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de Souza WM, Fumagalli MJ, de Lima STS, Parise PL, Carvalho DCM, Hernandez C, de Jesus R, Delafiori J, Candido DS, Carregari VC, Muraro SP, Souza GF, Simões Mello LM, Claro IM, Díaz Y, Kato RB, Trentin LN, Costa CHS, Maximo ACBM, Cavalcante KF, Fiuza TS, Viana VAF, Melo MEL, Ferraz CPM, Silva DB, Duarte LMF, Barbosa PP, Amorim MR, Judice CC, Toledo-Teixeira DA, Ramundo MS, Aguilar PV, Araújo ELL, Costa FTM, Cerqueira-Silva T, Khouri R, Boaventura VS, Figueiredo LTM, Fang R, Moreno B, López-Vergès S, Mello LP, Skaf MS, Catharino RR, Granja F, Martins-de-Souza D, Plante JA, Plante KS, Sabino EC, Diamond MS, Eugenin E, Proença-Módena JL, Faria NR, Weaver SC. Pathophysiology of chikungunya virus infection associated with fatal outcomes. Cell Host Microbe 2024; 32:606-622.e8. [PMID: 38479396 PMCID: PMC11018361 DOI: 10.1016/j.chom.2024.02.011] [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: 08/16/2023] [Revised: 12/08/2023] [Accepted: 02/16/2024] [Indexed: 03/28/2024]
Abstract
Chikungunya virus (CHIKV) is a mosquito-borne alphavirus that causes acute, subacute, and chronic human arthritogenic diseases and, in rare instances, can lead to neurological complications and death. Here, we combined epidemiological, virological, histopathological, cytokine, molecular dynamics, metabolomic, proteomic, and genomic analyses to investigate viral and host factors that contribute to chikungunya-associated (CHIK) death. Our results indicate that CHIK deaths are associated with multi-organ infection, central nervous system damage, and elevated serum levels of pro-inflammatory cytokines and chemokines compared with survivors. The histopathologic, metabolite, and proteomic signatures of CHIK deaths reveal hemodynamic disorders and dysregulated immune responses. The CHIKV East-Central-South-African lineage infecting our study population causes both fatal and survival cases. Additionally, CHIKV infection impairs the integrity of the blood-brain barrier, as evidenced by an increase in permeability and altered tight junction protein expression. Overall, our findings improve the understanding of CHIK pathophysiology and the causes of fatal infections.
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Affiliation(s)
- William M de Souza
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky, College of Medicine, Lexington, KY, USA; Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA; Global Virus Network, Baltimore, MD, USA.
| | - Marcilio J Fumagalli
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Shirlene T S de Lima
- Laboratório Central de Saúde Pública do Ceará, Fortaleza, Ceará, Brazil; Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Pierina L Parise
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil; Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Deyse C M Carvalho
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; Laboratory of Immunobiotechnology, Biotechnology Center, Federal University of Paraíba, João Pessoa, Paraíba, Brazil
| | - Cristian Hernandez
- Department of Neurobiology, University of Texas Medical Branch, Galveston, TX, USA
| | - Ronaldo de Jesus
- Coordenação Geral dos Laboratórios de Saúde Pública, Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília, Brazil; Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Jeany Delafiori
- Innovare Biomarkers Laboratory, School of Pharmaceutical Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Darlan S Candido
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK; Department of Zoology, University of Oxford, Oxford, UK; Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Victor C Carregari
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Stefanie P Muraro
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Gabriela F Souza
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | | | - Ingra M Claro
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK; Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil; Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Yamilka Díaz
- Department of Research in Virology and Biotechnology, Gorgas Memorial Institute of Health Studies, Panama, Panama
| | - Rodrigo B Kato
- Coordenação Geral dos Laboratórios de Saúde Pública, Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília, Brazil; Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Lucas N Trentin
- Institute of Chemistry and Center for Computing in Engineering and Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Clauber H S Costa
- Institute of Chemistry and Center for Computing in Engineering and Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | | | | | - Tayna S Fiuza
- Laboratório Central de Saúde Pública do Ceará, Fortaleza, Ceará, Brazil; Programa de Pós Graduação em Bioinformática, Instituto Metrópole Digital, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Vânia A F Viana
- Laboratório Central de Saúde Pública do Ceará, Fortaleza, Ceará, Brazil
| | | | | | - Débora B Silva
- Laboratório Central de Saúde Pública do Ceará, Fortaleza, Ceará, Brazil
| | | | - Priscilla P Barbosa
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Mariene R Amorim
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Carla C Judice
- Laboratory of Tropical Diseases, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Daniel A Toledo-Teixeira
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Mariana S Ramundo
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil; Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Patricia V Aguilar
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA; Center for Tropical Diseases, Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Emerson L L Araújo
- Coordenação Geral de Atenção às Doenças Transmissíveis na Atenção Primária, Departamento de Gestão ao cuidado Integral, Secretaria de Atenção Primária à Saúde, Ministério da Saúde, Brasília, Brazil
| | - Fabio T M Costa
- Laboratory of Tropical Diseases, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Thiago Cerqueira-Silva
- Universidade Federal da Bahia, Faculdade de Medicina, Salvador, Bahia, Brazil; Fundação Oswaldo Cruz, Instituto Gonçalo Muniz, Laboratório de Medicina e Saúde Pública de Precisão, Salvador, Bahia, Brazil
| | - Ricardo Khouri
- Universidade Federal da Bahia, Faculdade de Medicina, Salvador, Bahia, Brazil; Fundação Oswaldo Cruz, Instituto Gonçalo Muniz, Laboratório de Medicina e Saúde Pública de Precisão, Salvador, Bahia, Brazil
| | - Viviane S Boaventura
- Universidade Federal da Bahia, Faculdade de Medicina, Salvador, Bahia, Brazil; Fundação Oswaldo Cruz, Instituto Gonçalo Muniz, Laboratório de Medicina e Saúde Pública de Precisão, Salvador, Bahia, Brazil; Hospital Santa Izabel, Santa Casa de Misericórdia da Bahia, Serviço de Otorrinolaringologia, Salvador, Bahia, Brazil
| | - Luiz Tadeu M Figueiredo
- Virology Research Centre, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Rong Fang
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Brechla Moreno
- Department of Research in Virology and Biotechnology, Gorgas Memorial Institute of Health Studies, Panama, Panama
| | - Sandra López-Vergès
- Department of Research in Virology and Biotechnology, Gorgas Memorial Institute of Health Studies, Panama, Panama; Sistema Nacional de Investigación from SENACYT, Panama, Panama
| | | | - Munir S Skaf
- Institute of Chemistry and Center for Computing in Engineering and Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Rodrigo R Catharino
- Innovare Biomarkers Laboratory, School of Pharmaceutical Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Fabiana Granja
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil; Biodiversity Research Centre, Federal University of Roraima, Boa Vista, Roraima, Brazil
| | - Daniel Martins-de-Souza
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil; D'Or Institute for Research and Education, São Paulo, São Paulo, Brazil; Experimental Medicine Research Cluster, University of Campinas, Campinas, São Paulo, Brazil
| | - Jessica A Plante
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
| | - Kenneth S Plante
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
| | - Ester C Sabino
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil; Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Michael S Diamond
- Departments of Medicine, Molecular Microbiology, Pathology & Immunology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Eliseo Eugenin
- Department of Neurobiology, University of Texas Medical Branch, Galveston, TX, USA
| | - José Luiz Proença-Módena
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Nuno R Faria
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK; Department of Zoology, University of Oxford, Oxford, UK; Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Scott C Weaver
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA; Global Virus Network, Baltimore, MD, USA; Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX, USA
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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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de Souza WM, Ribeiro GS, de Lima ST, de Jesus R, Moreira FR, Whittaker C, Sallum MAM, Carrington CV, Sabino EC, Kitron U, Faria NR, Weaver SC. Chikungunya: a decade of burden in the Americas. Lancet Reg Health Am 2024; 30:100673. [PMID: 38283942 PMCID: PMC10820659 DOI: 10.1016/j.lana.2023.100673] [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] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/24/2023] [Accepted: 12/29/2023] [Indexed: 01/30/2024]
Abstract
In the Americas, one decade following its emergence in 2013, chikungunya virus (CHIKV) continues to spread and cause epidemics across the region. To date, 3.7 million suspected and laboratory-confirmed chikungunya cases have been reported in 50 countries or territories in the Americas. Here, we outline the current status and epidemiological aspects of chikungunya in the Americas and discuss prospects for future research and public health strategies to combat CHIKV in the region.
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Affiliation(s)
- William M. de Souza
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky, College of Medicine, Lexington, KY, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
- Global Virus Network, Baltimore, MD, USA
| | - Guilherme S. Ribeiro
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Bahia, Brazil
- Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Salvador, Bahia, Brazil
| | - Shirlene T.S. de Lima
- Laboratório Central de Saúde Pública do Ceará, Fortaleza, Ceará, Brazil
- Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Ronaldo de Jesus
- Coordenação Geral dos Laboratórios de Saúde Pública, Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília, Brazil
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Filipe R.R. Moreira
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK
| | - Maria Anice M. Sallum
- Departamento de Epidemiologia, Faculdade de Saúde Pública, Universidade de São Paulo, Brazil
| | - Christine V.F. Carrington
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Republic of Trinidad and Tobago
| | - Ester C. Sabino
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Uriel Kitron
- Department of Environmental Sciences, Emory University, Atlanta, GA, USA
| | - Nuno R. Faria
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Department of Biology, University of Oxford, Oxford, UK
| | - Scott C. Weaver
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
- Global Virus Network, Baltimore, MD, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
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4
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Li SL, Prete CA, Zarebski AE, de Souza Santos AA, Sabino EC, Nascimento VH, Wu CH, Messina JP. The Brazilian COVID-19 vaccination campaign: a modelling analysis of sociodemographic factors on uptake. BMJ Open 2024; 14:e076354. [PMID: 38233051 PMCID: PMC10806735 DOI: 10.1136/bmjopen-2023-076354] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 11/15/2023] [Indexed: 01/19/2024] Open
Abstract
OBJECTIVE Dose shortages delayed access to COVID-19 vaccination. We aim to characterise inequality in two-dose vaccination by sociodemographic group across Brazil. DESIGN This is a cross-sectional study. SETTING We used data retrieved from the Brazilian Ministry of Health databases published between 17 January 2021 and 6 September 2021. METHODS We assessed geographical inequalities in full vaccination coverage and dose by age, sex, race and socioeconomic status. We developed a Campaign Optimality Index to characterise inequality in vaccination access due to premature vaccination towards younger populations before older and vulnerable populations were fully vaccinated. Generalised linear regression was used to investigate the risk of death and hospitalisation by age group, socioeconomic status and vaccination coverage. RESULTS Vaccination coverage is higher in the wealthier South and Southeast. Men, people of colour and low-income groups were more likely to be only partially vaccinated due to missing or delaying a second dose. Vaccination started prematurely for age groups under 50 years which may have hindered uptake in older age groups. Vaccination coverage was associated with a lower risk of death, especially in older age groups (ORs 9.7 to 29.0, 95% CI 9. 4 to 29.9). Risk of hospitalisation was greater in areas with higher vaccination rates due to higher access to care and reporting. CONCLUSIONS Vaccination inequality persists between states, age and demographic groups despite increasing uptake. The association between hospitalisation rates and vaccination is attributed to preferential delivery to areas of greater transmission and access to healthcare.
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Affiliation(s)
- Sabrina L Li
- School of Geography, University of Nottingham, Nottingham, UK
- School of Geography and the Environment, University of Oxford, Oxford, UK
| | - Carlos A Prete
- Department of Electronic Systems Engineering, University of São Paulo, São Paulo, Brazil
| | - Alexander E Zarebski
- School of Mathematics and Statistics, The University of Melbourne, Melbourne, Victoria, Australia
- Department of Zoology, University of Oxford, Oxford, UK
| | - Andreza Aruska de Souza Santos
- Oxford School of Global and Area Studies and Latin American Centre, University of Oxford, Oxford, UK
- King's Brazil Institute, King's College London, London, UK
| | - Ester C Sabino
- Departamento de Molestias Infecciosas e Parasitarias & Instituto de Medicina Tropical da Faculdade de Medicina, University of São Paulo, São Paulo, Brazil
| | - Vitor H Nascimento
- Department of Electronic Systems Engineering, University of São Paulo, São Paulo, Brazil
| | - Chieh-Hsi Wu
- School of Mathematical Sciences, University of Southhampton, Southhampton, UK
| | - Jane P Messina
- School of Geography and the Environment, University of Oxford, Oxford, UK
- Oxford School of Global and Area Studies, University of Oxford, Oxford, UK
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5
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Mirza JD, de Oliveira Guimarães L, Wilkinson S, Rocha EC, Bertanhe M, Helfstein VC, de-Deus JT, Claro IM, Cumley N, Quick J, Faria NR, Sabino EC, Kirchgatter K, Loman NJ. Tracking arboviruses, their transmission vectors and potential hosts by nanopore sequencing of mosquitoes. Microb Genom 2024; 10:001184. [PMID: 38240642 PMCID: PMC10868619 DOI: 10.1099/mgen.0.001184] [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: 11/03/2023] [Accepted: 01/08/2024] [Indexed: 01/23/2024] Open
Abstract
The risk to human health from mosquito-borne viruses such as dengue, chikungunya and yellow fever is increasing due to increased human expansion, deforestation and climate change. To anticipate and predict the spread and transmission of mosquito-borne viruses, a better understanding of the transmission cycle in mosquito populations is needed. We present a pathogen-agnostic combined sequencing protocol for identifying vectors, viral pathogens and their hosts or reservoirs using portable Oxford Nanopore sequencing. Using mosquitoes collected in São Paulo, Brazil, we extracted RNA for virus identification and DNA for blood meal and mosquito identification. Mosquitoes and blood meals were identified by comparing cytochrome c oxidase I (COI) sequences against a curated Barcode of Life Data System (BOLD). Viruses were identified using the SMART-9N protocol, which allows amplified DNA to be prepared with native barcoding for nanopore sequencing. Kraken 2 was employed to detect viral pathogens and Minimap2 and BOLD identified the contents of the blood meal. Due to the high similarity of some species, mosquito identification was conducted using blast after generation of consensus COI sequences using RACON polishing. This protocol can simultaneously uncover viral diversity, mosquito species and mosquito feeding habits. It also has the potential to increase understanding of mosquito genetic diversity and transmission dynamics of zoonotic mosquito-borne viruses.
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Affiliation(s)
- Jeremy D. Mirza
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK
- Department of Biosciences, University of Birmingham, Birmingham, UK
| | | | - Sam Wilkinson
- Department of Biosciences, University of Birmingham, Birmingham, UK
| | - Esmenia C. Rocha
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Mayara Bertanhe
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | | | | | - Ingra M. Claro
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, Imperial College London, London, UK
| | - Nicola Cumley
- Department of Biosciences, University of Birmingham, Birmingham, UK
| | - Joshua Quick
- Department of Biosciences, University of Birmingham, Birmingham, UK
| | - Nuno R. Faria
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, Imperial College London, London, UK
| | - Ester C. Sabino
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Karin Kirchgatter
- Instituto Pasteur, São Paulo, Brazil
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
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6
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Sunderraj A, Cunha LM, Avila M, Alexandria S, Ferreira AM, de Oliveira-da Silva LC, Ribeiro ALP, Nunes MDCP, Sabino EC, Landay A, Kalil J, Chevillard C, Cunha-Neto E, Feinstein MJ. Parasite DNA and Markers of Decreased Immune Activation Associate Prospectively with Cardiac Functional Decline over 10 Years among Trypanosoma cruzi Seropositive Individuals in Brazil. Int J Mol Sci 2023; 25:44. [PMID: 38203212 PMCID: PMC10779141 DOI: 10.3390/ijms25010044] [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: 09/07/2023] [Revised: 11/27/2023] [Accepted: 12/12/2023] [Indexed: 01/12/2024] Open
Abstract
Parasitemia and inflammatory markers are cross-sectionally associated with chronic Chagas cardiomyopathy (CCC) among patients with Trypanosoma cruzi. However, the prospective association of the parasite load and host immune response-related characteristics with CCC (that is, progressors) among T. cruzi seropositive individuals has only been partially defined. In a cohort of T. cruzi seropositive patients in Montes Claros and São Paulo, Brazil who were followed over 10 years, we identified the association of a baseline T. cruzi parasite load and systemic markers of inflammation with a decline in cardiac function and/or the presence of cardiac congestion 10 years later. The progressors (n = 21) were individuals with a significant decline in the left ventricular ejection fraction and/or elevated markers of cardiac congestion after 10 years. The controls (n = 31) had normal markers of cardiac function and congestion at the baseline and at the follow-up. They were matched with the progressors on age, sex, and genetic ancestry. The progressors had higher mean parasite loads at the baseline than the controls (18.3 vs. 0.605 DNA parasite equivalents/20 mL, p < 0.05). Of the 384 inflammation-related proteins analyzed, 47 differed significantly at a false discovery rate- (FDR-) corrected p < 0.05 between the groups. There were 44 of these 47 proteins that were significantly higher in the controls compared to in the progressors, including the immune activation markers CCL21, CXCL12, and HCLS1 and several of the tumor necrosis factor superfamily of proteins. Among the individuals who were seropositive for T. cruzi at the baseline and who were followed over 10 years, those with incident CCC at the 10-year marker had a comparatively higher baseline of T. cruzi parasitemia and lower baseline markers of immune activation and chemotaxis. These findings generate the hypothesis that the early impairment of pathogen-killing immune responses predisposes individuals to CCC, which merits further study.
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Affiliation(s)
- Ashwin Sunderraj
- Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Luisa Marin Cunha
- Faculdade de Ciências Médicas de Santos, UNILUS, Santos 11045-101, Brazil
| | - Matheus Avila
- Faculdade de Ciências Médicas de Santos, UNILUS, Santos 11045-101, Brazil
| | - Shaina Alexandria
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA;
| | - Ariela Mota Ferreira
- Graduate Program in Health Sciences, State University of Montes Claros, Montes Claros 39401-089, Brazil;
| | | | - Antonio L. P. Ribeiro
- Department of Internal Medicine, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil; (A.L.P.R.); (M.d.C.P.N.)
| | - Maria do Carmo Pereira Nunes
- Department of Internal Medicine, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil; (A.L.P.R.); (M.d.C.P.N.)
| | - Ester C. Sabino
- Institute of Tropical Medicine, University of São Paulo, São Paulo 05403-000, Brazil; (L.C.d.O.-d.S.)
| | - Alan Landay
- Division of Geriatrics and Gerontology, Department of Medicine, Rush University Medical Center, Chicago, IL 60612, USA
| | - Jorge Kalil
- Laboratory of Immunology, Heart Institute Instituto do Coração (InCor), School of Medicine, University of São Paulo, São Paulo 05403-000, Brazil;
| | - Christophe Chevillard
- Institut MarMaRa, TAGC Theories and Approaches of Genomic Complexity, Aix Marseille Université, 13385 Marseille, France;
| | - Edecio Cunha-Neto
- Laboratory of Immunology, Heart Institute Instituto do Coração (InCor), School of Medicine, University of São Paulo, São Paulo 05403-000, Brazil;
| | - Matthew J. Feinstein
- Division of Cardiology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
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7
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Carrera JP, Araúz D, Rojas A, Cardozo F, Stittleburg V, Morales Claro I, Galue J, Lezcano-Coba C, Romero Rebello Moreira F, -Rivera LF, Chen-Germán M, Moreno B, Capitan-Barrios Z, López-Vergès S, Pascale JM, Sabino EC, Valderrama A, Hanley KA, Donnelly CA, Vasilakis N, Faria NR, Waggoner JJ. Real-time RT-PCR for Venezuelan equine encephalitis complex, Madariaga, and Eastern equine encephalitis viruses: application in human and mosquito public health surveillance in Panama. J Clin Microbiol 2023; 61:e0015223. [PMID: 37982611 PMCID: PMC10729654 DOI: 10.1128/jcm.00152-23] [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: 02/27/2023] [Accepted: 09/08/2023] [Indexed: 11/21/2023] Open
Abstract
Eastern equine encephalitis virus (EEEV), Madariaga virus (MADV), and Venezuelan equine encephalitis virus complex (VEEV) are New World alphaviruses transmitted by mosquitoes. They cause febrile and sometimes severe neurological diseases in human and equine hosts. Detecting them during the acute phase is hindered by non-specific symptoms and limited diagnostic tools. We designed and clinically assessed real-time reverse transcription polymerase chain reaction assays (rRT-PCRs) for VEEV complex, MADV, and EEEV using whole-genome sequences. Validation involved 15 retrospective serum samples from 2015 to 2017 outbreaks, 150 mosquito pools from 2015, and 118 prospective samples from 2021 to 2022 surveillance in Panama. The rRT-PCRs detected VEEV complex RNA in 10 samples (66.7%) from outbreaks, with one having both VEEV complex and MADV RNAs. VEEV complex RNA was found in five suspected dengue cases from disease surveillance. The rRT-PCR assays identified VEEV complex RNA in three Culex (Melanoconion) vomerifer pools, leading to VEEV isolates in two. Phylogenetic analysis revealed the VEEV ID subtype in positive samples. Notably, 11.9% of dengue-like disease patients showed VEEV infections. Together, our rRT-PCR validation in human and mosquito samples suggests that this method can be incorporated into mosquito and human encephalitic alphavirus surveillance programs in endemic regions.
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Affiliation(s)
- Jean-Paul Carrera
- Department of Biology, University of Oxford, Oxford, United Kingdom
- Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Department of Research in Virology and Biotechnology, Gorgas Memorial Institute of Health Studies, Panama City, Panama
- Viral Emerging Disease Dynamics Group, Gorgas Memorial Institute of Health Studies, Panama City, Panama
| | - Dimelza Araúz
- Department of Research in Virology and Biotechnology, Gorgas Memorial Institute of Health Studies, Panama City, Panama
| | - Alejandra Rojas
- Departamento de Producción, Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, San Lorenzo, Paraguay
| | - Fátima Cardozo
- Departamento de Producción, Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, San Lorenzo, Paraguay
| | - Victoria Stittleburg
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
| | - Ingra Morales Claro
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- MRC Centre for Global Infectious Disease Analysis (MRC-GIDA), Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Josefrancisco Galue
- Department of Research in Virology and Biotechnology, Gorgas Memorial Institute of Health Studies, Panama City, Panama
- Viral Emerging Disease Dynamics Group, Gorgas Memorial Institute of Health Studies, Panama City, Panama
| | - Carlos Lezcano-Coba
- Department of Research in Virology and Biotechnology, Gorgas Memorial Institute of Health Studies, Panama City, Panama
- Viral Emerging Disease Dynamics Group, Gorgas Memorial Institute of Health Studies, Panama City, Panama
| | - Filipe Romero Rebello Moreira
- MRC Centre for Global Infectious Disease Analysis (MRC-GIDA), Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Luis Felipe -Rivera
- Department of Research in Virology and Biotechnology, Gorgas Memorial Institute of Health Studies, Panama City, Panama
- Viral Emerging Disease Dynamics Group, Gorgas Memorial Institute of Health Studies, Panama City, Panama
| | - Maria Chen-Germán
- Department of Research in Virology and Biotechnology, Gorgas Memorial Institute of Health Studies, Panama City, Panama
| | - Brechla Moreno
- Department of Research in Virology and Biotechnology, Gorgas Memorial Institute of Health Studies, Panama City, Panama
| | - Zeuz Capitan-Barrios
- Department of Research in Virology and Biotechnology, Gorgas Memorial Institute of Health Studies, Panama City, Panama
- Viral Emerging Disease Dynamics Group, Gorgas Memorial Institute of Health Studies, Panama City, Panama
- Departamento de Microbiología y Parasitología, Facultad de Ciencias Naturales, Exactas y Tecnología, Universidad de Panamá, Ciudad de Panamá, Panama
| | - Sandra López-Vergès
- Department of Research in Virology and Biotechnology, Gorgas Memorial Institute of Health Studies, Panama City, Panama
| | - Juan Miguel Pascale
- Clinical of Tropical Diseases and Research Unit, Gorgas Memorial Institute of Health Studies, Panama City, Panama
| | - Ester C. Sabino
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Anayansi Valderrama
- Viral Emerging Disease Dynamics Group, Gorgas Memorial Institute of Health Studies, Panama City, Panama
- Department of Medical Entomology, Gorgas Memorial Institute of Health Studies, Panama City, Panama
| | - Kathryn A. Hanley
- Department of Biology, New Mexico State University, Las Cruces, New Mexico, USA
| | - Christl A. Donnelly
- Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- MRC Centre for Global Infectious Disease Analysis (MRC-GIDA), Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Nikos Vasilakis
- Department of Pathology, The University of Texas Medical Branch, Galveston, Texas, USA
- Department of Preventive Medicine and Population Health, The University of Texas Medical Branch, Galveston, Texas, USA
- Center for Biodefense and Emerging Infectious Diseases, The University of Texas Medical Branch, Galveston, Texas, USA
- Center for Vector-Borne and Zoonotic Diseases, The University of Texas Medical Branch, Galveston, Texas, USA
- Center for Tropical Diseases, The University of Texas Medical Branch, Galveston, Texas, USA
- Institute for Human Infection and Immunity, The University of Texas Medical Branch, Galveston, Texas, USA
| | - Nuno R. Faria
- Department of Biology, University of Oxford, Oxford, United Kingdom
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- MRC Centre for Global Infectious Disease Analysis (MRC-GIDA), Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Jesse J. Waggoner
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
- Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
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8
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Mattioli IA, Castro KR, Sedenho GC, Macedo LJA, Oliveira MN, Manuli ER, Sabino EC, Crespilho FN. Expanding the application of graphene vertical devices to dual femtomolar detection of SARS-CoV-2 receptor binding domain in serum and saliva. Biosens Bioelectron 2023; 239:115614. [PMID: 37607446 DOI: 10.1016/j.bios.2023.115614] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 08/16/2023] [Accepted: 08/17/2023] [Indexed: 08/24/2023]
Abstract
The emergence of the graphene-based hybrid electrical-electrochemical vertical device (EEVD) has introduced a promising nanostructured biosensor tailored for point-of-care applications. In this study, we present an innovative EEVD capable of simultaneously detecting the receptor binding domain (RBD) of the SARS-CoV-2 spike protein in both serum and saliva. The foundation of the EEVD lies in a poly-neutral red-graphene heterojunction, which has been enhanced with a bioconjugate of gold nanoparticles and antibodies. The biodevice demonstrates a remarkable limit of detection, registering at the femtomolar scale (2.86 fmol L-1 or 0.1 pg mL-1). Its sensitivity is characterized by a 6.1 mV/decade response, and its operational range spans 10-12 to 10-7 g mL-1 in both serum and saliva samples. With a 20.0 μL of biological samples and a rapid processing time of under 10 min, the EEVD achieves the feat of dual antigen detection. The tests achieved 100.0% specificity, accuracy, and sensitivity in saliva, and 100.0% specificity, 88.9% accuracy, and 80.0% sensitivity in serum. This study highlights the EEVD as a low-cost solution of rapid viral detection during the crucial initial phases of COVID-19 infections.
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Affiliation(s)
- Isabela A Mattioli
- São Carlos Institute of Chemistry, University of São Paulo, São Carlos, SP, 13560-970, Brazil
| | - Karla R Castro
- São Carlos Institute of Chemistry, University of São Paulo, São Carlos, SP, 13560-970, Brazil
| | - Graziela C Sedenho
- São Carlos Institute of Chemistry, University of São Paulo, São Carlos, SP, 13560-970, Brazil
| | - Lucyano J A Macedo
- São Carlos Institute of Chemistry, University of São Paulo, São Carlos, SP, 13560-970, Brazil
| | - Mona N Oliveira
- Biolinker Synthetic Biology EIRELI, Cotia, SP, 06715-862, Brazil
| | - Erika R Manuli
- Institute of Tropical Medicine, Faculty of Medicine, University of São Paulo, São Paulo, SP, 05403-000, Brazil; LIM-46 HC-FMUSP - Laboratory of Medical Investigation, Clinical Hospital, Faculty of Medicine, University of São Paulo, São Paulo, SP, 01246903, Brazil
| | - Ester C Sabino
- Institute of Tropical Medicine, Faculty of Medicine, University of São Paulo, São Paulo, SP, 05403-000, Brazil; LIM-46 HC-FMUSP - Laboratory of Medical Investigation, Clinical Hospital, Faculty of Medicine, University of São Paulo, São Paulo, SP, 01246903, Brazil
| | - Frank N Crespilho
- São Carlos Institute of Chemistry, University of São Paulo, São Carlos, SP, 13560-970, Brazil.
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9
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Policarpo JMP, Ramos AAGF, Dye C, Faria NR, Leal FE, Moraes OJS, Parag KV, Peixoto PS, Buss L, Sabino EC, Nascimento VH, Deppman A. Scale-free dynamics of COVID-19 in a Brazilian city. Appl Math Model 2023; 121:166-184. [PMID: 37151217 PMCID: PMC10154131 DOI: 10.1016/j.apm.2023.03.039] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 03/13/2023] [Accepted: 03/29/2023] [Indexed: 05/09/2023]
Abstract
A common basis to address the dynamics of directly transmitted infectious diseases, such as COVID-19, are compartmental (or SIR) models. SIR models typically assume homogenous population mixing, a simplification that is convenient but unrealistic. Here we validate an existing model of a scale-free fractal infection process using high-resolution data on COVID-19 spread in São Caetano, Brazil. We find that transmission can be described by a network in which each infectious individual has a small number of susceptible contacts, of the order of 2-5. This model parameter correlated tightly with physical distancing measured by mobile phone data, such that in periods of greater distancing the model recovered a lower average number of contacts, and vice versa. We show that the SIR model is a special case of our scale-free fractal process model in which the parameter that reflects population structure is set at unity, indicating homogeneous mixing. Our more general framework better explained the dynamics of COVID-19 in São Caetano, used fewer parameters than a standard SIR model and accounted for geographically localized clusters of disease. Our model requires further validation in other locations and with other directly transmitted infectious agents.
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Affiliation(s)
| | - A A G F Ramos
- Instituto de Física - Universidade de São Paulo, Brazil
| | - C Dye
- Department of Biology, University of Oxford, UK
| | - N R Faria
- Department of Biology, University of Oxford, UK
- Imperial Coll London, MRC Ctr Global Infect Dis Anal, Sch Publ Helth, London, England, UK
- Faculdade de Medicina - Universidade de São Paulo, Brazil
| | - F E Leal
- Universidade de São Caetano do Sul, São Caetano do Sul and Programa de Oncovirologia - Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - O J S Moraes
- Instituto de Física - Universidade de São Paulo, Brazil
| | - K V Parag
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London W2 1PG, UK
| | - P S Peixoto
- Instituto de Matemática e Estatística, Universidade de São Paulo, Brazil
| | - L Buss
- Faculdade de Medicina - Universidade de São Paulo, Brazil
| | - E C Sabino
- Faculdade de Medicina - Universidade de São Paulo, Brazil
| | | | - A Deppman
- Instituto de Física - Universidade de São Paulo, Brazil
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10
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Charlys da Costa A, Mendes-Correa MC, Tozetto-Mendoza TR, Villas-Boas LS, de Paula AV, Paiao HGO, Leal FE, Ferreira NE, Honorato L, Leal E, Grandi G, dos Santos Morais V, Manuli ER, Sabino EC, Witkin SS. Detailed characterization of Redondovirus in saliva of SARS-CoV-2-infected individuals in Sao Paulo, Brazil. PLoS One 2023; 18:e0291027. [PMID: 37651462 PMCID: PMC10470920 DOI: 10.1371/journal.pone.0291027] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 08/20/2023] [Indexed: 09/02/2023] Open
Abstract
BACKGROUND Redondovirus (ReDoV) is a DNA virus present in the respiratory tract of many healthy individuals. Since SARS-CoV-2, the virus responsible for COVID-19, also primarily infects the same site, we evaluated whether ReDoV was present at increased frequency in patients with COVID-19 and influenced infection parameters. METHODS Saliva samples were collected weekly from 59 individuals with COVID-19 and from 132 controls. ReDoV was detected by polymerase chain reaction and the genotypes were identified by metagenomics. Torque Teno Virus (TTV) in these samples were previously reported. RESULTS ReDoV was detected in saliva more frequently from COVID-19 patients (72.9%) than from controls (50.0%) (p = 0.0015). There were no associations between ReDoV detection and either continuous or intermittent SARS-CoV-2 shedding, the duration of SARS-CoV-2 detection in saliva, patients' sex or if infection was by the B1 or Gamma strain. The two ReDoV strains, Brisavirus and Vientovirus, were present in equivalent frequencies in ReDoV-positive COVID-19 patients and controls. Phylogenetic analysis suggested that the two ReDoV strains in Brazil were similar to strains previously detected on other continents. CONCLUSION ReDoV expression in saliva is increased in males and females in Brazil with mild COVID-19 but its presence does not appear to influence properties of the SARS-CoV-2 infection.
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Affiliation(s)
- Antonio Charlys da Costa
- Laboratório de Investigação Médica em Virologia, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Maria C. Mendes-Correa
- Laboratório de Investigação Médica em Virologia, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Molestias Infecciosas e Parasitarias da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Tania Regina Tozetto-Mendoza
- Laboratório de Investigação Médica em Virologia, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Faculdade de Medicina da Universidade Municipal de Sao Caetano do Sul, São Paulo, Brazil
| | - Lucy S. Villas-Boas
- Laboratório de Investigação Médica em Virologia, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Faculdade de Medicina da Universidade Municipal de Sao Caetano do Sul, São Paulo, Brazil
| | - Anderson Vicente de Paula
- Laboratório de Investigação Médica em Virologia, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Heuder Gustavo Oliveira Paiao
- Laboratório de Investigação Médica em Virologia, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Molestias Infecciosas e Parasitarias da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Fabio E. Leal
- Faculdade de Medicina da Universidade Municipal de Sao Caetano do Sul, São Paulo, Brazil
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Noely E. Ferreira
- Laboratório de Investigação Médica em Virologia, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Layla Honorato
- Laboratório de Investigação Médica em Virologia, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Molestias Infecciosas e Parasitarias da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Elcio Leal
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Pará, Brazil
| | | | - Vanessa dos Santos Morais
- Departamento de Molestias Infecciosas e Parasitarias da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Erika R. Manuli
- Departamento de Molestias Infecciosas e Parasitarias da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Faculdade de Medicina da Universidade Municipal de Sao Caetano do Sul, São Paulo, Brazil
| | - Ester C. Sabino
- Laboratório de Investigação Médica em Virologia, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Molestias Infecciosas e Parasitarias da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Faculdade de Medicina da Universidade Municipal de Sao Caetano do Sul, São Paulo, Brazil
| | - Steven S. Witkin
- Laboratório de Investigação Médica em Virologia, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Molestias Infecciosas e Parasitarias da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY, United States of America
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11
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Pereira GM, Manuli ER, Coulon L, Côrtes MF, Ramundo MS, Dromenq L, Larue-Triolet A, Raymond F, Tourneur C, Lázari CDS, Brasil P, Filippis AMBD, Paranhos-Baccalà G, Banz A, Sabino EC. Performance Evaluation of VIDAS ® Diagnostic Assays Detecting Anti-Chikungunya Virus IgM and IgG Antibodies: An International Study. Diagnostics (Basel) 2023; 13:2306. [PMID: 37443699 DOI: 10.3390/diagnostics13132306] [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: 04/25/2023] [Revised: 06/26/2023] [Accepted: 06/30/2023] [Indexed: 07/15/2023] Open
Abstract
Chikungunya (CHIK) is a debilitating mosquito-borne disease with an epidemiology and early clinical symptoms similar to those of other arboviruses-triggered diseases such as dengue or Zika. Accurate and rapid diagnosis of CHIK virus (CHIKV) infection is therefore challenging. This international study evaluated the performance of the automated VIDAS® anti-CHIKV IgM and IgG assays compared to that of manual competitor IgM and IgG ELISA for the detection of anti-CHIKV IgM and IgG antibodies in 660 patients with suspected CHIKV infection. Positive and negative agreements of the VIDAS® CHIKV assays with ELISA ranged from 97.5% to 100.0%. The sensitivity of the VIDAS® CHIKV assays evaluated in patients with a proven CHIKV infection confirmed reported kinetics of anti-CHIKV IgM and IgG response, with a positive detection of 88.2-100.0% for IgM ≥ 5 days post symptom onset and of 100.0% for IgG ≥ 11 days post symptom onset. Our study also demonstrated the superiority of ELISA and VIDAS® assays over rapid diagnostic IgM/IgG tests. The analytical performance of VIDAS® anti-CHIKV IgM and IgG assays was excellent, with a high precision (coefficients of variation ≤ 7.4%) and high specificity (cross-reactivity rate ≤ 2.9%). This study demonstrates the suitability of the automated VIDAS® anti-CHIKV IgM and IgG assays to diagnose CHIKV infections and supports its applicability for epidemiological surveillance and differential diagnosis in regions endemic for CHIKV.
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Affiliation(s)
- Geovana M Pereira
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Erika R Manuli
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, Brazil
- Faculdade de Medicina da Universidade Municipal de São Caetano do Sul, São Paulo 09521-160, Brazil
- Laboratório de Investigação Médica/Parasitologia LIM/46, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-010, Brazil
| | | | - Marina F Côrtes
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Mariana S Ramundo
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, Brazil
| | | | | | | | | | - Carolina Dos Santos Lázari
- Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-010, Brazil
| | - Patricia Brasil
- Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-360, Brazil
| | - Ana Maria Bispo de Filippis
- Laboratório de Arbovírus e Vírus Hemorrágicos, Instituto Oswaldo Cruz/Fiocruz, Rio de Janeiro 21040-360, Brazil
| | - Glaucia Paranhos-Baccalà
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, Brazil
- bioMérieux, 69280 Marcy l'Etoile, France
| | - Alice Banz
- bioMérieux, 69280 Marcy l'Etoile, France
| | - Ester C Sabino
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, Brazil
- Faculdade de Medicina da Universidade Municipal de São Caetano do Sul, São Paulo 09521-160, Brazil
- Laboratório de Investigação Médica/Parasitologia LIM/46, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-010, Brazil
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12
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Jidling C, Gedon D, Schön TB, Oliveira CDL, Cardoso CS, Ferreira AM, Giatti L, Barreto SM, Sabino EC, Ribeiro ALP, Ribeiro AH. Screening for Chagas disease from the electrocardiogram using a deep neural network. PLoS Negl Trop Dis 2023; 17:e0011118. [PMID: 37399207 PMCID: PMC10361500 DOI: 10.1371/journal.pntd.0011118] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 07/21/2023] [Accepted: 05/25/2023] [Indexed: 07/05/2023] Open
Abstract
BACKGROUND Worldwide, it is estimated that over 6 million people are infected with Chagas disease (ChD). It is a neglected disease that can lead to severe heart conditions in its chronic phase. While early treatment can avoid complications, the early-stage detection rate is low. We explore the use of deep neural networks to detect ChD from electrocardiograms (ECGs) to aid in the early detection of the disease. METHODS We employ a convolutional neural network model that uses 12-lead ECG data to compute the probability of a ChD diagnosis. Our model is developed using two datasets which jointly comprise over two million entries from Brazilian patients: The SaMi-Trop study focusing on ChD patients, enriched with data from the CODE study from the general population. The model's performance is evaluated on two external datasets: the REDS-II, a study focused on ChD with 631 patients, and the ELSA-Brasil study, with 13,739 civil servant patients. FINDINGS Evaluating our model, we obtain an AUC-ROC of 0.80 (CI 95% 0.79-0.82) for the validation set (samples from CODE and SaMi-Trop), and in external validation datasets: 0.68 (CI 95% 0.63-0.71) for REDS-II and 0.59 (CI 95% 0.56-0.63) for ELSA-Brasil. In the latter, we report a sensitivity of 0.52 (CI 95% 0.47-0.57) and 0.36 (CI 95% 0.30-0.42) and a specificity of 0.77 (CI 95% 0.72-0.81) and 0.76 (CI 95% 0.75-0.77), respectively. Additionally, when considering only patients with Chagas cardiomyopathy as positive, the model achieved an AUC-ROC of 0.82 (CI 95% 0.77-0.86) for REDS-II and 0.77 (CI 95% 0.68-0.85) for ELSA-Brasil. INTERPRETATION The neural network detects chronic Chagas cardiomyopathy (CCC) from ECG-with weaker performance for early-stage cases. Future work should focus on curating large higher-quality datasets. The CODE dataset, our largest development dataset includes self-reported and therefore less reliable labels, limiting performance for non-CCC patients. Our findings can improve ChD detection and treatment, particularly in high-prevalence areas.
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Affiliation(s)
- Carl Jidling
- Department of Information Technology, Uppsala University, Uppsala, Sweden
| | - Daniel Gedon
- Department of Information Technology, Uppsala University, Uppsala, Sweden
| | - Thomas B. Schön
- Department of Information Technology, Uppsala University, Uppsala, Sweden
| | | | - Clareci Silva Cardoso
- Preventive Medicine, School of Medicine, Universidade Federal de São João del-Rei, Divinópolis, Brazil
| | - Ariela Mota Ferreira
- Graduate Program in Health Sciences, Universidade Estadual de Montes Claros, Montes Claros, Brazil
| | - Luana Giatti
- Preventive Medicine, School of Medicine, Clinical Hospital/EBSERH, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Sandhi Maria Barreto
- Preventive Medicine, School of Medicine, Clinical Hospital/EBSERH, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Ester C. Sabino
- Instituto de Medicina Tropical da Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Antonio L. P. Ribeiro
- Department of Internal Medicine, Faculdade de Medicina, Telehealth Center, Hospital das Clínicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Antônio H. Ribeiro
- Department of Information Technology, Uppsala University, Uppsala, Sweden
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13
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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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14
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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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15
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de Souza WM, de Lima STS, Simões Mello LM, Candido DS, Buss L, Whittaker C, Claro IM, Chandradeva N, Granja F, de Jesus R, Lemos PS, Toledo-Teixeira DA, Barbosa PP, Firmino ACL, Amorim MR, Duarte LMF, Pessoa IB, Forato J, Vasconcelos IL, Maximo ACBM, Araújo ELL, Perdigão Mello L, Sabino EC, Proença-Módena JL, Faria NR, Weaver SC. Spatiotemporal dynamics and recurrence of chikungunya virus in Brazil: an epidemiological study. Lancet Microbe 2023; 4:e319-e329. [PMID: 37031687 PMCID: PMC10281060 DOI: 10.1016/s2666-5247(23)00033-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 12/13/2022] [Accepted: 01/27/2023] [Indexed: 04/09/2023]
Abstract
BACKGROUND Chikungunya virus (CHIKV) is an Aedes mosquito-borne virus that has caused large epidemics linked to acute, chronic, and severe clinical outcomes. Currently, Brazil has the highest number of chikungunya cases in the Americas. We aimed to investigate the spatiotemporal dynamics and recurrence pattern of chikungunya in Brazil since its introduction in 2013. METHODS In this epidemiological study, we used CHIKV genomic sequencing data, CHIKV vector information, and aggregate clinical data on chikungunya cases from Brazil. The genomic data comprised 241 Brazilian CHIKV genome sequences from GenBank (n=180) and the 2022 CHIKV outbreak in Ceará state (n=61). The vector data (Breteau index and House index) were obtained from the Brazilian Ministry of Health for all 184 municipalities in Ceará state and 116 municipalities in Tocantins state in 2022. Epidemiological data on laboratory-confirmed cases of chikungunya between 2013 and 2022 were obtained from the Brazilian Ministry of Health and Laboratory of Public Health of Ceará. We assessed the spatiotemporal dynamics of chikungunya in Brazil via time series, mapping, age-sex distribution, cumulative case-fatality, linear correlation, logistic regression, and phylogenetic analyses. FINDINGS Between March 3, 2013, and June 4, 2022, 253 545 laboratory-confirmed chikungunya cases were reported in 3316 (59·5%) of 5570 municipalities, mainly distributed in seven epidemic waves from 2016 to 2022. To date, Ceará in the northeast has been the most affected state, with 77 418 cases during the two largest epidemic waves in 2016 and 2017 and the third wave in 2022. From 2016 to 2022 in Ceará, the odds of being CHIKV-positive were higher in females than in males (odds ratio 0·87, 95% CI 0·85-0·89, p<0·0001), and the cumulative case-fatality ratio was 1·3 deaths per 1000 cases. Chikungunya recurrences in the states of Ceará, Tocantins (recurrence in 2022), and Pernambuco (recurrence in 2021) were limited to municipalities with few or no previously reported cases in the previous epidemic waves. The recurrence of chikungunya in Ceará in 2022 was associated with a new East-Central-South-African lineage. Population density metrics of the main CHIKV vector in Brazil, Aedes aegypti, were not correlated spatially with locations of chikungunya recurrence in Ceará and Tocantins. INTERPRETATION Spatial heterogeneity of CHIKV spread and population immunity might explain the recurrence pattern of chikungunya in Brazil. These results can be used to inform public health interventions to prevent future chikungunya epidemic waves in urban settings. FUNDING Global Virus Network, Burroughs Wellcome Fund, Wellcome Trust, US National Institutes of Health, São Paulo Research Foundation, Brazil Ministry of Education, UK Medical Research Council, Brazilian National Council for Scientific and Technological Development, and UK Royal Society. TRANSLATION For the Portuguese translation of the abstract see Supplementary Materials section.
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Affiliation(s)
- William M de Souza
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA.
| | - Shirlene T S de Lima
- Laboratório Central de Saúde Pública do Ceará, Fortaleza, Brazil; Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
| | | | - Darlan S Candido
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK; Department of Zoology, University of Oxford, Oxford, UK; Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Lewis Buss
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK
| | - Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK; The Abdul Latif Jameel Institute for Disease and Emergency Analytics, School of Public Health, Imperial College London, London, UK
| | - Ingra M Claro
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK; Department of Zoology, University of Oxford, Oxford, UK; Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Nilani Chandradeva
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK
| | - Fabiana Granja
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil; Biodiversity Research Centre, Federal University of Roraima, Boa Vista, Brazil
| | - Ronaldo de Jesus
- Ministério da Saúde, Departamento de Articulação Estratégica de Vigilância em Saúde, Brasilia, Brazil; Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Poliana S Lemos
- Ministério da Saúde, Departamento de Articulação Estratégica de Vigilância em Saúde, Brasilia, Brazil
| | - Daniel A Toledo-Teixeira
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Priscilla P Barbosa
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
| | | | - Mariene R Amorim
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
| | | | - Ivan B Pessoa
- Laboratório Central de Saúde Pública do Ceará, Fortaleza, Brazil
| | - Julia Forato
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
| | | | | | - Emerson L L Araújo
- Ministério da Saúde, Departamento de Articulação Estratégica de Vigilância em Saúde, Brasilia, Brazil
| | | | - Ester C Sabino
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil; Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - José Luiz Proença-Módena
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil; Hub of Global Health, University of Campinas, Campinas, Brazil
| | - Nuno R Faria
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK; Department of Zoology, University of Oxford, Oxford, UK; Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Scott C Weaver
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
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16
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Claro IM, Ramundo MS, Coletti TM, da Silva CAM, Valenca IN, Candido DS, Sales FCS, Manuli ER, de Jesus JG, de Paula A, Felix AC, Andrade PDS, Pinho MC, Souza WM, Amorim MR, Proenca-Modena JL, Kallas EG, Levi JE, Faria NR, Sabino EC, Loman NJ, Quick J. Rapid viral metagenomics using SMART-9N amplification and nanopore sequencing. Wellcome Open Res 2023; 6:241. [PMID: 37224315 PMCID: PMC10189296 DOI: 10.12688/wellcomeopenres.17170.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [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] [Accepted: 04/05/2023] [Indexed: 12/08/2023] Open
Abstract
Emerging and re-emerging viruses are a global health concern. Genome sequencing as an approach for monitoring circulating viruses is currently hampered by complex and expensive methods. Untargeted, metagenomic nanopore sequencing can provide genomic information to identify pathogens, prepare for or even prevent outbreaks. SMART (Switching Mechanism at the 5' end of RNA Template) is a popular approach for RNA-Seq but most current methods rely on oligo-dT priming to target polyadenylated mRNA molecules. We have developed two random primed SMART-Seq approaches, a sequencing agnostic approach 'SMART-9N' and a version compatible rapid adapters available from Oxford Nanopore Technologies 'Rapid SMART-9N'. The methods were developed using viral isolates, clinical samples, and compared to a gold-standard amplicon-based method. From a Zika virus isolate the SMART-9N approach recovered 10kb of the 10.8kb RNA genome in a single nanopore read. We also obtained full genome coverage at a high depth coverage using the Rapid SMART-9N, which takes only 10 minutes and costs up to 45% less than other methods. We found the limits of detection of these methods to be 6 focus forming units (FFU)/mL with 99.02% and 87.58% genome coverage for SMART-9N and Rapid SMART-9N respectively. Yellow fever virus plasma samples and SARS-CoV-2 nasopharyngeal samples previously confirmed by RT-qPCR with a broad range of Ct-values were selected for validation. Both methods produced greater genome coverage when compared to the multiplex PCR approach and we obtained the longest single read of this study (18.5 kb) with a SARS-CoV-2 clinical sample, 60% of the virus genome using the Rapid SMART-9N method. This work demonstrates that SMART-9N and Rapid SMART-9N are sensitive, low input, and long-read compatible alternatives for RNA virus detection and genome sequencing and Rapid SMART-9N improves the cost, time, and complexity of laboratory work.
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Affiliation(s)
- Ingra M. Claro
- Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, SW7 2AZ, UK
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Mariana S. Ramundo
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
| | - Thais M. Coletti
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
| | - Camila A. M. da Silva
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
| | - Ian N. Valenca
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
| | - Darlan S. Candido
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, SW7 2AZ, UK
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
- Department of Zoology, University of Oxford, Oxford, OX1 3SZ, UK
| | - Flavia C. S. Sales
- Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
| | - Erika R. Manuli
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
| | - Jaqueline G. de Jesus
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, SW7 2AZ, UK
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
| | - Anderson de Paula
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
| | - Alvina Clara Felix
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
| | - Pamela dos Santos Andrade
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
- Faculdade de Saúde Pública da Universidade de São Paulo, Sao Paulo, 01246-904, Brazil
| | - Mariana C. Pinho
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
| | - William M. Souza
- World Reference Center for Emerging Viruses and Arboviruses and Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Mariene R. Amorim
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, 13083-862, Brazil
| | - José Luiz Proenca-Modena
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, 13083-862, Brazil
- Experimental Medicine Research Cluster, University of Campinas, Campinas, 13083-862, Brazil
| | - Esper G. Kallas
- Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
| | - José Eduardo Levi
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
- DASA, Sao Paulo, 06455-010, Brazil
| | - Nuno Rodrigues Faria
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, SW7 2AZ, UK
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
- Department of Zoology, University of Oxford, Oxford, OX1 3SZ, UK
| | - Ester C. Sabino
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
| | - Nicholas J. Loman
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Joshua Quick
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
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17
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Claro IM, Ramundo MS, Coletti TM, da Silva CAM, Valenca IN, Candido DS, Sales FCS, Manuli ER, de Jesus JG, de Paula A, Felix AC, Andrade PDS, Pinho MC, Souza WM, Amorim MR, Proenca-Modena JL, Kallas EG, Levi JE, Faria NR, Sabino EC, Loman NJ, Quick J. Rapid viral metagenomics using SMART-9N amplification and nanopore sequencing. Wellcome Open Res 2023; 6:241. [PMID: 37224315 PMCID: PMC10189296 DOI: 10.12688/wellcomeopenres.17170.2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/05/2023] [Indexed: 05/26/2023] Open
Abstract
Emerging and re-emerging viruses are a global health concern. Genome sequencing as an approach for monitoring circulating viruses is currently hampered by complex and expensive methods. Untargeted, metagenomic nanopore sequencing can provide genomic information to identify pathogens, prepare for or even prevent outbreaks. SMART (Switching Mechanism at the 5' end of RNA Template) is a popular approach for RNA-Seq but most current methods rely on oligo-dT priming to target polyadenylated mRNA molecules. We have developed two random primed SMART-Seq approaches, a sequencing agnostic approach 'SMART-9N' and a version compatible rapid adapters available from Oxford Nanopore Technologies 'Rapid SMART-9N'. The methods were developed using viral isolates, clinical samples, and compared to a gold-standard amplicon-based method. From a Zika virus isolate the SMART-9N approach recovered 10kb of the 10.8kb RNA genome in a single nanopore read. We also obtained full genome coverage at a high depth coverage using the Rapid SMART-9N, which takes only 10 minutes and costs up to 45% less than other methods. We found the limits of detection of these methods to be 6 focus forming units (FFU)/mL with 99.02% and 87.58% genome coverage for SMART-9N and Rapid SMART-9N respectively. Yellow fever virus plasma samples and SARS-CoV-2 nasopharyngeal samples previously confirmed by RT-qPCR with a broad range of Ct-values were selected for validation. Both methods produced greater genome coverage when compared to the multiplex PCR approach and we obtained the longest single read of this study (18.5 kb) with a SARS-CoV-2 clinical sample, 60% of the virus genome using the Rapid SMART-9N method. This work demonstrates that SMART-9N and Rapid SMART-9N are sensitive, low input, and long-read compatible alternatives for RNA virus detection and genome sequencing and Rapid SMART-9N improves the cost, time, and complexity of laboratory work.
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Affiliation(s)
- Ingra M. Claro
- Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, SW7 2AZ, UK
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Mariana S. Ramundo
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
| | - Thais M. Coletti
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
| | - Camila A. M. da Silva
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
| | - Ian N. Valenca
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
| | - Darlan S. Candido
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, SW7 2AZ, UK
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
- Department of Zoology, University of Oxford, Oxford, OX1 3SZ, UK
| | - Flavia C. S. Sales
- Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
| | - Erika R. Manuli
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
| | - Jaqueline G. de Jesus
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, SW7 2AZ, UK
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
| | - Anderson de Paula
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
| | - Alvina Clara Felix
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
| | - Pamela dos Santos Andrade
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
- Faculdade de Saúde Pública da Universidade de São Paulo, Sao Paulo, 01246-904, Brazil
| | - Mariana C. Pinho
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
| | - William M. Souza
- World Reference Center for Emerging Viruses and Arboviruses and Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Mariene R. Amorim
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, 13083-862, Brazil
| | - José Luiz Proenca-Modena
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, 13083-862, Brazil
- Experimental Medicine Research Cluster, University of Campinas, Campinas, 13083-862, Brazil
| | - Esper G. Kallas
- Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
| | - José Eduardo Levi
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
- DASA, Sao Paulo, 06455-010, Brazil
| | - Nuno Rodrigues Faria
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, SW7 2AZ, UK
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
- Department of Zoology, University of Oxford, Oxford, OX1 3SZ, UK
| | - Ester C. Sabino
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, 05403-000, Brazil
| | - Nicholas J. Loman
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Joshua Quick
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
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18
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Cato LD, Li R, Lu HY, Yu F, Wissman M, Mkumbe BS, Ekwattanakit S, Deelen P, Mwita L, Sangeda R, Suksangpleng T, Riolueang S, Bronson PG, Paul DS, Kawabata E, Astle WJ, Aguet F, Ardlie K, de Lapuente Portilla AL, Kang G, Zhang Y, Nouraie SM, Gordeuk VR, Gladwin MT, Garrett ME, Ashley-Koch A, Telen MJ, Custer B, Kelly S, Dinardo CL, Sabino EC, Loureiro P, Carneiro-Proietti AB, Maximo C, Méndez A, Hammerer-Lercher A, Sheehan VA, Weiss MJ, Franke L, Nilsson B, Butterworth AS, Viprakasit V, Nkya S, Sankaran VG. Genetic regulation of fetal hemoglobin across global populations. medRxiv 2023:2023.03.24.23287659. [PMID: 36993312 PMCID: PMC10055601 DOI: 10.1101/2023.03.24.23287659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
Human genetic variation has enabled the identification of several key regulators of fetal-to-adult hemoglobin switching, including BCL11A, resulting in therapeutic advances. However, despite the progress made, limited further insights have been obtained to provide a fuller accounting of how genetic variation contributes to the global mechanisms of fetal hemoglobin (HbF) gene regulation. Here, we have conducted a multi-ancestry genome-wide association study of 28,279 individuals from several cohorts spanning 5 continents to define the architecture of human genetic variation impacting HbF. We have identified a total of 178 conditionally independent genome-wide significant or suggestive variants across 14 genomic windows. Importantly, these new data enable us to better define the mechanisms by which HbF switching occurs in vivo. We conduct targeted perturbations to define BACH2 as a new genetically-nominated regulator of hemoglobin switching. We define putative causal variants and underlying mechanisms at the well-studied BCL11A and HBS1L-MYB loci, illuminating the complex variant-driven regulation present at these loci. We additionally show how rare large-effect deletions in the HBB locus can interact with polygenic variation to influence HbF levels. Our study paves the way for the next generation of therapies to more effectively induce HbF in sickle cell disease and β-thalassemia.
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Affiliation(s)
- Liam D. Cato
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Rick Li
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Henry Y. Lu
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Fulong Yu
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Mariel Wissman
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Baraka S. Mkumbe
- Sickle Cell Program, Department of Hematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- Department of Biochemistry, Muhimbili University of Health and Allied Science, Dar es Salaam, Tanzania
- Department of Artificial Intelligence and Innovative Medicine, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Supachai Ekwattanakit
- Siriraj Thalassemia Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Patrick Deelen
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Oncode Institute, Amsterdam, the Netherlands
| | - Liberata Mwita
- Department of Pharmaceutical Microbiology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Raphael Sangeda
- Sickle Cell Program, Department of Hematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- Department of Pharmaceutical Microbiology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Thidarat Suksangpleng
- Siriraj Thalassemia Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Suchada Riolueang
- Siriraj Thalassemia Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Paola G. Bronson
- R&D Translational Biology, Biogen, Cambridge, Massachusetts, USA
| | - Dirk S. Paul
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK
| | - Emily Kawabata
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - William J. Astle
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- National Institute for Health and Care Research Blood and Transplant Research Unit in Donor Health and Behaviour, University of Cambridge, Cambridge, UK
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
- NHS Blood and Transplant, Cambridge, UK
| | - Francois Aguet
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Kristin Ardlie
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | | | - Guolian Kang
- St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Yingze Zhang
- Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Seyed Mehdi Nouraie
- Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Victor R. Gordeuk
- Division of Hematology and Oncology, Department of Medicine, Comprehensive Sickle Cell Center, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Mark T. Gladwin
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Melanie E. Garrett
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Allison Ashley-Koch
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Marilyn J. Telen
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Brian Custer
- Vitalant Research Institute, San Francisco, California, USA
- Department of Laboratory Medicine, UCSF, San Francisco, California, USA
| | - Shannon Kelly
- Vitalant Research Institute, San Francisco, California, USA
- Division of Pediatric Hematology, UCSF Benioff Children's Hospital, Oakland, California, USA
| | - Carla Luana Dinardo
- Fundacao Pro-Sangue Hemocentro de Sao Paulo, Sao Paulo, Brazil
- Institute of Tropical Medicine, Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Ester C. Sabino
- Institute of Tropical Medicine, Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil
| | | | | | | | | | | | - Adriana Méndez
- Institute of Laboratory Medicine, Cantonal Hospital Aarau, 5000 Aarau, Switzerland
| | | | - Vivien A. Sheehan
- Aflac Cancer & Blood Disorders Center, Children's Healthcare of Atlanta & Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
| | | | - Lude Franke
- Oncode Institute, Amsterdam, the Netherlands
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Björn Nilsson
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Lund Stem Cell Center, Lund University, 221 84 Lund, Sweden
- Department of Laboratory Medicine, Lund University, 221 84 Lund, Sweden
| | - Adam S. Butterworth
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK
- National Institute for Health and Care Research Blood and Transplant Research Unit in Donor Health and Behaviour, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
| | - Vip Viprakasit
- Siriraj Thalassemia Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Department of Pediatrics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Siana Nkya
- Sickle Cell Program, Department of Hematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- Department of Biochemistry, Muhimbili University of Health and Allied Science, Dar es Salaam, Tanzania
- Tanzania Human Genetics Organisation, Tanzania
| | - Vijay G. Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard Stem Cell Institute, Cambridge, Massachusetts, USA
- Department of Biochemistry, Muhimbili University of Health and Allied Science
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19
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Custer B, Grebe E, Buccheri R, Bakkour S, Stone M, Capuani L, Alencar C, Amorim L, Loureiro P, Carneiro-Proietti AB, Mendrone-Junior A, Gonçalez T, Gao K, Livezey KW, Linnen JM, Brambilla D, McClure C, Busch MP, Sabino EC. Surveillance for Zika, Chikungunya, and Dengue Virus Incidence and RNAemia in Blood Donors at 4 Brazilian Blood Centers During 2016-2019. J Infect Dis 2023; 227:696-707. [PMID: 35687888 PMCID: PMC10152499 DOI: 10.1093/infdis/jiac173] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 01/27/2022] [Revised: 04/12/2022] [Accepted: 05/03/2022] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Except for public health case reports, the incidence of Zika virus (ZIKV), chikungunya virus (CHIKV), and dengue virus (DENV) infection are not available to assess the potential blood transfusion safety threat in Brazil. METHODS Pools of 6 donation samples (MP6) left over from human immunodeficiency virus, hepatitis B virus, and hepatitis C virus nucleic acid testing were combined to create MP18 pools (3 MP6 pools). Samples were tested using the Grifols triplex ZIKV, CHIKV, and DENV real-time transcription mediated amplification assay to estimate prevalence of RNAemia and incidence, and to compare these results to case reports in São Paulo, Belo Horizonte, Recife, and Rio de Janeiro, from April 2016 through June 2019. RESULTS ZIKV, CHIKV, and DENV RNAemia were found from donors who donated without overt symptoms of infection that would have led to deferral. The highest RNAemic donation prevalence was 1.2% (95% CI, .8%-1.9%) for DENV in Belo Horizonte in May 2019. Arbovirus infections varied by location and time of year, and were not always aligned with annual arbovirus outbreak seasons in different regions of the country. CONCLUSIONS Testing donations for arboviruses in Brazil can contribute to public health. Transfusion recipients were likely exposed to ZIKV, CHIKV, and DENV viremic blood components during the study period.
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Affiliation(s)
- Brian Custer
- Vitalant Research Institute, San Francisco, California, USA.,Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Eduard Grebe
- Vitalant Research Institute, San Francisco, California, USA.,Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA.,Department of Science and Innovation, National Research Foundation Centre of Excellence in Epidemiological Modelling and Analysis, Stellenbosch University, Stellenbosch, South Africa
| | | | - Sonia Bakkour
- Vitalant Research Institute, San Francisco, California, USA.,Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Mars Stone
- Vitalant Research Institute, San Francisco, California, USA.,Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Ligia Capuani
- Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Cecilia Alencar
- Hospital das Clinicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | | | - Paula Loureiro
- Fundação Hemope, Recife, Brazil.,Faculdade de Medicina da Universidade de Pernambuco, Recife, Brazil
| | | | | | | | - Kui Gao
- Grifols Diagnostics Solutions, San Diego, California, USA
| | | | | | - Don Brambilla
- Research Triangle Institute International, Rockville, Maryland, USA
| | - Chris McClure
- Research Triangle Institute International, Rockville, Maryland, USA
| | - Michael P Busch
- Vitalant Research Institute, San Francisco, California, USA.,Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Ester C Sabino
- Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
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20
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Fernandes AE, Rosa PWL, Melo ME, Martins RCR, Santin FGO, Moura AMSH, Coelho GSMA, Sabino EC, Cercato C, Mancini MC. Differences in the gut microbiota of women according to ultra-processed food consumption. Nutr Metab Cardiovasc Dis 2023; 33:84-89. [PMID: 36411218 DOI: 10.1016/j.numecd.2022.09.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 09/28/2022] [Accepted: 09/30/2022] [Indexed: 11/19/2022]
Abstract
BACKGROUND AND AIMS High consumption of ultra-processed food (UPF) has been associated with increased risk of obesity and other metabolic diseases, and this dietary pattern seems to be responsible for chronic changes in the gut microbiota. The aim of this study was to assess the associations of UPF with the gut microbiota and obesity-associated biometrics in women. METHODS AND RESULTS This cross-sectional study examined 59 women. The following parameters were evaluated: food consumption using NOVA classification, anthropometric and metabolic parameters, and gut microbiome by next-generation sequencing. The mean age was 28.0 ± 6.6 years. The mean caloric intake was 1624 ± 531 kcal, of which unprocessed or minimally processed food (G1) accounted for 52.4 ± 13.5%, and UPF accounted for 31.4 ± 13.6%. Leptin levels adjusted for fat mass were negatively associated with G1 and positively associated with UPF. We found 15 species in the gut microbiota that correlated with G1 (3 positively and 12 negatively) and 9 species associated with UPF (5 positively and 4 negatively). CONCLUSION Higher consumption of UPF was directly associated with leptin resistance, and this study suggests that the consumption of UPF or G1 may affect the composition of the gut microbiota.
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Affiliation(s)
- Ariana E Fernandes
- Hospital Das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, Brazil.
| | - Paula W L Rosa
- Hospital Das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Maria E Melo
- Hospital Das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Roberta C R Martins
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Fernanda G O Santin
- Departamento de Nutricao, Faculdade de Saude Publica, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Aline M S H Moura
- Hospital Das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Graziele S M A Coelho
- Hospital Das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Ester C Sabino
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Cintia Cercato
- Hospital Das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Marcio C Mancini
- Hospital Das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
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21
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Rodrigues DS, Nastri ACS, Magri MM, Oliveira MSD, Sabino EC, Figueiredo PHMF, Levin AS, Freire MP, Harima LS, Nunes FLS, Ferreira JE, Busatto G, Bonfá E, Utiyama E, Segurado A, Perondi B, Morais AM, Montal A, Fusco S, Fregonesi M, Rocha M, Marcilio I, Rios IC, Kawano FYO, de Jesus MA, Kallas EG, Marmo C, Tanaka C, de Souza HP, Marchini JFM, Carvalho C, Ferreira JC, Guimaraes T, Lazari CS, Duarte AJS, Francisco MCPB, Costa SF. Predicting the outcome for COVID-19 patients by applying time series classification to electronic health records. BMC Med Inform Decis Mak 2022; 22:187. [PMID: 35843930 PMCID: PMC9288836 DOI: 10.1186/s12911-022-01931-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 07/07/2022] [Indexed: 12/12/2022] Open
Abstract
Background COVID-19 caused more than 622 thousand deaths in Brazil. The infection can be asymptomatic and cause mild symptoms, but it also can evolve into a severe disease and lead to death. It is difficult to predict which patients will develop severe disease. There are, in the literature, machine learning models capable of assisting diagnose and predicting outcomes for several diseases, but usually these models require laboratory tests and/or imaging. Methods We conducted a observational cohort study that evaluated vital signs and measurements from patients who were admitted to Hospital das Clínicas (São Paulo, Brazil) between March 2020 and October 2021 due to COVID-19. The data was then represented as univariate and multivariate time series, that were used to train and test machine learning models capable of predicting a patient’s outcome. Results Time series-based machine learning models are capable of predicting a COVID-19 patient’s outcome with up to 96% general accuracy and 81% accuracy considering only the first hospitalization day. The models can reach up to 99% sensitivity (discharge prediction) and up to 91% specificity (death prediction). Conclusions Results indicate that time series-based machine learning models combined with easily obtainable data can predict COVID-19 outcomes and support clinical decisions. With further research, these models can potentially help doctors diagnose other diseases.
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22
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Borin A, Coimbra LD, Bispo-Dos-Santos K, Naciuk FF, Fontoura M, Simeoni CL, Gomes GV, Amorim MR, Gravina HD, Shimizu JF, Passos ASC, de Oliveira IM, de Carvalho AC, Cardoso AC, Parise PL, Toledo-Teixeira DA, Sotorilli GE, Persinoti GF, Claro IM, Sabino EC, Alborghetti MR, Rocco SA, Franchini KG, de Souza WM, Oliveira PSL, Cunha TM, Granja F, Proença-Módena JL, Trivella DBB, Bruder M, Cordeiro AT, Marques RE. Identification and characterization of the anti-SARS-CoV-2 activity of cationic amphiphilic steroidal compounds. Virulence 2022; 13:1031-1048. [PMID: 35734825 PMCID: PMC9235892 DOI: 10.1080/21505594.2022.2085793] [Citation(s) in RCA: 2] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The ongoing COVID-19 pandemic caused a significant loss of human lives and a worldwide decline in quality of life. Treatment of COVID-19 patients is challenging, and specific treatments to reduce COVID-19 aggravation and mortality are still necessary. Here, we describe the discovery of a novel class of epiandrosterone steroidal compounds with cationic amphiphilic properties that present antiviral activity against SARS-CoV-2 in the low micromolar range. Compounds were identified in screening campaigns using a cytopathic effect-based assay in Vero CCL81 cells, followed by hit compound validation and characterization. Compounds LNB167 and LNB169 were selected due to their ability to reduce the levels of infectious viral progeny and viral RNA levels in Vero CCL81, HEK293, and HuH7.5 cell lines. Mechanistic studies in Vero CCL81 cells indicated that LNB167 and LNB169 inhibited the initial phase of viral replication through mechanisms involving modulation of membrane lipids and cholesterol in host cells. Selection of viral variants resistant to steroidal compound treatment revealed single mutations on transmembrane, lipid membrane-interacting Spike and Envelope proteins. Finally, in vivo testing using the hACE2 transgenic mouse model indicated that SARS-CoV-2 infection could not be ameliorated by LNB167 treatment. We conclude that anti-SARS-CoV-2 activities of steroidal compounds LNB167 and LNB169 are likely host-targeted, consistent with the properties of cationic amphiphilic compounds that modulate host cell lipid biology. Although effective in vitro, protective effects were cell-type specific and did not translate to protection in vivo, indicating that subversion of lipid membrane physiology is an important, yet complex mechanism involved in SARS-CoV-2 replication and pathogenesis.
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Affiliation(s)
- Alexandre Borin
- Brazilian Biosciences National Laboratory - LNBio, Brazilian Center for Research in Energy and Materials - CNPEM, Campinas, Brazil.,Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Laís D Coimbra
- Brazilian Biosciences National Laboratory - LNBio, Brazilian Center for Research in Energy and Materials - CNPEM, Campinas, Brazil.,Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Karina Bispo-Dos-Santos
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil.,Laboratory of Emerging Viruses (LEVE), Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Fabrício F Naciuk
- Brazilian Biosciences National Laboratory - LNBio, Brazilian Center for Research in Energy and Materials - CNPEM, Campinas, Brazil
| | - Marina Fontoura
- Brazilian Biosciences National Laboratory - LNBio, Brazilian Center for Research in Energy and Materials - CNPEM, Campinas, Brazil.,Department of Cellular and Structural Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Camila L Simeoni
- Laboratory of Emerging Viruses (LEVE), Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Giovanni V Gomes
- Center for Research in Inflammatory Diseases (CRID), Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Mariene R Amorim
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil.,Laboratory of Emerging Viruses (LEVE), Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Humberto D Gravina
- Brazilian Biosciences National Laboratory - LNBio, Brazilian Center for Research in Energy and Materials - CNPEM, Campinas, Brazil
| | - Jacqueline Farinha Shimizu
- Brazilian Biosciences National Laboratory - LNBio, Brazilian Center for Research in Energy and Materials - CNPEM, Campinas, Brazil
| | - Amanda S C Passos
- Center for Research in Inflammatory Diseases (CRID), Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Isadora M de Oliveira
- Brazilian Biosciences National Laboratory - LNBio, Brazilian Center for Research in Energy and Materials - CNPEM, Campinas, Brazil
| | - Ana Carolina de Carvalho
- Brazilian Biosciences National Laboratory - LNBio, Brazilian Center for Research in Energy and Materials - CNPEM, Campinas, Brazil.,Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Alisson Campos Cardoso
- Brazilian Biosciences National Laboratory - LNBio, Brazilian Center for Research in Energy and Materials - CNPEM, Campinas, Brazil
| | - Pierina L Parise
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil.,Laboratory of Emerging Viruses (LEVE), Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Daniel A Toledo-Teixeira
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil.,Laboratory of Emerging Viruses (LEVE), Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Giuliana E Sotorilli
- Brazilian Biosciences National Laboratory - LNBio, Brazilian Center for Research in Energy and Materials - CNPEM, Campinas, Brazil.,Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Gabriela F Persinoti
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), São Paulo, Brazil
| | - Ingra Morales Claro
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, Brazil
| | - Ester C Sabino
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, Brazil
| | - Marcos R Alborghetti
- Brazilian Biosciences National Laboratory - LNBio, Brazilian Center for Research in Energy and Materials - CNPEM, Campinas, Brazil
| | - Silvana A Rocco
- Brazilian Biosciences National Laboratory - LNBio, Brazilian Center for Research in Energy and Materials - CNPEM, Campinas, Brazil
| | - Kleber G Franchini
- Brazilian Biosciences National Laboratory - LNBio, Brazilian Center for Research in Energy and Materials - CNPEM, Campinas, Brazil
| | - William M de Souza
- World Reference Center for Emerging Viruses and Arboviruses and Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Paulo S L Oliveira
- Brazilian Biosciences National Laboratory - LNBio, Brazilian Center for Research in Energy and Materials - CNPEM, Campinas, Brazil
| | - Thiago M Cunha
- Center for Research in Inflammatory Diseases (CRID), Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Fabiana Granja
- Laboratory of Emerging Viruses (LEVE), Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil.,Biodiversity Research Center, Federal University of Roraima (UFRR), Boa Vista, Brazil
| | - José Luiz Proença-Módena
- Laboratory of Emerging Viruses (LEVE), Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil.,Experimental Medicine Research Cluster, University of Campinas (UNICAMP), Campinas, Brazil
| | - Daniela B B Trivella
- Brazilian Biosciences National Laboratory - LNBio, Brazilian Center for Research in Energy and Materials - CNPEM, Campinas, Brazil
| | - Marjorie Bruder
- Brazilian Biosciences National Laboratory - LNBio, Brazilian Center for Research in Energy and Materials - CNPEM, Campinas, Brazil
| | - Artur T Cordeiro
- Brazilian Biosciences National Laboratory - LNBio, Brazilian Center for Research in Energy and Materials - CNPEM, Campinas, Brazil
| | - Rafael Elias Marques
- Brazilian Biosciences National Laboratory - LNBio, Brazilian Center for Research in Energy and Materials - CNPEM, Campinas, Brazil
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23
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Brito AF, Semenova E, Dudas G, Hassler GW, Kalinich CC, Kraemer MUG, Ho J, Tegally H, Githinji G, Agoti CN, Matkin LE, Whittaker C, Howden BP, Sintchenko V, Zuckerman NS, Mor O, Blankenship HM, de Oliveira T, Lin RTP, Siqueira MM, Resende PC, Vasconcelos ATR, Spilki FR, Aguiar RS, Alexiev I, Ivanov IN, Philipova I, Carrington CVF, Sahadeo NSD, Branda B, Gurry C, Maurer-Stroh S, Naidoo D, von Eije KJ, Perkins MD, van Kerkhove M, Hill SC, Sabino EC, Pybus OG, Dye C, Bhatt S, Flaxman S, Suchard MA, Grubaugh ND, Baele G, Faria NR. Global disparities in SARS-CoV-2 genomic surveillance. Nat Commun 2022; 13:7003. [PMID: 36385137 PMCID: PMC9667854 DOI: 10.1038/s41467-022-33713-y] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 09/29/2022] [Indexed: 11/17/2022] Open
Abstract
Genomic sequencing is essential to track the evolution and spread of SARS-CoV-2, optimize molecular tests, treatments, vaccines, and guide public health responses. To investigate the global SARS-CoV-2 genomic surveillance, we used sequences shared via GISAID to estimate the impact of sequencing intensity and turnaround times on variant detection in 189 countries. In the first two years of the pandemic, 78% of high-income countries sequenced >0.5% of their COVID-19 cases, while 42% of low- and middle-income countries reached that mark. Around 25% of the genomes from high income countries were submitted within 21 days, a pattern observed in 5% of the genomes from low- and middle-income countries. We found that sequencing around 0.5% of the cases, with a turnaround time <21 days, could provide a benchmark for SARS-CoV-2 genomic surveillance. Socioeconomic inequalities undermine the global pandemic preparedness, and efforts must be made to support low- and middle-income countries improve their local sequencing capacity.
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Affiliation(s)
- Anderson F Brito
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.
- Instituto Todos pela Saúde, São Paulo, SP, Brazil.
| | | | - Gytis Dudas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Gabriel W Hassler
- Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Chaney C Kalinich
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- Yale School of Medicine, Yale University, New Haven, CT, USA
| | | | - Joses Ho
- GISAID Global Data Science Initiative, Munich, Germany
- Bioinformatics Institute & ID Labs, Agency for Science Technology and Research, Singapore, Singapore
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - George Githinji
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya
| | - Charles N Agoti
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- School of Health and Human Sciences, Pwani University, Kilifi, Kenya
| | - Lucy E Matkin
- Department of Biology, University of Oxford, Oxford, UK
| | - Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK
| | | | | | | | | | | | | | | | | | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Vitali Sintchenko
- Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW, Australia
- Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
| | - Neta S Zuckerman
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
| | - Orna Mor
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
| | - Heather M Blankenship
- Michigan Department of Health and Human Services, Bureau of Laboratories, Lansing, MI, USA
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Raymond T P Lin
- National Centre for Infectious Diseases, Singapore, Singapore
| | - Marilda Mendonça Siqueira
- Laboratory of Respiratory Viruses and Measles, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Paola Cristina Resende
- Laboratory of Respiratory Viruses and Measles, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Ana Tereza R Vasconcelos
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | - Fernando R Spilki
- Feevale University, Institute of Health Sciences, Novo Hamburgo, RS, Brazil
| | - Renato Santana Aguiar
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Instituto D'Or de Pesquisa e Ensino (IDOR), Rio de Janeiro, Brazil
| | - Ivailo Alexiev
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Ivan N Ivanov
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Ivva Philipova
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Christine V F Carrington
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Nikita S D Sahadeo
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Ben Branda
- GISAID Global Data Science Initiative, Munich, Germany
| | - Céline Gurry
- GISAID Global Data Science Initiative, Munich, Germany
| | - Sebastian Maurer-Stroh
- GISAID Global Data Science Initiative, Munich, Germany
- Bioinformatics Institute & ID Labs, Agency for Science Technology and Research, Singapore, Singapore
- National Centre for Infectious Diseases, Singapore, Singapore
| | - Dhamari Naidoo
- Health Emergencies Programme, World Health Organization Regional Office for South-East Asia, New Delhi, India
| | - Karin J von Eije
- Department of Medical Microbiology and Infection Prevention, Division of Clinical Virology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Emerging Diseases and Zoonoses Unit, Health Emergencies Programme, World Health Organization, Geneva, Switzerland
| | - Mark D Perkins
- Emerging Diseases and Zoonoses Unit, Health Emergencies Programme, World Health Organization, Geneva, Switzerland
| | - Maria van Kerkhove
- Emerging Diseases and Zoonoses Unit, Health Emergencies Programme, World Health Organization, Geneva, Switzerland
| | | | - Ester C Sabino
- Instituto Todos pela Saúde, São Paulo, SP, Brazil
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Oliver G Pybus
- Department of Biology, University of Oxford, Oxford, UK
- Royal Veterinary College, Hawkshead, UK
| | | | - Samir Bhatt
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Seth Flaxman
- Department of Computer Science, University of Oxford, Oxford, UK
| | - Marc A Suchard
- Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Nuno R Faria
- Department of Biology, University of Oxford, Oxford, UK.
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK.
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK.
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.
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24
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Andrade PS, Valença IN, Heinisch MRS, Rocha EC, Fernandes LN, Faria NR, Sabino EC, Lima-Camara TN. First Report of Wenzhou sobemo-like virus 4 in Aedes albopictus (Diptera: Culicidae) in Latin America. Viruses 2022; 14:v14112341. [PMID: 36366436 PMCID: PMC9696862 DOI: 10.3390/v14112341] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/21/2022] [Accepted: 10/22/2022] [Indexed: 02/01/2023] Open
Abstract
Insect-specific viruses (ISVs) are viruses that replicate exclusively in arthropod cells. Many ISVs have been studied in mosquitoes as many of them act as vectors for human etiological agents, such as arboviruses. Aedes (Stegomyia) albopictus is an important potential vector of several arboviruses in Brazil, such as dengue (DENV), Zika (ZIKV) and chikungunya (CHIKV). The development of next-generation sequencing metagenomics has enabled the discovery and characterization of new ISVs. Ae. albopictus eggs were collected using oviposition traps placed in two urban parks in the city of São Paulo, Brazil. The Aedes albopictus females were divided into pools and the genetic material was extracted and processed for sequencing by metagenomics. Complete genomes of ISV Wenzhou sobemo-like virus 4 (WSLV4) were obtained in three of the four pools tested. This is the first detection of ISV WSLV4 in Ae. albopictus females in Latin America. Further studies on ISVs in Ae. albopictus are needed to better understand the role of this species in the dynamics of arbovirus transmission in the Americas.
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Affiliation(s)
- Pâmela S. Andrade
- Department of Epidemiology, Faculdade de Saúde Pública, Universidade de São Paulo, São Paulo 01246-904, Brazil
- Institute of Tropical Medicine, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
- Correspondence:
| | - Ian N. Valença
- Institute of Tropical Medicine, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
- Department of Infectious and Parasitic Diseases, Faculdade de Medicina, Universidade de São Paulo, São Paulo 01246-903, Brazil
| | - Marta R. S. Heinisch
- Department of Epidemiology, Faculdade de Saúde Pública, Universidade de São Paulo, São Paulo 01246-904, Brazil
| | - Esmenia C. Rocha
- Institute of Tropical Medicine, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Lícia N. Fernandes
- Medical Research Laboratory 49, Institute of Tropical Medicine, Faculdade de Medicina, Universidade de São Paulo, São Paulo 01246-903, Brazil
| | - Nuno R. Faria
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London W2 1PG, UK
| | - Ester C. Sabino
- Institute of Tropical Medicine, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
- Department of Infectious and Parasitic Diseases, Faculdade de Medicina, Universidade de São Paulo, São Paulo 01246-903, Brazil
| | - Tamara N. Lima-Camara
- Department of Epidemiology, Faculdade de Saúde Pública, Universidade de São Paulo, São Paulo 01246-904, Brazil
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25
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Oliveira BA, Moura ICG, Ozahata MC, Mateos SOG, Belisário AR, Duarte J, Sabino EC, Kelly S, Dinardo CL. CLINICAL PREDICTORS OF VASO-OCCLUSIVE PAIN HOSPITALIZATION IN PATIENTS WITH SICKLE CELL DISEASE (SCD). Hematol Transfus Cell Ther 2022. [DOI: 10.1016/j.htct.2022.09.095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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26
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Luna-Muschi A, Noguera SV, Borges IC, De Paula AV, Côrtes MF, Larocca C, Mari JF, Pereira Guimarães LS, Torres PM, Scaccia N, Villas-Boas LS, da Silva AR, Andrade PS, Teixeira JC, Escadafal C, de Oliveira VF, Tozetto-Mendoza TR, Mendes-Correa MC, Levin AS, Sabino EC, Costa SF. Characterization of SARS-CoV-2 Omicron variant shedding and predictors of viral culture positivity on vaccinated healthcare workers with mild COVID-19. J Infect Dis 2022; 226:1726-1730. [PMID: 36134610 PMCID: PMC9619435 DOI: 10.1093/infdis/jiac391] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 09/20/2022] [Indexed: 11/25/2022] Open
Abstract
In this prospective cohort of 30 vaccinated healthcare workers with mild Omicron variant infection, we evaluated viral culture, rapid antigen test (RAT), and real-time reverse-transcription polymerase chain reaction (RT-PCR) of respiratory samples at days 5, 7, 10, and 14. Viral culture was positive in 46% (11/24) and 20% (6/30) of samples at days 5 and 7, respectively. RAT and RT-PCR (Ct ≤35) showed 100% negative predictive value (NPV), with positive predictive values (PPVs) of 32% and 17%, respectively, for predicting viral culture positivity. A lower RT-PCR threshold (Ct ≤24) improved culture prediction (PPV = 39%; NPV = 100%). Vaccinated persons with mild Omicron infection are potentially transmissible up to day 7. RAT and RT-PCR might be useful tools for shortening the isolation period.
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Affiliation(s)
- Alessandra Luna-Muschi
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.,Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Saidy Vásconez Noguera
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.,Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Igor C Borges
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.,Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.,Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Anderson V De Paula
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.,Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Marina Farrel Côrtes
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.,Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Carolina Larocca
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.,Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Julia Ferreira Mari
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.,Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Lara Silva Pereira Guimarães
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.,Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Pablo Munoz Torres
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.,Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Nazareno Scaccia
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.,Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Lucy S Villas-Boas
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.,Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Almir Ribeiro da Silva
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.,Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Pâmela S Andrade
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.,Faculdade de Saúde Pública da Universidade de São Paulo, São Paulo, Brazil
| | - Juliana C Teixeira
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.,Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | | | - Victor Falcão de Oliveira
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.,Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Tania R Tozetto-Mendoza
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.,Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Maria Cássia Mendes-Correa
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.,Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.,Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Anna S Levin
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.,Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Ester C Sabino
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.,Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Silvia F Costa
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.,Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.,Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
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27
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Prete CA, Buss LF, Whittaker C, Salomon T, Oikawa MK, Pereira RHM, Moura ICG, Delerino L, Barral-Netto M, Tavares NM, Franca RFO, Boaventura VS, Miyajima F, Mendrone-Junior A, de Almeida-Neto C, Salles NA, Ferreira SC, Fladzinski KA, de Souza LM, Schier LK, Inoue PM, Xabregas LA, Crispim MAE, Fraiji N, Araujo FLV, Carlos LMB, Pessoa V, Ribeiro MA, de Souza RE, da Silva SMN, Cavalcante AF, Valença MIB, da Silva MV, Lopes E, Filho LA, Mateos SOG, Nunes GT, Silva-Junior AL, Busch MP, Castro MC, Dye C, Ratmann O, Faria NR, Nascimento VH, Sabino EC. SARS-CoV-2 antibody dynamics in blood donors and COVID-19 epidemiology in eight Brazilian state capitals: A serial cross-sectional study. eLife 2022; 11:e78233. [PMID: 36135358 PMCID: PMC9545556 DOI: 10.7554/elife.78233] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 02/28/2022] [Accepted: 09/17/2022] [Indexed: 11/13/2022] Open
Abstract
Background The COVID-19 situation in Brazil is complex due to large differences in the shape and size of regional epidemics. Understanding these patterns is crucial to understand future outbreaks of SARS-CoV-2 or other respiratory pathogens in the country. Methods We tested 97,950 blood donation samples for IgG antibodies from March 2020 to March 2021 in 8 of Brazil's most populous cities. Residential postal codes were used to obtain representative samples. Weekly age- and sex-specific seroprevalence were estimated by correcting the crude seroprevalence by test sensitivity, specificity, and antibody waning. Results The inferred attack rate of SARS-CoV-2 in December 2020, before the Gamma variant of concern (VOC) was dominant, ranged from 19.3% (95% credible interval [CrI] 17.5-21.2%) in Curitiba to 75.0% (95% CrI 70.8-80.3%) in Manaus. Seroprevalence was consistently smaller in women and donors older than 55 years. The age-specific infection fatality rate (IFR) differed between cities and consistently increased with age. The infection hospitalisation rate increased significantly during the Gamma-dominated second wave in Manaus, suggesting increased morbidity of the Gamma VOC compared to previous variants circulating in Manaus. The higher disease penetrance associated with the health system's collapse increased the overall IFR by a minimum factor of 2.91 (95% CrI 2.43-3.53). Conclusions These results highlight the utility of blood donor serosurveillance to track epidemic maturity and demonstrate demographic and spatial heterogeneity in SARS-CoV-2 spread. Funding This work was supported by Itaú Unibanco 'Todos pela Saude' program; FAPESP (grants 18/14389-0, 2019/21585-0); Wellcome Trust and Royal Society Sir Henry Dale Fellowship 204311/Z/16/Z; the Gates Foundation (INV- 034540 and INV-034652); REDS-IV-P (grant HHSN268201100007I); the UK Medical Research Council (MR/S0195/1, MR/V038109/1); CAPES; CNPq (304714/2018-6); Fundação Faculdade de Medicina; Programa Inova Fiocruz-CE/Funcap - Edital 01/2020 Number: FIO-0167-00065.01.00/20 SPU N°06531047/2020; JBS - Fazer o bem faz bem.
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Affiliation(s)
- Carlos A Prete
- Department of Electronic Systems Engineering, University of São PauloSão PauloBrazil
| | | | - Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis, Imperial College LondonLondonUnited Kingdom
- Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College LondonLondonUnited Kingdom
| | - Tassila Salomon
- Faculdade Ciências Médicas de Minas GeraisBelo HorizonteBrazil
| | | | | | - Isabel CG Moura
- Faculdade Ciências Médicas de Minas GeraisBelo HorizonteBrazil
| | | | | | | | | | | | - Fabio Miyajima
- Fundação Oswaldo CruzManguinhosBrazil
- Universidade Federal do CearáFortalezaBrazil
| | | | | | - Nanci A Salles
- Fundação Pró Sangue Hemocentro de São Paulo (FPS)São PauloBrazil
| | | | | | - Luana M de Souza
- Centro de Hematologia e Hemoterapia do Paraná (HEMEPAR)CuritibaBrazil
| | - Luciane K Schier
- Centro de Hematologia e Hemoterapia do Paraná (HEMEPAR)CuritibaBrazil
| | - Patricia M Inoue
- Centro de Hematologia e Hemoterapia do Paraná (HEMEPAR)CuritibaBrazil
| | - Lilyane A Xabregas
- Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas (HEMOAM)ManausBrazil
| | - Myuki AE Crispim
- Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas (HEMOAM)ManausBrazil
| | - Nelson Fraiji
- Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas (HEMOAM)ManausBrazil
| | | | - Luciana MB Carlos
- Centro de Hematologia e Hemoterapia do Ceará (HEMOCE)FortalezaBrazil
| | - Veridiana Pessoa
- Centro de Hematologia e Hemoterapia do Ceará (HEMOCE)FortalezaBrazil
| | | | | | | | - Anna F Cavalcante
- Fundação de Hematologia e Hemoterapia de Pernambuco (HEMOPE)RecifeBrazil
| | - Maria IB Valença
- Fundação de Hematologia e Hemoterapia de Pernambuco (HEMOPE)RecifeBrazil
| | - Maria V da Silva
- Fundação de Hematologia e Hemoterapia de Pernambuco (HEMOPE)RecifeBrazil
| | - Esther Lopes
- Instituto Estadual de Hematologia Arthur de Siqueira Cavalcanti (HEMORIO)Rio de JaneiroBrazil
| | - Luiz A Filho
- Instituto Estadual de Hematologia Arthur de Siqueira Cavalcanti (HEMORIO)Rio de JaneiroBrazil
| | - Sheila OG Mateos
- Instituto Estadual de Hematologia Arthur de Siqueira Cavalcanti (HEMORIO)Rio de JaneiroBrazil
| | - Gabrielle T Nunes
- Fundação Oswaldo CruzManguinhosBrazil
- Instituto Estadual de Hematologia Arthur de Siqueira Cavalcanti (HEMORIO)Rio de JaneiroBrazil
| | - Alexander L Silva-Junior
- Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas (HEMOAM)ManausBrazil
- Universidade Federal do AmazonasManausBrazil
- Centro Universitário do NorteManausBrazil
| | - Michael P Busch
- Vitalant Research InstituteSan FranscicoUnited States
- University of California, San FranciscoSan FranciscoUnited States
| | | | - Christopher Dye
- Department of Zoology, University of OxfordOxfordUnited Kingdom
| | | | - Nuno R Faria
- MRC Centre for Global Infectious Disease Analysis, Imperial College LondonLondonUnited Kingdom
- Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College LondonLondonUnited Kingdom
- Department of Zoology, University of OxfordOxfordUnited Kingdom
- Instituto de Medicina Tropical, University of São PauloSão PauloBrazil
| | - Vítor H Nascimento
- Department of Electronic Systems Engineering, University of São PauloSão PauloBrazil
| | - Ester C Sabino
- Instituto de Medicina Tropical, University of São PauloSão PauloBrazil
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28
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Levin AS, Freire MP, Oliveira MSD, Nastri ACS, Harima LS, Perdigão-Neto LV, Magri MM, Fialkovitz G, Figueiredo PHMF, Siciliano RF, Sabino EC, Carlotti DPN, Rodrigues DS, Nunes FLS, Ferreira JE. Correlating drug prescriptions with prognosis in severe COVID-19: first step towards resource management. BMC Med Inform Decis Mak 2022; 22:246. [PMID: 36131274 PMCID: PMC9490728 DOI: 10.1186/s12911-022-01983-7] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 08/29/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Optimal COVID-19 management is still undefined. In this complicated scenario, the construction of a computational model capable of extracting information from electronic medical records, correlating signs, symptoms and medical prescriptions, could improve patient management/prognosis. METHODS The aim of this study is to investigate the correlation between drug prescriptions and outcome in patients with COVID-19. We extracted data from 3674 medical records of hospitalized patients: drug prescriptions, outcome, and demographics. The outcome evaluated was hospital outcome. We applied correlation analysis using a Logistic Regression algorithm for machine learning with Lasso and Matthews correlation coefficient. RESULTS We found correlations between drugs and patient outcomes (death/discharged alive). Anticoagulants, used very frequently during all phases of the disease, were associated with good prognosis only after the first week of symptoms. Antibiotics very frequently prescribed, especially early, were not correlated with outcome, suggesting that bacterial infections may not be important in determining prognosis. There were no differences between age groups. CONCLUSIONS In conclusion, we achieved an important result in the area of Artificial Intelligence, as we were able to establish a correlation between concrete variables in a real and extremely complex environment of clinical data from COVID-19. Our results are an initial and promising contribution in decision-making and real-time environments to support resource management and forecasting prognosis of patients with COVID-19.
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Affiliation(s)
- Anna S Levin
- Department of Infectious Diseases, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil. .,Department of Infection Control, Hospital das Clínicas, Universidade de São Paulo, São Paulo, Brazil. .,Division of Infectious Diseases, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil.
| | - Maristela P Freire
- Department of Infection Control, Hospital das Clínicas, Universidade de São Paulo, São Paulo, Brazil
| | | | - Ana Catharina S Nastri
- Division of Infectious Diseases, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Leila S Harima
- Clinical Director's Office, Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | | | - Marcello M Magri
- Division of Infectious Diseases, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Gabriel Fialkovitz
- Division of Infectious Diseases, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Pedro H M F Figueiredo
- Núcleo de Vigilância Epidemiológica, Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | | | - Ester C Sabino
- Department of Infectious Diseases, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Danilo P N Carlotti
- Computer Science Department, Institute of Mathematics and Statistics, Universidade de São Paulo, São Paulo, Brazil
| | - Davi Silva Rodrigues
- Laboratory of Computer Applications for Health Care; School of Arts, Sciences and Humanities, Universidade de São Paulo, São Paulo, Brazil
| | - Fátima L S Nunes
- Laboratory of Computer Applications for Health Care; School of Arts, Sciences and Humanities, Universidade de São Paulo, São Paulo, Brazil
| | - João Eduardo Ferreira
- Computer Science Department, Institute of Mathematics and Statistics, Universidade de São Paulo, São Paulo, Brazil
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29
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Luna-Muschi A, Borges IC, Faria E, Santos LG, Santos RE, Sabino EC, Mendes-Correa MC, Levin AS, Costa SF. PREDITORES DE PROTEÇÃO CONTRA INFECÇÃO POR SARS-COV-2 APÓS DUAS DOSES DE CORONAVAC EM UMA COORTE DE PROFISSIONAIS DE SAÚDE. Braz J Infect Dis 2022. [PMCID: PMC9461066 DOI: 10.1016/j.bjid.2022.102410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Introdução A elucidação dos preditores de proteção contra infecção pelo SARS-CoV-2 após a vacinação contra o mesmo pode auxiliar no controle da pandemia. Objetivo Identificar fatores de proteção contra infecção por SARS-CoV-2 após recebimento de duas doses de CoronaVac. Método Trata-se de uma coorte prospectiva de profissionais de saúde (PS) do HC-FMUSP vacinados com 2 doses da CoronaVac. O desfecho avaliado foi infecção pelo SARS-CoV-2 (confirmada por RT-PCR) desde 10 semanas após a segunda dose da vacina até pararem de trabalhar no HC-FMUSP ou até a data 08/03/2022. A infecção pelo SARS-CoV-2 foi verificada através dos registros do Centro de Atendimento ao Colaborador (CEAC) e do Núcleo de Vigilância Epidemiológica (NUVE) do HCFMUSP e através de entrevistas aos participantes do estudo. Os PS foram submetidos a sorologia para o SARS-CoV-2 para detecção de IgG anti-S (Liaison®/DiaSorin). Fatores de proteção contra infecção pelo SARS-CoV-2 foram avaliados com modelos de regressão de Cox. Os participantes assinaram um TCLE antes de ingressarem no estudo e o projeto foi aprovado no CEP do HC-FMUSP. Resultados Entre a 2ª e a 3ª dose da vacina, 3.979 PS foram avaliados. A idade mediana foi 44 anos e 79% era do sexo feminino. Casos de COVID-19 antes da 1ª dose da vacina foram detectados em 18% dos participantes. Sorologia reagente (título ≥ 33,8) foi detectada em 90% dos participantes em um teste realizado 10 semanas após a 2ª dose da vacina e houve 247 (6%) casos de COVID-19 entre a coleta desta sorologia e o recebimento da 3ª dose da vacina. Fatores de proteção contra infecção pelo SARS-CoV-2 neste período foram: diagnóstico de COVID-19 antes da 1ª dose da vacina (adjHR = 0,35), sorologia reagente coletada 10 semanas após 2ª dose da vacina (adjHR = 0,50) e idade entre 50-70 anos (adjHR = 0,52). Após a 3ª dose da vacina, 1305 PS foram avaliados. Sorologia reagente foi detectada em 99,8% dos participantes em um teste realizado 8 semanas após a 3ª dose da vacina e houve 159 (12%) casos de COVID-19 entre a coleta desta sorologia e o término do seguimento. Fatores de proteção contra infecção pelo SARS-CoV-2 no período foram: diagnóstico de COVID-19 antes da 3ª dose da vacina (adjHR = 0,57) e altos títulos da sorologia coletada 8 semanas após a terceira dose da vacina (adjHR = 0,99). Conclusão Diagnóstico prévio de COVID-19 e altos títulos de IgG contra o SARS-CoV-2 8-10 semanas após a vacinação são fatores protetores de infecção pelo SARS-CoV-2 em PS vacinados com CoronaVac. Ag. Financiadora: Instituto todos pela saúde. Nr. Processo: C1864.
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30
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Buss L, Prete CA, Whittaker C, Salomon T, Oikawa MK, Pereira RHM, Moura ICG, Delerino L, Franca RFO, Miyajima F, Mendrone Jr. A, Almeida-Neto C, Salles NA, Ferreira SC, Fladzinski KA, de Souza LM, Schier LK, Inoue PM, Xabregas LA, Crispim MAE, Fraiji N, Carlos LMB, Pessoa V, Ribeiro MA, de Souza RE, Cavalcante AF, Valença MIB, da Silva MV, Lopes E, Filho LA, Mateos SOG, Nunes GT, Schlesinger D, da Silva SMN, Silva-Junior AL, Castro MC, Nascimento VH, Dye C, Busch MP, Faria NR, Sabino EC. Predicting SARS-CoV-2 Variant Spread in a Completely Seropositive Population Using Semi-Quantitative Antibody Measurements in Blood Donors. Vaccines (Basel) 2022; 10:vaccines10091437. [PMID: 36146515 PMCID: PMC9501043 DOI: 10.3390/vaccines10091437] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/21/2022] [Accepted: 08/24/2022] [Indexed: 11/16/2022] Open
Abstract
SARS-CoV-2 serologic surveys estimate the proportion of the population with antibodies against historical variants, which nears 100% in many settings. New approaches are required to fully exploit serosurvey data. Using a SARS-CoV-2 anti-Spike (S) protein chemiluminescent microparticle assay, we attained a semi-quantitative measurement of population IgG titers in serial cross-sectional monthly samples of blood donations across seven Brazilian state capitals (March 2021−November 2021). Using an ecological analysis, we assessed the contributions of prior attack rate and vaccination to antibody titer. We compared anti-S titer across the seven cities during the growth phase of the Delta variant and used this to predict the resulting age-standardized incidence of severe COVID-19 cases. We tested ~780 samples per month, per location. Seroprevalence rose to >95% across all seven capitals by November 2021. Driven by vaccination, mean antibody titer increased 16-fold over the study, with the greatest increases occurring in cities with the highest prior attack rates. Mean anti-S IgG was strongly correlated (adjusted R2 = 0.89) with the number of severe cases caused by Delta. Semi-quantitative anti-S antibody titers are informative about prior exposure and vaccination coverage and may also indicate the potential impact of future SARS-CoV-2 variants.
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Affiliation(s)
- Lewis Buss
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London SW7 2BX, UK
- Correspondence: (L.B.); (E.C.S.)
| | - Carlos A. Prete
- Department of Electronic Systems Engineering, University of São Paulo, São Paulo 05508-010, Brazil
| | - Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London SW7 2BX, UK
| | - Tassila Salomon
- Faculdade Ciências Médicas de Minas Gerais, Belo Horizonte 30130-110, Brazil
| | - Marcio K. Oikawa
- Center of Mathematics, Computing and Cognition, Universidade Federal do ABC, Santo André 09210-170, Brazil
| | | | - Isabel C. G. Moura
- Faculdade Ciências Médicas de Minas Gerais, Belo Horizonte 30130-110, Brazil
| | | | | | - Fabio Miyajima
- Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, Brazil
- Universidade Federal do Ceará, Fortaleza 60455-760, Brazil
| | | | - Cesar Almeida-Neto
- Fundação Pró Sangue Hemocentro de São Paulo (FPS), Sao Paulo 05403-000, Brazil
| | - Nanci A. Salles
- Fundação Pró Sangue Hemocentro de São Paulo (FPS), Sao Paulo 05403-000, Brazil
| | - Suzete C. Ferreira
- Fundação Pró Sangue Hemocentro de São Paulo (FPS), Sao Paulo 05403-000, Brazil
| | - Karine A. Fladzinski
- Centro de Hematologia e Hemoterapia do Paraná (HEMEPAR), Curitiba 80045-145, Brazil
| | - Luana M. de Souza
- Centro de Hematologia e Hemoterapia do Paraná (HEMEPAR), Curitiba 80045-145, Brazil
| | - Luciane K. Schier
- Centro de Hematologia e Hemoterapia do Paraná (HEMEPAR), Curitiba 80045-145, Brazil
| | - Patricia M. Inoue
- Centro de Hematologia e Hemoterapia do Paraná (HEMEPAR), Curitiba 80045-145, Brazil
| | - Lilyane A. Xabregas
- Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas (HEMOAM), Manaus 69050-001, Brazil
| | - Myuki A. E. Crispim
- Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas (HEMOAM), Manaus 69050-001, Brazil
| | - Nelson Fraiji
- Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas (HEMOAM), Manaus 69050-001, Brazil
| | - Luciana M. B. Carlos
- Centro de Hematologia e Hemoterapia do Ceará (HEMOCE), Fortaleza 60140-200, Brazil
| | - Veridiana Pessoa
- Centro de Hematologia e Hemoterapia do Ceará (HEMOCE), Fortaleza 60140-200, Brazil
| | | | | | - Anna F. Cavalcante
- Fundação de Hematologia e Hemoterapia de Pernambuco (HEMOPE), Recife 52011-000, Brazil
| | - Maria I. B. Valença
- Fundação de Hematologia e Hemoterapia de Pernambuco (HEMOPE), Recife 52011-000, Brazil
| | - Maria V. da Silva
- Fundação de Hematologia e Hemoterapia de Pernambuco (HEMOPE), Recife 52011-000, Brazil
| | - Esther Lopes
- Instituto Estadual de Hematologia Arthur de Siqueira Cavalcanti (HEMORIO), Rio de Janeiro 20211-030, Brazil
| | - Luiz A. Filho
- Instituto Estadual de Hematologia Arthur de Siqueira Cavalcanti (HEMORIO), Rio de Janeiro 20211-030, Brazil
| | - Sheila O. G. Mateos
- Instituto Estadual de Hematologia Arthur de Siqueira Cavalcanti (HEMORIO), Rio de Janeiro 20211-030, Brazil
| | - Gabrielle T. Nunes
- Instituto Estadual de Hematologia Arthur de Siqueira Cavalcanti (HEMORIO), Rio de Janeiro 20211-030, Brazil
| | | | | | - Alexander L. Silva-Junior
- Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas (HEMOAM), Manaus 69050-001, Brazil
- Universidade Federal do Amazonas, Manaus 69067-005, Brazil
| | - Marcia C. Castro
- Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Vítor H. Nascimento
- Department of Electronic Systems Engineering, University of São Paulo, São Paulo 05508-010, Brazil
| | - Christopher Dye
- Department of Zoology, University of Oxford, Oxford OX1 3SZ, UK
| | - Michael P. Busch
- Vitalant Research Institute, Denver, CO 80230, USA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94158, USA
| | - Nuno R. Faria
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London SW7 2BX, UK
- Department of Zoology, University of Oxford, Oxford OX1 3SZ, UK
- Departamento de Moléstias Infecciosas e Parasitárias e Instituto de Medicina Tropical da Faculdade de Medicina, Universidade de São Paulo, São Paulo 05508-010, Brazil
- Department of Infectious Disease Epidemiology, Imperial College London, London SW7 2BX, UK
| | - Ester C. Sabino
- Departamento de Moléstias Infecciosas e Parasitárias e Instituto de Medicina Tropical da Faculdade de Medicina, Universidade de São Paulo, São Paulo 05508-010, Brazil
- Correspondence: (L.B.); (E.C.S.)
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Whittaker C, Watson OJ, Alvarez-Moreno C, Angkasekwinai N, Boonyasiri A, Carlos Triana L, Chanda D, Charoenpong L, Chayakulkeeree M, Cooke GS, Croda J, Cucunubá ZM, Djaafara BA, Estofolete CF, Grillet ME, Faria NR, Figueiredo Costa S, Forero-Peña DA, Gibb DM, Gordon AC, Hamers RL, Hamlet A, Irawany V, Jitmuang A, Keurueangkul N, Kimani TN, Lampo M, Levin AS, Lopardo G, Mustafa R, Nayagam S, Ngamprasertchai T, Njeri NIH, Nogueira ML, Ortiz-Prado E, Perroud MW, Phillips AN, Promsin P, Qavi A, Rodger AJ, Sabino EC, Sangkaew S, Sari D, Sirijatuphat R, Sposito AC, Srisangthong P, Thompson HA, Udwadia Z, Valderrama-Beltrán S, Winskill P, Ghani AC, Walker PGT, Hallett TB. Understanding the Potential Impact of Different Drug Properties on Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Transmission and Disease Burden: A Modelling Analysis. Clin Infect Dis 2022; 75:e224-e233. [PMID: 34549260 PMCID: PMC9402649 DOI: 10.1093/cid/ciab837] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 06/24/2021] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The public health impact of the coronavirus disease 2019 (COVID-19) pandemic has motivated a rapid search for potential therapeutics, with some key successes. However, the potential impact of different treatments, and consequently research and procurement priorities, have not been clear. METHODS Using a mathematical model of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission, COVID-19 disease and clinical care, we explore the public-health impact of different potential therapeutics, under a range of scenarios varying healthcare capacity, epidemic trajectories; and drug efficacy in the absence of supportive care. RESULTS The impact of drugs like dexamethasone (delivered to the most critically-ill in hospital and whose therapeutic benefit is expected to depend on the availability of supportive care such as oxygen and mechanical ventilation) is likely to be limited in settings where healthcare capacity is lowest or where uncontrolled epidemics result in hospitals being overwhelmed. As such, it may avert 22% of deaths in high-income countries but only 8% in low-income countries (assuming R = 1.35). Therapeutics for different patient populations (those not in hospital, early in the course of infection) and types of benefit (reducing disease severity or infectiousness, preventing hospitalization) could have much greater benefits, particularly in resource-poor settings facing large epidemics. CONCLUSIONS Advances in the treatment of COVID-19 to date have been focused on hospitalized-patients and predicated on an assumption of adequate access to supportive care. Therapeutics delivered earlier in the course of infection that reduce the need for healthcare or reduce infectiousness could have significant impact, and research into their efficacy and means of delivery should be a priority.
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Affiliation(s)
- Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Oliver J Watson
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Carlos Alvarez-Moreno
- Clínica Universitaria Colombia, Clínica Colsanitas, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Nasikarn Angkasekwinai
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | | | - Luis Carlos Triana
- Hospital Universitario San Ignacio -Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Duncan Chanda
- Adult Infectious Diseases Centre, University Teaching Hospital, Lusaka, Zambia
- Department of Internal Medicine, University of Zambia School of Medicine, Lusaka, Zambia
| | - Lantharita Charoenpong
- Bamrasnaradura Infectious Diseases Institute, Department of Diseases Control, Ministry of Public Health, Nonthaburi, Thailand
| | - Methee Chayakulkeeree
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Graham S Cooke
- Department of Infectious Diseases, Imperial College London, London, UK
- NIHR Biomedical Research Centre, Imperial College NHS Trust, London, UK
| | - Julio Croda
- Oswaldo Cruz Foudantion, Mato Grosso do Sul, Campo Grande, Brazil
- School of Medicine, Federal University of Mato Grosso do Sul, Campo Grande, Brazil
- Yale School of Public Health, New Haven, Connecticut, USA
| | - Zulma M Cucunubá
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
- Departamento de Epidemiología Clínica y Bioestadística. Facultad de Medicina, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Bimandra A Djaafara
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
- Eijkman-Oxford Clinical Research Unit, Jakarta, Indonesia
| | - Cassia F Estofolete
- Faculdade de Medicina de São José do Rio Preto (FAMERP), São José do Rio Preto, Brazil
| | - Maria Eugenia Grillet
- Instituto de Zoologia y Ecologia Tropical, Facultad de Ciencias, Universidad Central de Venezuela, Caracas, Venezuela
| | - Nuno R Faria
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
- Departamento de Molestias Infecciosas e Parasitarias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Department of Zoology, University of Oxford, Oxford, UK
| | - Silvia Figueiredo Costa
- Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - David A Forero-Peña
- Biomedical Research and Therapeutic Vaccines Institute, Ciudad Bolívar, Venezuela
| | - Diana M Gibb
- MRC Clinical Trials Unit at University College London, London, UK
| | - Anthony C Gordon
- Division of Anaesthetics, Pain Medicine and Intensive Care, Imperial College London, London, UK
| | - Raph L Hamers
- Eijkman-Oxford Clinical Research Unit, Jakarta, Indonesia
- Centre for Tropical Medicine and Global Health, Nuffield Dept of Medicine, University of Oxford, Oxford, UK
| | - Arran Hamlet
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Vera Irawany
- Fatmawati General Hospital, Faculty of Medicine University of Indonesia, Jakarta, Indonesia
| | - Anupop Jitmuang
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | | | | | - Margarita Lampo
- Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela
| | - Anna S Levin
- Department of Infectious Diseases, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | | | - Rima Mustafa
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
| | - Shevanthi Nayagam
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Thundon Ngamprasertchai
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | | | - Mauricio L Nogueira
- Faculdade de Medicina de São José do Rio Preto (FAMERP), São José do Rio Preto, Brazil
| | - Esteban Ortiz-Prado
- OneHealth Global Research Group, Universidad de las Américas, Quito, Ecuador
| | | | | | - Panuwat Promsin
- Critical Care Division, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Ambar Qavi
- School of Public Health, Imperial College London, London, UK
| | - Alison J Rodger
- Institute for Global Health, University College London, London, UK
| | - Ester C Sabino
- Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Sorawat Sangkaew
- Section of Adult Infectious Disease, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Djayanti Sari
- Department of Anesthesiology and Intensive Theraphy, Faculty of Medicine, Public Health and Nursing Universitas Gadjah Mada. Public Hospital Dr. Sardjito, Yogyakarta, Indonesia
| | - Rujipas Sirijatuphat
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Andrei C Sposito
- Atherosclerosis and Vascular Biology Laboratory, State University of Campinas, Campinas, Brazil
| | | | - Hayley A Thompson
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | | | - Sandra Valderrama-Beltrán
- Division of Infectious Diseases. School of Medicine. Pontificia Universidad Javeriana, Hospital Universitario San Ignacio, Bogotá, Colombia
| | - Peter Winskill
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Azra C Ghani
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Patrick G T Walker
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Timothy B Hallett
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
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Oliveira TGM, Venturini G, Alvim JM, Feijó LL, Dinardo CL, Sabino EC, Seidman JG, Seidman CE, Krieger JE, Pereira AC. Different Transcriptomic Response to T. cruzi Infection in hiPSC-Derived Cardiomyocytes From Chagas Disease Patients With and Without Chronic Cardiomyopathy. Front Cell Infect Microbiol 2022; 12:904747. [PMID: 35873155 PMCID: PMC9301326 DOI: 10.3389/fcimb.2022.904747] [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: 03/25/2022] [Accepted: 06/16/2022] [Indexed: 11/16/2022] Open
Abstract
Chagas disease is a tropical zoonosis caused by Trypanosoma cruzi. After infection, the host present an acute phase, usually asymptomatic, in which an extensive parasite proliferation and intense innate immune activity occurs, followed by a chronic phase, characterized by low parasitemia and development of specific immunity. Most individuals in the chronic phase remain without symptoms or organ damage, a state called indeterminate IND form. However, 20 to 40% of individuals develop cardiac or gastrointestinal complications at any time in life. Cardiomyocytes have an important role in the development of Chronic Chagas Cardiomyopathy (CCC) due to transcriptional and metabolic alterations that are crucial for the parasite survival and replication. However, it still not clear why some infected individuals progress to a cardiomyopathy phase, while others remain asymptomatic. In this work, we used hiPSCs-derived cardiomyocytes (hiPSC-CM) to investigate patterns of infection, proliferation and transcriptional response in IND and CCC patients. Our data show that T. cruzi infection and proliferation efficiency do not differ significantly in PBMCs and hiPSC-CM from both groups. However, RNA-seq analysis in hiPSC-CM infected for 24 hours showed a significantly different transcriptional response to the parasite in cells from IND or CCC patients. Cardiomyocytes from IND showed significant differences in the expression of genes related to antigen processing and presentation, as well as, immune co-stimulatory molecules. Furthermore, the downregulation of collagen production genes and extracellular matrix components was significantly different in these cells. Cardiomyocytes from CCC, in turn, showed increased expression of mTORC1 pathway and unfolded protein response genes, both associated to increased intracellular ROS production. These data point to a differential pattern of response, determined by baseline genetic differences between groups, which may have an impact on the development of a chronic outcome with or without the presentation of cardiac symptoms.
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Affiliation(s)
- Theo G. M. Oliveira
- Laboratório de Genética e Cardiologia Molecular, Instituto do Coração (InCor), Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo (HC/FMUSP), São Paulo, Brazil
- Instituto do Coração (InCor), Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo (HC/FMUSP), São Paulo, Brazil
- Fundação Pró-Sangue Hemocentro de São Paulo, Divisão de Pesquisa – São Paulo, SP, Brazil
- *Correspondence: Theo G. M. Oliveira,
| | - Gabriela Venturini
- Laboratório de Genética e Cardiologia Molecular, Instituto do Coração (InCor), Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo (HC/FMUSP), São Paulo, Brazil
- Genetics Department, Harvard Medical School, MA, United States
| | - Juliana M. Alvim
- Laboratório de Genética e Cardiologia Molecular, Instituto do Coração (InCor), Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo (HC/FMUSP), São Paulo, Brazil
| | - Larissa L. Feijó
- Fundação Pró-Sangue Hemocentro de São Paulo, Divisão de Pesquisa – São Paulo, SP, Brazil
| | - Carla L. Dinardo
- Fundação Pró-Sangue Hemocentro de São Paulo, Divisão de Pesquisa – São Paulo, SP, Brazil
| | - Ester C. Sabino
- Instituto do Medicina Tropical (IMT), Universidade de São Paulo – São Paulo, SP, Brazil
| | | | - Christine E. Seidman
- Genetics Department, Harvard Medical School, MA, United States
- Cardiovascular Division, Brigham and Women’s Hospital, & Harvard Medical School, Boston, MA, United States
- Howard Hughes Medical Institute, Chevy Chase, MD, United States
| | - Jose E. Krieger
- Laboratório de Genética e Cardiologia Molecular, Instituto do Coração (InCor), Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo (HC/FMUSP), São Paulo, Brazil
- Instituto do Coração (InCor), Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo (HC/FMUSP), São Paulo, Brazil
| | - Alexandre C. Pereira
- Laboratório de Genética e Cardiologia Molecular, Instituto do Coração (InCor), Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo (HC/FMUSP), São Paulo, Brazil
- Instituto do Coração (InCor), Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo (HC/FMUSP), São Paulo, Brazil
- Genetics Department, Harvard Medical School, MA, United States
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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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Brizzi A, Whittaker C, Servo LMS, Hawryluk I, Prete CA, de Souza WM, Aguiar RS, Araujo LJT, Bastos LS, Blenkinsop A, Buss LF, Candido D, Castro MC, Costa SF, Croda J, de Souza Santos AA, Dye C, Flaxman S, Fonseca PLC, Geddes VEV, Gutierrez B, Lemey P, Levin AS, Mellan T, Bonfim DM, Miscouridou X, Mishra S, Monod M, Moreira FRR, Nelson B, Pereira RHM, Ranzani O, Schnekenberg RP, Semenova E, Sonabend R, Souza RP, Xi X, Sabino EC, Faria NR, Bhatt S, Ratmann O. Spatial and temporal fluctuations in COVID-19 fatality rates in Brazilian hospitals. Nat Med 2022; 28:1476-1485. [PMID: 35538260 PMCID: PMC9307484 DOI: 10.1038/s41591-022-01807-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [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: 11/04/2021] [Accepted: 03/31/2022] [Indexed: 02/07/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Gamma variant of concern has spread rapidly across Brazil since late 2020, causing substantial infection and death waves. Here we used individual-level patient records after hospitalization with suspected or confirmed coronavirus disease 2019 (COVID-19) between 20 January 2020 and 26 July 2021 to document temporary, sweeping shocks in hospital fatality rates that followed the spread of Gamma across 14 state capitals, during which typically more than half of hospitalized patients aged 70 years and older died. We show that such extensive shocks in COVID-19 in-hospital fatality rates also existed before the detection of Gamma. Using a Bayesian fatality rate model, we found that the geographic and temporal fluctuations in Brazil's COVID-19 in-hospital fatality rates were primarily associated with geographic inequities and shortages in healthcare capacity. We estimate that approximately half of the COVID-19 deaths in hospitals in the 14 cities could have been avoided without pre-pandemic geographic inequities and without pandemic healthcare pressure. Our results suggest that investments in healthcare resources, healthcare optimization and pandemic preparedness are critical to minimize population-wide mortality and morbidity caused by highly transmissible and deadly pathogens such as SARS-CoV-2, especially in low- and middle-income countries.
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Affiliation(s)
- Andrea Brizzi
- Department of Mathematics, Imperial College London, London, UK
| | - Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | | | - Iwona Hawryluk
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Carlos A Prete
- Departamento de Engenharia de Sistemas Eletrônicos, Escola Politécnica, Universidade de São Paulo, São Paulo, Brazil
| | - William M de Souza
- World Reference Center for Emerging Viruses and Arboviruses and Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston TX, USA
| | - Renato S Aguiar
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Instituto D'Or de Pesquisa e Ensino (IDOR), Rio de Janeiro, Brazil
| | - Leonardo J T Araujo
- Laboratory of Quantitative Pathology, Center of Pathology, Adolfo Lutz Institute, São Paulo, Brazil
| | - Leonardo S Bastos
- Programa de Computação Científica, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | | | - Lewis F Buss
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
- Departamento de Moléstias Infecciosas e Parasitárias e Instituto de Medicina Tropical da Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | | | - Marcia C Castro
- Department of Global Health and Population, Harvard T. H. Chan School of Public Health, Boston MA, USA
| | - Silvia F Costa
- Departamento de Moléstias Infecciosas e Parasitárias e Instituto de Medicina Tropical da Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Julio Croda
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven CT, USA
| | | | | | - Seth Flaxman
- Department of Computer Science, University of Oxford, Oxford, UK
| | - Paula L C Fonseca
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Victor E V Geddes
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven - University of Leuven, Leuven, Belgium
| | - Anna S Levin
- Departamento de Moléstias Infecciosas e Parasitárias e Instituto de Medicina Tropical da Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Thomas Mellan
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Diego M Bonfim
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Swapnil Mishra
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
- Section of Epidemiology, School of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Mélodie Monod
- Department of Mathematics, Imperial College London, London, UK
| | - Filipe R R Moreira
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Bruce Nelson
- Environmental Dynamics, INPA, National Institute for Amazon Research, Manaus, Brazil
| | | | - Otavio Ranzani
- Barcelona Institute for Global Health, ISGlobal, Barcelona, Spain
| | | | | | - Raphael Sonabend
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Renan P Souza
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Xiaoyue Xi
- Department of Mathematics, Imperial College London, London, UK
| | - Ester C Sabino
- Departamento de Moléstias Infecciosas e Parasitárias e Instituto de Medicina Tropical da Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil.
| | - Nuno R Faria
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK.
- Departamento de Moléstias Infecciosas e Parasitárias e Instituto de Medicina Tropical da Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil.
- Department of Zoology, University of Oxford, Oxford, UK.
- Department of Infectious Disease Epidemiology, Imperial College London, London, UK.
| | - Samir Bhatt
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK.
- Section of Epidemiology, School of Public Health, University of Copenhagen, Copenhagen, Denmark.
| | - Oliver Ratmann
- Department of Mathematics, Imperial College London, London, UK.
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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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36
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da Silva H, Oliveira TMP, Sabino EC, Alonso DP, Sallum MAM. Bacterial diversity in Haemagogus leucocelaenus (Diptera: Culicidae) from Vale do Ribeira, São Paulo, Brazil. BMC Microbiol 2022; 22:161. [PMID: 35733096 PMCID: PMC9215073 DOI: 10.1186/s12866-022-02571-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 06/06/2022] [Indexed: 01/29/2023] Open
Abstract
INTRODUCTION Mosquitoes (Diptera: Culicidae) are vectors that transmit numerous pathogens to humans and other vertebrates. Haemagogus leucocelaenus is a mosquito associated with transmission of yellow fever virus. The insect gut harbors a variety of microorganisms that can live and multiply within it, thus contributing to digestion, nutrition, and development of its host. The composition of bacterial communities in mosquitoes can be influenced by both biotic and abiotic factors. The goal of this study was to investigate the bacterial diversity of Hg. leucocelaenus and verify the differences between the bacterial communities in Hg. leucocelaenus from three different locations in the Atlantic tropical rain forest and southeastern state of São Paulo State, Brazil. RESULTS The phylum Proteobacteria was found in mosquitoes collected from the three selected study sites. More than 50% of the contigs belong to Wolbachia, followed by 5% Swaminathania, and 3% Acinetobacter. The genus Serratia was found in samples from two locations. CONCLUSIONS Wolbachia was reported for the first time in this species and may indicates that the vector competence of the populations of the species can vary along its geographical distribution area. The presence of Serratia might facilitate viral invasion caused by the disruption of the midgut barrier via action of the SmEnhancin protein, which digests the mucins present in the intestinal epithelium.
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Affiliation(s)
- Herculano da Silva
- Departamento de Epidemiologia, Faculdade de Saúde Pública, Universidade de São Paulo, Av. Dr. Arnaldo 715, São Paulo, SP 01246-904 Brazil
| | - Tatiane M. P. Oliveira
- Departamento de Epidemiologia, Faculdade de Saúde Pública, Universidade de São Paulo, Av. Dr. Arnaldo 715, São Paulo, SP 01246-904 Brazil
| | - Ester C. Sabino
- Departamento de Moléstias Infecciosas e Parasitarias, Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, Av. Dr. Eneas de Carvalho 470, 1º andar, São Paulo, 05403-000 Brazil
| | - Diego Peres Alonso
- Departamento de Epidemiologia, Faculdade de Saúde Pública, Universidade de São Paulo, Av. Dr. Arnaldo 715, São Paulo, SP 01246-904 Brazil
- Biotechnology Institute and Bioscience Institute, Sao Paulo State University (UNESP), Botucatu, 18618-689 Brazil
| | - Maria Anice M. Sallum
- Departamento de Epidemiologia, Faculdade de Saúde Pública, Universidade de São Paulo, Av. Dr. Arnaldo 715, São Paulo, SP 01246-904 Brazil
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Sabino JS, Amorim MR, de Souza WM, Marega LF, Mofatto LS, Toledo-Teixeira DA, Forato J, Stabeli RG, Costa ML, Spilki FR, Sabino EC, Faria NR, Benites BD, Addas-Carvalho M, Stucchi RSB, Vasconcelos DM, Weaver SC, Granja F, Proenca-Modena JL, Vilela MMDS. Clearance of Persistent SARS-CoV-2 RNA Detection in a NFκB-Deficient Patient in Association with the Ingestion of Human Breast Milk: A Case Report. Viruses 2022; 14:1042. [PMID: 35632784 PMCID: PMC9143223 DOI: 10.3390/v14051042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 04/11/2022] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 02/01/2023] Open
Abstract
Currently, there are no evidence-based treatment options for long COVID-19, and it is known that SARS-CoV-2 can persist in part of the infected patients, especially those with immunosuppression. Since there is a robust secretion of SARS-CoV-2-specific highly-neutralizing IgA antibodies in breast milk, and because this immunoglobulin plays an essential role against respiratory virus infection in mucosa cells, being, in addition, more potent in neutralizing SARS-CoV-2 than IgG, here we report the clinical course of an NFκB-deficient patient chronically infected with the SARS-CoV-2 Gamma variant, who, after a non-full effective treatment with plasma infusion, received breast milk from a vaccinated mother by oral route as treatment for COVID-19. After such treatment, the symptoms improved, and the patient was systematically tested negative for SARS-CoV-2. Thus, we hypothesize that IgA and IgG secreted antibodies present in breast milk could be useful to treat persistent SARS-CoV-2 infection in immunodeficient patients.
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Affiliation(s)
- Janine S. Sabino
- Laboratory of Pediatric Immunology, Center for Investigation in Pediatrics, Faculty of Medical Sciences, University of Campinas, Campinas 13083-887, Brazil; (J.S.S.); (L.F.M.)
| | - Mariene R. Amorim
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas 13083-862, Brazil; (M.R.A.); (L.S.M.); (D.A.T.-T.); (J.F.); (F.G.)
| | - William M. de Souza
- World Reference Center for Emerging Viruses, Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA; (W.M.d.S.); (S.C.W.)
| | - Lia F. Marega
- Laboratory of Pediatric Immunology, Center for Investigation in Pediatrics, Faculty of Medical Sciences, University of Campinas, Campinas 13083-887, Brazil; (J.S.S.); (L.F.M.)
| | - Luciana S. Mofatto
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas 13083-862, Brazil; (M.R.A.); (L.S.M.); (D.A.T.-T.); (J.F.); (F.G.)
| | - Daniel A. Toledo-Teixeira
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas 13083-862, Brazil; (M.R.A.); (L.S.M.); (D.A.T.-T.); (J.F.); (F.G.)
| | - Julia Forato
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas 13083-862, Brazil; (M.R.A.); (L.S.M.); (D.A.T.-T.); (J.F.); (F.G.)
| | - Rodrigo G. Stabeli
- Oswaldo Cruz Foundation (Fiocruz-SP), Ribeirão Preto 14049-900, Brazil;
- Department of Public Health Emergency, Preparedness and Disaster, PAHO/WHO, Brasilia 70312-970, Brazil
| | - Maria Laura Costa
- Department of Obstetrics and Gynecology, Faculty of Medical Sciences, University of Campinas, Campinas 13083-887, Brazil;
| | - Fernando R. Spilki
- One Health Laboratory, Feevale University, Novo Hamburgo 93510-235, Brazil;
| | - Ester C. Sabino
- Tropical Medicine Institute, Medical School, University of São Paulo, São Paulo 5403-907, Brazil;
- Department of Infectious and Parasitic Disease, Medical School, University of São Paulo, São Paulo 05403-000, Brazil;
| | - Nuno R. Faria
- Department of Infectious and Parasitic Disease, Medical School, University of São Paulo, São Paulo 05403-000, Brazil;
- Department of Zoology, University of Oxford, Oxford OX1 2JD, UK
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London SW7 2AZ, UK
| | - Bruno D. Benites
- Hematology and Transfusion Medicine Center, University of Campinas, Campinas 13083-878, Brazil; (B.D.B.); (M.A.-C.)
| | - Marcelo Addas-Carvalho
- Hematology and Transfusion Medicine Center, University of Campinas, Campinas 13083-878, Brazil; (B.D.B.); (M.A.-C.)
| | - Raquel S. B. Stucchi
- Division of Infectious Diseases, University of Campinas, Campinas 13083-887, Brazil;
| | - Dewton M. Vasconcelos
- Laboratory of Investigation in Dermatology and Immunodeficiencies, Department of Dermatology, Medical School, University of São Paulo, São Paulo 05403-000, Brazil;
| | - Scott C. Weaver
- World Reference Center for Emerging Viruses, Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA; (W.M.d.S.); (S.C.W.)
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Fabiana Granja
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas 13083-862, Brazil; (M.R.A.); (L.S.M.); (D.A.T.-T.); (J.F.); (F.G.)
- Biodiversity Research Centre, Federal University of Roraima, Boa Vista 72000-000, Brazil
| | - José Luiz Proenca-Modena
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas 13083-862, Brazil; (M.R.A.); (L.S.M.); (D.A.T.-T.); (J.F.); (F.G.)
- Experimental Medicine Research Cluster (EMRC), University of Campinas, Campinas 13083-862, Brazil
- Hub of Global Health (HGH), University of Campinas, Campinas 13083-862, Brazil
| | - Maria Marluce dos S. Vilela
- Laboratory of Pediatric Immunology, Center for Investigation in Pediatrics, Faculty of Medical Sciences, University of Campinas, Campinas 13083-887, Brazil; (J.S.S.); (L.F.M.)
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Miranda C, Utsch-Gonçalves D, Piassi FCC, Loureiro P, Gomes I, Ribeiro MA, de Almeida-Neto C, Blatyta P, Amorim L, Garcia Mateos SO, Murphy EL, Custer B, Carneiro-Proietti ABF, Sabino EC. Prevalence and Risk Factors for Human T-Cell Lymphotropic Virus (HTLV) in Blood Donors in Brazil-A 10-Year Study (2007-2016). Front Med (Lausanne) 2022; 9:844265. [PMID: 35355612 PMCID: PMC8959844 DOI: 10.3389/fmed.2022.844265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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] [Received: 12/27/2021] [Accepted: 02/10/2022] [Indexed: 12/12/2022] Open
Abstract
It is unknown whether HTLV-1/2 prevalence has been stable or changing with time in Brazil. We present a 10-year (2007–2016) analysis of HTLV-1/2 infection in first-time blood donors from four blood banks in Brazil. The Brazilian blood centers participating in this multicenter Recipient Epidemiology and Donor Evaluation Study (REDS) are located in Recife in the Northeast and in São Paulo, Rio de Janeiro and Belo Horizonte located in the Southeast of the country. A previous REDS study using the same database from 2007 to 2009 showed that the prevalence per 100,000 donors was 222 in Recife, 83 in Belo Horizonte and 101 in São Paulo. From 2007 to 2016, HTLV-1/2 prevalence was calculated by year, blood center and birth cohort. Covariates included age, gender, schooling, self-reported skin color and type of donation. From 1,092,174 first-blood donations, in the general analysis, HTLV-1/2 infection predominated in females, donors over 50 years of age, black skin color and less educated. The average prevalence was 228 per 100,000 donors in Recife, 222 in Rio de Janeiro, 104 in Belo Horizonte and 103 in São Paulo. In the 10-year analysis, HTLV-1/2 prevalence was stable, but a trend was observed toward an increase in HTLV-1/2 infection among younger people (p < 0.001), males (p = 0.049), those with white skin color (p < 0.001), and higher education (p = 0.014). Therefore, this 10-year surveillance of the infection showed stable HTLV-1/2 prevalence overall but a trend toward increased prevalence among the younger and more educated donors despite Brazilian policies to control sexually transmitted infections being in place for more than 10 years.
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Affiliation(s)
- Carolina Miranda
- Programa de Pós-Graduação em Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Denise Utsch-Gonçalves
- Programa de Pós-Graduação em Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Fabiana Chagas Camargos Piassi
- Departamento de Propedêutica Complementar, Faculdade de Medicina da Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Paula Loureiro
- Fundação Hemope, Recife, Brazil.,Department of Clinical Medicine, Universidade de Pernambuco, Recife, Brazil
| | - Isabel Gomes
- Faculdade Ciências Médicas de Minas Gerais, Belo Horizonte, Brazil
| | | | | | - Paula Blatyta
- Fundação Pró-Sangue, Hemocentro de São Paulo, São Paulo, Brazil
| | - Luiz Amorim
- Fundação Hemorio, Hemocentro do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Edward L Murphy
- Department of Laboratory Medicine, Vitalant Research Institute, San Francisco, CA, United States.,Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Brian Custer
- Department of Laboratory Medicine, Vitalant Research Institute, San Francisco, CA, United States.,Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, United States
| | | | - Ester C Sabino
- Faculdade de Medicina da Universidade de São Paulo, Instituto de Medicina Tropical, São Paulo, Brazil
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39
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Nicolete VC, Rodrigues PT, Fernandes ARJ, Corder RM, Tonini J, Buss LF, Sales FC, Faria NR, Sabino EC, Castro MC, Ferreira MU. Epidemiology of COVID-19 after Emergence of SARS-CoV-2 Gamma Variant, Brazilian Amazon, 2020-2021. Emerg Infect Dis 2022; 28:709-712. [PMID: 34963505 PMCID: PMC8888227 DOI: 10.3201/eid2803.211993] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Gamma variant has been hypothesized to cause more severe illness than previous variants, especially in children. Successive SARS-CoV-2 IgG serosurveys in the Brazilian Amazon showed that age-specific attack rates and proportions of symptomatic SARS-CoV-2 infections were similar before and after Gamma variant emergence.
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40
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Lazari LC, Zerbinati RM, Rosa-Fernandes L, Santiago VF, Rosa KF, Angeli CB, Schwab G, Palmieri M, Sarmento DJS, Marinho CRF, Almeida JD, To K, Giannecchini S, Wrenger C, Sabino EC, Martinho H, Lindoso JAL, Durigon EL, Braz-Silva PH, Palmisano G. MALDI-TOF mass spectrometry of saliva samples as a prognostic tool for COVID-19. J Oral Microbiol 2022; 14:2043651. [PMID: 35251522 PMCID: PMC8890567 DOI: 10.1080/20002297.2022.2043651] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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] [Indexed: 11/02/2022] Open
Abstract
Background Methods Results Conclusion
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Affiliation(s)
- Lucas C. Lazari
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil
| | - Rodrigo M. Zerbinati
- Laboratory of Virology (LIM-52-HC-FMUSP), Institute of Tropical Medicine of São Paulo, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Livia Rosa-Fernandes
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil
- Laboratory of Experimental Immunoparasitology, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil
| | - Veronica Feijoli Santiago
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil
| | - Klaise F. Rosa
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil
| | - Claudia B. Angeli
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil
| | - Gabriela Schwab
- Laboratory of Virology (LIM-52-HC-FMUSP), Institute of Tropical Medicine of São Paulo, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Michelle Palmieri
- Department of Stomatology, School of Dentistry, University of São Paulo, São Paulo, Brazil
| | - Dmitry J. S. Sarmento
- Department of Stomatology, School of Dentistry, University of São Paulo, São Paulo, Brazil
| | - Claudio R. F. Marinho
- Laboratory of Experimental Immunoparasitology, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil
| | - Janete Dias Almeida
- Department of Biosciences and Oral Diagnosis, Institute of Science and Technology, São Paulo State University, São José dos Campos, Brazil
| | - Kelvin 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, Hong Kong, Special Administrative Region, China
| | - Simone Giannecchini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Carsten Wrenger
- Unit for Drug Discovery, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil
| | - Ester C. Sabino
- Institute of Tropical Medicine of São Paulo, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Herculano Martinho
- Centro de Ciencias Naturais e Humanas, Universidade Federal do ABC, Santo André, Brazil
| | - José A. L. Lindoso
- Institute of Infectious Diseases Emílio Ribas, São Paulo, Brazil
- Laboratory of Protozoology (LIM-49-HC-FMUSP), Institute of Tropical Medicine of São Paulo, School of Medicine, University of São Paulo, São Paulo, Brazil
- Department of Infectious Diseases, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Edison L. Durigon
- Laboratory of Clinical and Molecular Virology, Department of Microbiology, ICB, University of São Paulo, São Paulo, Brazil
| | - Paulo H. Braz-Silva
- Laboratory of Virology (LIM-52-HC-FMUSP), 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 São Paulo, São Paulo, Brazil
| | - Giuseppe Palmisano
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil
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41
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Aikawa NE, Kupa LVK, Pasoto SG, Medeiros-Ribeiro AC, Yuki EFN, Saad CGS, Pedrosa T, Fuller R, Shinjo SK, Sampaio-Barros PD, Andrade DCO, Pereira RMR, Seguro LPC, Valim JML, Waridel F, Sartori AMC, Duarte AJS, Antonangelo L, Sabino EC, Menezes PR, Kallas EG, Silva CA, Bonfa E. Immunogenicity and safety of two doses of the CoronaVac SARS-CoV-2 vaccine in SARS-CoV-2 seropositive and seronegative patients with autoimmune rheumatic diseases in Brazil: a subgroup analysis of a phase 4 prospective study. The Lancet Rheumatology 2022; 4:e113-e124. [PMID: 34901885 PMCID: PMC8641960 DOI: 10.1016/s2665-9913(21)00327-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Background We aimed to examine the immunogenicity pattern induced by the inactivated SARS-CoV-2 vaccine CoronaVac (Sinovac Life Sciences, Beijing, China) in SARS-CoV-2 seropositive patients with autoimmune rheumatic diseases compared with seropositive controls, seronegative patients with autoimmune rheumatic diseases, and seronegative controls. Methods CoronavRheum is an ongoing, prospective, controlled, phase 4 study, in which patients aged 18 years or older with autoimmune rheumatic diseases, and healthy controls were recruited from a single site (Rheumatology Division of Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo) in São Paulo, Brazil Participants were vaccinated with two doses of CoronaVac (intramuscular injection, 3 μg in 0·5 mL of β-propiolactone inactivated SARS-CoV-2) on day 0 and on day 28. Blood samples were taken pre-vaccination on day 0, day 28, and also on day 69. For this subgroup analysis, participants were defined as being SARS-CoV-2 seropositive or seronegative prevaccination via anti-SARS-CoV-2 spike (S)1 or S2 IgG (cutoff of 15·0 arbitrary units [AU] per mL) or neutralising antibody titres (cutoff of ≥30%) and were matched for age and sex, via convenience sampling, in a 1:3:1:1 ratio (seropositive patients to seronegative patients to seropositive controls to seronegative controls). The primary outcomes were rates of anti-SARS-CoV-2 S1 and S2 IgG seropositivity and SARS-CoV-2 neutralising antibody positivity at day 28 and day 69 and immunogenicity dynamics assessed by geometric mean titres (GMTs) of IgG and median neutralising activity in seropositive patients with autoimmune rheumatic diseases compared with seronegative patients and seropositive and seronegative controls. We assessed safety in all participants randomly selected for this subgroup analysis. This study is registered with ClinicalTrials.gov, NCT04754698, and is ongoing for long-term immunogenicity evaluation. Findings Between Feb 4 and Feb 8, 2021, 1418 patients and 542 controls were recruited, of whom 1685 received two vaccinations (1193 patients and 492 controls). After random sampling, our immunogenicity analysis population comprised 942 participants, of whom 157 were SARS-CoV-2 seropositive patients with autoimmune rheumatic diseases, 157 were seropositive controls, 471 were seronegative patients, and 157 were seronegative controls; the median age was 48 years (IQR 38–56) and 594 (63%) were female and 348 (37%) were male. For seropositive patients and controls, an increase in anti-SARS-CoV-2 S1 and S2 IgG titres (seropositive patients GMT 52·3 [95% CI 42·9–63·9] at day 0 vs 128·9 [105·6–157·4] at day 28; seropositive controls 53·3 [45·4–62·5] at day 0 vs 202·0 [174·8–233·4] at day 28) and neutralising antibody activity (seropositive patients 59% [IQR 39–83] at day 0 vs 82% [54–96] at day 28; seropositive controls 58% [41–79] at day 0 vs 92% [79–96] at day 28), was observed from day 0 to day 28, without further increases from day 28 to day 69 (at day 69 seropositive patients' GMT was 137·1 [116·2–161·9] and neutralising antibody activity was 79% [57–94]); and seropositive controls' GMT was 188·6 [167·4–212·6] and neutralising antibody activity was 92% [75–96]). By contrast, for seronegative patients and controls, the second dose was required for maximum response at day 69, which was lower in seronegative patients than in seronegative controls. GMTs in seronegative patients were 2·3 (95% CI 2·2–2·3) at day 0, 5·7 (5·1–6·4) at day 28, and 29·6 (26·4–33·3) at day 69, and in seronegative controls were 2·3 (2·1–2·5) at day 0, 10·6 (8·7–13·1) at day 28, and 71·7 (63·5–81·0) at day 69; neutralising antibody activity in seronegative patients was 15% (IQR 15–15) on day 0, 15% (15–15) at day 28, and 39% (15–65) at day 69, and in seronegative controls was 15% (15–15) at day 0, 24% (15–37) at day 28, and 61% (37–79) at day 69. Neither seronegative patients nor seronegative controls reached the GMT or antibody activity levels of seropositive patients at day 69. Interpretation By contrast with seronegative patients with autoimmune rheumatic diseases, seropositive patients have a robust response after a single dose of CoronaVac. Our findings raise the possibility that the reduced immunogenicity observed in seronegative patients might not be the optimum response potential to SARS-CoV-2 vaccination, and therefore emphasise the importance of at least a single booster vaccination in these patients. Funding Fundação de Amparo à Pesquisa do Estado de São Paulo, Conselho Nacional de Desenvolvimento Científico e Tecnológico, and B3-Bolsa de Valores do Brasil. Translation For the Portuguese translation of the abstract see Supplementary Materials section.
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Taub MA, Conomos MP, Keener R, Iyer KR, Weinstock JS, Yanek LR, Lane J, Miller-Fleming TW, Brody JA, Raffield LM, McHugh CP, Jain D, Gogarten SM, Laurie CA, Keramati A, Arvanitis M, Smith AV, Heavner B, Barwick L, Becker LC, Bis JC, Blangero J, Bleecker ER, Burchard EG, Celedón JC, Chang YPC, Custer B, Darbar D, de las Fuentes L, DeMeo DL, Freedman BI, Garrett ME, Gladwin MT, Heckbert SR, Hidalgo BA, Irvin MR, Islam T, Johnson WC, Kaab S, Launer L, Lee J, Liu S, Moscati A, North KE, Peyser PA, Rafaels N, Seidman C, Weeks DE, Wen F, Wheeler MM, Williams LK, Yang IV, Zhao W, Aslibekyan S, Auer PL, Bowden DW, Cade BE, Chen Z, Cho MH, Cupples LA, Curran JE, Daya M, Deka R, Eng C, Fingerlin TE, Guo X, Hou L, Hwang SJ, Johnsen JM, Kenny EE, Levin AM, Liu C, Minster RL, Naseri T, Nouraie M, Reupena MS, Sabino EC, Smith JA, Smith NL, Lasky-Su J, Taylor JG, Telen MJ, Tiwari HK, Tracy RP, White MJ, Zhang Y, Wiggins KL, Weiss ST, Vasan RS, Taylor KD, Sinner MF, Silverman EK, Shoemaker MB, Sheu WHH, Sciurba F, Schwartz DA, Rotter JI, Roden D, Redline S, Raby BA, Psaty BM, Peralta JM, Palmer ND, Nekhai S, Montgomery CG, Mitchell BD, Meyers DA, McGarvey ST, Mak AC, Loos RJ, Kumar R, Kooperberg C, Konkle BA, Kelly S, Kardia SL, Kaplan R, He J, Gui H, Gilliland FD, Gelb BD, Fornage M, Ellinor PT, de Andrade M, Correa A, Chen YDI, Boerwinkle E, Barnes KC, Ashley-Koch AE, Arnett DK, Albert C, Laurie CC, Abecasis G, Nickerson DA, Wilson JG, Rich SS, Levy D, Ruczinski I, Aviv A, Blackwell TW, Thornton T, O’Connell J, Cox NJ, Perry JA, Armanios M, Battle A, Pankratz N, Reiner AP, Mathias RA. Genetic determinants of telomere length from 109,122 ancestrally diverse whole-genome sequences in TOPMed. Cell Genom 2022; 2:S2666-979X(21)00105-1. [PMID: 35530816 PMCID: PMC9075703 DOI: 10.1016/j.xgen.2021.100084] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 09/03/2021] [Accepted: 12/10/2021] [Indexed: 01/16/2023]
Abstract
Genetic studies on telomere length are important for understanding age-related diseases. Prior GWAS for leukocyte TL have been limited to European and Asian populations. Here, we report the first sequencing-based association study for TL across ancestrally-diverse individuals (European, African, Asian and Hispanic/Latino) from the NHLBI Trans-Omics for Precision Medicine (TOPMed) program. We used whole genome sequencing (WGS) of whole blood for variant genotype calling and the bioinformatic estimation of telomere length in n=109,122 individuals. We identified 59 sentinel variants (p-value <5×10-9) in 36 loci associated with telomere length, including 20 newly associated loci (13 were replicated in external datasets). There was little evidence of effect size heterogeneity across populations. Fine-mapping at OBFC1 indicated the independent signals colocalized with cell-type specific eQTLs for OBFC1 (STN1). Using a multi-variant gene-based approach, we identified two genes newly implicated in telomere length, DCLRE1B (SNM1B) and PARN. In PheWAS, we demonstrated our TL polygenic trait scores (PTS) were associated with increased risk of cancer-related phenotypes.
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Affiliation(s)
- Margaret A. Taub
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Matthew P. Conomos
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA, USA
| | - Rebecca Keener
- Department of Biomedical Engineering, Johns Hopkins Whiting School of Engineering, Baltimore, MD, USA
| | - Kruthika R. Iyer
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Joshua S. Weinstock
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Lisa R. Yanek
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - John Lane
- Department of Laboratory Medicine & Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Tyne W. Miller-Fleming
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jennifer A. Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Laura M. Raffield
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Caitlin P. McHugh
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA, USA
| | - Deepti Jain
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA, USA
| | - Stephanie M. Gogarten
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA, USA
| | - Cecelia A. Laurie
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA, USA
| | - Ali Keramati
- Department of Cardiology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Marios Arvanitis
- Department of Medicine, Division of Cardiology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Albert V. Smith
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Benjamin Heavner
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA, USA
| | - Lucas Barwick
- LTRC Data Coordinating Center, The Emmes Company, LLC, Rockville, MD, USA
| | - Lewis C. Becker
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Joshua C. Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - John Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Eugene R. Bleecker
- Department of Medicine, Division of Genetics, Genomics, and Precision Medicine, University of Arizona, Tucson, AZ, USA
- Division of Pharmacogenomics, University of Arizona, Tucson, AZ, USA
| | - Esteban G. Burchard
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Juan C. Celedón
- Division of Pediatric Pulmonary Medicine, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yen Pei C. Chang
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Brian Custer
- Vitalant Research Institute, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Dawood Darbar
- Division of Cardiology, University of Illinois at Chicago, Chicago, IL, USA
| | - Lisa de las Fuentes
- Cardiovascular Division, Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Dawn L. DeMeo
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Barry I. Freedman
- Department of Internal Medicine, Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Melanie E. Garrett
- Department of Medicine and Duke Comprehensive Sickle Cell Center, Duke University Medical Center, Durham, NC, USA
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
| | - Mark T. Gladwin
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Susan R. Heckbert
- Cardiovascular Health Research Unit and Department of Epidemiology, University of Washington, Seattle, WA, USA
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Bertha A. Hidalgo
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Marguerite R. Irvin
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Talat Islam
- Division of Environmental Health, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA, USA
| | - W. Craig Johnson
- Department of Biostatistics, Collaborative Health Studies Coordinating Center, University of Washington, Seattle, WA, USA
| | - Stefan Kaab
- Department of Medicine I, University Hospital Munich, Ludwig-Maximilian’s University, Munich, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, Munich, Germany
| | - Lenore Launer
- Laboratory of Epidemiology and Population Science, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Jiwon Lee
- Department of Medicine, Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA, USA
| | - Simin Liu
- Department of Epidemiology and Brown Center for Global Cardiometabolic Health, Brown University, Providence, RI, USA
| | - Arden Moscati
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kari E. North
- Department of Epidemiology, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Patricia A. Peyser
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Nicholas Rafaels
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | | | - Daniel E. Weeks
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Fayun Wen
- Center for Sickle Cell Disease and Department of Medicine, College of Medicine, Howard University, Washington, DC 20059, USA
| | - Marsha M. Wheeler
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - L. Keoki Williams
- Center for Individualized and Genomic Medicine Research (CIGMA), Department of Internal Medicine, Henry Ford Health System, Detroit, MI, USA
| | - Ivana V. Yang
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Wei Zhao
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Stella Aslibekyan
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Paul L. Auer
- Zilber School of Public Health, University of Wisconsin, Milwaukee, Milwaukee, WI, USA
| | - Donald W. Bowden
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Brian E. Cade
- Harvard Medical School, Boston, MA, USA
- Division of Sleep Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Zhanghua Chen
- Division of Environmental Health, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA, USA
| | - Michael H. Cho
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - L. Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- The National Heart, Lung, and Blood Institute, Boston University’s Framingham Heart Study, Framingham, MA, USA
| | - Joanne E. Curran
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Michelle Daya
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Ranjan Deka
- Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Celeste Eng
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Tasha E. Fingerlin
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
- Department of Biostatistics and Informatics, University of Colorado, Denver, Aurora, CO, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Lifang Hou
- Department of Preventive Medicine, Northwestern University, Chicago, IL, USA
| | - Shih-Jen Hwang
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jill M. Johnsen
- Bloodworks Northwest Research Institute, Seattle, WA, USA
- University of Washington, Department of Medicine, Seattle, WA, USA
| | - Eimear E. Kenny
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Albert M. Levin
- Department of Public Health Sciences, Henry Ford Health System, Detroit, MI, USA
| | - Chunyu Liu
- The National Heart, Lung, and Blood Institute, Boston University’s Framingham Heart Study, Framingham, MA, USA
- The Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, MD, USA
| | - Ryan L. Minster
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Take Naseri
- Ministry of Health, Government of Samoa, Apia, Samoa
- Department of Epidemiology & International Health Institute, School of Public Health, Brown University, Providence, RI, USA
| | - Mehdi Nouraie
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | | | - Ester C. Sabino
- Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Jennifer A. Smith
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Nicholas L. Smith
- Cardiovascular Health Research Unit and Department of Epidemiology, University of Washington, Seattle, WA, USA
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Jessica Lasky-Su
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - James G. Taylor
- Center for Sickle Cell Disease and Department of Medicine, College of Medicine, Howard University, Washington, DC 20059, USA
| | - Marilyn J. Telen
- Department of Medicine and Duke Comprehensive Sickle Cell Center, Duke University Medical Center, Durham, NC, USA
- Duke Comprehensive Sickle Cell Center, Duke University Medical Center, Durham, NC, USA
| | - Hemant K. Tiwari
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Russell P. Tracy
- Departments of Pathology & Laboratory Medicine and Biochemistry, Larrner College of Medicine, University of Vermont, Colchester, VT, USA
| | - Marquitta J. White
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Yingze Zhang
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Kerri L. Wiggins
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Scott T. Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Ramachandran S. Vasan
- The National Heart, Lung, and Blood Institute, Boston University’s Framingham Heart Study, Framingham, MA, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA
| | - Kent D. Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Moritz F. Sinner
- Department of Medicine I, University Hospital Munich, Ludwig-Maximilian’s University, Munich, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, Munich, Germany
| | - Edwin K. Silverman
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - M. Benjamin Shoemaker
- Departments of Medicine, Pharmacology, and Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Wayne H.-H. Sheu
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Frank Sciurba
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - David A. Schwartz
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Jerome I. Rotter
- Institute for Translational Genomics and Population Sciences, Departments of Pediatrics and Medicine, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Daniel Roden
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Susan Redline
- Division of Sleep Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Benjamin A. Raby
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Pulmonary Medicine, Boston Children’s Hospital, Boston, MA, USA
| | - Bruce M. Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, and Health Services, University of Washington, Seattle, WA, USA
| | - Juan M. Peralta
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Nicholette D. Palmer
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Sergei Nekhai
- Center for Sickle Cell Disease and Department of Medicine, College of Medicine, Howard University, Washington, DC 20059, USA
| | - Courtney G. Montgomery
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Braxton D. Mitchell
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Geriatrics Research and Education Clinical Center, Baltimore Veterans Administration Medical Center, Baltimore, MD, USA
| | - Deborah A. Meyers
- Department of Medicine, Division of Genetics, Genomics, and Precision Medicine, University of Arizona, Tucson, AZ, USA
- Division of Pharmacogenomics, University of Arizona, Tucson, AZ, USA
| | - Stephen T. McGarvey
- Department of Epidemiology & International Health Institute, School of Public Health, Brown University, Providence, RI, USA
| | | | - Angel C.Y. Mak
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Ruth J.F. Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rajesh Kumar
- Division of Allergy and Clinical Immunology, The Ann and Robert H. Lurie Children’s Hospital of Chicago, and Department of Pediatrics, Northwestern University, Chicago, IL, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Barbara A. Konkle
- Bloodworks Northwest Research Institute, Seattle, WA, USA
- University of Washington, Department of Medicine, Seattle, WA, USA
| | - Shannon Kelly
- Vitalant Research Institute, San Francisco, CA, USA
- UCSF Benioff Children’s Hospital, Oakland, CA, USA
| | - Sharon L.R. Kardia
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Robert Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jiang He
- Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | - Hongsheng Gui
- Center for Individualized and Genomic Medicine Research (CIGMA), Department of Internal Medicine, Henry Ford Health System, Detroit, MI, USA
| | - Frank D. Gilliland
- Division of Environmental Health, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA, USA
| | - Bruce D. Gelb
- Mindich Child Health and Development Institute, Departments of Pediatrics and Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Patrick T. Ellinor
- Cardiology Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Mariza de Andrade
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Adolfo Correa
- Jackson Heart Study and Departments of Medicine and Population Health Science, Jackson, MS, USA
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Kathleen C. Barnes
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Allison E. Ashley-Koch
- Department of Medicine and Duke Comprehensive Sickle Cell Center, Duke University Medical Center, Durham, NC, USA
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
| | - Donna K. Arnett
- College of Public Health, University of Kentucky, Lexington, KY, USA
| | - Christine Albert
- Harvard Medical School, Boston, MA, USA
- Division of Cardiovascular Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | | | | | | | - Cathy C. Laurie
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA, USA
| | - Goncalo Abecasis
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | | | - James G. Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MI, USA
| | - Stephen S. Rich
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Daniel Levy
- The National Heart, Lung, and Blood Institute, Boston University’s Framingham Heart Study, Framingham, MA, USA
- The Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, MD, USA
| | - Ingo Ruczinski
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Abraham Aviv
- Center of Human Development and Aging, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Thomas W. Blackwell
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Timothy Thornton
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Jeff O’Connell
- Division of Endocrinology, Diabetes, and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Nancy J. Cox
- Vanderbilt Genetics Institute and Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - James A. Perry
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Mary Armanios
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Alexis Battle
- Department of Biomedical Engineering, Johns Hopkins Whiting School of Engineering, Baltimore, MD, USA
- Departments of Computer Science and Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Nathan Pankratz
- Department of Laboratory Medicine & Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Alexander P. Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Rasika A. Mathias
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
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Liggett LA, Cato LD, Weinstock JS, Zhang Y, Nouraie SM, Gladwin MT, Garrett ME, Ashley-Koch A, Telen M, Custer B, Kelly S, Dinardo C, Sabino EC, Loureiro P, Carneiro-Proietti A, Maximo C, Reiner AP, Abecasis GR, Williams DA, Natarajan P, Bick AG, Sankaran VG. Clonal hematopoiesis in sickle cell disease. J Clin Invest 2022; 132:156060. [PMID: 34990411 PMCID: PMC8843701 DOI: 10.1172/jci156060] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [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] [Received: 10/21/2021] [Accepted: 01/04/2022] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Curative gene therapies for sickle cell disease (SCD) are currently undergoing clinical evaluation. The occurrence of myeloid malignancies in these trials has prompted safety concerns. Individuals with SCD are predisposed to myeloid malignancies, but the underlying causes remain undefined. Clonal hematopoiesis (CH) is a pre-malignant condition that also confers significant predisposition to myeloid cancers. While it has been speculated that CH may play a role in SCD-associated cancer predisposition, limited data addressing this issue have been reported. METHODS Here, we leveraged 74,190 whole genome sequences to robustly study CH in SCD. Somatic mutation calling methods were used to assess CH in all samples and comparisons between individuals with and without SCD were performed. RESULTS While we had sufficient power to detect a greater than 2-fold increased rate of CH, we found no detectable variation in rate or clone properties between individuals affected by SCD and controls. The rate of CH in individuals with SCD was unaltered by hydroxyurea use. CONCLUSIONS We did not observe an increased risk for acquiring detectable CH in SCD, at least as measured by whole genome sequencing. These results should help guide ongoing efforts and further studies that seek to better define the risk factors underlying myeloid malignancy predisposition in SCD and help ensure that curative therapies can be more safely applied. FUNDING Funding was provided by the New York Stem Cell Foundation and National Institutes of Health. The funders had no role in study design or reporting.
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Affiliation(s)
- L Alexander Liggett
- Division of Hematology and Oncology, Boston Children's Hospital, Boston, United States of America
| | - Liam D Cato
- Department of Human Genetics, Broad Institute of MIT and Harvard, Cambridge, United States of America
| | - Joshua S Weinstock
- Department of Biostatistics, University of Michigan, Ann Arbor, United States of America
| | - Yingze Zhang
- Department of Medicine, University of Pittsburgh, Pittsburgh, United States of America
| | - S Mehdi Nouraie
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, United States of America
| | - Mark T Gladwin
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, United States of America
| | - Melanie E Garrett
- Department of Medicine, Duke University Medical Center, Durham, United States of America
| | - Allison Ashley-Koch
- Department of Medicine, Duke University Medical Center, Durham, United States of America
| | - Marilyn Telen
- Department of Medicine, Duke University Medical Center, Durham, United States of America
| | - Brian Custer
- Department of Epidemiology and Policy Science, Vitalant Research Institute, San Francisco, United States of America
| | - Shannon Kelly
- Division of Pediatric Hematology, UCSF Benioff Children's Hospital, Oakland, United States of America
| | - Carla Dinardo
- Department of Immunohematology, Fundação Pró-Sangue Hemocentro de São Paulo, Sao Paulo, Brazil
| | - Ester C Sabino
- Institute of Tropical Medicine, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil, Sao Paulo, Brazil
| | - Paula Loureiro
- Pernambuco State Center of Hematology and Hemotherapy, Fundação Hemope, Recife, Brazil
| | | | | | - Alexander P Reiner
- Department of Epidemiology, University of Washington, Seattle, United States of America
| | - Gonçalo R Abecasis
- Department of Biostatistics, University of Michigan, Ann Arbor, United States of America
| | - David A Williams
- Division of Hematology and Oncology, Boston Children's Hospital, Boston, United States of America
| | - Pradeep Natarajan
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, United States of America
| | - Alexander G Bick
- Department of Medicine, Vanderbilt University Medical Center, Nashville, United States of America
| | - Vijay G Sankaran
- Division of Hematology and Oncology, Boston Children's Hospital, Boston, United States of America
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Brizzi A, Whittaker C, Servo LMS, Hawryluk I, Prete CA, de Souza WM, Aguiar RS, Araujo LJT, Bastos LS, Blenkinsop A, Buss LF, Candido D, Castro MC, Costa SF, Croda J, de Souza Santos AA, Dye C, Flaxman S, Fonseca PLC, Geddes VEV, Gutierrez B, Lemey P, Levin AS, Mellan T, Bonfim DM, Miscouridou X, Mishra S, Monod M, Moreira FRR, Nelson B, Pereira RHM, Ranzani O, Schnekenberg RP, Semenova E, Sonabend R, Souza RP, Xi X, Sabino EC, Faria NR, Bhatt S, Ratmann O. Author Correction: Spatial and temporal fluctuations in COVID-19 fatality rates in Brazilian hospitals. Nat Med 2022; 28:1509. [PMID: 35835884 PMCID: PMC9282140 DOI: 10.1038/s41591-022-01939-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Andrea Brizzi
- grid.7445.20000 0001 2113 8111Department of Mathematics, Imperial College London, London, UK
| | - Charles Whittaker
- grid.7445.20000 0001 2113 8111MRC Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Luciana M. S. Servo
- grid.457041.30000 0001 2324 8955Institute for Applied Economic Research, IPEA, Brasília, Brazil
| | - Iwona Hawryluk
- grid.7445.20000 0001 2113 8111MRC Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Carlos A. Prete
- grid.11899.380000 0004 1937 0722Departamento de Engenharia de Sistemas Eletrônicos, Escola Politécnica, Universidade de São Paulo, São Paulo, Brazil
| | - William M. de Souza
- grid.176731.50000 0001 1547 9964World Reference Center for Emerging Viruses and Arboviruses and Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston TX, USA
| | - Renato S. Aguiar
- grid.8430.f0000 0001 2181 4888Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil ,grid.472984.4Instituto D’Or de Pesquisa e Ensino (IDOR), Rio de Janeiro, Brazil
| | - Leonardo J. T. Araujo
- grid.414596.b0000 0004 0602 9808Laboratory of Quantitative Pathology, Center of Pathology, Adolfo Lutz Institute, São Paulo, Brazil
| | - Leonardo S. Bastos
- grid.418068.30000 0001 0723 0931Programa de Computação Científica, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Alexandra Blenkinsop
- grid.7445.20000 0001 2113 8111Department of Mathematics, Imperial College London, London, UK
| | - Lewis F. Buss
- grid.7445.20000 0001 2113 8111MRC Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK ,grid.11899.380000 0004 1937 0722Departamento de Moléstias Infecciosas e Parasitárias e Instituto de Medicina Tropical da Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Darlan Candido
- grid.4991.50000 0004 1936 8948Department of Zoology, University of Oxford, Oxford, UK
| | - Marcia C. Castro
- grid.38142.3c000000041936754XDepartment of Global Health and Population, Harvard T. H. Chan School of Public Health, Boston MA, USA
| | - Silvia F. Costa
- grid.11899.380000 0004 1937 0722Departamento de Moléstias Infecciosas e Parasitárias e Instituto de Medicina Tropical da Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Julio Croda
- grid.47100.320000000419368710Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven CT, USA
| | | | - Christopher Dye
- grid.4991.50000 0004 1936 8948Department of Zoology, University of Oxford, Oxford, UK
| | - Seth Flaxman
- grid.4991.50000 0004 1936 8948Department of Computer Science, University of Oxford, Oxford, UK
| | - Paula L. C. Fonseca
- grid.8430.f0000 0001 2181 4888Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Victor E. V. Geddes
- grid.8430.f0000 0001 2181 4888Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Bernardo Gutierrez
- grid.4991.50000 0004 1936 8948Department of Zoology, University of Oxford, Oxford, UK
| | - Philippe Lemey
- grid.5596.f0000 0001 0668 7884Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven – University of Leuven, Leuven, Belgium
| | - Anna S. Levin
- grid.11899.380000 0004 1937 0722Departamento de Moléstias Infecciosas e Parasitárias e Instituto de Medicina Tropical da Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Thomas Mellan
- grid.7445.20000 0001 2113 8111MRC Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Diego M. Bonfim
- grid.8430.f0000 0001 2181 4888Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Xenia Miscouridou
- grid.7445.20000 0001 2113 8111Department of Mathematics, Imperial College London, London, UK
| | - Swapnil Mishra
- grid.7445.20000 0001 2113 8111MRC Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK ,grid.5254.60000 0001 0674 042XSection of Epidemiology, School of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Mélodie Monod
- grid.7445.20000 0001 2113 8111Department of Mathematics, Imperial College London, London, UK
| | - Filipe R. R. Moreira
- grid.8536.80000 0001 2294 473XDepartamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Bruce Nelson
- grid.419220.c0000 0004 0427 0577Environmental Dynamics, INPA, National Institute for Amazon Research, Manaus, Brazil
| | - Rafael H. M. Pereira
- grid.457041.30000 0001 2324 8955Institute for Applied Economic Research, IPEA, Brasília, Brazil
| | - Otavio Ranzani
- grid.434607.20000 0004 1763 3517Barcelona Institute for Global Health, ISGlobal, Barcelona, Spain
| | - Ricardo P. Schnekenberg
- grid.4991.50000 0004 1936 8948Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Elizaveta Semenova
- grid.7445.20000 0001 2113 8111Department of Mathematics, Imperial College London, London, UK
| | - Raphael Sonabend
- grid.7445.20000 0001 2113 8111MRC Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Renan P. Souza
- grid.8430.f0000 0001 2181 4888Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Xiaoyue Xi
- grid.7445.20000 0001 2113 8111Department of Mathematics, Imperial College London, London, UK
| | - Ester C. Sabino
- grid.11899.380000 0004 1937 0722Departamento de Moléstias Infecciosas e Parasitárias e Instituto de Medicina Tropical da Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Nuno R. Faria
- grid.7445.20000 0001 2113 8111MRC Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK ,grid.11899.380000 0004 1937 0722Departamento de Moléstias Infecciosas e Parasitárias e Instituto de Medicina Tropical da Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil ,grid.4991.50000 0004 1936 8948Department of Zoology, University of Oxford, Oxford, UK ,grid.7445.20000 0001 2113 8111Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Samir Bhatt
- grid.7445.20000 0001 2113 8111MRC Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK ,grid.5254.60000 0001 0674 042XSection of Epidemiology, School of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Oliver Ratmann
- grid.7445.20000 0001 2113 8111Department of Mathematics, Imperial College London, London, UK
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Mee P, Alexander N, Mayaud P, González FDJC, Abbott S, Santos AADS, Acosta AL, Parag KV, Pereira RH, Prete CA, Sabino EC, Faria NR, Brady OJ. Tracking the emergence of disparities in the subnational spread of COVID-19 in Brazil using an online application for real-time data visualisation: A longitudinal analysis. Lancet Reg Health Am 2022; 5:None. [PMID: 35098203 PMCID: PMC8782271 DOI: 10.1016/j.lana.2021.100119] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BACKGROUND Brazil is one of the countries worst affected by the COVID-19 pandemic with over 20 million cases and 557,000 deaths reported by August 2021. Comparison of real-time local COVID-19 data between areas is essential for understanding transmission, measuring the effects of interventions, and predicting the course of the epidemic, but are often challenging due to different population sizes and structures. METHODS We describe the development of a new app for the real-time visualisation of COVID-19 data in Brazil at the municipality level. In the CLIC-Brazil app, daily updates of case and death data are downloaded, age standardised and used to estimate the effective reproduction number (Rt ). We show how such platforms can perform real-time regression analyses to identify factors associated with the rate of initial spread and early reproduction number. We also use survival methods to predict the likelihood of occurrence of a new peak of COVID-19 incidence. FINDINGS After an initial introduction in São Paulo and Rio de Janeiro states in early March 2020, the epidemic spread to northern states and then to highly populated coastal regions and the Central-West. Municipalities with higher metrics of social development experienced earlier arrival of COVID-19 (decrease of 11·1 days [95% CI:8.9,13.2] in the time to arrival for each 10% increase in the social development index). Differences in the initial epidemic intensity (mean Rt ) were largely driven by geographic location and the date of local onset. INTERPRETATION This study demonstrates that platforms that monitor, standardise and analyse the epidemiological data at a local level can give useful real-time insights into outbreak dynamics that can be used to better adapt responses to the current and future pandemics. FUNDING This project was supported by a Medical Research Council UK (MRC-UK) -São Paulo Research Foundation (FAPESP) CADDE partnership award (MR/S0195/1 and FAPESP 18/14389-0).
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Affiliation(s)
- Paul Mee
- Faculty of Epidemiology and Public Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- International Statistics and Epidemiology Group, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Neal Alexander
- Faculty of Epidemiology and Public Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
- International Statistics and Epidemiology Group, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Philippe Mayaud
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Felipe de Jesus Colón González
- Faculty of Epidemiology and Public Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Sam Abbott
- Faculty of Epidemiology and Public Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | | - André Luís Acosta
- Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Kris V. Parag
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, United Kingdom
| | | | - Carlos A. Prete
- Department of Electronic Systems Engineering, University of São Paulo, São Paulo, Brazil
| | - Ester C. Sabino
- Departamento de Molestias Infecciosas e Parasitarias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, Brazil
| | - Nuno R. Faria
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, United Kingdom
- Departamento de Molestias Infecciosas e Parasitarias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, Brazil
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | | | - Oliver J Brady
- Faculty of Epidemiology and Public Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
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46
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Brito AF, Semenova E, Dudas G, Hassler GW, Kalinich CC, Kraemer MU, Ho J, Tegally H, Githinji G, Agoti CN, Matkin LE, Whittaker C, Howden BP, Sintchenko V, Zuckerman NS, Mor O, Blankenship HM, de Oliveira T, Lin RTP, Siqueira MM, Resende PC, Vasconcelos ATR, Spilki FR, Aguiar RS, Alexiev I, Ivanov IN, Philipova I, Carrington CVF, Sahadeo NSD, Gurry C, Maurer-Stroh S, Naidoo D, von Eije KJ, Perkins MD, van Kerkhove M, Hill SC, Sabino EC, Pybus OG, Dye C, Bhatt S, Flaxman S, Suchard MA, Grubaugh ND, Baele G, Faria NR. Global disparities in SARS-CoV-2 genomic surveillance. medRxiv 2021:2021.08.21.21262393. [PMID: 34462754 PMCID: PMC8404891 DOI: 10.1101/2021.08.21.21262393] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Genomic sequencing provides critical information to track the evolution and spread of SARS-CoV-2, optimize molecular tests, treatments and vaccines, and guide public health responses. To investigate the spatiotemporal heterogeneity in the global SARS-CoV-2 genomic surveillance, we estimated the impact of sequencing intensity and turnaround times (TAT) on variant detection in 167 countries. Most countries submit genomes >21 days after sample collection, and 77% of low and middle income countries sequenced <0.5% of their cases. We found that sequencing at least 0.5% of the cases, with a TAT <21 days, could be a benchmark for SARS-CoV-2 genomic surveillance efforts. Socioeconomic inequalities substantially impact our ability to quickly detect SARS-CoV-2 variants, and undermine the global pandemic preparedness.
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Affiliation(s)
- Anderson F. Brito
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
- Instituto Todos pela Saúde, São Paulo, São Paulo, Brazil
| | - Elizaveta Semenova
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
- Department of Mathematics, Imperial College London, London, UK
| | - Gytis Dudas
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Gabriel W. Hassler
- Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Chaney C. Kalinich
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
- Yale School of Medicine, Yale University, New Haven, Connecticut, USA
| | | | - Joses Ho
- GISAID Global Data Science Initiative, Munich, Germany
- Bioinformatics Institute & ID Labs, Agency for Science Technology and Research, Singapore, Singapore
| | - Houriiyah Tegally
- KwaZulu–Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu–Natal, Durban, South Africa
| | - George Githinji
- KEMRI-Wellcome Trust Research Programme, Kenya
- Department of Biochemistry and Biotechnology, Pwani University, Kenya
| | | | - Lucy E. Matkin
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, United Kingdom
| | | | | | | | | | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Vitali Sintchenko
- Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, New South Wales, Australia
- Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, New South Wales 2145, Australia
| | - Neta S. Zuckerman
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Israel
| | - Orna Mor
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Israel
| | - Heather M Blankenship
- Michigan Department of Health and Human Services, Bureau of Laboratories, Lansing, Michigan, USA
| | - Tulio de Oliveira
- KwaZulu–Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu–Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | | | | | | | | | - Fernando R. Spilki
- Feevale University, Institute of Health Sciences, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Renato Santana Aguiar
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Instituto D’Or de Pesquisa e Ensino (IDOR), Rio de Janeiro, Brazil
| | - Ivailo Alexiev
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Ivan N. Ivanov
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Ivva Philipova
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Christine V. F. Carrington
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Nikita S. D. Sahadeo
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Céline Gurry
- GISAID Global Data Science Initiative, Munich, Germany
| | - Sebastian Maurer-Stroh
- GISAID Global Data Science Initiative, Munich, Germany
- Bioinformatics Institute & ID Labs, Agency for Science Technology and Research, Singapore, Singapore
- National Centre for Infectious Diseases, Singapore
| | - Dhamari Naidoo
- Health Emergencies Programme, World Health Organization Regional Office for South-East Asia, New Delhi, India
| | - Karin J von Eije
- Department of Medical Microbiology and Infection Prevention, Division of Clinical Virology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Emerging Diseases and Zoonoses Unit, Health Emergencies Programme, World Health Organization, Geneva, Switzerland
| | - Mark D. Perkins
- Emerging Diseases and Zoonoses Unit, Health Emergencies Programme, World Health Organization, Geneva, Switzerland
| | - Maria van Kerkhove
- Emerging Diseases and Zoonoses Unit, Health Emergencies Programme, World Health Organization, Geneva, Switzerland
| | | | - Ester C. Sabino
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Oliver G. Pybus
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Royal Veterinary College, Hawkshead, United Kingdom
| | - Christopher Dye
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Samir Bhatt
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, United Kingdom
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Seth Flaxman
- Department of Computer Science, University of Oxford, Oxford, United Kingdom
| | - Marc A. Suchard
- Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, California, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Nuno R. Faria
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom
- Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, New South Wales, Australia
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
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Mattioli IA, Castro KR, Macedo LJA, Sedenho GC, Oliveira MN, Todeschini I, Vitale PM, Ferreira SC, Manuli ER, Pereira GM, Sabino EC, Crespilho FN. Graphene-based hybrid electrical-electrochemical point-of-care device for serologic COVID-19 diagnosis. Biosens Bioelectron 2021; 199:113866. [PMID: 34915214 PMCID: PMC8648586 DOI: 10.1016/j.bios.2021.113866] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/27/2021] [Accepted: 12/03/2021] [Indexed: 02/08/2023]
Abstract
The outbreak of COVID-19 pandemics highlighted the need of sensitive, selective, and easy-to-handle biosensing devices. In the contemporary scenario, point-of-care devices for mass testing and infection mapping within a population have proven themselves as of primordial importance. Here, we introduce a graphene-based Electrical-Electrochemical Vertical Device (EEVD) point-of-care biosensor, strategically engineered for serologic COVID-19 diagnosis. EEVD uses serologic IgG quantifications on SARS-CoV-2 Receptor Binding Domain (RBD) bioconjugate immobilized onto device surface. EEVD combines graphene basal plane with high charge carrier mobility, high conductivity, low intrinsic resistance, and interfacial sensitivity to capacitance alterations. EEVD application was carried out in real human serum samples. Since EEVD is a miniaturized device, it requires just 40 μL of sample for a point-of-care COVID-19 infections detection. When compared to serologic assays such ELISA and other immunochromatographic methods, EEVD presents some advantages such as time of analyses (15 min), sample preparation, and a LOD of 1.0 pg mL-1. We glimpse that EEVD meets the principles of robustness and accuracy, desirable analytic parameters for assays destined to pandemics control strategies.
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Affiliation(s)
- Isabela A Mattioli
- São Carlos Institute of Chemistry, University of São Paulo, São Carlos, SP, 13560-970, Brazil
| | - Karla R Castro
- São Carlos Institute of Chemistry, University of São Paulo, São Carlos, SP, 13560-970, Brazil
| | - Lucyano J A Macedo
- São Carlos Institute of Chemistry, University of São Paulo, São Carlos, SP, 13560-970, Brazil
| | - Graziela C Sedenho
- São Carlos Institute of Chemistry, University of São Paulo, São Carlos, SP, 13560-970, Brazil
| | - Mona N Oliveira
- Biolinker Synthetic Biology EIRELI, São Paulo, 05508-000, Brazil
| | - Iris Todeschini
- Biolinker Synthetic Biology EIRELI, São Paulo, 05508-000, Brazil
| | - Phelipe M Vitale
- Biolinker Synthetic Biology EIRELI, São Paulo, 05508-000, Brazil
| | - Suzete Cleusa Ferreira
- Laboratory of Medical Investigation in Pathogenesis and Targeted Therapy in Onco-Immuno-Hematology (LIM-31), Department of Hematology, Clinical Hospital HCFMUSP, Faculty of Medicine, University of São Paulo, São Paulo, 01246903, Brazil; Division of Research and Transfusion Medicine, São Paulo Hemocentre Pro-Blood Foundation, São Paulo, 05403000, Brazil
| | - Erika R Manuli
- Institute of Tropical Medicine, Faculty of Medicine, University of São Paulo, 05403-000, Brazil; LIM-46 HC-FMUSP - Laboratory of Medical Investigation, Clinical Hospital, Faculty of Medicine, University of São Paulo, 01246903, Brazil
| | - Geovana M Pereira
- Institute of Tropical Medicine, Faculty of Medicine, University of São Paulo, 05403-000, Brazil
| | - Ester C Sabino
- Institute of Tropical Medicine, Faculty of Medicine, University of São Paulo, 05403-000, Brazil; LIM-46 HC-FMUSP - Laboratory of Medical Investigation, Clinical Hospital, Faculty of Medicine, University of São Paulo, 01246903, Brazil
| | - Frank N Crespilho
- São Carlos Institute of Chemistry, University of São Paulo, São Carlos, SP, 13560-970, Brazil.
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Nicolete VC, Rodrigues PT, Johansen IC, Corder RM, Tonini J, Cardoso MA, de Jesus JG, Claro IM, Faria NR, Sabino EC, Castro MC, Ferreira MU. Interacting Epidemics in Amazonian Brazil: Prior Dengue Infection Associated With Increased Coronavirus Disease 2019 (COVID-19) Risk in a Population-Based Cohort Study. Clin Infect Dis 2021; 73:2045-2054. [PMID: 33956939 PMCID: PMC8135953 DOI: 10.1093/cid/ciab410] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Immunity after dengue virus (DENV) infection has been suggested to cross-protect from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and mortality. METHODS We tested whether serologically proven prior DENV infection diagnosed in September-October 2019, before the coronavirus disease 2019 (COVID-19) pandemic, reduced the risk of SARS-CoV-2 infection and clinically apparent COVID-19 over the next 13 months in a population-based cohort in Amazonian Brazil. Mixed-effects multiple logistic regression analysis was used to identify predictors of infection and disease, adjusting for potential individual and household-level confounders. Virus genomes from 14 local SARS-CoV-2 isolates were obtained using whole-genome sequencing. RESULTS Anti-DENV immunoglobulin G (IgG) was found in 37.0% of 1285 cohort participants (95% confidence interval [CI]: 34.3% to 39.7%) in 2019, with 10.4 (95% CI: 6.7-15.5) seroconversion events per 100 person-years during the follow-up. In 2020, 35.2% of the participants (95% CI: 32.6% to 37.8%) had anti-SARS-CoV-2 IgG and 57.1% of the 448 SARS-CoV-2 seropositives (95% CI: 52.4% to 61.8%) reported clinical manifestations at the time of infection. Participants aged >60 years were twice more likely to have symptomatic COVID-19 than children under 5 years. Locally circulating SARS-CoV-2 isolates were assigned to the B.1.1.33 lineage. Contrary to the cross-protection hypothesis, prior DENV infection was associated with twice the risk of clinically apparent COVID-19 upon SARS-CoV-2 infection, with P values between .025 and .039 after adjustment for identified confounders. CONCLUSIONS Higher risk of clinically apparent COVID-19 among individuals with prior dengue has important public health implications for communities sequentially exposed to DENV and SARS-CoV-2 epidemics.
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Affiliation(s)
- Vanessa C Nicolete
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Priscila T Rodrigues
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Igor C Johansen
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Rodrigo M Corder
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Juliana Tonini
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Marly A Cardoso
- Department of Nutrition, School of Public Health, University of São Paulo, São Paulo, Brazil
| | - Jaqueline G de Jesus
- Institute of Tropical Medicine and Department of Infectious and Parasitic Diseases, Medical School, University of São Paulo, São Paulo, Brazil
| | - Ingra M Claro
- Institute of Tropical Medicine and Department of Infectious and Parasitic Diseases, Medical School, University of São Paulo, São Paulo, Brazil
| | - Nuno R Faria
- Institute of Tropical Medicine and Department of Infectious and Parasitic Diseases, Medical School, University of São Paulo, São Paulo, Brazil.,Department of Infectious Disease Epidemiology, Imperial College London, ,London, UK.,Department of Zoology, University of Oxford, Oxford, UK
| | - Ester C Sabino
- Institute of Tropical Medicine and Department of Infectious and Parasitic Diseases, Medical School, University of São Paulo, São Paulo, Brazil
| | - Marcia C Castro
- Department of Global Health and Population, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Marcelo U Ferreira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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Pepe Razzolini MT, Funada Barbosa MR, Silva de Araújo R, Freitas de Oliveira I, Mendes-Correa MC, Sabino EC, Garcia SC, de Paula AV, Villas-Boas LS, Costa SF, Dropa M, Brandão de Assis D, Levin BS, Pedroso de Lima AC, Levin AS. SARS-CoV-2 in a stream running through an underprivileged, underserved, urban settlement in São Paulo, Brazil: A 7-month follow-up. Environ Pollut 2021; 290:118003. [PMID: 34425371 PMCID: PMC8373523 DOI: 10.1016/j.envpol.2021.118003] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 08/15/2021] [Accepted: 08/17/2021] [Indexed: 05/11/2023]
Abstract
COVID-19 pandemic has led to concerns on the circulation of SARS-CoV-2 in the environment, its infectivity from the environment and, the relevance of transmission via environmental compartments. During 31 weeks, water samples were collected from a heavily contaminated stream going through an urban, underprivileged community without sewage collection. Our results showed a statistically significant correlation between cases of COVID-19 and SARS in the community, and SARS-CoV-2 concentrations in the water. Based on the model, if the concentrations of SARS-CoV-RNA (N1 and N2 target regions) increase 10 times, there is an expected increase of 104% [95%CI: (62-157%)] and 92% [95%CI: (51-143%)], respectively, in the number of cases of COVID-19 and SARS. We believe that differences in concentration of the virus in the environment reflect the epidemiological status in the community, which may be important information for surveillance and controlling dissemination in areas with vulnerable populations and poor sanitation. None of the samples were found infectious based cultures. Our results may be applicable globally as similar communities exist worldwide.
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Affiliation(s)
- Maria Tereza Pepe Razzolini
- School of Public Health of Universidade de São Paulo, Brazil; NARA - Center for Research in Environmental Risk Assessment, Brazil.
| | - Mikaela Renata Funada Barbosa
- NARA - Center for Research in Environmental Risk Assessment, Brazil; CETESB - Environmental Company of São Paulo State, Brazil
| | | | | | - Maria Cássia Mendes-Correa
- Department of Infectious Diseases and Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, Brazil
| | - Ester C Sabino
- Department of Infectious Diseases and Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, Brazil
| | | | - Anderson V de Paula
- Department of Infectious Diseases and Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, Brazil
| | - Lucy S Villas-Boas
- Department of Infectious Diseases and Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, Brazil
| | - Silvia Figueiredo Costa
- Department of Infectious Diseases and Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, Brazil
| | - Milena Dropa
- School of Public Health of Universidade de São Paulo, Brazil
| | | | - Beatriz S Levin
- Guttman Community College, City University of New York, New York, USA
| | | | - Anna S Levin
- Department of Infectious Diseases and Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, Brazil
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50
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Brizzi A, Whittaker C, Servo LMS, Hawryluk I, Prete CA, de Souza WM, Aguiar RS, Araujo LJT, Bastos LS, Blenkinsop A, Buss LF, Candido D, Castro MC, Costa SF, Croda J, de Souza Santos AA, Dye C, Flaxman S, Fonseca PLC, Geddes VEV, Gutierrez B, Lemey P, Levin AS, Mellan T, Bonfim DM, Miscouridou X, Mishra S, Monod M, Moreira FRR, Nelson B, Pereira RHM, Ranzani O, Schnekenberg RP, Semenova E, Sonnabend R, Souza RP, Xi X, Sabino EC, Faria NR, Bhatt S, Ratmann O. Report 46: Factors driving extensive spatial and temporal fluctuations in COVID-19 fatality rates in Brazilian hospitals. medRxiv 2021:2021.11.01.21265731. [PMID: 34751273 PMCID: PMC8575144 DOI: 10.1101/2021.11.01.21265731] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The SARS-CoV-2 Gamma variant spread rapidly across Brazil, causing substantial infection and death waves. We use individual-level patient records following hospitalisation with suspected or confirmed COVID-19 to document the extensive shocks in hospital fatality rates that followed Gamma's spread across 14 state capitals, and in which more than half of hospitalised patients died over sustained time periods. We show that extensive fluctuations in COVID-19 in-hospital fatality rates also existed prior to Gamma's detection, and were largely transient after Gamma's detection, subsiding with hospital demand. Using a Bayesian fatality rate model, we find that the geographic and temporal fluctuations in Brazil's COVID-19 in-hospital fatality rates are primarily associated with geographic inequities and shortages in healthcare capacity. We project that approximately half of Brazil's COVID-19 deaths in hospitals could have been avoided without pre-pandemic geographic inequities and without pandemic healthcare pressure. Our results suggest that investments in healthcare resources, healthcare optimization, and pandemic preparedness are critical to minimize population wide mortality and morbidity caused by highly transmissible and deadly pathogens such as SARS-CoV-2, especially in low- and middle-income countries. NOTE The following manuscript has appeared as 'Report 46 - Factors driving extensive spatial and temporal fluctuations in COVID-19 fatality rates in Brazilian hospitals' at https://spiral.imperial.ac.uk:8443/handle/10044/1/91875 . ONE SENTENCE SUMMARY COVID-19 in-hospital fatality rates fluctuate dramatically in Brazil, and these fluctuations are primarily associated with geographic inequities and shortages in healthcare capacity.
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Affiliation(s)
- Andrea Brizzi
- Department of Mathematics, Imperial College London, London, United Kingdom
| | - Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, United Kingdom
| | | | - Iwona Hawryluk
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, United Kingdom
| | - Carlos A Prete
- Departamento de Engenharia de Sistemas Eletrônicos, Escola Politécnica da Universidade de São Paulo, São Paulo, Brazil
| | - William M de Souza
- World Reference Center for Emerging Viruses and Arboviruses and Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Renato S Aguiar
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Instituto D'Or de Pesquisa e Ensino (IDOR), Rio de Janeiro, Brazil
| | - Leonardo J T Araujo
- Laboratory of Quantitative Pathology, Center of Pathology, Adolfo Lutz Institute, São Paulo, Brazil
| | - Leonardo S Bastos
- Programa de Computação Científica, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | | | - Lewis F Buss
- Departamento de Moléstias Infecciosas e Parasitárias e Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brasil
| | - Darlan Candido
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Marcia C Castro
- Department of Global Health and Population, Harvard T.H. Chan School of Public Health, Boston, United States
| | - Silvia F Costa
- Departamento de Moléstias Infecciosas e Parasitárias e Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brasil
| | - Julio Croda
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, United States
| | | | - Christopher Dye
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Seth Flaxman
- Department of Computer Science, University of Oxford, Oxford, United Kingdom
| | - Paula L C Fonseca
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Victor E V Geddes
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, KU Leuven - University of Leuven, Leuven, Belgium
| | - Anna S Levin
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Thomas Mellan
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, United Kingdom
| | - Diego M Bonfim
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Xenia Miscouridou
- Department of Mathematics, Imperial College London, London, United Kingdom
| | - Swapnil Mishra
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, United Kingdom
- Section of Epidemiology, School of Public Health, University of Copenhagen, Denmark, Copenhagen
| | - Mélodie Monod
- Department of Mathematics, Imperial College London, London, United Kingdom
| | - Filipe R R Moreira
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Bruce Nelson
- Environmental Dynamics, INPA, National Institute for Amazon Research, Bairro Petropolis, Brazil
| | | | - Otavio Ranzani
- Barcelona Institute for Global Health, ISGlobal, Barcelona, Spain
| | - Ricardo P Schnekenberg
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Elizaveta Semenova
- Department of Mathematics, Imperial College London, London, United Kingdom
| | - Raphael Sonnabend
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, United Kingdom
| | - Renan P Souza
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Xiaoyue Xi
- Department of Mathematics, Imperial College London, London, United Kingdom
| | - Ester C Sabino
- Programa de Computação Científica, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Nuno R Faria
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, United Kingdom
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Samir Bhatt
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, United Kingdom
- Section of Epidemiology, School of Public Health, University of Copenhagen
| | - Oliver Ratmann
- Department of Mathematics, Imperial College London, London, United Kingdom
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