RJ, Romano CM, Beatty PR, Sabino EC, Harris E. Sulfated β-glucan from Agaricus subrufescens inhibits flavivirus infection and nonstructural protein 1-mediated pathogenesis. Antiviral Res 2022; 203:105330. [PMID: 35533778 PMCID: PMC10416543 DOI: 10.1016/j.antiviral.2022.105330] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 04/28/2022] [Accepted: 05/03/2022] [Indexed: 11/23/2022]
Abstract
Despite substantial morbidity and mortality, no therapeutic agents exist for treatment of dengue or Zika, and the currently available dengue vaccine is only recommended for dengue virus (DENV)-immune individuals. Thus, development of therapeutic and/or preventive drugs is urgently needed. DENV and Zika virus (ZIKV) nonstructural protein 1 (NS1) can directly trigger endothelial barrier dysfunction and induce inflammatory responses, contributing to vascular leak in vivo. Here we evaluated the efficacy of the (1-6,1-3)-β-D-glucan isolated from Agaricus subrufescens fruiting bodies (FR) and its sulfated derivative (FR-S) against DENV-2 and ZIKV infection and NS1-mediated pathogenesis. FR-S, but not FR, significantly inhibited DENV-2 and ZIKV replication in human monocytic cells (EC50 = 36.5 and 188.7 μg/mL, respectively) when added simultaneously with viral infection. No inhibitory effect was observed when FR or FR-S were added post-infection, suggesting inhibition of viral entry as a mechanism of action. In an in vitro model of endothelial permeability using human pulmonary microvascular endothelial cells (HPMECs), FR and FR-S (0.12 μg/mL) inhibited DENV-2 NS1- and ZIKV NS1-induced hyperpermeability by 50% and 100%, respectively, as measured by Trans-Endothelial Electrical Resistance. Treatment with 0.25 μg/mL of FR and FR-S inhibited DENV-2 NS1 binding to HPMECs. Further, FR-S significantly reduced intradermal hyperpermeability induced by DENV-2 NS1 in C57BL/6 mice and protected against DENV-induced morbidity and mortality in a murine model of dengue vascular leak syndrome. Thus, we demonstrate efficacy of FR-S against DENV and ZIKV infection and NS1-induced endothelial permeability in vitro and in vivo. These findings encourage further exploration of FR-S and other glycan candidates for flavivirus treatment alone or in combination with compounds with different mechanisms of action.
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Affiliation(s)
- Francielle Tramontini Gomes de Sousa
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, 94720-3370, USA; Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, 05403000, Brazil
| | - Scott B Biering
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, 94720-3370, USA
| | - Trishna S Patel
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, 94720-3370, USA
| | - Sophie F Blanc
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, 94720-3370, USA
| | - Carla M Camelini
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de Santa Catarina, Florianópolis, SC, 88.040-900, Brazil
| | - Dalila Venzke
- Departamento de Química, Universidade Federal de Santa Catarina, Florianópolis, SC, 88.040-900, Brazil
| | - Ricardo J Nunes
- Departamento de Química, Universidade Federal de Santa Catarina, Florianópolis, SC, 88.040-900, Brazil
| | - Camila M Romano
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, 05403000, Brazil; Laboratório de Virologia (LIMHC 52), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (HCFMUSP), São Paulo, SP, Brazil
| | - P Robert Beatty
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, 94720-3370, USA
| | - Ester C Sabino
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, 05403000, Brazil
| | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, 94720-3370, USA.
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6
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Mills MG, Bruce E, Huang ML, Crothers JW, Hyrien O, Oura CAL, Blake L, Brown Jordan A, Hester S, Wehmas L, Mari B, Barby P, Lacoux C, Fassy J, Vial P, Vial C, Martinez JRW, Oladipo OO, Inuwa B, Shittu I, Meseko CA, Chammas R, Santos CF, Dionísio TJ, Garbieri TF, Parisi VA, Mendes-Correa MC, de Paula AV, Romano CM, Góes LGB, Minoprio P, Campos AC, Cunha MP, Vilela APP, Nyirenda T, Mkakosya RS, Muula AS, Dumm RE, Harris RM, Mitchell CA, Pettit S, Botten J, Jerome KR. An international, interlaboratory ring trial confirms the feasibility of an extraction-less "direct" RT-qPCR method for reliable detection of SARS-CoV-2 RNA in clinical samples. PLoS One 2022; 17:e0261853. [PMID: 35025926 PMCID: PMC8758094 DOI: 10.1371/journal.pone.0261853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 12/11/2021] [Indexed: 11/29/2022] Open
Abstract
Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) is used worldwide to test and trace the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). "Extraction-less" or "direct" real time-reverse transcription polymerase chain reaction (RT-PCR) is a transparent and accessible qualitative method for SARS-CoV-2 detection from nasopharyngeal or oral pharyngeal samples with the potential to generate actionable data more quickly, at a lower cost, and with fewer experimental resources than full RT-qPCR. This study engaged 10 global testing sites, including laboratories currently experiencing testing limitations due to reagent or equipment shortages, in an international interlaboratory ring trial. Participating laboratories were provided a common protocol, common reagents, aliquots of identical pooled clinical samples, and purified nucleic acids and used their existing in-house equipment. We observed 100% concordance across laboratories in the correct identification of all positive and negative samples, with highly similar cycle threshold values. The test also performed well when applied to locally collected patient nasopharyngeal samples, provided the viral transport media did not contain charcoal or guanidine, both of which appeared to potently inhibit the RT-PCR reaction. Our results suggest that direct RT-PCR assay methods can be clearly translated across sites utilizing readily available equipment and expertise and are thus a feasible option for more efficient COVID-19 coronavirus disease testing as demanded by the continuing pandemic.
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Affiliation(s)
- Margaret G. Mills
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Emily Bruce
- Division of Immunobiology, Department of Medicine, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
| | - Meei-Li Huang
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Jessica W. Crothers
- Division of Immunobiology, Department of Medicine, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
| | - Ollivier Hyrien
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Christopher A. L. Oura
- School of Veterinary Medicine, University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Lemar Blake
- School of Veterinary Medicine, University of the West Indies, St. Augustine, Trinidad and Tobago
| | | | - Susan Hester
- Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, United States of America
| | - Leah Wehmas
- Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, United States of America
| | - Bernard Mari
- Université Côte d’Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, FHU-OncoAge, Valbonne, France
| | - Pascal Barby
- Université Côte d’Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, FHU-OncoAge, Valbonne, France
| | - Caroline Lacoux
- Université Côte d’Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, FHU-OncoAge, Valbonne, France
| | - Julien Fassy
- Université Côte d’Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, FHU-OncoAge, Valbonne, France
| | - Pablo Vial
- Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Programa Hantavirus, Instituto de Ciencias e Innovación en Medicina, Santiago, Chile
| | - Cecilia Vial
- Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Programa Hantavirus, Instituto de Ciencias e Innovación en Medicina, Santiago, Chile
| | - Jose R. W. Martinez
- Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Programa Hantavirus, Instituto de Ciencias e Innovación en Medicina, Santiago, Chile
| | | | - Bitrus Inuwa
- Infectious and Transboundary Animal Diseases, National Veterinary Research Institute, Vom, Nigeria
| | - Ismaila Shittu
- Infectious and Transboundary Animal Diseases, National Veterinary Research Institute, Vom, Nigeria
| | - Clement A. Meseko
- Infectious and Transboundary Animal Diseases, National Veterinary Research Institute, Vom, Nigeria
| | - Roger Chammas
- Faculdade de Medicina da Universidade de São Paulo, Departamento de Radiologia e Oncologia, Centro de Investigação Translacional em Oncologia, Instituto do Cancer do Estado de São Paulo, São Paulo, Brazil
| | - Carlos Ferreira Santos
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, São Paulo, Brazil
| | - Thiago José Dionísio
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, São Paulo, Brazil
| | - Thais Francini Garbieri
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, São Paulo, Brazil
| | - Viviane Aparecida Parisi
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, São Paulo, Brazil
| | | | - Anderson V. de Paula
- Department of Infectious Diseases, Institute of Tropical Medicine of São Paulo, São Paulo, Brazil
| | - Camila M. Romano
- Department of Infectious Diseases, Institute of Tropical Medicine of São Paulo, São Paulo, Brazil
| | - Luiz Gustavo Bentim Góes
- Scientific Platform Pasteur-USP, Universidade de São Paulo, São Paulo, Brazil
- Department of Microbiology, Biomedical Sciences Institute, University of São Paulo, São Paulo, Brazil
| | - Paola Minoprio
- Scientific Platform Pasteur-USP, Universidade de São Paulo, São Paulo, Brazil
| | - Angelica C. Campos
- Scientific Platform Pasteur-USP, Universidade de São Paulo, São Paulo, Brazil
| | - Marielton P. Cunha
- Scientific Platform Pasteur-USP, Universidade de São Paulo, São Paulo, Brazil
| | - Ana Paula P. Vilela
- Scientific Platform Pasteur-USP, Universidade de São Paulo, São Paulo, Brazil
| | - Tonney Nyirenda
- Department of Pathology, College of Medicine, University of Malawi, Blantyre, Malawi
| | | | - Adamson S. Muula
- Department of Public Health, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Rebekah E. Dumm
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Rebecca M. Harris
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Constance A. Mitchell
- Health and Environmental Sciences Institute, Washington, DC, United States of America
| | - Syril Pettit
- Health and Environmental Sciences Institute, Washington, DC, United States of America
| | - Jason Botten
- Division of Immunobiology, Department of Medicine, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
| | - Keith R. Jerome
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
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7
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Nali LH, Olival GS, Montenegro H, da Silva IT, Dias-Neto E, Naya H, Spangenberg L, Penalva-de-Oliveira AC, Romano CM. Human endogenous retrovirus and multiple sclerosis: A review and transcriptome findings. Mult Scler Relat Disord 2021; 57:103383. [PMID: 34922254 DOI: 10.1016/j.msard.2021.103383] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 10/15/2021] [Accepted: 11/05/2021] [Indexed: 12/14/2022]
Abstract
Multiple Sclerosis is an autoimmune disease with an unknown etiology. Both genetic and environmental factors are believed to trigger MS autoimmunity. Among the environmental factors, infectious agents have been extensively investigated, and the Human Endogenous Retroviruses (HERVs), especially HERV-W, are believed to be associated with MS pathogenesis. HERVs are derived from ancestral infections and comprise around 8% of the human genome. Although most HERVs are silenced, retroviral genes may be expressed with virion formation. There is extensive evidence of the relationship between HERV-W and MS, including higher levels of HERV-W expression in MS patients, HERV-W protein detection in MS plaques, and the HERV-W env protein inducing an inflammatory response in in vitro and in vivo models. Here we discuss possible links of HERVs and the pathogenesis of MS and present new data regarding the diversity of HERVs expression in samples derived from MS patients.
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Affiliation(s)
- Luiz H Nali
- Laboratório de Virologia, Instituto de Medicina Tropical de São Paulo, LIM-52 (LIMHC) Universidade de São Paulo, Rua Dr. Enéas de Carvalho Aguiar, 470, São Paulo 05403-000, Brazil; Post-graduation Program in Health Sciences, Santo Amaro University, Rua Prof. Enéas de Siqueira Neto, 340, São Paulo 04829-300, Brazil
| | - Guilherme S Olival
- Departamento de Neurologia Santa Casa de Misericórdia de São Paulo, R. Dr. Cesário Mota Júnior, 112, São Paulo 01221-020 Brazil
| | | | - Israel T da Silva
- Laboratory of Medical Genomics, A.C. Camargo Cancer Center, São Paulo 01525-001, Brazil
| | - Emmanuel Dias-Neto
- Laboratory of Medical Genomics, A.C. Camargo Cancer Center, São Paulo 01525-001, Brazil; Laboratory of Neurosciences (LIM-27), Institute of Psychiatry, São Paulo Medical School, University of São Paulo, São Paulo, Brazil
| | - Hugo Naya
- Unidad de Bioinformática Institut Pasteur de Montevideo, Mataojo 2020, CP11400 Montevideo, Uruguay; Departamento de Producción Animal y Pasturas, Facultad de Agronomía, Universidad de la República, Av. Gral. Eugenio Garzón 780, CP12900 Montevideo, Uruguay
| | - Lucia Spangenberg
- Unidad de Bioinformática Institut Pasteur de Montevideo, Mataojo 2020, CP11400 Montevideo, Uruguay
| | - Augusto C Penalva-de-Oliveira
- Departamento de Neurologia Santa Casa de Misericórdia de São Paulo, R. Dr. Cesário Mota Júnior, 112, São Paulo 01221-020 Brazil; Departamento de Neurologia, Instituto de Infectologia Emilio Ribas, Avenida Doutor Arnaldo, 165, São Paulo 01246-900, Brazil
| | - Camila M Romano
- Laboratório de Virologia, Instituto de Medicina Tropical de São Paulo, LIM-52 (LIMHC) Universidade de São Paulo, Rua Dr. Enéas de Carvalho Aguiar, 470, São Paulo 05403-000, Brazil; Hospital das Clinicas HCFMUSP (LIM52), Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil.
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8
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Mendes Correa MC, Leal FE, Villas Boas LS, Witkin SS, de Paula A, Tozetto Mendonza TR, Ferreira NE, Curty G, de Carvalho PS, Buss LF, Costa SF, da Cunha Carvalho FM, Kawakami J, Taniwaki NN, Paiao H, da Silva Bizário JC, de Jesus JG, Sabino EC, Romano CM, Grepan RMZ, Sesso A. Prolonged presence of replication-competent SARS-CoV-2 in mildly symptomatic individuals: A report of two cases. J Med Virol 2021; 93:5603-5607. [PMID: 33851749 PMCID: PMC8250959 DOI: 10.1002/jmv.27021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 04/07/2021] [Accepted: 04/12/2021] [Indexed: 12/17/2022]
Abstract
It has been estimated that individuals with COVID-19 can shed replication-competent virus up to a maximum of 20 days after initiation of symptoms. The majority of studies that addressed this situation involved hospitalized individuals and those with severe disease. Studies to address the possible presence of SARS-CoV-2 during the different phases of COVID-19 disease in mildly infected individuals, and utilization of viral culture techniques to identify replication-competent viruses, have been limited. This report describes two patients with mild forms of the disease who shed replication-competent virus for 24 and 37 days, respectively, after symptom onset.
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Affiliation(s)
- Maria C. Mendes Correa
- Laboratorio de Investigacao Medica em Virologia (LIM52), Instituto de Medicina Tropical de Sao Paulo, Faculdade de MedicinaUniversidade de Sao PauloSão PauloBrazil
- Departamento de Molestias Infecciosas e Parasitarias da Faculdade de MedicinaUniversidade de São PauloSão PauloSão PauloBrazil
| | - Fabio E. Leal
- Faculdade de MedicinaUniversidade Municipal de Sao Caetano do SulSão Caetano do SulSão PauloBrazil
- Instituto Nacional do Cancer Rio de JaneiroRio de JaneiroRio de JaneiroBrazil
| | - Lucy S. Villas Boas
- Laboratorio de Investigacao Medica em Virologia (LIM52), Instituto de Medicina Tropical de Sao Paulo, Faculdade de MedicinaUniversidade de Sao PauloSão PauloBrazil
| | - Steven S. Witkin
- Laboratorio de Investigacao Medica em Virologia (LIM52), Instituto de Medicina Tropical de Sao Paulo, Faculdade de MedicinaUniversidade de Sao PauloSão PauloBrazil
- Weill Cornell MedicineNew YorkNew YorkUSA
| | - Anderson de Paula
- Laboratorio de Investigacao Medica em Virologia (LIM52), Instituto de Medicina Tropical de Sao Paulo, Faculdade de MedicinaUniversidade de Sao PauloSão PauloBrazil
| | - Tania R. Tozetto Mendonza
- Laboratorio de Investigacao Medica em Virologia (LIM52), Instituto de Medicina Tropical de Sao Paulo, Faculdade de MedicinaUniversidade de Sao PauloSão PauloBrazil
| | - Noely E. Ferreira
- Laboratorio de Investigacao Medica em Virologia (LIM52), Instituto de Medicina Tropical de Sao Paulo, Faculdade de MedicinaUniversidade de Sao PauloSão PauloBrazil
| | - Gislaine Curty
- Instituto Nacional do Cancer Rio de JaneiroRio de JaneiroRio de JaneiroBrazil
| | | | - Lewis F. Buss
- Departamento de Molestias Infecciosas e Parasitarias da Faculdade de MedicinaUniversidade de São PauloSão PauloSão PauloBrazil
| | - Silvia F. Costa
- Departamento de Molestias Infecciosas e Parasitarias da Faculdade de MedicinaUniversidade de São PauloSão PauloSão PauloBrazil
- Instituto de Medicina Tropical de Sao Paulo, Faculdade de MedicinaUniversidade de Sao PauloSão PauloSão PauloBrazil
| | - Flavia M. da Cunha Carvalho
- Instituto de Medicina Tropical de Sao Paulo, Faculdade de MedicinaUniversidade de Sao PauloSão PauloSão PauloBrazil
| | - Joyce Kawakami
- Instituto do Coracao do Hospital das Clinicas da Faculdade de MedicinaUniversidade de Sao PauloSão PauloSão PauloBrazil
| | | | - Heuder Paiao
- Laboratorio de Investigacao Medica em Virologia (LIM52), Instituto de Medicina Tropical de Sao Paulo, Faculdade de MedicinaUniversidade de Sao PauloSão PauloBrazil
| | - Joao C. da Silva Bizário
- Faculdade de MedicinaUniversidade Municipal de Sao Caetano do SulSão Caetano do SulSão PauloBrazil
| | - Jaqueline G. de Jesus
- Departamento de Molestias Infecciosas e Parasitarias da Faculdade de MedicinaUniversidade de São PauloSão PauloSão PauloBrazil
- Instituto de Medicina Tropical de Sao Paulo, Faculdade de MedicinaUniversidade de Sao PauloSão PauloSão PauloBrazil
| | - Ester C. Sabino
- Departamento de Molestias Infecciosas e Parasitarias da Faculdade de MedicinaUniversidade de São PauloSão PauloSão PauloBrazil
- Instituto de Medicina Tropical de Sao Paulo, Faculdade de MedicinaUniversidade de Sao PauloSão PauloSão PauloBrazil
| | - Camila M. Romano
- Laboratorio de Investigacao Medica em Virologia (LIM52), Instituto de Medicina Tropical de Sao Paulo, Faculdade de MedicinaUniversidade de Sao PauloSão PauloBrazil
| | - Regina M. Z. Grepan
- Faculdade de MedicinaUniversidade Municipal de Sao Caetano do SulSão Caetano do SulSão PauloBrazil
| | - Antonio Sesso
- Instituto de Medicina Tropical de Sao Paulo, Faculdade de MedicinaUniversidade de Sao PauloSão PauloSão PauloBrazil
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9
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Affiliation(s)
- Camila M Romano
- Laboratório de Virologia (LIMHC 52), Hospital das Clinicas HCFMUSP da Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brazil,Instituto de Medicina Tropical de São Paulo, SP, Brazil,Corresponding author at: Laboratório de Virologia (LIMHC 52), Hospital das Clinicas HCFMUSP da Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brazil.
| | - Fernando L Melo
- Departamento de Biologia Celular, Instituto de Biologia, Universidade de Brasília, Brasília, DF, Brazil
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10
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Mills MG, Bruce E, Huang ML, Crothers JW, Hyrien O, Oura CAL, Blake L, Jordan AB, Hester S, Wehmas L, Mari B, Barby P, Lacoux C, Fassy J, Vial P, Vial C, Martinez JRW, Oladipo OO, Inuwa B, Shittu I, Meseko CA, Chammas R, Santos CF, José Dionísio T, Garbieri TF, Parisi VA, Mendes-Correa MC, dePaula AV, Romano CM, Góes LGB, Minoprio P, Campos AC, Cunha MP, Vilela APP, Nyirenda T, Mkakosya RS, Muula AS, Dumm RE, Harris RM, Mitchell CA, Pettit S, Botten J, Jerome KR. An international, interlaboratory ring trial confirms the feasibility of an open-source, extraction-less "direct" RT-qPCR method for reliable detection of SARS-CoV-2 RNA in clinical samples. medRxiv 2021:2021.04.10.21254091. [PMID: 33880478 PMCID: PMC8057246 DOI: 10.1101/2021.04.10.21254091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) is used worldwide to test and trace the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). "Extraction-less" or "direct" real time-reverse transcription polymerase chain reaction (RT-PCR) is an open-access qualitative method for SARS-CoV-2 detection from nasopharyngeal or oral pharyngeal samples with the potential to generate actionable data more quickly, at a lower cost, and with fewer experimental resources than full RT-qPCR. This study engaged 10 global testing sites, including laboratories currently experiencing testing limitations due to reagent or equipment shortages, in an international interlaboratory ring trial. Participating laboratories were provided a common protocol, common reagents, aliquots of identical pooled clinical samples, and purified nucleic acids and used their existing in-house equipment. We observed 100% concordance across laboratories in the correct identification of all positive and negative samples, with highly similar cycle threshold values. The test also performed well when applied to locally collected patient nasopharyngeal samples, provided the viral transport media did not contain charcoal or guanidine, both of which appeared to potently inhibit the RT-PCR reaction. Our results suggest that open-access, direct RT-PCR assays are a feasible option for more efficient COVID-19 coronavirus disease testing as demanded by the continuing pandemic.
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11
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Costa PVA, Ishiy PS, Urbano PRP, Romano CM, Tyring SK, Oliveira WRP, Festa-Neto C. Identification of Polyomaviruses in Skin Cancers. Intervirology 2021; 64:119-125. [PMID: 33592613 DOI: 10.1159/000513544] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 11/22/2020] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Polyomaviruses (PyVs) were initially described in animals. They have also been detected in humans with some evidence that could play a role in skin carcinogenesis. OBJECTIVES This study aimed to verify the presence of PyVs in different skin tumour samples and to make clinical correlations with patients' epidemiological data from Clinics Hospital of Medical School of University of São Paulo, Brazil. METHODS This is a cross-sectional study. A random selection was performed of 120 patients with histopathological exams of different cutaneous neoplasms equally divided into 6 groups and 20 patients with normal skin. The available skin specimens were analysed with 2 different techniques of PCR (conventional and real time) for detection of PyV DNA. Concomitantly, retrospective analysis of the respective medical records for the collection of epidemiological data was done. Analyses suitable for categorical data were used to compare the proportion of patients in each group. RESULTS PyV DNA was found in 25.69% of the samples: 15% in basal cell carcinoma group, 15% in squamous cell carcinoma, 28.57% in melanoma, 15% in dermatofibrosarcoma protuberans, 13.33% in Kaposi sarcoma, 65% in Merkel cell carcinoma (MCC), and none in normal skin. Merkel cell PyV detection was statistically significant in MCC patients (p value <0.01), but no correlations were found between PyVs and others skin tumours. CONCLUSION This study demonstrated the presence of PyVs in different skin tumours; however, no association of any PyVs found in any skin tumour with epidemiological data could be shown. Further studies are still needed to elucidate the mechanisms of PyVs in skin carcinogenesis.
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Affiliation(s)
- Pedro V A Costa
- Department of Dermatology, Clinics Hospital of the Medical School of the University of São Paulo, São Paulo, Brazil
| | - Patricia S Ishiy
- Department of Dermatology, Clinics Hospital of the Medical School of the University of São Paulo, São Paulo, Brazil
| | - Paulo R P Urbano
- Virology Research Laboratory (LIMHC 52), Clinics Hospital of the Medical School of the University of São Paulo, São Paulo, Brazil
| | - Camila M Romano
- Virology Research Laboratory (LIMHC 52), Clinics Hospital of the Medical School of the University of São Paulo, São Paulo, Brazil
| | - Stephen K Tyring
- Department of Dermatology, University of Texas Health Science Center, Houston, Texas, USA
| | - Walmar R P Oliveira
- Department of Dermatology, Clinics Hospital of the Medical School of the University of São Paulo, São Paulo, Brazil,
| | - Cyro Festa-Neto
- Department of Dermatology, Clinics Hospital of the Medical School of the University of São Paulo, São Paulo, Brazil
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12
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Braz-Silva PH, Mamana AC, Romano CM, Felix AC, de Paula AV, Fereira NE, Buss LF, Tozetto-Mendoza TR, Caixeta RAV, Leal FE, Grespan RMZ, Bizário JCS, Ferraz ABC, Sapkota D, Giannecchini S, To KK, Doglio A, Mendes-Correa MC. Performance of at-home self-collected saliva and nasal-oropharyngeal swabs in the surveillance of COVID-19. J Oral Microbiol 2020; 13:1858002. [PMID: 33391631 PMCID: PMC7733974 DOI: 10.1080/20002297.2020.1858002] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Background: SARS-CoV-2 quickly spreads in the worldwide population, imposing social restrictions to control the infection, being the massive testing another essential strategy to break the chain of transmission. Aim: To compare the performance of at-home self-collected samples – saliva and combined nasal-oropharyngeal swabs (NOP) – for SARS-CoV-2 detection in a telemedicine platform for COVID-19 surveillance. Material and methods: We analyzed 201 patients who met the criteria of suspected COVID-19. NOP sampling was combined (nostrils and oropharynx) and saliva collected using a cotton pad device. Detection of SARS-COV-2 was performed by using the Altona RealStar® SARS-CoV-2 RT-PCR Kit 1.0. Results: There was an overall significant agreement (κ coefficient value of 0.58) between saliva and NOP. Considering results in either sample, 70 patients positive for SARS-CoV-2 were identified, with 52/70 being positive in NOP and 55/70 in saliva. This corresponds to sensitivities of 74.2% (95% CI; 63.7% to 83.1%) for NOP and 78.6% (95% CI; 67.6% to 86.6%) for saliva. Conclusion: Our data show the feasibility of using at-home self-collected samples (especially saliva), as an adequate alternative for SARS-CoV-2 detection. This new approach of testing can be useful to develop strategies for COVID-19 surveillance and for guiding public health decisions.
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Affiliation(s)
- Paulo H Braz-Silva
- Laboratory of Virology (LIM-52), Institute of Tropical Medicine of São Paulo, School of Medicine, University of São Paulo, São Paulo, Brazil.,Department of Stomatology, School of Dentistry, University of Sao Paulo, Sao Paulo, Brazil
| | - Ana C Mamana
- Laboratory of Virology (LIM-52), Institute of Tropical Medicine of São Paulo, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Camila M Romano
- Laboratory of Virology (LIM-52), Institute of Tropical Medicine of São Paulo, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Alvina C Felix
- Laboratory of Virology (LIM-52), Institute of Tropical Medicine of São Paulo, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Anderson V de Paula
- Laboratory of Virology (LIM-52), Institute of Tropical Medicine of São Paulo, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Noeli E Fereira
- Laboratory of Virology (LIM-52), Institute of Tropical Medicine of São Paulo, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Lewis F Buss
- Laboratory of Virology (LIM-52), Institute of Tropical Medicine of São Paulo, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Tania R Tozetto-Mendoza
- Laboratory of Virology (LIM-52), Institute of Tropical Medicine of São Paulo, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Rafael A V Caixeta
- Department of Stomatology, School of Dentistry, University of Sao Paulo, Sao Paulo, Brazil
| | - Fabio E Leal
- Department of Medicine, Municipal University of São Caetano do Sul, São Caetano Do Sul, Brazil
| | - Regina M Z Grespan
- Department of Medicine, Municipal University of São Caetano do Sul, São Caetano Do Sul, Brazil
| | - João C S Bizário
- Department of Medicine, Municipal University of São Caetano do Sul, São Caetano Do Sul, Brazil
| | - Andrea B C Ferraz
- Department of Medicine, Municipal University of São Caetano do Sul, São Caetano Do Sul, Brazil
| | - Dipak Sapkota
- Department of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Simone Giannecchini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Kelvin K To
- State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, Carol Yu Centre for Infection, Li KaShing Faculty of Medicine of the University of Hong Kong, Special Administrative Region, China.,Department of Microbiology, Queen Mary Hospital, Hong Kong Special Administrative Region, China.,Department of Clinical Microbiology and Infection Control, The University of Hong Kong - Shenzhen Hospital, Shenzhen, China
| | - Alain Doglio
- Laboratory MICORALIS (Microbiologie Orale, Immunité Et Santé) School of Dentistry, University of Côte d'Azur, Nice, France
| | - Maria C Mendes-Correa
- Laboratory of Virology (LIM-52), Institute of Tropical Medicine of São Paulo, School of Medicine, University of São Paulo, São Paulo, Brazil
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13
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Nali LH, Olival GS, Sousa FTG, de Oliveira ACS, Montenegro H, da Silva IT, Dias-Neto E, Naya H, Spangenberg L, Penalva-de-Oliveira AC, Romano CM. Whole transcriptome analysis of multiple Sclerosis patients reveals active inflammatory profile in relapsing patients and downregulation of neurological repair pathways in secondary progressive cases. Mult Scler Relat Disord 2020; 44:102243. [PMID: 32559700 DOI: 10.1016/j.msard.2020.102243] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 04/21/2020] [Accepted: 05/25/2020] [Indexed: 01/03/2023]
Abstract
BACKGROUND Multiple sclerosis (MS) is an inflammatory autoimmune neurologic disease that causes progressive destruction of myelin sheath and axons. Affecting more than 2 million people worldwide, MS may presents distinct clinical courses. However, information regarding key gene expression and genic pathways related to each clinical form is still limited. OBJECTIVE To assess the whole transcriptome of blood leukocytes from patients with remittent-recurrent (RRMS) and secondary-progressive (SPMS) forms to explore the gene expression profile of each form. METHODS Total RNA was obtained and sequenced in Illumina HiSeq platform. Reads were aligned to human genome (GRCh38/hg38), BAM files were mapped and differential expression was obtained with DeSeq2. Up or downregulated pathways were obtained through Ingenuity IPA. Pro-inflammatory cytokines levels were also assessed. RESULTS The transcriptome was generated for nine patients (6 SPMS and 3 RRMS) and 5 healthy controls. A total of 731 and 435 differentially expressed genes were identified in SPMS and RRMS, respectively. RERE, IRS2, SIPA1L1, TANC2 and PLAGL1 were upregulated in both forms, whereas PAD2 and PAD4 were upregulated in RRMS and downregulated in SPMS. Inflammatory and neuronal repair pathways were upregulated in RRMS, which was also observed in cytokine analysis. Conversely, SPMS patients presented IL-8, IL-1, Neurothrophin and Neuregulin pathways down regulated. CONCLUSIONS Overall, the transcriptome of RRMS and SPMS clearly indicated distinct inflammatory profiles, where RRMS presented marked pro-inflammatory profile but SPMS did not. SPMS individuals also presented a decrease on expression of neuronal repair pathways.
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Affiliation(s)
- Luiz H Nali
- Laboratório de Virologia, Instituto de Medicina Tropical de São Paulo, LIM-52 (LIMHC) Universidade de São Paulo, Rua Dr. Enéas de Carvalho Aguiar, 470, São Paulo, 05403-000, Brazil.; Post-graduation Program in Health Sciences, Santo Amaro University, Rua Prof. Enéas de Siqueira Neto, 340, São Paulo, 04829-300, Brazil
| | - Guilherme S Olival
- Departamento de Neurologia Santa Casa de Misericórdia de São Paulo, R. Dr. Cesário Mota Júnior, 112, São Paulo, 01221-020 Brazil
| | - Francielle T G Sousa
- Laboratório de Virologia, Instituto de Medicina Tropical de São Paulo, LIM-52 (LIMHC) Universidade de São Paulo, Rua Dr. Enéas de Carvalho Aguiar, 470, São Paulo, 05403-000, Brazil
| | - Ana Carolina S de Oliveira
- Laboratório de Virologia, Instituto de Medicina Tropical de São Paulo, LIM-52 (LIMHC) Universidade de São Paulo, Rua Dr. Enéas de Carvalho Aguiar, 470, São Paulo, 05403-000, Brazil
| | | | - Israel T da Silva
- Laboratory of Medical Genomics, A.C.Camargo Cancer Center, São Paulo, 01525-001, Brazil
| | - Emamnuel Dias-Neto
- Laboratory of Medical Genomics, A.C.Camargo Cancer Center, São Paulo, 01525-001, Brazil; Laboratory of Neurosciences (LIM-27), Institute of Psychiatry, São Paulo Medical School, University of São Paulo, São Paulo, Brazil
| | - Hugo Naya
- Unidad de Bioinformática Institut Pasteur de Montevideo, Mataojo 2020, Montevideo, 11400, Uruguay
| | - Lucia Spangenberg
- Unidad de Bioinformática Institut Pasteur de Montevideo, Mataojo 2020, Montevideo, 11400, Uruguay
| | - Augusto C Penalva-de-Oliveira
- Departamento de Neurologia Santa Casa de Misericórdia de São Paulo, R. Dr. Cesário Mota Júnior, 112, São Paulo, 01221-020 Brazil; Departamento de Neurologia, Instituto de Infectologia Emilio Ribas, Avenida Doutor Arnaldo, 165, São Paulo, 01246-900, Brazil
| | - Camila M Romano
- Laboratório de Virologia, Instituto de Medicina Tropical de São Paulo, LIM-52 (LIMHC) Universidade de São Paulo, Rua Dr. Enéas de Carvalho Aguiar, 470, São Paulo, 05403-000, Brazil.; Hospital das Clinicas HCFMUSP (LIM52), Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil.
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14
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Rodrigues LS, da Silva Nali LH, Leal COD, Sabino EC, Lacerda EM, Kingdon CC, Nacul L, Romano CM. HERV-K and HERV-W transcriptional activity in myalgic encephalomyelitis/chronic fatigue syndrome. Auto Immun Highlights 2019; 10:12. [PMID: 32257068 PMCID: PMC7065355 DOI: 10.1186/s13317-019-0122-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 10/09/2019] [Indexed: 02/08/2023]
Abstract
Background Chronic fatigue syndrome/myalgic encephalomyelitis (CFS/MS) is an incapacitating chronic disease that dramatically compromise the life quality. The CFS/ME pathogenesis is multifactorial, and it is believed that immunological, metabolic and environmental factors play a role. It is well documented an increased activity of Human endogenous retroviruses (HERVs) from different families in autoimmune and neurological diseases, making these elements good candidates for biomarkers or even triggers for such diseases. Methods Here the expression of Endogenous retroviruses K and W (HERV-K and HERV-W) was determined in blood from moderately and severely affected ME/CFS patients through real time PCR. Results HERV-K was overexpressed only in moderately affected individuals but HERV-W showed no difference. Conclusions This is the first report about HERV-K differential expression in moderate ME/CFS. Although the relationship between HERVs and ME/CFS has yet to be proven, the observation of this phenomenon deserves further attention.
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Affiliation(s)
- Lucas S Rodrigues
- 1Laboratório de Virologia, Instituto de Medicina Tropical de São Paulo, Universidade de São Paulo, Rua Dr. Enéas de Carvalho Aguiar, 470, São Paulo, SP 05403-000 Brazil
| | - Luiz H da Silva Nali
- 1Laboratório de Virologia, Instituto de Medicina Tropical de São Paulo, Universidade de São Paulo, Rua Dr. Enéas de Carvalho Aguiar, 470, São Paulo, SP 05403-000 Brazil.,2Pós-Graduação em Ciências da Saúde, Universidade Santo Amaro, São Paulo, Brazil
| | - Cibele O D Leal
- 1Laboratório de Virologia, Instituto de Medicina Tropical de São Paulo, Universidade de São Paulo, Rua Dr. Enéas de Carvalho Aguiar, 470, São Paulo, SP 05403-000 Brazil
| | - Ester C Sabino
- 1Laboratório de Virologia, Instituto de Medicina Tropical de São Paulo, Universidade de São Paulo, Rua Dr. Enéas de Carvalho Aguiar, 470, São Paulo, SP 05403-000 Brazil.,3Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Eliana M Lacerda
- 4Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Caroline C Kingdon
- 4Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Luis Nacul
- 4Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Camila M Romano
- 1Laboratório de Virologia, Instituto de Medicina Tropical de São Paulo, Universidade de São Paulo, Rua Dr. Enéas de Carvalho Aguiar, 470, São Paulo, SP 05403-000 Brazil.,5Hospital das Clinicas HCFMUSP (LIM52), Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
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15
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Urbano PRP, Nali LHDS, Oliveira RDR, Sumita LM, Fink MCDDS, Pierrotti LC, Bicalho CDS, David-Neto E, Pannuti CS, Romano CM. Variable sources of Bk virus in renal allograft recipients. J Med Virol 2019; 91:1136-1141. [PMID: 30680753 DOI: 10.1002/jmv.25409] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 01/07/2019] [Accepted: 01/21/2019] [Indexed: 01/22/2023]
Abstract
BK virus is the causative agent of polyomavirus-associated nephropathy, a major cause of kidney transplant failure affecting 1%-10% of recipients. Previous studies that investigated the viral source on the kidney recipient pointed that the donor is implicated in the origin of human polyomavirus BK (BKPyV) infection in recipients, but giving the low genetic variability of BKPyV this subject is still controversial. The aim of this study was to determine if BKPyV replicating in kidney recipients after transplantation is always originated from the donor. Urine and blood samples from 68 pairs of living donors and kidney recipients who underwent renal transplantation from August 2010-September 2011 were screened for BKPyV by real time polymerase chain reaction. Only three recipients presented viremia. When both donors and recipients were BKPyV positive, a larger fragment of VP1 region was obtained and sequenced to determine the level of similarity between them. A phylogenetic tree was built for the 12 pairs of sequences obtained from urine and high level of similarity among all sequences was observed, indicating that homology inferences for donor and recipient viruses must be cautiously interpreted. However, a close inspection on the donor-recipient pairs sequences revealed that 3 of 12 pairs presented considerably different viruses and 4 of 12 presented mixed infection, indicating that the source of BKPyV infection is not exclusively derived from the donor. We report that about 60% of the renal recipients shed BKPyV genetically distinct from the donor, confronting the accepted concept that the donor is the main source of recipients' infection.
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Affiliation(s)
- Paulo Roberto P Urbano
- Laboratório de Virologia, Instituto de Medicina Tropical de São Paulo, Universidade de São Paulo, Sao Paulo, Brasil
| | - Luiz H da Silva Nali
- Laboratório de Virologia, Instituto de Medicina Tropical de São Paulo, Universidade de São Paulo, Sao Paulo, Brasil
| | - Renato Dos R Oliveira
- Laboratório de Virologia, Instituto de Medicina Tropical de São Paulo, Universidade de São Paulo, Sao Paulo, Brasil
| | - Laura M Sumita
- Laboratório de Virologia, Instituto de Medicina Tropical de São Paulo, Universidade de São Paulo, Sao Paulo, Brasil
| | | | - Lígia C Pierrotti
- Divisão de Moléstias Infecciosas e Parasitárias, do Hospital das Clinicas da Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, Brasil.,Serviço de Transplante Renal do Hospital das Clinicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brasil
| | - Camila da Silva Bicalho
- Divisão de Moléstias Infecciosas e Parasitárias, do Hospital das Clinicas da Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, Brasil
| | - Elias David-Neto
- Divisão de Moléstias Infecciosas e Parasitárias, do Hospital das Clinicas da Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, Brasil.,Serviço de Transplante Renal do Hospital das Clinicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brasil
| | - Cláudio S Pannuti
- Laboratório de Virologia, Instituto de Medicina Tropical de São Paulo, Universidade de São Paulo, Sao Paulo, Brasil
| | - Camila M Romano
- Laboratório de Virologia, Instituto de Medicina Tropical de São Paulo, Universidade de São Paulo, Sao Paulo, Brasil.,Hospital das Clinicas HCFMUSP (LIM52), Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brasil
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16
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Neto CF, Oliveira WRP, Costa PVA, Cardoso MK, Barreto PG, Romano CM, Urbano PR. The first observation of the association of Merkel cell polyomavirus and Merkel cell carcinoma in Brazil. Int J Dermatol 2019; 58:703-706. [DOI: 10.1111/ijd.14325] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 09/28/2018] [Accepted: 11/14/2018] [Indexed: 12/14/2022]
Affiliation(s)
- Cyro Festa Neto
- Department of Dermatology Clinics Hospital of the Medical School University of São Paulo São Paulo Brazil
| | - Walmar R. P. Oliveira
- Department of Dermatology Clinics Hospital of the Medical School University of São Paulo São Paulo Brazil
| | - Pedro V. A. Costa
- Department of Dermatology Clinics Hospital of the Medical School University of São Paulo São Paulo Brazil
| | - Melina K. Cardoso
- Department of Dermatology Clinics Hospital of the Medical School University of São Paulo São Paulo Brazil
| | - Paula G. Barreto
- Department of Dermatology Clinics Hospital of the Medical School University of São Paulo São Paulo Brazil
| | - Camila M. Romano
- Virology Medical Research Laboratory Institute of Tropical Medicine University of São Paulo São Paulo Brazil
| | - Paulo R. Urbano
- Virology Medical Research Laboratory Institute of Tropical Medicine University of São Paulo São Paulo Brazil
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17
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Tozetto-Mendoza TR, Ibrahim KY, Tateno AF, Oliveira CM, Sumita LM, Sanchez MC, Luna EJ, Pierrotti LC, Drexler JF, Braz-Silva PH, Pannuti CS, Romano CM. A50 Genotypic distribution of HHV-8 in aids individuals without and with Kaposi sarcoma. Virus Evol 2018. [PMCID: PMC5905436 DOI: 10.1093/ve/vey010.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
- T R Tozetto-Mendoza
- Laboratory of Virology, Institute of Tropical Medicine, Universidade de Sao Paulo, Brazil
| | - K Y Ibrahim
- Department of Infectious Diseases, Clinics Hospital of the School of Medicine, Universidade de Sao Paulo, Brazil
| | - A F Tateno
- Laboratory of Virology, Institute of Tropical Medicine, Universidade de Sao Paulo, Brazil
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany Centre for Infection Research (DZIF), Partner Site, BonnCologne, Germany
| | - C M Oliveira
- Laboratory of Virology, Institute of Tropical Medicine, Universidade de Sao Paulo, Brazil
| | - L M Sumita
- Laboratory of Virology, Institute of Tropical Medicine, Universidade de Sao Paulo, Brazil
| | - M C Sanchez
- Laboratory of Virology, Institute of Tropical Medicine, Universidade de Sao Paulo, Brazil
| | - E J Luna
- Laboratory of Virology, Institute of Tropical Medicine, Universidade de Sao Paulo, Brazil
| | - L C Pierrotti
- Laboratory of Virology, Institute of Tropical Medicine, Universidade de Sao Paulo, Brazil
| | - J F Drexler
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany Centre for Infection Research (DZIF), Partner Site, BonnCologne, Germany
| | - P H Braz-Silva
- Department of Pathology, School of Dentistry, University of São Paulo, Brazil
| | - C S Pannuti
- Laboratory of Virology, Institute of Tropical Medicine, Universidade de Sao Paulo, Brazil
| | - C M Romano
- Laboratory of Virology, Institute of Tropical Medicine, Universidade de Sao Paulo, Brazil
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18
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Pereira BBS, Batista AM, Souza ACMF, Romano CM, Machado CM. A37 Genome sequencing, genetic characterization, and vaccine-match analysis of influenza B virus detected in hematopoietic stem cell transplant recipients (HSCT), an overview from 2010 to 2017. Virus Evol 2018. [PMCID: PMC5905454 DOI: 10.1093/ve/vey010.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Affiliation(s)
- B B S Pereira
- Virology Laboratory, São Paulo Institute of Tropical Medicine, University of Sao Paulo, SP, Brazil
| | - A M Batista
- Virology Laboratory, São Paulo Institute of Tropical Medicine, University of Sao Paulo, SP, Brazil
| | - A C M F Souza
- Virology Laboratory, São Paulo Institute of Tropical Medicine, University of Sao Paulo, SP, Brazil
| | - C M Romano
- Virology Laboratory, São Paulo Institute of Tropical Medicine, University of Sao Paulo, SP, Brazil
| | - C M Machado
- Virology Laboratory, São Paulo Institute of Tropical Medicine, University of Sao Paulo, SP, Brazil
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19
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Lisboa Neto G, Malta FM, Gomes-Gouvêa MS, Noble CF, Romano CM, Rebello Pinho JR, Silva MH, Leite AG, Piccoli LZ, Carrilho FJ, Mendes-Correa MC. Characterization of clinical predictors of naturally occurring NS3/NS4A protease polymorphism in genotype 1 hepatitis C virus mono and HIV co-infected patients. J Med Virol 2017; 89:2249-2254. [DOI: 10.1002/jmv.24900] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 07/02/2017] [Indexed: 01/09/2023]
Affiliation(s)
- Gaspar Lisboa Neto
- Department of Infectious Diseases; University of São Paulo School of Medicine; São Paulo São Paulo Brazil
- Laboratory of Virology- LIM 52. Institute of Tropical Medicine; University of São Paulo School of Medicine São Paulo; São Paulo Brazil
| | - Fernanda M. Malta
- Laboratory of Tropical Gastroenterology and Hepatology - LIM-07. Institute of Tropical Medicine; University of São Paulo School of Medicine; São Paulo São Paulo Brazil
| | - Michele S. Gomes-Gouvêa
- Laboratory of Tropical Gastroenterology and Hepatology - LIM-07. Institute of Tropical Medicine; University of São Paulo School of Medicine; São Paulo São Paulo Brazil
| | - Caroline F. Noble
- Laboratory of Tropical Gastroenterology and Hepatology - LIM-07. Institute of Tropical Medicine; University of São Paulo School of Medicine; São Paulo São Paulo Brazil
| | - Camila M. Romano
- Laboratory of Virology- LIM 52. Institute of Tropical Medicine; University of São Paulo School of Medicine São Paulo; São Paulo Brazil
| | - João R. Rebello Pinho
- Laboratory of Tropical Gastroenterology and Hepatology - LIM-07. Institute of Tropical Medicine; University of São Paulo School of Medicine; São Paulo São Paulo Brazil
- Albert Einstein Medicina Diagnóstica; Hospital Israelita Albert Einstein; São Paulo São Paulo Brazil
| | - Mariliza H. Silva
- Centro de Referência e Treinamento em DST/AIDS do Estado de São Paulo; São Paulo São Paulo Brazil
- Clínicas de Especialidades; São Bernardo do Campo São Paulo Brazil
| | | | | | - Flair J. Carrilho
- Laboratory of Tropical Gastroenterology and Hepatology - LIM-07. Institute of Tropical Medicine; University of São Paulo School of Medicine; São Paulo São Paulo Brazil
| | - Maria C. Mendes-Correa
- Department of Infectious Diseases; University of São Paulo School of Medicine; São Paulo São Paulo Brazil
- Laboratory of Virology- LIM 52. Institute of Tropical Medicine; University of São Paulo School of Medicine São Paulo; São Paulo Brazil
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20
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Sotelo JR, Sotelo AB, Sotelo FJB, Doi AM, Pinho JRR, Oliveira RDC, Bezerra AMPS, Deutsch AD, Villas-Boas LS, Felix AC, Romano CM, Machado CM, Mendes-Correa MCJ, Santana RAF, Menezes FG, Mangueira CLP. Persistence of Zika Virus in Breast Milk after Infection in Late Stage of Pregnancy. Emerg Infect Dis 2017; 23:856-857. [PMID: 28192072 PMCID: PMC5403055 DOI: 10.3201/eid2305.161538] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We detected Zika virus in breast milk of a woman in Brazil infected with the virus during the 36th week of pregnancy. Virus was detected 33 days after onset of signs and symptoms and 9 days after delivery. No abnormalities were found during fetal assessment or after birth of the infant.
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21
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Nali LHS, Oliveira ACS, Alves DO, Caleiro GS, Nunes CF, Gerhardt D, Succi RCM, Romano CM, Machado DM. Expression of human endogenous retrovirus K and W in babies. Arch Virol 2016; 162:857-861. [PMID: 27885560 DOI: 10.1007/s00705-016-3167-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 11/03/2016] [Indexed: 01/09/2023]
Abstract
Here we determined the relative expression of HERV-K and W proviruses in HIV infected and non-infected mothers as well as their respective babies up to 1 year-old. HIV-infected mothers, their babies and uninfected control groups presented expression of both HERV-K and HERV-W with relatively high frequency. While the level of HERV-K expression was similar among groups, the level of HERV-W expression in HIV-infected mothers was four-fold higher than the uninfected mothers from the control group (p < 0.01). HERV-W was down regulated in HIV-exposed babies in comparison to non-exposed babies. To our knowledge, this is the first report of HERV transcriptional activity in babies from 0-1 year-old.
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Affiliation(s)
- L H S Nali
- Laboratório de Virologia, Instituto de Medicina Tropical de São Paulo, LIM-52 (LIMHC) Universidade de São Paulo, Rua Dr. Enéas de Carvalho Aguiar, 470, São Paulo, 05403-000, Brazil
| | - A C S Oliveira
- Laboratório de Virologia, Instituto de Medicina Tropical de São Paulo, LIM-52 (LIMHC) Universidade de São Paulo, Rua Dr. Enéas de Carvalho Aguiar, 470, São Paulo, 05403-000, Brazil
| | - D O Alves
- Laboratório de Virologia, Instituto de Medicina Tropical de São Paulo, LIM-52 (LIMHC) Universidade de São Paulo, Rua Dr. Enéas de Carvalho Aguiar, 470, São Paulo, 05403-000, Brazil
| | - G S Caleiro
- Laboratório de Virologia, Instituto de Medicina Tropical de São Paulo, LIM-52 (LIMHC) Universidade de São Paulo, Rua Dr. Enéas de Carvalho Aguiar, 470, São Paulo, 05403-000, Brazil
| | - C F Nunes
- Laboratório de Virologia, Instituto de Medicina Tropical de São Paulo, LIM-52 (LIMHC) Universidade de São Paulo, Rua Dr. Enéas de Carvalho Aguiar, 470, São Paulo, 05403-000, Brazil
| | - D Gerhardt
- Laboratório de Virologia, Instituto de Medicina Tropical de São Paulo, LIM-52 (LIMHC) Universidade de São Paulo, Rua Dr. Enéas de Carvalho Aguiar, 470, São Paulo, 05403-000, Brazil.,Departamento de Pediatria, Universidade Federal de São Paulo, Rua Sena Madureira 1500, São Paulo, 04021-001, Brazil
| | - R C M Succi
- Departamento de Pediatria, Universidade Federal de São Paulo, Rua Sena Madureira 1500, São Paulo, 04021-001, Brazil
| | - Camila M Romano
- Laboratório de Virologia, Instituto de Medicina Tropical de São Paulo, LIM-52 (LIMHC) Universidade de São Paulo, Rua Dr. Enéas de Carvalho Aguiar, 470, São Paulo, 05403-000, Brazil.
| | - D M Machado
- Laboratório de Virologia, Instituto de Medicina Tropical de São Paulo, LIM-52 (LIMHC) Universidade de São Paulo, Rua Dr. Enéas de Carvalho Aguiar, 470, São Paulo, 05403-000, Brazil.,Departamento de Pediatria, Universidade Federal de São Paulo, Rua Sena Madureira 1500, São Paulo, 04021-001, Brazil
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Nali LH, Fink MC, do Olival GS, Moraes L, Callegaro D, Tilbery CP, Vidal JE, Sumita LM, de Oliveira ACP, Romano CM. Polyomavirus detection in multiple sclerosis patients under natalizumab therapy: Profile and frequency of urinary shedding. J Med Virol 2016; 89:528-534. [PMID: 27464945 DOI: 10.1002/jmv.24646] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2016] [Indexed: 11/07/2022]
Abstract
Patients undergoing Natalizumab (NTZ) therapy are at risk of progressive multifocal leukoencephalopathy (PML). Besides John Cunningham virus (JCV), BK polyomavirus might represent an additional concern for such patients since it can also infect CNS cells. Currently, data regarding the presence of anti-JCV antibodies added to previous immunosuppressive therapy and prolonged NTZ therapy has been used to classify patients at risk of developing PML. Here, we investigated the profile shedding of JCV and BKV in multiple sclerosis (MS) patients during treatment with NTZ. Serial blood and urine samples from 97 MS patients receiving either NTZ or β-interferon were investigated for polyomavirus shedding. While all blood samples tested negative, 36% of the patients shed polyomavirus in the urine in at least one time point. From these, 21.7%, 9.3%, and 5.1% shed JCV, BKV, and both polyomavirus, respectively. No difference was observed between the rates of urinary shedding of patients treated with NTZ (38.9%) and patients treated with other drugs (34.5%), also no PML event was diagnosed during the follow-up. Therefore, urinary shedding might not be interfered by therapy condition. In our study, we also observed 14/27 (52%) of anti-JCV antibodies prevalence, and nearly half of them (42%) did not present any event of urinary shedding during the follow-up. J. Med. Virol. 89:528-534, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Luiz Henrique Nali
- Laboratório de Virologia, Instituto de Medicina Tropical de São Paulo, Universidade de São Paulo, São Paulo, Brazil
| | - Maria Cristina Fink
- Laboratório de Virologia, Instituto de Medicina Tropical de São Paulo, Universidade de São Paulo, São Paulo, Brazil
| | - Guilherme S do Olival
- Laboratório de Virologia, Instituto de Medicina Tropical de São Paulo, Universidade de São Paulo, São Paulo, Brazil.,Departamento de Neurologia, Santa Casa de Misericórdia de São Paulo, São Paulo, Brazil
| | - Lenira Moraes
- Hospital das Clínicas de São Paulo-HCFMUSP, São Paulo, Brazil
| | | | - Charles Peter Tilbery
- Departamento de Neurologia, Santa Casa de Misericórdia de São Paulo, São Paulo, Brazil
| | - Jose Ernesto Vidal
- Grupo de Neurociências, Instituto de Infectologia Emílio Ribas, São Paulo, Brazil
| | - Laura Masami Sumita
- Laboratório de Virologia, Instituto de Medicina Tropical de São Paulo, Universidade de São Paulo, São Paulo, Brazil
| | - Augusto C Penalva de Oliveira
- Departamento de Neurologia, Santa Casa de Misericórdia de São Paulo, São Paulo, Brazil.,Grupo de Neurociências, Instituto de Infectologia Emílio Ribas, São Paulo, Brazil
| | - Camila M Romano
- Laboratório de Virologia, Instituto de Medicina Tropical de São Paulo, Universidade de São Paulo, São Paulo, Brazil
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Gaspareto KV, Ribeiro RM, de Mello Malta F, Gomes-Gouvêa MS, Muto NH, Romano CM, Mendes-Correa MC, Carrilho FJ, Sabino EC, Rebello Pinho JR. Resistance-associated variants in HCV subtypes 1a and 1b detected by Ion Torrent sequencing platform. Antivir Ther 2016; 21:653-660. [PMID: 27314166 DOI: 10.3851/imp3057] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/20/2016] [Indexed: 10/21/2022]
Abstract
BACKGROUND As a result of increased understanding of the HCV life cycle, a new generation of drugs known as direct-acting antivirals (DAAs) was developed and is constantly being improved. At baseline, HCV variants resistant to DAA therapy may pre-exist, increasing the likelihood of treatment failure. The aim of this study was to investigate the presence of resistance-associated variants (RAVs) in treatment-naive patients infected with HCV subtypes 1a and 1b. METHODS Next-generation sequencing was used to assess the frequencies of NS3-4A, NS5A and NS5B RAVs in 100 HCV monoinfected DAA-naive patients (HCV-1a: n=51; HCV-1b: n=49). RESULTS Complete HCV sequence information was obtained for most samples. RAVs were detected in the NS3-4A (T54S, V55A, Q80K and R155K), NS5A (Q30H/R, H58P and Y93C/H/N) and NS5B (A421V) regions in 10%, 22% and 8%, respectively, of patients infected with HCV subtype-1a. Among the patients infected with HCV subtype-1b, mutations in the NS3-4A (F43I, T54S, Q80H, D168E and M175L), NS5A (L28M, R30Q, L31M, Q54H, A92T and Y93H) and NS5B (L159F, C316N, A421V and S556G) regions were observed in 12%, 53% and 31% of patients, respectively. CONCLUSIONS High-throughput DNA sequencing allows an easier and more complete analysis of DAA RAVs, including mutations that represent only a minor variant of the whole viral population. RAVs to the three different classes of DAAs were found in our population. The characterization of their profile in the circulating virus is relevant to determine the better treatment option for infected individuals or to guide the implementation of treatment policies.
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Affiliation(s)
- Karine V Gaspareto
- Laboratory of Tropical Gastroenterology and Hepatology 'João Alves de Queiroz and Castorina Bittencourt Alves', LIM-07, Institute of Tropical Medicine and Department of Gastroenterology, School of Medicine, University of São Paulo, São Paulo, Brazil.,Graduate Program in Biotechnology Interunits (USP/Butantan/IPT), University of São Paulo, São Paulo, Brazil
| | - Roberto M Ribeiro
- Laboratory of Parasitology, LIM-46, Institute of Tropical Medicine and Department of Infectious and Parasitic Diseases, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Fernanda de Mello Malta
- Laboratory of Tropical Gastroenterology and Hepatology 'João Alves de Queiroz and Castorina Bittencourt Alves', LIM-07, Institute of Tropical Medicine and Department of Gastroenterology, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Michele S Gomes-Gouvêa
- Laboratory of Tropical Gastroenterology and Hepatology 'João Alves de Queiroz and Castorina Bittencourt Alves', LIM-07, Institute of Tropical Medicine and Department of Gastroenterology, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Nair H Muto
- Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Camila M Romano
- Laboratory of Virology, LIM-52, Institute of Tropical Medicine and Department of Infectious and Parasitic Diseases, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Maria C Mendes-Correa
- Laboratory of Virology, LIM-52, Institute of Tropical Medicine and Department of Infectious and Parasitic Diseases, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Flair J Carrilho
- Laboratory of Tropical Gastroenterology and Hepatology 'João Alves de Queiroz and Castorina Bittencourt Alves', LIM-07, Institute of Tropical Medicine and Department of Gastroenterology, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Ester C Sabino
- Laboratory of Parasitology, LIM-46, Institute of Tropical Medicine and Department of Infectious and Parasitic Diseases, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - João R Rebello Pinho
- Laboratory of Tropical Gastroenterology and Hepatology 'João Alves de Queiroz and Castorina Bittencourt Alves', LIM-07, Institute of Tropical Medicine and Department of Gastroenterology, School of Medicine, University of São Paulo, São Paulo, Brazil.,Graduate Program in Biotechnology Interunits (USP/Butantan/IPT), University of São Paulo, São Paulo, Brazil.,Hospital Israelita Albert Einstein, São Paulo, Brazil
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24
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Urbano PR, Nali LHS, Bicalho CS, Pierrotti LC, David-Neto E, Pannuti CS, Romano CM. New findings about trichodysplasia spinulosa-associated polyomavirus (TSPyV)--novel qPCR detects TSPyV-DNA in blood samples. Diagn Microbiol Infect Dis 2015; 84:123-4. [PMID: 26602950 DOI: 10.1016/j.diagmicrobio.2015.10.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 09/15/2015] [Accepted: 10/15/2015] [Indexed: 10/22/2022]
Abstract
A new real-time PCR assay for trichodysplasia spinulosa-associated polyomavirus (TSPyV) DNA detection was designed, and blood samples from kidney transplant recipients and healthy individuals were screened. TSPyV-DNA was not detected in blood from healthy individuals, but 26.8% of kidney recipients presented TSPyV-DNA. This is the first report of TSPyV viremia.
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Affiliation(s)
- Paulo R Urbano
- São Paulo Institute of Tropical Medicine, São Paulo, Brazil
| | - Luiz H S Nali
- São Paulo Institute of Tropical Medicine, São Paulo, Brazil
| | | | | | | | | | - Camila M Romano
- São Paulo Institute of Tropical Medicine, São Paulo, Brazil.
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25
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Levi JE, Cabral SPN, Nishiya A, Ferreira S, Romano CM, Polite MBC, Pereira RAA, Mota MA, Kutner JM. Absence of nonprimate hepacivirus-related genomes in blood donors seroreactive for hepatitis C virus displaying indeterminate blot patterns. J Viral Hepat 2014; 21:e164-6. [PMID: 24689976 DOI: 10.1111/jvh.12252] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2013] [Accepted: 02/13/2014] [Indexed: 12/09/2022]
Abstract
Despite intensive search, no primate homologue to the Hepatitis C Virus (HCV) has ever been found. The search for a zoonotic origin for HCV has been renewed recently when a virus, now known as non-primate hepacivirus (NPHV), with a high homology to HCV was found in dogs. A variable proportion of anti-HCV reactive blood donors submitted to the immunoblot (IB) to confirm their HCV status, present indeterminate results. The degree of homology between HCV and NPHV suggests that humans may be infected by NPHV or NPHV-like viruses. Maximum similarity between NHPV and HCV is observed in the nonstructural regions 3 and 5. Peptides representing both domains are present in IB assays, so it is reasonable to suppose that blood donors harboring such viruses may display cross-reactivity to the HCV antigenic fractions. Fifty-nine plasma samples from blood donors found reactive for anti-HCV and presenting IB indeterminate results were submitted to five distinct PCR reactions under low-stringency conditions, employing primers targeting GBV-C 5'UTR and NS3, Flavivirus-genus NS5 and NPHV 5'UTR and NS3. No amplification was obtained with all primer pairs tested except for five samples that amplified both 5'UTR and NS3 fragments from GBV-C. Unbiased next-generation sequencing may prove or rule out the existence of HCV-related viruses in IB indeterminate samples.
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Affiliation(s)
- J E Levi
- Hospital Israelita Albert Einstein Blood Bank, São Paulo, Brazil; Molecular Biology Department, Fundação Pró-Sangue/Hemocentro de São Paulo, São Paulo, Brazil; Virology Lab, Instituto de Medicina Tropical, University of São Paulo, São Paulo, Brazil
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26
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van de Weg CAM, Pannuti CS, van den Ham HJ, de Araújo ESA, Boas LSV, Felix AC, Carvalho KI, Levi JE, Romano CM, Centrone CC, Rodrigues CLDL, Luna E, van Gorp ECM, Osterhaus ADME, Kallas EG, Martina BEE. Serum angiopoietin-2 and soluble VEGF receptor 2 are surrogate markers for plasma leakage in patients with acute dengue virus infection. J Clin Virol 2014; 60:328-35. [PMID: 24928471 DOI: 10.1016/j.jcv.2014.05.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2014] [Revised: 05/04/2014] [Accepted: 05/05/2014] [Indexed: 12/07/2022]
Abstract
BACKGROUND Endothelial cell dysfunction is believed to play an important role in the pathogenesis of plasma leakage in patients with acute dengue virus (DENV) infection. Several factors, produced by activated endothelial cells, have been associated with plasma leakage or severe disease in patients with infectious diseases. OBJECTIVES The aim of this study was to investigate which of these markers could serve as a surrogate marker for the occurrence of plasma leakage in patients with acute DENV infection. STUDY DESIGN A case-control study was performed in patients with acute DENV infection in Santos, Brazil. Plasma leakage was detected with X-ray and/or ultrasound examination at admission. Serum levels of soluble endoglin, endothelin-1, angiopoietin-2, VEGF, soluble VEGFR-2, MMP-2, MMP-9, TIMP-1 and TIMP-2 were determined using commercially available ELISAs. RESULTS Increased levels of angiopoietin-2, endothelin-1 and MMP-2 and decreased levels of soluble VEGFR-2 were significantly associated with the occurrence of plasma leakage. An unsupervised cluster analysis confirmed that angiopoietin-2 and soluble VEGFR-2 were strongly associated with clinical apparent vascular leakage. CONCLUSION Angiopoietin-2 and soluble VEGFR-2 can serve as surrogate markers for the occurrence of plasma leakage in patients with acute DENV infection.
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Affiliation(s)
- Cornelia A M van de Weg
- Department of Viroscience, Erasmus Medical Center, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Cláudio S Pannuti
- Instituto de Medicina Tropical de São Paulo e Departamento de Moléstias Infecciosas e Parasitárias (LIM-52), Faculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas de Carvalho Aguiar 470, 05403-000 São Paulo, Brazil
| | - Henk-Jan van den Ham
- Department of Viroscience, Erasmus Medical Center, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Evaldo S A de Araújo
- Instituto de Medicina Tropical de São Paulo e Departamento de Moléstias Infecciosas e Parasitárias (LIM-52), Faculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas de Carvalho Aguiar 470, 05403-000 São Paulo, Brazil; Department of Infectious Diseases, Hospital Ana Costa, Rua Pedro Américo 60, Campo Grande 11075-400, Santos, Brazil
| | - Lucy S V Boas
- Instituto de Medicina Tropical de São Paulo e Departamento de Moléstias Infecciosas e Parasitárias (LIM-52), Faculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas de Carvalho Aguiar 470, 05403-000 São Paulo, Brazil
| | - Alvina C Felix
- Instituto de Medicina Tropical de São Paulo e Departamento de Moléstias Infecciosas e Parasitárias (LIM-52), Faculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas de Carvalho Aguiar 470, 05403-000 São Paulo, Brazil
| | - Karina I Carvalho
- Hospital Albert Einstein, Av. Albert Einstein 627, CEP 05652-000 São Paulo, Brazil
| | - José E Levi
- Instituto de Medicina Tropical de São Paulo e Departamento de Moléstias Infecciosas e Parasitárias (LIM-52), Faculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas de Carvalho Aguiar 470, 05403-000 São Paulo, Brazil
| | - Camila M Romano
- Instituto de Medicina Tropical de São Paulo e Departamento de Moléstias Infecciosas e Parasitárias (LIM-52), Faculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas de Carvalho Aguiar 470, 05403-000 São Paulo, Brazil
| | - Cristiane C Centrone
- Instituto de Medicina Tropical de São Paulo e Departamento de Moléstias Infecciosas e Parasitárias (LIM-52), Faculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas de Carvalho Aguiar 470, 05403-000 São Paulo, Brazil
| | - Celia L de Lima Rodrigues
- Instituto de Medicina Tropical de São Paulo e Departamento de Moléstias Infecciosas e Parasitárias (LIM-52), Faculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas de Carvalho Aguiar 470, 05403-000 São Paulo, Brazil
| | - Expedito Luna
- Instituto de Medicina Tropical de São Paulo e Departamento de Moléstias Infecciosas e Parasitárias (LIM-52), Faculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas de Carvalho Aguiar 470, 05403-000 São Paulo, Brazil
| | - Eric C M van Gorp
- Department of Viroscience, Erasmus Medical Center, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Albert D M E Osterhaus
- Department of Viroscience, Erasmus Medical Center, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Esper G Kallas
- Disciplina de Imunologia Clínica e Alergia (LIM-60), Faculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas de Carvalho Aguiar 155, CEP 05403-000 São Paulo, Brazil
| | - Byron E E Martina
- Department of Viroscience, Erasmus Medical Center, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands.
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Nali LHS, Olival GS, de Oliveira ACP, Casseb J, Vidal JE, Moraes L, Fink MCD, Sumita LM, Romano CM. HERV-W/MRSV envelope transcripts detection in blood of multiple sclerosis patients after Natalizumab treatment. Retrovirology 2014. [PMCID: PMC4042368 DOI: 10.1186/1742-4690-11-s1-p131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
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28
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Romano CM, Oliveira D, Gerhardt D, Nali LHS, Caleiro GS, Nunes CF, Granato F, do Carmo FB, Succi RCM, Machado DM. Human endogenous retrovirus K (HERV-K) transcripts detection in babies exposed to HIV-1 during pregnancy. Retrovirology 2014. [PMCID: PMC4042532 DOI: 10.1186/1742-4690-11-s1-p134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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29
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do Olival GS, Faria TS, Nali LHS, de Oliveira ACP, Casseb J, Vidal JE, Cavenaghi VB, Tilbery CP, Moraes L, Fink MCS, Sumita LM, Perron H, Romano CM. Genomic analysis of ERVWE2 locus in patients with multiple sclerosis: absence of genetic association but potential role of human endogenous retrovirus type W elements in molecular mimicry with myelin antigen. Front Microbiol 2013; 4:172. [PMID: 23805135 PMCID: PMC3693062 DOI: 10.3389/fmicb.2013.00172] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 06/05/2013] [Indexed: 12/11/2022] Open
Abstract
Human endogenous retroviruses (HERVs) arise from ancient infections of the host germline cells by exogenous retroviruses, constituting 8% of the human genome. Elevated level of envelope transcripts from HERVs-W has been detected in CSF, plasma and brain tissues from patients with Multiple Sclerosis (MS), most of them from Xq22.3, 15q21.3, and 6q21 chromosomes. However, since the locus Xq22.3 (ERVWE2) lack the 5' LTR promoter and the putative protein should be truncated due to a stop codon, we investigated the ERVWE2 genomic loci from 84 individuals, including MS patients with active HERV-W expression detected in PBMC. In addition, an automated search for promoter sequences in 20 kb nearby region of ERVWE2 reference sequence was performed. Several putative binding sites for cellular cofactors and enhancers were found, suggesting that transcription may occur via alternative promoters. However, ERVWE2 DNA sequencing of MS and healthy individuals revealed that all of them harbor a stop codon at site 39, undermining the expression of a full-length protein. Finally, since plaque formation in central nervous system (CNS) of MS patients is attributed to immunological mechanisms triggered by autoimmune attack against myelin, we also investigated the level of similarity between envelope protein and myelin oligodendrocyte glycoprotein (MOG). Comparison of the MOG to the envelope identified five retroviral regions similar to the Ig-like domain of MOG. Interestingly, one of them includes T and B cell epitopes, capable to induce T effector functions and circulating Abs in rats. In sum, although no DNA substitutions that would link ERVWE2 to the MS pathogeny was found, the similarity between the envelope protein to MOG extends the idea that ERVEW2 may be involved on the immunopathogenesis of MS, maybe facilitating the MOG recognizing by the immune system. Although awaiting experimental evidences, the data presented here may expand the scope of the endogenous retroviruses involvement on MS pathogenesis.
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Affiliation(s)
- Guilherme S. do Olival
- Departamento de Neurologia, Irmandade da Santa Casa de Misericórdia de São PauloSão Paulo, Brazil
| | - Thiago S. Faria
- Departamento de Moléstias Infecciosas e Parasitárias – (LIMHC), Instituto de Medicina Tropical de São Paulo e Faculdade de Medicina, Universidade de São PauloSão Paulo, Brazil
| | - Luiz H. S. Nali
- Departamento de Moléstias Infecciosas e Parasitárias – (LIMHC), Instituto de Medicina Tropical de São Paulo e Faculdade de Medicina, Universidade de São PauloSão Paulo, Brazil
| | | | - Jorge Casseb
- Departamento de Neurologia, Instituto de Infectologia Emilio RibasSão Paulo, Brazil
- Laboratório de Imunodeficiências e Dermatologia, Instituto de Medicina Tropical de São Paulo e Faculdade de Medicina, Universidade de São PauloSão Paulo, Brazil
| | - Jose E. Vidal
- Departamento de Neurologia, Instituto de Infectologia Emilio RibasSão Paulo, Brazil
| | - Vitor B. Cavenaghi
- Departamento de Neurologia, Irmandade da Santa Casa de Misericórdia de São PauloSão Paulo, Brazil
| | - Charles P. Tilbery
- Departamento de Neurologia, Irmandade da Santa Casa de Misericórdia de São PauloSão Paulo, Brazil
| | - Lenira Moraes
- Departamento de Neurologia, Hospital das Clínicas da Faculdade de Medicina, Universidade de São PauloSão Paulo, Brazil
| | - Maria C. S. Fink
- Departamento de Moléstias Infecciosas e Parasitárias – (LIMHC), Instituto de Medicina Tropical de São Paulo e Faculdade de Medicina, Universidade de São PauloSão Paulo, Brazil
| | - Laura M. Sumita
- Departamento de Moléstias Infecciosas e Parasitárias – (LIMHC), Instituto de Medicina Tropical de São Paulo e Faculdade de Medicina, Universidade de São PauloSão Paulo, Brazil
| | | | - Camila M. Romano
- Departamento de Moléstias Infecciosas e Parasitárias – (LIMHC), Instituto de Medicina Tropical de São Paulo e Faculdade de Medicina, Universidade de São PauloSão Paulo, Brazil
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30
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van de Weg CAM, Pannuti CS, de Araújo ESA, van den Ham HJ, Andeweg AC, Boas LSV, Felix AC, Carvalho KI, de Matos AM, Levi JE, Romano CM, Centrone CC, de Lima Rodrigues CL, Luna E, van Gorp ECM, Osterhaus ADME, Martina BEE, Kallas EG. Microbial translocation is associated with extensive immune activation in dengue virus infected patients with severe disease. PLoS Negl Trop Dis 2013; 7:e2236. [PMID: 23717702 PMCID: PMC3662706 DOI: 10.1371/journal.pntd.0002236] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Accepted: 04/15/2013] [Indexed: 11/18/2022] Open
Abstract
Background Severe dengue virus (DENV) disease is associated with extensive immune activation, characterized by a cytokine storm. Previously, elevated lipopolysaccharide (LPS) levels in dengue were found to correlate with clinical disease severity. In the present cross-sectional study we identified markers of microbial translocation and immune activation, which are associated with severe manifestations of DENV infection. Methods Serum samples from DENV-infected patients were collected during the outbreak in 2010 in the State of São Paulo, Brazil. Levels of LPS, lipopolysaccharide binding protein (LBP), soluble CD14 (sCD14) and IgM and IgG endotoxin core antibodies were determined by ELISA. Thirty cytokines were quantified using a multiplex luminex system. Patients were classified according to the 2009 WHO classification and the occurrence of plasma leakage/shock and hemorrhage. Moreover, a (non-supervised) cluster analysis based on the expression of the quantified cytokines was applied to identify groups of patients with similar cytokine profiles. Markers of microbial translocation were linked to groups with similar clinical disease severity and clusters with similar cytokine profiles. Results Cluster analysis indicated that LPS levels were significantly increased in patients with a profound pro-inflammatory cytokine profile. LBP and sCD14 showed significantly increased levels in patients with severe disease in the clinical classification and in patients with severe inflammation in the cluster analysis. With both the clinical classification and the cluster analysis, levels of IL-6, IL-8, sIL-2R, MCP-1, RANTES, HGF, G-CSF and EGF were associated with severe disease. Conclusions The present study provides evidence that both microbial translocation and extensive immune activation occur during severe DENV infection and may play an important role in the pathogenesis. The pathogenesis of severe dengue virus (DENV) infection is still not fully understood. It is hypothesized that it is caused by a cytokine storm as is described in severe sepsis. In the sepsis field, the potent immunostimulator lipopolysaccharide (LPS) is proposed to play an important role in the development of a cytokine storm. In a previous study we have found elevated levels of LPS in children with severe DENV infection. In this study we have investigated if we could confirm that microbial translocation occurs in DENV-infected patients. Moreover, we have determined the levels of thirty cytokines to get more insight in the cytokine storm during DENV infections and we have investigated whether microbial translocation is associated with immune activation. The patients in this cohort were classified according to their clinical presentation. Furthermore, a cluster analysis based on the expression of the determined cytokines was applied to identify patients with similar cytokine profiles. With these two techniques, we identified cytokines that may contribute significantly to the cytokine storm, and we could relate elevated levels of LPS to patients with a pro-inflammatory cytokine profile.
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Affiliation(s)
| | - Cláudio S. Pannuti
- Instituto de Medicina Tropical de São Paulo e Departamento de Moléstias Infecciosas e Parasitárias (LIM-52), Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Evaldo S. A. de Araújo
- Instituto de Medicina Tropical de São Paulo e Departamento de Moléstias Infecciosas e Parasitárias (LIM-52), Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
- Department of Infectious Diseases, Hospital Ana Costa, Santos, Brazil
| | | | - Arno C. Andeweg
- Viroscience Lab, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Lucy S. V. Boas
- Instituto de Medicina Tropical de São Paulo e Departamento de Moléstias Infecciosas e Parasitárias (LIM-52), Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Alvina C. Felix
- Instituto de Medicina Tropical de São Paulo e Departamento de Moléstias Infecciosas e Parasitárias (LIM-52), Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Karina I. Carvalho
- Disciplina de Imunologia Clínica e Alergia (LIM-60), Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Andreia M. de Matos
- Disciplina de Imunologia Clínica e Alergia (LIM-60), Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - José E. Levi
- Instituto de Medicina Tropical de São Paulo e Departamento de Moléstias Infecciosas e Parasitárias (LIM-52), Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Camila M. Romano
- Instituto de Medicina Tropical de São Paulo e Departamento de Moléstias Infecciosas e Parasitárias (LIM-52), Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Cristiane C. Centrone
- Instituto de Medicina Tropical de São Paulo e Departamento de Moléstias Infecciosas e Parasitárias (LIM-52), Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Celia L. de Lima Rodrigues
- Instituto de Medicina Tropical de São Paulo e Departamento de Moléstias Infecciosas e Parasitárias (LIM-52), Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Expedito Luna
- Instituto de Medicina Tropical de São Paulo e Departamento de Moléstias Infecciosas e Parasitárias (LIM-52), Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | | | | | | | - Esper G. Kallas
- Disciplina de Imunologia Clínica e Alergia (LIM-60), Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
- * E-mail:
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Alvarado-Mora MV, Romano CM, Gomes-Gouvêa MS, Gutierrez MF, Carrilho FJ, Pinho JRR. Phylogenetic analysis of complete genome sequences of hepatitis B virus from an Afro-Colombian community: presence of HBV F3/A1 recombinant strain. Virol J 2012; 9:244. [PMID: 23092209 PMCID: PMC3499267 DOI: 10.1186/1743-422x-9-244] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Accepted: 10/22/2012] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Hepatitis B virus (HBV) infection is one of the most prevalent viral infections in humans and represents a serious public health problem. In Colombia, our group reported recently the presence of subgenotypes F3, A2 and genotype G in Bogotá. The aim of this study was to characterize the HBV genotypes circulating in Quibdó, the largest Afro-descendant community in Colombia. Sixty HBsAg-positive samples were studied. A fragment of 1306 bp (S/POL) was amplified by nested PCR. Positive samples to S/POL fragment were submitted to PCR amplification of the HBV complete genome. FINDINGS The distribution of HBV genotypes was: A1 (52.17%), E (39.13%), D3 (4.3%) and F3/A1 (4.3%). An HBV recombinant strain subgenotype F3/A1 was found for the first time. CONCLUSIONS This study is the first analysis of complete HBV genome sequences from Afro-Colombian population. It was found an important presence of HBV/A1 and HBV/E genotypes. A new recombinant strain of HBV genotype F3/A1 was reported in this population. This fact may be correlated with the introduction of these genotypes in the times of slavery.
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Affiliation(s)
- Mónica V Alvarado-Mora
- Laboratory of Gastroenterology and Hepatology, São Paulo Institute of Tropical Medicine and Department of Gastroenterology, School of Medicine, University of São Paulo, São Paulo, Brazil.
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Romano CM, Nali LHS, Faria TS, Olival GS, Vidal JE, Fink MCD, Sumita LM, Oliveira ACP. Lack of evidence of ERVWE1/Xq22.3 involvement in MRSV transcripts detected in Multiple Sclerosis patients. Retrovirology 2011. [PMCID: PMC3112695 DOI: 10.1186/1742-4690-8-s1-a217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Romano CM, Ramalho RF, Zanotto PMDA. Tempo and mode of ERV-K evolution in human and chimpanzee genomes. Arch Virol 2006; 151:2215-28. [PMID: 16830071 DOI: 10.1007/s00705-006-0792-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2005] [Accepted: 04/24/2006] [Indexed: 11/25/2022]
Abstract
Several families of endogenous retrovirus (ERV) exist in copious numbers in the genomes of primate species. Therefore, we undertook a systematic search for endogenous retrovirus sequences from the ERV-K family, comparing across both human (Homo sapiens) and chimpanzee (Pan troglodytes) genomes. Using conserved motifs of the ERV-K as query we identified and characterized 76 complete ERV-K elements, 54 in human (HERV-K), 34 of which were described previously, and 21 in the chimpanzee (CERV-K). Phylogenetic analysis using coding regions and LTRs showed the existence of two main branches. Group I was the most heterogeneous and had an average integration time of 18.3 MYBP (million years before present), using rates ranging from 1.5 to 4.0 x 10(-9) s/s/y (substitution per site per year). Group O/N integrated around 19.4 MYBP and nested Group N integrated about 14 MYBP. We found evidence for strong positive selection on the gag, pol and env coding regions and for A/T hypermutation. Our data suggest that the endogenous elements were possibly involved in chromosomal rearrangements and retained a great deal of information from their active stage, most likely as a consequence of host interactions. This study also contributes to the annotation effort of both human and chimpanzee genomes.
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Affiliation(s)
- C M Romano
- Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, Biomedical Sciences Institute - ICB II, University of São Paulo, São Paulo, Brazil
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Ferreira EN, Pires LC, Parmigiani RB, Bettoni F, Puga RD, Pinheiro DG, Andrade LEC, Cruz LO, Degaki TL, Faria M, Festa F, Giannella-Neto D, Giorgi RR, Goldman GH, Granja F, Gruber A, Hackel C, Henrique-Silva F, Malnic B, Manzini CVB, Marie SKN, Martinez-Rossi NM, Oba-Shinjo SM, Pardini MIMC, Rahal P, Rainho CA, Rogatto SR, Romano CM, Rodrigues V, Sales MM, Savoldi M, da Silva IDCG, da Silva NP, de Souza SJ, Tajara EH, Silva WA, Simpson AJG, Sogayar MC, Camargo AA, Carraro DM. Identification and complete sequencing of novel human transcripts through the use of mouse orthologs and testis cDNA sequences. Genet Mol Res 2004; 3:493-511. [PMID: 15688316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
The correct identification of all human genes, and their derived transcripts, has not yet been achieved, and it remains one of the major aims of the worldwide genomics community. Computational programs suggest the existence of 30,000 to 40,000 human genes. However, definitive gene identification can only be achieved by experimental approaches. We used two distinct methodologies, one based on the alignment of mouse orthologous sequences to the human genome, and another based on the construction of a high-quality human testis cDNA library, in an attempt to identify new human transcripts within the human genome sequence. We generated 47 complete human transcript sequences, comprising 27 unannotated and 20 annotated sequences. Eight of these transcripts are variants of previously known genes. These transcripts were characterized according to size, number of exons, and chromosomal localization, and a search for protein domains was undertaken based on their putative open reading frames. In silico expression analysis suggests that some of these transcripts are expressed at low levels and in a restricted set of tissues.
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Affiliation(s)
- Elisa N Ferreira
- Laboratory of Molecular Biology and Genomics, Ludwig Institute for Cancer Research, São Paulo, SP, Brazil
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Sogayar MC, Camargo AA, Bettoni F, Carraro DM, Pires LC, Parmigiani RB, Ferreira EN, de Sá Moreira E, do Rosário D de O Latorre M, Simpson AJG, Cruz LO, Degaki TL, Festa F, Massirer KB, Sogayar MC, Filho FC, Camargo LP, Cunha MAV, De Souza SJ, Faria M, Giuliatti S, Kopp L, de Oliveira PSL, Paiva PB, Pereira AA, Pinheiro DG, Puga RD, S de Souza JE, Albuquerque DM, Andrade LEC, Baia GS, Briones MRS, Cavaleiro-Luna AMS, Cerutti JM, Costa FF, Costanzi-Strauss E, Espreafico EM, Ferrasi AC, Ferro ES, Fortes MAHZ, Furchi JRF, Giannella-Neto D, Goldman GH, Goldman MHS, Gruber A, Guimarães GS, Hackel C, Henrique-Silva F, Kimura ET, Leoni SG, Macedo C, Malnic B, Manzini B CV, Marie SKN, Martinez-Rossi NM, Menossi M, Miracca EC, Nagai MA, Nobrega FG, Nobrega MP, Oba-Shinjo SM, Oliveira MK, Orabona GM, Otsuka AY, Paço-Larson ML, Paixão BMC, Pandolfi JRC, Pardini MIMC, Passos Bueno MR, Passos GAS, Pesquero JB, Pessoa JG, Rahal P, Rainho CA, Reis CP, Ricca TI, Rodrigues V, Rogatto SR, Romano CM, Romeiro JG, Rossi A, Sá RG, Sales MM, Sant'Anna SC, Santarosa PL, Segato F, Silva WA, Silva IDCG, Silva NP, Soares-Costa A, Sonati MF, Strauss BE, Tajara EH, Valentini SR, Villanova FE, Ward LS, Zanette DL. A transcript finishing initiative for closing gaps in the human transcriptome. Genome Res 2004; 14:1413-23. [PMID: 15197164 PMCID: PMC442158 DOI: 10.1101/gr.2111304] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2003] [Accepted: 03/12/2004] [Indexed: 11/24/2022]
Abstract
We report the results of a transcript finishing initiative, undertaken for the purpose of identifying and characterizing novel human transcripts, in which RT-PCR was used to bridge gaps between paired EST clusters, mapped against the genomic sequence. Each pair of EST clusters selected for experimental validation was designated a transcript finishing unit (TFU). A total of 489 TFUs were selected for validation, and an overall efficiency of 43.1% was achieved. We generated a total of 59,975 bp of transcribed sequences organized into 432 exons, contributing to the definition of the structure of 211 human transcripts. The structure of several transcripts reported here was confirmed during the course of this project, through the generation of their corresponding full-length cDNA sequences. Nevertheless, for 21% of the validated TFUs, a full-length cDNA sequence is not yet available in public databases, and the structure of 69.2% of these TFUs was not correctly predicted by computer programs. The TF strategy provides a significant contribution to the definition of the complete catalog of human genes and transcripts, because it appears to be particularly useful for identification of low abundance transcripts expressed in a restricted set of tissues as well as for the delineation of gene boundaries and alternatively spliced isoforms.
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