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Castiñeiras ACP, Sales AC, Picone CDM, Diogo CL, Rossi ÁD, Galliez RM, Ferreira ODC, Castiñeiras TMPP, Lopes MH, Sartori AMC. The decline of measles antibody titers in previously vaccinated adults: a cross-sectional analysis. Rev Inst Med Trop Sao Paulo 2024; 66:e4. [PMID: 38198377 PMCID: PMC10768653 DOI: 10.1590/s1678-9946202466004] [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: 07/10/2023] [Accepted: 11/01/2023] [Indexed: 01/12/2024] Open
Abstract
The global reemergence of measles in 2018-2019 reinforces the relevance of high-coverage immunization to maintain the disease elimination. During an outbreak in the Sao Paulo State in 2019, several measles cases were reported in individuals who were adequately vaccinated according to the current immunization schedule recommends. This study aimed to assess measles IgG antibody seropositivity and titers in previously vaccinated adults. A cross-sectional study was conducted at CRIE-HC-FMUSP (Sao Paulo, Brazil) in 2019. It included healthy adults who had received two or more Measles-Mumps-Rubella vaccines (MMR) and excluded individuals with immunocompromising conditions. Measles IgG antibodies were measured and compared by ELISA (Euroimmun®) and chemiluminescence (LIASON®). The association of seropositivity and titers with variables of interest (age, sex, profession, previous measles, number of measles-containing vaccine doses, interval between MMR doses, and time elapsed since the last MMR dose) was analyzed. A total of 162 participants were evaluated, predominantly young (median age 30 years), women (69.8%) and healthcare professionals (61.7%). The median interval between MMR doses was 13.2 years, and the median time since the last dose was 10.4 years. The seropositivity rate was 32.7% by ELISA and 75.3% by CLIA, and a strong positive correlation was found between the tests. Multivariate analyses revealed that age and time since the last dose were independently associated with positivity. Despite being a single-center evaluation, our results suggest that measles seropositivity may be lower than expected in adequately immunized adults. Seropositivity was higher among older individuals and those with a shorter time since the last MMR vaccine dose.
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Affiliation(s)
- Anna Carla Pinto Castiñeiras
- Universidade de São Paulo, Faculdade de Medicina, Departamento de Moléstias Infecciosas e Parasitárias, São Paulo, São Paulo, Brazil
- Universidade de São Paulo, Faculdade de Medicina, Hospital das Clínicas, Centro de Referência para Imunobiológicos Especiais, São Paulo, São Paulo, Brazil
- Universidade Federal do Rio de Janeiro, Núcleo de Enfrentamento e Estudos de Doenças Infecciosas e Emergentes e Reemergentes, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Amanda Caroline Sales
- Universidade de São Paulo, Faculdade de Medicina, Departamento de Moléstias Infecciosas e Parasitárias, São Paulo, São Paulo, Brazil
- Universidade de São Paulo, Faculdade de Medicina, Hospital das Clínicas, Centro de Referência para Imunobiológicos Especiais, São Paulo, São Paulo, Brazil
| | - Camila de Melo Picone
- Universidade de São Paulo, Faculdade de Medicina, Departamento de Moléstias Infecciosas e Parasitárias, São Paulo, São Paulo, Brazil
- Universidade de São Paulo, Faculdade de Medicina, Hospital das Clínicas, Centro de Referência para Imunobiológicos Especiais, São Paulo, São Paulo, Brazil
| | - Constância Lima Diogo
- Universidade Federal do Rio de Janeiro, Núcleo de Enfrentamento e Estudos de Doenças Infecciosas e Emergentes e Reemergentes, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Átila Duque Rossi
- Universidade Federal do Rio de Janeiro, Núcleo de Enfrentamento e Estudos de Doenças Infecciosas e Emergentes e Reemergentes, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rafael Mello Galliez
- Universidade Federal do Rio de Janeiro, Núcleo de Enfrentamento e Estudos de Doenças Infecciosas e Emergentes e Reemergentes, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Orlando da Costa Ferreira
- Universidade Federal do Rio de Janeiro, Núcleo de Enfrentamento e Estudos de Doenças Infecciosas e Emergentes e Reemergentes, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Terezinha Marta Pereira Pinto Castiñeiras
- Universidade Federal do Rio de Janeiro, Núcleo de Enfrentamento e Estudos de Doenças Infecciosas e Emergentes e Reemergentes, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marta Heloísa Lopes
- Universidade de São Paulo, Faculdade de Medicina, Departamento de Moléstias Infecciosas e Parasitárias, São Paulo, São Paulo, Brazil
- Universidade de São Paulo, Faculdade de Medicina, Hospital das Clínicas, Centro de Referência para Imunobiológicos Especiais, São Paulo, São Paulo, Brazil
- Universidade de São Paulo, Faculdade de Medicina, Hospital das Clínicas, Laboratório de Investigação Médica em Imunologia (LIM-48), São Paulo, São Paulo, Brazil
| | - Ana Marli Christovam Sartori
- Universidade de São Paulo, Faculdade de Medicina, Departamento de Moléstias Infecciosas e Parasitárias, São Paulo, São Paulo, Brazil
- Universidade de São Paulo, Faculdade de Medicina, Hospital das Clínicas, Centro de Referência para Imunobiológicos Especiais, São Paulo, São Paulo, Brazil
- Universidade de São Paulo, Faculdade de Medicina, Hospital das Clínicas, Laboratório de Investigação Médica em Imunologia (LIM-48), São Paulo, São Paulo, Brazil
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Melo Mendes IC, Martins de Oliveira AL, Martins Pinheiro Trindade P, Mendes da Silva W, Pontes Frankel P, Carvalho Mocarzel C, de Alencar Rosa M, Santos Nascimento AP, de Melo Rodrigues G, Pimentel C, de Moraes Perlingeiro R, Gonçalves Lisbôa Pereira A, Caminha Escosteguy C, Mello Galliez R. Severe Covid-19 in pregnant and postpartum women admitted to an intensive care unit: A retrospective cohort study. PLoS One 2023; 18:e0295444. [PMID: 38096234 PMCID: PMC10721012 DOI: 10.1371/journal.pone.0295444] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 11/21/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND SARS-CoV-2 infection is associated with worse maternal and fetal outcomes. This study aims to describe the characteristics of pregnant and postpartum women with severe Covid-19 admitted to ICU. METHODS AND FINDINGS It's a retrospective cohort study evaluating pregnant and postpartum women referenced to a specialized ICU between May 2020 and June 2022. Covid-19 was confirmed with RT-PCR or rapid antigen test on a nasopharyngeal swab. Variables were described by median and IQR when numerical, and by frequency and percentage when categorical. OR with 95% CI were calculated for the evaluation of factors related to death. P-values were calculated using Pearson's ꭓ2-test, Fisher's exact test, Wilcoxon rank sum test, and Kruskall-Wallis test, and statistical significance was established as < 0·05. Missing data were excluded. All statistical analysis were performed using R software version 4.2.2. Of the 101 admissions, 85 (84·2%) were of pregnant women. Obesity (23·0%) and systemic arterial hypertension (13·0%) were the most prevalent medical conditions. Sixty-six (65·3%) were admitted using some type of oxygen support. Forty-seven (46·5%) evolved to mechanical ventilation. There were 61 events considered obstetric complications, with 8 stillbirths/fetal losses. The overall lethality was 15·8%. Pregnancy interruption, need for non-invasive mechanical ventilation, level of oxygen support at admission, prone maneuver, hemodialysis, and healthcare-related infections were factors associated with death. Evaluating the WHO 7-category ordinary scale, there was a trend of increase in the risk of death with higher punctuation, with a statistically significant difference of women with 5 (OR = 7·27; 95% IC = 1·17-194; p = 0·031) or 6 points (OR = 12·0; 95% IC = 1·15-391; p = 0·038) when compared to the ones with 3 points, i.e., of women admitted with a high-flow non-rebreathing mask or invasive mechanical ventilation, compared with the ones admitted at room air, respectively. The main limitations of this study are the relatively small number of participants, and the use of data derived of medical records-which are susceptible to misclassification and variable amounts of missing data. CONCLUSIONS Pregnant and postpartum women with severe Covid-19 have high lethality and a high incidence of clinical and obstetric complications. These findings support that this population should be prioritized in public health strategies that address Covid-19.
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Affiliation(s)
- Isabel Cristina Melo Mendes
- Infectious Diseases Post-Graduation Program, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Instituto Estadual de Infectologia São Sebastião, Rio de Janeiro, Brazil
| | | | | | - Wallace Mendes da Silva
- Hospital Federal dos Servidores do Estado, Rio de Janeiro, Brazil
- Faculty of Medicine, Estácio de Sá University (UNESA/IDOMED), Rio de Janeiro, Brazil
| | | | | | | | | | | | - Clarisse Pimentel
- Instituto Estadual de Infectologia São Sebastião, Rio de Janeiro, Brazil
| | | | | | | | - Rafael Mello Galliez
- Instituto Estadual de Infectologia São Sebastião, Rio de Janeiro, Brazil
- Faculty of Medicine, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Center for Response and Studies on Emerging and Reemerging Infectious Diseases (NEEDIER), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
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Schiffler FB, Pereira AHB, Moreira SB, Arruda IF, Moreira FRR, D’arc M, Claro IM, Pissinatti TDA, Cavalcante LTDF, Miranda TDS, Cosentino MAC, de Oliveira RC, Fernandes J, Assis MRDS, de Oliveira JG, da Silva TAC, Galliez RM, Faffe DS, de Jesus JG, Sobreira Bezerra da Silva M, Bezerra MF, Ferreira Junior ODC, Tanuri A, Castiñeiras TM, Aguiar RS, Faria NR, de Almeida AP, Pissinatti A, Sabino EC, Amendoeira MRR, de Lemos ERS, Ubiali DG, Santos AFA. Lessons from a Multilaboratorial Task Force for Diagnosis of a Fatal Toxoplasmosis Outbreak in Captive Primates in Brazil. Microorganisms 2023; 11:2888. [PMID: 38138032 PMCID: PMC10745312 DOI: 10.3390/microorganisms11122888] [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: 10/26/2023] [Revised: 11/16/2023] [Accepted: 11/23/2023] [Indexed: 12/24/2023] Open
Abstract
Toxoplasmosis is an important zoonotic disease caused by the parasite Toxoplasma gondii and is especially fatal for neotropical primates. In Brazil, the Ministry of Health is responsible for national epizootic surveillance, but some diseases are still neglected. Here, we present an integrated investigation of an outbreak that occurred during the first year of the COVID-19 pandemic among eleven neotropical primates housed at a primatology center in Brazil. After presenting non-specific clinical signs, all animals died within four days. A wide range of pathogens were evaluated, and we successfully identified T. gondii as the causative agent within four days after necropsies. The liver was the most affected organ, presenting hemorrhage and hepatocellular necrosis. Tachyzoites and bradyzoite cysts were observed in histological examinations and immunohistochemistry in different organs; in addition, parasitic DNA was detected through PCR in blood samples from all specimens evaluated. A high prevalence of Escherichia coli was also observed, indicating sepsis. This case highlights some of the obstacles faced by the current Brazilian surveillance system. A diagnosis was obtained through the integrated action of researchers since investigation for toxoplasmosis is currently absent in national guidelines. An interdisciplinary investigation could be a possible model for future epizootic investigations in animals.
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Affiliation(s)
- Francine Bittencourt Schiffler
- Laboratório de Diversidade e Doenças Virais (LDDV), Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-617, RJ, Brazil; (F.B.S.); (M.D.); (L.T.d.F.C.); (T.d.S.M.); (M.A.C.C.)
| | - Asheley Henrique Barbosa Pereira
- Setor de Anatomia Patológica (SAP), Departamento de Epidemiologia e Saúde Pública, Instituto de Veterinária, Universidade Federal Rural do Rio de Janeiro, Seropédica 23890-000, RJ, Brazil; (A.H.B.P.); (D.G.U.)
| | - Silvia Bahadian Moreira
- Centro de Primatologia do Rio de Janeiro (CPRJ), Instituto Estadual do Ambiente, Guapimirim 25940-000, RJ, Brazil; (S.B.M.); (A.P.)
| | - Igor Falco Arruda
- Laboratório de Toxoplasmose e outras Protozooses (LabTOXO), Instituto Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil; (I.F.A.); (M.R.R.A.)
| | - Filipe Romero Rebello Moreira
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London SW7 2BX, UK; (F.R.R.M.); (I.M.C.); (N.R.F.)
- Laboratório de Virologia Molecular (LVM), Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-617, RJ, Brazil; (O.d.C.F.J.); (A.T.)
| | - Mirela D’arc
- Laboratório de Diversidade e Doenças Virais (LDDV), Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-617, RJ, Brazil; (F.B.S.); (M.D.); (L.T.d.F.C.); (T.d.S.M.); (M.A.C.C.)
| | - Ingra Morales Claro
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London SW7 2BX, UK; (F.R.R.M.); (I.M.C.); (N.R.F.)
- Instituto de Medicina Tropical (IMT), Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (J.G.d.J.); (E.C.S.)
| | - Thalita de Abreu Pissinatti
- Serviço de Criação de Primatas Não Humanos (SCPrim), Instituto de Ciência e Tecnologia em Biomodelos, Fundação Oswaldo Cruz, Rio de Janeiro 26382-462, RJ, Brazil;
| | - Liliane Tavares de Faria Cavalcante
- Laboratório de Diversidade e Doenças Virais (LDDV), Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-617, RJ, Brazil; (F.B.S.); (M.D.); (L.T.d.F.C.); (T.d.S.M.); (M.A.C.C.)
| | - Thamiris dos Santos Miranda
- Laboratório de Diversidade e Doenças Virais (LDDV), Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-617, RJ, Brazil; (F.B.S.); (M.D.); (L.T.d.F.C.); (T.d.S.M.); (M.A.C.C.)
| | - Matheus Augusto Calvano Cosentino
- Laboratório de Diversidade e Doenças Virais (LDDV), Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-617, RJ, Brazil; (F.B.S.); (M.D.); (L.T.d.F.C.); (T.d.S.M.); (M.A.C.C.)
| | - Renata Carvalho de Oliveira
- Laboratório de Hantaviroses e Rickettsioses, Instituto Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil; (R.C.d.O.); (J.F.); (M.R.d.S.A.); (J.G.d.O.); (T.A.C.d.S.); (E.R.S.d.L.)
| | - Jorlan Fernandes
- Laboratório de Hantaviroses e Rickettsioses, Instituto Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil; (R.C.d.O.); (J.F.); (M.R.d.S.A.); (J.G.d.O.); (T.A.C.d.S.); (E.R.S.d.L.)
| | - Matheus Ribeiro da Silva Assis
- Laboratório de Hantaviroses e Rickettsioses, Instituto Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil; (R.C.d.O.); (J.F.); (M.R.d.S.A.); (J.G.d.O.); (T.A.C.d.S.); (E.R.S.d.L.)
| | - Jonathan Gonçalves de Oliveira
- Laboratório de Hantaviroses e Rickettsioses, Instituto Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil; (R.C.d.O.); (J.F.); (M.R.d.S.A.); (J.G.d.O.); (T.A.C.d.S.); (E.R.S.d.L.)
| | - Thayssa Alves Coelho da Silva
- Laboratório de Hantaviroses e Rickettsioses, Instituto Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil; (R.C.d.O.); (J.F.); (M.R.d.S.A.); (J.G.d.O.); (T.A.C.d.S.); (E.R.S.d.L.)
| | - Rafael Mello Galliez
- Núcleo de Enfrentamento e Estudos de Doenças Infecciosas Emergentes e Reemergentes (NEEDIER), Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-599, RJ, Brazil; (R.M.G.); (D.S.F.); (T.M.C.)
| | - Debora Souza Faffe
- Núcleo de Enfrentamento e Estudos de Doenças Infecciosas Emergentes e Reemergentes (NEEDIER), Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-599, RJ, Brazil; (R.M.G.); (D.S.F.); (T.M.C.)
| | - Jaqueline Goes de Jesus
- Instituto de Medicina Tropical (IMT), Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (J.G.d.J.); (E.C.S.)
| | - Marise Sobreira Bezerra da Silva
- Serviço de Referência Nacional em Peste, Instituto Aggeu Magalhães, Fundação Oswaldo Cruz, Recife 50740-465, PE, Brazil; (M.S.B.d.S.); (M.F.B.); (A.P.d.A.)
| | - Matheus Filgueira Bezerra
- Serviço de Referência Nacional em Peste, Instituto Aggeu Magalhães, Fundação Oswaldo Cruz, Recife 50740-465, PE, Brazil; (M.S.B.d.S.); (M.F.B.); (A.P.d.A.)
| | - Orlando da Costa Ferreira Junior
- Laboratório de Virologia Molecular (LVM), Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-617, RJ, Brazil; (O.d.C.F.J.); (A.T.)
| | - Amilcar Tanuri
- Laboratório de Virologia Molecular (LVM), Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-617, RJ, Brazil; (O.d.C.F.J.); (A.T.)
| | - Terezinha Marta Castiñeiras
- Núcleo de Enfrentamento e Estudos de Doenças Infecciosas Emergentes e Reemergentes (NEEDIER), Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-599, RJ, Brazil; (R.M.G.); (D.S.F.); (T.M.C.)
| | - Renato Santana Aguiar
- Laboratório de Biologia Integrativa, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil;
- Instituto D’OR de Pesquisa e Ensino (ID’or), Rio de Janeiro 22281-100, RJ, Brazil
| | - Nuno Rodrigues Faria
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London SW7 2BX, UK; (F.R.R.M.); (I.M.C.); (N.R.F.)
- Instituto de Medicina Tropical (IMT), Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (J.G.d.J.); (E.C.S.)
| | - Alzira Paiva de Almeida
- Serviço de Referência Nacional em Peste, Instituto Aggeu Magalhães, Fundação Oswaldo Cruz, Recife 50740-465, PE, Brazil; (M.S.B.d.S.); (M.F.B.); (A.P.d.A.)
| | - Alcides Pissinatti
- Centro de Primatologia do Rio de Janeiro (CPRJ), Instituto Estadual do Ambiente, Guapimirim 25940-000, RJ, Brazil; (S.B.M.); (A.P.)
| | - Ester Cerdeira Sabino
- Instituto de Medicina Tropical (IMT), Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (J.G.d.J.); (E.C.S.)
| | - Maria Regina Reis Amendoeira
- Laboratório de Toxoplasmose e outras Protozooses (LabTOXO), Instituto Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil; (I.F.A.); (M.R.R.A.)
| | - Elba Regina Sampaio de Lemos
- Laboratório de Hantaviroses e Rickettsioses, Instituto Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil; (R.C.d.O.); (J.F.); (M.R.d.S.A.); (J.G.d.O.); (T.A.C.d.S.); (E.R.S.d.L.)
| | - Daniel Guimarães Ubiali
- Setor de Anatomia Patológica (SAP), Departamento de Epidemiologia e Saúde Pública, Instituto de Veterinária, Universidade Federal Rural do Rio de Janeiro, Seropédica 23890-000, RJ, Brazil; (A.H.B.P.); (D.G.U.)
| | - André F. A. Santos
- Laboratório de Diversidade e Doenças Virais (LDDV), Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-617, RJ, Brazil; (F.B.S.); (M.D.); (L.T.d.F.C.); (T.d.S.M.); (M.A.C.C.)
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Lima VC, Rijo RPCL, Bernardi FA, Filho MEC, Barbosa-Junior F, Pellison FC, Galliez RM, Kritski AL, Alves D. REDbox: a comprehensive semantic framework for data collection and management in tuberculosis research. Sci Rep 2023; 13:7686. [PMID: 37169802 PMCID: PMC10173910 DOI: 10.1038/s41598-023-33492-6] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 04/13/2023] [Indexed: 05/13/2023] Open
Abstract
Clinical research outcomes depend on the correct definition of the research protocol, the data collection strategy, and the data management plan. Furthermore, researchers often need to work within challenging contexts, as is the case in tuberculosis services, where human and technological resources for research may be scarce. Electronic Data Capture Systems mitigate such risks and enable a reliable environment to conduct health research and promote result dissemination and data reusability. The proposed solution is based on needs pinpointed by researchers, considering the need for an accommodating solution to conduct research in low-resource environments. The REDbox framework was developed to facilitate data collection, management, sharing, and availability in tuberculosis research and improve the user experience through user-friendly, web-based tools. REDbox combines elements of the REDCap and KoBoToolbox electronic data capture systems and semantics to deliver new valuable tools that meet the needs of tuberculosis researchers in Brazil. The framework was implemented in five cross-institutional, nationwide projects to evaluate the users' perceptions of the system's usefulness and the information and user experience. Seventeen responses (representing 40% of active users) to an anonymous survey distributed to active users indicated that REDbox was perceived to be helpful for the particular audience of researchers and health professionals. The relevance of this article lies in the innovative approach to supporting tuberculosis research by combining existing technologies and tailoring supporting features.
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Affiliation(s)
- Vinícius Costa Lima
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.
| | - Rui Pedro Charters Lopes Rijo
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
- School of Technology and Management, Polytechnic Institute of Leiria, Leiria, Portugal
- Institute for Systems Engineering and Computers at Coimbra, Coimbra, Portugal
- Center for Research in Health Technologies and Services, Faculty of Medicine, University of Porto, Porto, Portugal
| | | | | | | | | | - Rafael Mello Galliez
- Faculty of Medicine, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Domingos Alves
- Department of Social Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
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5
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Faffe DS, Byrne RL, Body R, Castiñeiras TMP, Castiñeiras AP, Finch LS, Kontogianni K, Bengey D, Galliez RM, Ferreira OC, Mariani D, da Silva BO, Ribeiro SS, de Vos M, Escadafal C, Adams ER, Tanuri A, Cubas Atienzar AI. Multicenter Diagnostic Evaluation of a Novel Coronavirus Antigen Lateral Flow Test among Symptomatic Individuals in Brazil and the United Kingdom. Microbiol Spectr 2022; 10:e0201222. [PMID: 36448777 PMCID: PMC9769746 DOI: 10.1128/spectrum.02012-22] [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] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 10/31/2022] [Indexed: 12/05/2022] Open
Abstract
The COVID-19 pandemic has led to the commercialization of many antigen-based rapid diagnostic tests (Ag-RDTs), requiring independent evaluations. This report describes the clinical evaluation of the Novel Coronavirus 2019-nCoV Antigen Test (Colloidal Gold) (Beijing Hotgen Biotech Co., Ltd.), at two sites within Brazil and one in the United Kingdom. The collected samples (446 nasal swabs from Brazil and 246 nasopharyngeal samples from the UK) were analyzed by the Ag-RDT and compared to reverse transcription-quantitative PCR (RT-qPCR). Analytical evaluation of the Ag-RDT was performed using direct culture supernatants of SARS-CoV-2 strains from the wild-type (B.1), Alpha (B.1.1.7), Delta (B.1.617.2), Gamma (P.1), and Omicron (B.1.1.529) lineages. An overall sensitivity and specificity of 88.2% (95% confidence interval [CI], 81.3 to 93.3) and 100.0% (95% CI, 99.1 to 100.0), respectively, were obtained for the Brazilian and UK cohorts. The analytical limit of detection was determined as 1.0 × 103 PFU/mL (Alpha), 2.5 × 102 PFU/mL (Delta), 2.5 × 103 PFU/mL (Gamma), and 1.0 × 103 PFU/mL (Omicron), giving a viral copy equivalent of approximately 2.1 × 104 copies/mL, 9.0 × 105 copies/mL, 1.7 × 106 copies/mL, and 1.8 × 105 copies/mL for the Ag-RDT, respectively. Overall, while a higher sensitivity was claimed by the manufacturers than that found in this study, this evaluation finds that the Ag-RDT meets the WHO minimum performance requirements for sensitivity and specificity of COVID-19 Ag-RDTs. This study illustrates the comparative performance of the Hotgen Ag-RDT across two global settings and considers the different approaches in evaluation methods. IMPORTANCE Since the beginning of the SARS-CoV-2 pandemic, we have witnessed growing numbers of antigen rapid diagnostic tests (Ag-RDTs) being brought to market. In the United Kingdom, this was somewhat controlled indirectly as the government offered free tests from a small number of companies. However, as this has now ceased, individuals are responsible for their own acquisition of test kits. Similarly in Brazil, as of January 2022, pharmacies and other health care retailers are permitted to sell Ag-RDTs directly to the community. Many of these Ag-RDTs have not been externally evaluated, and results are not readily available to the public. Thus, there is now a need for a transparent evaluation of Ag-RDTs with both analytical and clinical evaluation. We present an independent review of the Novel Coronavirus 2019-nCoV Antigen Test (Colloidal Gold) (Beijing Hotgen Biotech Co., Ltd.), at two sites within Brazil and one in the United Kingdom.
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Affiliation(s)
- Debora S. Faffe
- Universidade Federal do Rio de Janeiro (UFRJ), Núcleo de Enfrentamento e Estudos de Doenças Infecciosas e Emergentes e Reemergentes (NEEDIER), Rio de Janeiro, Brazil
| | - Rachel L. Byrne
- Liverpool School of Tropical Medicine, Centre for Drugs and Diagnostics, Liverpool, United Kingdom
| | - Richard Body
- Oxford University, Oxford, United Kingdom
- Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - Terezinha Marta P. Castiñeiras
- Universidade Federal do Rio de Janeiro (UFRJ), Núcleo de Enfrentamento e Estudos de Doenças Infecciosas e Emergentes e Reemergentes (NEEDIER), Rio de Janeiro, Brazil
| | - Anna P. Castiñeiras
- Universidade Federal do Rio de Janeiro (UFRJ), Núcleo de Enfrentamento e Estudos de Doenças Infecciosas e Emergentes e Reemergentes (NEEDIER), Rio de Janeiro, Brazil
| | - Lorna S. Finch
- Liverpool School of Tropical Medicine, Centre for Drugs and Diagnostics, Liverpool, United Kingdom
| | - Konstantina Kontogianni
- Liverpool School of Tropical Medicine, Centre for Drugs and Diagnostics, Liverpool, United Kingdom
| | - Daisy Bengey
- Liverpool School of Tropical Medicine, Centre for Drugs and Diagnostics, Liverpool, United Kingdom
| | - Rafael Mello Galliez
- Universidade Federal do Rio de Janeiro (UFRJ), Núcleo de Enfrentamento e Estudos de Doenças Infecciosas e Emergentes e Reemergentes (NEEDIER), Rio de Janeiro, Brazil
| | - Orlando C. Ferreira
- Universidade Federal do Rio de Janeiro (UFRJ), Núcleo de Enfrentamento e Estudos de Doenças Infecciosas e Emergentes e Reemergentes (NEEDIER), Rio de Janeiro, Brazil
| | - Diana Mariani
- Universidade Federal do Rio de Janeiro (UFRJ), Núcleo de Enfrentamento e Estudos de Doenças Infecciosas e Emergentes e Reemergentes (NEEDIER), Rio de Janeiro, Brazil
| | - Bianca Ortiz da Silva
- Universidade Federal do Rio de Janeiro (UFRJ), Núcleo de Enfrentamento e Estudos de Doenças Infecciosas e Emergentes e Reemergentes (NEEDIER), Rio de Janeiro, Brazil
| | - Sabrina Santana Ribeiro
- Universidade Federal do Rio de Janeiro (UFRJ), Núcleo de Enfrentamento e Estudos de Doenças Infecciosas e Emergentes e Reemergentes (NEEDIER), Rio de Janeiro, Brazil
| | | | - LSTM Diagnostic Group
- Liverpool School of Tropical Medicine, Centre for Drugs and Diagnostics, Liverpool, United Kingdom
| | | | | | - Emily R. Adams
- Liverpool School of Tropical Medicine, Centre for Drugs and Diagnostics, Liverpool, United Kingdom
| | - Amilcar Tanuri
- Universidade Federal do Rio de Janeiro (UFRJ), Núcleo de Enfrentamento e Estudos de Doenças Infecciosas e Emergentes e Reemergentes (NEEDIER), Rio de Janeiro, Brazil
| | - Ana I. Cubas Atienzar
- Liverpool School of Tropical Medicine, Centre for Drugs and Diagnostics, Liverpool, United Kingdom
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Thornhill JP, Palich R, Ghosn J, Walmsley S, Moschese D, Cortes CP, Galliez RM, Garlin AB, Nozza S, Mitja O, Radix AE, Blanco JL, Crabtree-Ramirez B, Thompson M, Wiese L, Schulbin H, Levcovich A, Falcone M, Lucchini A, Sendagorta E, Treutiger CJ, Byrne R, Coyne K, Meyerowitz EA, Grahn AM, Hansen ABE, Pourcher V, DellaPiazza M, Lee R, Stoeckle M, Hazra A, Apea V, Rubenstein E, Jones J, Wilkin A, Ganesan A, Henao-Martínez AF, Chow EJ, Titanji BK, Zucker JE, Ogoina D, Orkin CM. Human monkeypox virus infection in women and non-binary individuals during the 2022 outbreaks: a global case series. Lancet 2022; 400:1953-1965. [PMID: 36403584 PMCID: PMC9671743 DOI: 10.1016/s0140-6736(22)02187-0] [Citation(s) in RCA: 63] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/01/2022] [Accepted: 11/01/2022] [Indexed: 11/19/2022]
Abstract
BACKGROUND Between May and November, 2022, global outbreaks of human monkeypox virus infection have been reported in more than 78 000 people worldwide, predominantly in men who have sex with men. We describe the epidemiological and clinical characteristics of monkeypox virus infection in cisgender (cis) and transgender (trans) women and non-binary individuals assigned female sex at birth to improve identification and understanding of risk factors. METHODS International collaborators in geographical locations with high numbers of diagnoses of monkeypox virus infection were approached and invited to contribute data on women and non-binary individuals with confirmed monkeypox virus infection. Contributing centres completed deidentified structured case-report spreadsheets, adapted and developed by participating clinicians, to include variables of interest relevant to women and non-binary individuals assigned female at birth. We describe the epidemiology and clinical course observed in the reported infections. FINDINGS Collaborators reported data for a total of 136 individuals with monkeypox virus infection who presented between May 11 and Oct 4, 2022, across 15 countries. Overall median age was 34 years (IQR 28-40; range 19-84). The cohort comprised 62 trans women, 69 cis women, and five non-binary individuals (who were, because of small numbers, grouped with cis women to form a category of people assigned female at birth for the purpose of comparison). 121 (89%) of 136 individuals reported sex with men. 37 (27%) of all individuals were living with HIV, with a higher proportion among trans women (31 [50%] of 62) than among cis women and non-binary individuals (six [8%] of 74). Sexual transmission was suspected in 55 (89%) trans women (with the remainder having an unknown route of transmission) and 45 (61%) cis women and non-binary individuals; non-sexual routes of transmission (including household and occupational exposures) were reported only in cis women and non-binary individuals. 25 (34%) of 74 cis women and non-binary individuals submitted to the case series were initially misdiagnosed. Overall, among individuals with available data, rash was described in 124 (93%) of 134 individuals and described as anogenital in 95 (74%) of 129 and as vesiculopustular in 105 (87%) of 121. Median number of lesions was ten (IQR 5-24; range 1-200). Mucosal lesions involving the vagina, anus, or oropharynx or eye occurred in 65 (55%) of 119 individuals with available data. Vaginal and anal sex were associated with lesions at those sites. Monkeypox virus DNA was detected by PCR from vaginal swab samples in all 14 samples tested. 17 (13%) individuals were hospitalised, predominantly for bacterial superinfection of lesions and pain management. 33 (24%) individuals were treated with tecovirimat and six (4%) received post-exposure vaccinations. No deaths were reported. INTERPRETATION The clinical features of monkeypox in women and non-binary individuals were similar to those described in men, including the presence of anal and genital lesions with prominent mucosal involvement. Anatomically, anogenital lesions were reflective of sexual practices: vulvovaginal lesions predominated in cis women and non-binary individuals and anorectal features predominated in trans women. The prevalence of HIV co-infection in the cohort was high. FUNDING None.
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Affiliation(s)
- John P Thornhill
- Department of Infection and Immunity, Blizard Institute and SHARE Collaborative, Queen Mary University of London, Barts Health NHS Trust, London, UK
| | - Romain Palich
- Infectious Diseases Department, Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Pierre Louis Epidemiology and Public Health Institute, Sorbonne University, INSERM 1136, Paris, France
| | - Jade Ghosn
- Department of Infectious Diseases, Bichât University Hospital, Assistance Publique-Hôpitaux de Paris Nord, Université Paris Cité, INSERM U1137, IAME, Paris, France
| | - Sharon Walmsley
- University Health Network, University of Toronto, Toronto, ON, Canada
| | - Davide Moschese
- Department of Infectious Diseases, Luigi Sacco Hospital, ASST Fatebenefratelli Sacco, Milan, Italy
| | | | - Rafael Mello Galliez
- Núcleo de Enfrentamento e Estudos de Doenças Infecciosas Emergentes e Reemergentes, Departamento de Doenças Infecciosas e Parasitárias, Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Amy B Garlin
- Disease Prevention and Control Branch, Population Health Division, San Francisco Department of Public Health, San Francisco, CA, USA; Division of Infectious Diseases and Vaccinology, Berkeley School of Public Health, University of California, San Francisco, CA, USA
| | - Silvia Nozza
- Department of Infectious and Tropical Diseases, IRCCS-Ospedale San Raffaele, Milan, Italy
| | - Oriol Mitja
- Skin Neglected Tropical Diseases and Sexually Transmitted Infections Section, Fight Infectious Diseases Foundation, University Hospital Germans Trias i Pujol, Badalona, Spain
| | - Asa E Radix
- Department of Medicine, Callen-Lorde Community Health Center, NYU Grossman School of Medicine, New York, NY, USA
| | - Jose Luis Blanco
- Servicio de Enfermedades Infecciosas, Hospital Clinic de Barcelona, Universidad de Barcelona, Instituto para la Investigación Médica August Pi I Suñe, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Brenda Crabtree-Ramirez
- Departamento de Infectología, Instituto Nacional de Ciencias Médicas y Nutrición, Salvador Zubirán, Mexico City, Mexico
| | | | - Lothar Wiese
- Department of Infectious Diseases, Zealand University Hospital, Roskilde, Denmark
| | | | | | - Marco Falcone
- Infectious Diseases Unit, Cisanello University Hospital, Department of Clinical and Experimental Medicine, University of Pisa, Italy
| | - Anna Lucchini
- Sexual Health Clinic, National Health Service, Torino, Italy
| | - Elena Sendagorta
- Servicio de Dermatología, Hospital Universitario La Paz, Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Investigación Hospital Universitario La Paz (IdiPAZ), Madrid, Spain
| | - Carl-Johan Treutiger
- Department of Infectious Diseases/Venhälsan, South General Hospital, Stockholm, Sweden
| | - Ruth Byrne
- Chelsea and Westminster Hospital NHS Foundation Trust, London, UK
| | | | | | - Anna M Grahn
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Ann-Brit Eg Hansen
- Department of Infectious Diseases, Copenhagen University Hospital-Hvidovre, Hvidovre, Denmark
| | - Valerie Pourcher
- Infectious Diseases Department, Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Pierre Louis Epidemiology and Public Health Institute, Sorbonne University, INSERM 1136, Paris, France
| | - Michelle DellaPiazza
- Division of Infectious Diseases, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Rachel Lee
- George Washington University Hospital, Washington, DC, USA
| | - Marcel Stoeckle
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Aniruddha Hazra
- Section of Infectious Diseases and Global Health, University of Chicago Medicine, Chicago, IL, USA
| | - Vanessa Apea
- Department of Global Health, Wolfson Institute and SHARE Collaborative, Queen Mary University of London, Barts Health NHS Trust, London, UK
| | - Emma Rubenstein
- Department of Infectious Diseases, Saint-Louis and Lariboisière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Joyce Jones
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Aimee Wilkin
- Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Anuradha Ganesan
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, The Henry M Jackson Foundation for the Advancement of Military Medicine, Walter Reed National Military Medical Center, Bethesda, MD, USA
| | | | - Eric J Chow
- Public Health-Seattle & King County, Seattle, WA, USA; Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA; Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | - Boghuma K Titanji
- Department of Infectious Diseases, Emory University School of Medicine, Atlanta, GA, USA
| | - Jason E Zucker
- Columbia University Irving Medical Center, New York, NY, USA
| | - Dimie Ogoina
- Infectious Diseases Unit, Department of Internal Medicine, Niger Delta University, Amassoma, Niger; Niger Delta University Teaching Hospital, Okolobir, Bayelsa, Nigeria
| | - Chloe M Orkin
- Department of Infection and Immunity, Blizard Institute and SHARE Collaborative, Queen Mary University of London, Barts Health NHS Trust, London, UK.
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7
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Cardoso CC, Rossi ÁD, Galliez RM, Faffe DS, Tanuri A, Castiñeiras TMPP. Olfactory Dysfunction in Patients With Mild COVID-19 During Gamma, Delta, and Omicron Waves in Rio de Janeiro, Brazil. JAMA 2022; 328:582-583. [PMID: 35749125 PMCID: PMC9364123 DOI: 10.1001/jama.2022.11006] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
This study uses data obtained through an updated version of the Brazilian National Health System Questionnaire for COVID-19 to assess olfactory dysfunction in patients with mild COVID-19 in Rio de Janeiro, Brazil.
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Affiliation(s)
| | - Átila Duque Rossi
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rafael Mello Galliez
- Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Débora Souza Faffe
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Amilcar Tanuri
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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8
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Corrêa IA, Faffe DS, Galliez RM, Gonçalves CCA, Maia RA, da Silva GP, Moreira FRR, Mariani D, Campos MF, Leitão IDC, de Souza MR, Cunha MS, Nascimento ÉRDS, Ribeiro LDJ, da Cruz TFC, Policarpo C, Gonzales L, Rodgers MA, Berg M, Vijesurier R, Cloherty GA, Hackett J, Ferreira ODC, Castiñeiras TMPP, Tanuri A, da Costa LJ. A SARS-CoV-2 Negative Antigen Rapid Diagnostic in RT-qPCR Positive Samples Correlates With a Low Likelihood of Infectious Viruses in the Nasopharynx. Front Microbiol 2022; 13:912138. [PMID: 35966714 PMCID: PMC9364907 DOI: 10.3389/fmicb.2022.912138] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 05/31/2022] [Indexed: 11/13/2022] Open
Abstract
Severe acute respiratory syndrome-related coronavirus (SARS-CoV-2) transmission occurs even among fully vaccinated individuals; thus, prompt identification of infected patients is central to control viral circulation. Antigen rapid diagnostic tests (Ag-RDTs) are highly specific, but sensitivity is variable. Discordant RT-qPCR vs. Ag-RDT results are reported, raising the question of whether negative Ag-RDT in positive RT-qPCR samples could imply the absence of infectious viruses. To study the relationship between negative Ag-RDT results with virological, molecular, and serological parameters, we selected a cross-sectional and a follow-up dataset and analyzed virus culture, subgenomic RNA quantification, and sequencing to determine infectious viruses and mutations. We demonstrated that RT-qPCR positive while SARS-CoV-2 Ag-RDT negative discordant results correlate with the absence of infectious virus in nasopharyngeal samples. A decrease in sgRNA detection together with an expected increase in detectable anti-S and anti-N IgGs was also verified in these samples. The data clearly demonstrate that a negative Ag-RDT sample is less likely to harbor infectious SARS-CoV-2 and, consequently, has a lower transmissible potential.
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Affiliation(s)
- Isadora Alonso Corrêa
- Laboratório de Genética e Imunologia das Infecções Virais, Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Débora Souza Faffe
- Departamento de Doenças Infecciosas e Parasitárias, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rafael Mello Galliez
- Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Richard Araújo Maia
- Laboratório de Virologia Molecular, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gustavo Peixoto da Silva
- Laboratório de Genética e Imunologia das Infecções Virais, Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Filipe Romero Rebello Moreira
- Laboratório de Virologia Molecular, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Diana Mariani
- Laboratório de Virologia Molecular, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Mariana Freire Campos
- Departamento de Doenças Infecciosas e Parasitárias, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Isabela de Carvalho Leitão
- Departamento de Doenças Infecciosas e Parasitárias, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marcos Romário de Souza
- Laboratório de Genética e Imunologia das Infecções Virais, Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marcela Sabino Cunha
- Laboratório de Genética e Imunologia das Infecções Virais, Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Liane de Jesus Ribeiro
- Laboratório de Virologia Molecular, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Thais Felix Cordeiro da Cruz
- Laboratório de Virologia Molecular, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Cintia Policarpo
- Laboratório de Virologia Molecular, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Luis Gonzales
- Abbott Laboratories Inc., Chicago, IL, United States
| | | | - Michael Berg
- Abbott Laboratories Inc., Chicago, IL, United States
| | | | | | - John Hackett
- Abbott Laboratories Inc., Chicago, IL, United States
| | - Orlando da Costa Ferreira
- Laboratório de Virologia Molecular, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Amilcar Tanuri
- Laboratório de Virologia Molecular, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Luciana Jesus da Costa
- Laboratório de Genética e Imunologia das Infecções Virais, Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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9
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Galliez RM, Bomfim L, Mariani D, Leitão IDC, Castiñeiras ACP, Gonçalves CCA, Ortiz da Silva B, Cardoso PH, Arruda MB, Alvarez P, Brindeiro R, Ota VA, Rodrigues DGM, da Costa LJ, Ferreira ODC, Castiñeiras TMPP, Faffe DS, Tanuri A. Evaluation of the Panbio COVID-19 Antigen Rapid Diagnostic Test in Subjects Infected with Omicron Using Different Specimens. Microbiol Spectr 2022; 10:e0125022. [PMID: 35652635 PMCID: PMC9241948 DOI: 10.1128/spectrum.01250-22] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [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: 04/04/2022] [Accepted: 05/17/2022] [Indexed: 12/22/2022] Open
Abstract
Community testing is a crucial tool for the early identification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and transmission control. The emergence of the highly mutated Omicron variant (B.1.1.529) raised concerns about its primary site of replication, impacting sample collection and its detectability by rapid antigen tests. We tested the performance of the Panbio antigen rapid diagnostic test (Ag-RDT) using nasal and oral specimens for COVID-19 diagnosis in 192 symptomatic individuals, with quantitative reverse transcription-PCR (RT-qPCR) of nasopharyngeal samples as a control. Variant of concern (VOC) investigation was performed with the 4Plex SARS-CoV-2 screening kit. The SARS-CoV-2 positivity rate was 66.2%, with 99% of the positive samples showing an amplification profile consistent with that of the Omicron variant. Nasal Ag-RDT showed higher sensitivity (89%) than oral (12.6%) Ag-RDT. Our data showed good performance of the Ag-RDT in a pandemic scenario dominated by the Omicron VOC. Furthermore, our data also demonstrated that the Panbio COVID-19 antigen rapid diagnostic test does not provide good sensitivity with oral swabs for Omicron Ag-RDT detection. IMPORTANCE This study showed that the antigen rapid test for COVID19 worked fine using nasal swabs when it was utilized in patients infected with the Omicron variant, showing a concordance with PCR in 93% of patients tested. The nasal swab yielded more reliable results than the oral swab when an antigen rapid diagnosis test (the Panbio COVID-19 antigen rapid diagnostic test) was used in patients infected with the Omicron variant.
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Affiliation(s)
- Rafael Mello Galliez
- Núcleo de Enfrentamento e Estudos de Doenças Infecciosas Emergentes e Reemergentes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Departamento de Doenças Infecciosas e Parasitárias, Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Larissa Bomfim
- Laboratório de Virologia Molecular, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Diana Mariani
- Laboratório de Virologia Molecular, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Isabela de Carvalho Leitão
- Núcleo de Enfrentamento e Estudos de Doenças Infecciosas Emergentes e Reemergentes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Anna Carla Pinto Castiñeiras
- Núcleo de Enfrentamento e Estudos de Doenças Infecciosas Emergentes e Reemergentes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Hospital Universitário Clementino Fraga Filho, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Cassia Cristina Alves Gonçalves
- Laboratório de Virologia Molecular, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Bianca Ortiz da Silva
- Núcleo de Enfrentamento e Estudos de Doenças Infecciosas Emergentes e Reemergentes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Decania, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Pedro Henrique Cardoso
- Instituto de Tecnologia de Imunobiológicos Bio-manguinhos, Fundação Oswaldo Cruz/Fiocruz, Rio de Janeiro, Brazil
| | - Monica Barcelos Arruda
- Instituto de Tecnologia de Imunobiológicos Bio-manguinhos, Fundação Oswaldo Cruz/Fiocruz, Rio de Janeiro, Brazil
| | - Patricia Alvarez
- Instituto de Tecnologia de Imunobiológicos Bio-manguinhos, Fundação Oswaldo Cruz/Fiocruz, Rio de Janeiro, Brazil
| | - Rodrigo Brindeiro
- Laboratório de Virologia Molecular, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Instituto de Tecnologia de Imunobiológicos Bio-manguinhos, Fundação Oswaldo Cruz/Fiocruz, Rio de Janeiro, Brazil
| | - Victor Akira Ota
- Núcleo de Enfrentamento e Estudos de Doenças Infecciosas Emergentes e Reemergentes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Débora Gomes Marins Rodrigues
- Núcleo de Enfrentamento e Estudos de Doenças Infecciosas Emergentes e Reemergentes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Luciana Jesus da Costa
- Núcleo de Enfrentamento e Estudos de Doenças Infecciosas Emergentes e Reemergentes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Orlando da Costa Ferreira
- Núcleo de Enfrentamento e Estudos de Doenças Infecciosas Emergentes e Reemergentes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Laboratório de Virologia Molecular, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Terezinha Marta Pereira Pinto Castiñeiras
- Núcleo de Enfrentamento e Estudos de Doenças Infecciosas Emergentes e Reemergentes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Departamento de Doenças Infecciosas e Parasitárias, Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Debora Souza Faffe
- Núcleo de Enfrentamento e Estudos de Doenças Infecciosas Emergentes e Reemergentes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Amilcar Tanuri
- Núcleo de Enfrentamento e Estudos de Doenças Infecciosas Emergentes e Reemergentes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Laboratório de Virologia Molecular, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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Herlinger AL, Monteiro FLL, D'arc M, Moreira FRR, Westgarth HJ, Galliez RM, Mariani D, da Costa LJ, de Almeida LGP, Voloch CM, Melo ASDO, Aguiar RSD, Dos Santos AFA, Castiñeiras TMPP, de Vasconcelos ATR, João Filho EC, Escosteguy CC, Ferreira Junior ODC, Tanuri A, Higa LM. Identification and characterisation of SARS-CoV-2 and Human alphaherpesvirus 1 from a productive coinfection in a fatal COVID-19 case. Mem Inst Oswaldo Cruz 2022; 116:e210176. [PMID: 35019069 PMCID: PMC8752051 DOI: 10.1590/0074-02760210176] [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] [Received: 05/19/2021] [Accepted: 10/28/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND During routine Coronavirus disease 2019 (COVID-19) diagnosis, an unusually high viral load was detected by reverse transcription real-time polymerase chain reaction (RT-qPCR) in a nasopharyngeal swab sample collected from a patient with respiratory and neurological symptoms who rapidly succumbed to the disease. Therefore we sought to characterise the infection. OBJECTIVES We aimed to determine and characterise the etiological agent responsible for the poor outcome. METHODS Classical virological methods, such as plaque assay and plaque reduction neutralisation test combined with amplicon-based sequencing, as well as a viral metagenomic approach, were performed to characterise the etiological agents of the infection. FINDINGS Plaque assay revealed two distinct plaque phenotypes, suggesting either the presence of two severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains or a productive coinfection of two different species of virus. Amplicon-based sequencing did not support the presence of any SARS-CoV-2 genetic variants that would explain the high viral load and suggested the presence of a single SARS-CoV-2 strain. Nonetheless, the viral metagenomic analysis revealed that Coronaviridae and Herpesviridae were the predominant virus families within the sample. This finding was confirmed by a plaque reduction neutralisation test and PCR. MAIN CONCLUSIONS We characterised a productive coinfection of SARS-CoV-2 and Herpes simplex virus 1 (HSV-1) in a patient with severe symptoms that succumbed to the disease. Although we cannot establish the causal relationship between the coinfection and the severity of the clinical case, this work serves as a warning for future studies focused on the interplay between SARS-CoV-2 and HSV-1 coinfection and COVID-19 severity.
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Affiliation(s)
- Alice Laschuk Herlinger
- Universidade Federal do Rio de Janeiro, Instituto de Biologia, Departamento de Genética, Laboratório de Virologia Molecular, Rio de Janeiro, RJ, Brasil
| | - Fábio Luís Lima Monteiro
- Universidade Federal do Rio de Janeiro, Instituto de Biologia, Departamento de Genética, Laboratório de Virologia Molecular, Rio de Janeiro, RJ, Brasil
| | - Mirela D'arc
- Universidade Federal do Rio de Janeiro, Instituto de Biologia, Departamento de Genética, Laboratório de Diversidade e Doenças Virais, Rio de Janeiro, RJ, Brasil
| | - Filipe Romero Rebello Moreira
- Universidade Federal do Rio de Janeiro, Instituto de Biologia, Departamento de Genética, Laboratório de Virologia Molecular, Rio de Janeiro, RJ, Brasil
| | - Harrison James Westgarth
- Universidade Federal do Rio de Janeiro, Instituto de Biologia, Departamento de Genética, Laboratório de Virologia Molecular, Rio de Janeiro, RJ, Brasil
| | - Rafael Mello Galliez
- Hospital Federal dos Servidores do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | - Diana Mariani
- Universidade Federal do Rio de Janeiro, Instituto de Biologia, Departamento de Genética, Laboratório de Virologia Molecular, Rio de Janeiro, RJ, Brasil
| | - Luciana Jesus da Costa
- Universidade Federal do Rio de Janeiro, Instituto de Microbiologia Paulo de Góes, Departamento de Virologia, Laboratório de Genética e Imunologia das Infecções Virais, Rio de Janeiro, RJ, Brasil
| | | | - Carolina Moreira Voloch
- Universidade Federal do Rio de Janeiro, Instituto de Biologia, Departamento de Genética, Laboratório de Virologia Molecular, Rio de Janeiro, RJ, Brasil
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- Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | | | - Renato Santana de Aguiar
- Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Departamento de Genética, Ecologia e Evolução, Belo Horizonte, MG, Brasil
| | - André Felipe Andrade Dos Santos
- Universidade Federal do Rio de Janeiro, Instituto de Biologia, Departamento de Genética, Laboratório de Diversidade e Doenças Virais, Rio de Janeiro, RJ, Brasil
| | | | | | | | | | - Orlando da Costa Ferreira Junior
- Universidade Federal do Rio de Janeiro, Instituto de Biologia, Departamento de Genética, Laboratório de Virologia Molecular, Rio de Janeiro, RJ, Brasil
| | - Amilcar Tanuri
- Universidade Federal do Rio de Janeiro, Instituto de Biologia, Departamento de Genética, Laboratório de Virologia Molecular, Rio de Janeiro, RJ, Brasil
| | - Luiza Mendonça Higa
- Universidade Federal do Rio de Janeiro, Instituto de Biologia, Departamento de Genética, Laboratório de Virologia Molecular, Rio de Janeiro, RJ, Brasil
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11
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Krüger LJ, Tanuri A, Lindner AK, Gaeddert M, Köppel L, Tobian F, Brümmer LE, Klein JAF, Lainati F, Schnitzler P, Nikolai O, Mockenhaupt FP, Seybold J, Corman VM, Jones TC, Drosten C, Gottschalk C, Weber SF, Weber S, Ferreira OC, Mariani D, Dos Santos Nascimento ER, Pereira Pinto Castineiras TM, Galliez RM, Faffe DS, Leitão IDC, Dos Santos Rodrigues C, Frauches TS, Nocchi KJCV, Feitosa NM, Ribeiro SS, Pollock NR, Knorr B, Welker A, de Vos M, Sacks J, Ongarello S, Denkinger CM. Accuracy and ease-of-use of seven point-of-care SARS-CoV-2 antigen-detecting tests: A multi-centre clinical evaluation. EBioMedicine 2022; 75:103774. [PMID: 34959134 PMCID: PMC8702380 DOI: 10.1016/j.ebiom.2021.103774] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [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: 11/05/2021] [Revised: 12/02/2021] [Accepted: 12/09/2021] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND Antigen-detecting rapid diagnostic tests (Ag-RDTs) for SARS-CoV-2 are important diagnostic tools. We assessed clinical performance and ease-of-use of seven Ag-RDTs in a prospective, manufacturer-independent, multi-centre cross-sectional diagnostic accuracy study to inform global decision makers. METHODS Unvaccinated participants suspected of a first SARS-CoV-2 infection were recruited at six sites (Germany, Brazil). Ag-RDTs were evaluated sequentially, with collection of paired swabs for routine reverse transcription polymerase chain reaction (RT-PCR) testing and Ag-RDT testing. Performance was compared to RT-PCR overall and in sub-group analyses (viral load, symptoms, symptoms duration). To understandusability a System Usability Scale (SUS) questionnaire and ease-of-use (EoU) assessment were performed. FINDINGS 7471 participants were included in the analysis. Sensitivities across Ag-RDTs ranged from 70·4%-90·1%, specificities were above 97·2% for all Ag-RDTs but one (93·1%).Ag-RDTs, Mologic, Bionote, Standard Q, showed diagnostic accuracy in line with WHO targets (> 80% sensitivity, > 97% specificity). All tests showed high sensitivity in the first three days after symptom onset (≥87·1%) and in individuals with viral loads≥ 6 log10SARS-CoV2 RNA copies/mL (≥ 88·7%). Usability varied, with Rapigen, Bionote and Standard Q reaching very good scores; 90, 88 and 84/100, respectively. INTERPRETATION Variability in test performance is partially explained by variable viral loads in population evaluated over the course of the pandemic. All Ag-RDTs reach high sensitivity early in the disease and in individuals with high viral loads, supporting their role in identifying transmission relevant infections. For easy-to-use tests, performance shown will likely be maintained in routine implementation. FUNDING Ministry of Science, Research and Arts, State of Baden-Wuerttemberg, Germany, internal funds from Heidelberg University Hospital, University Hospital Charité - Universitätsmedizin Berlin, UK Department of International Development, WHO, Unitaid.
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Affiliation(s)
- Lisa J Krüger
- Division of Infectious Disease and Tropical Medicine, Heidelberg University Hospital, Im Neuenheimer Feld 324, Heidelberg 69120, Germany
| | - Amilcar Tanuri
- Laboratório de Virologia Molecular, Instituto de Biologia - Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Cidade Universitária, Rio de Janeiro, RJ 21941-902, Brazil
| | - Andreas K Lindner
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Tropical Medicine and International Health, Augustenburger Pl. 1, Berlin 13353, Germany
| | - Mary Gaeddert
- Division of Infectious Disease and Tropical Medicine, Heidelberg University Hospital, Im Neuenheimer Feld 324, Heidelberg 69120, Germany
| | - Lisa Köppel
- Division of Infectious Disease and Tropical Medicine, Heidelberg University Hospital, Im Neuenheimer Feld 324, Heidelberg 69120, Germany
| | - Frank Tobian
- Division of Infectious Disease and Tropical Medicine, Heidelberg University Hospital, Im Neuenheimer Feld 324, Heidelberg 69120, Germany
| | - Lukas E Brümmer
- Division of Infectious Disease and Tropical Medicine, Heidelberg University Hospital, Im Neuenheimer Feld 324, Heidelberg 69120, Germany
| | - Julian A F Klein
- Division of Infectious Disease and Tropical Medicine, Heidelberg University Hospital, Im Neuenheimer Feld 324, Heidelberg 69120, Germany
| | - Federica Lainati
- Division of Infectious Disease and Tropical Medicine, Heidelberg University Hospital, Im Neuenheimer Feld 324, Heidelberg 69120, Germany
| | - Paul Schnitzler
- Virology, Heidelberg University Hospital, Im Neuenheimer Feld 324, Heidelberg 69120, Germany
| | - Olga Nikolai
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Tropical Medicine and International Health, Augustenburger Pl. 1, Berlin 13353, Germany
| | - Frank P Mockenhaupt
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Tropical Medicine and International Health, Augustenburger Pl. 1, Berlin 13353, Germany
| | - Joachim Seybold
- Medical Directorate, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Pl. 1, Berlin 13353, Germany
| | - Victor M Corman
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Virology, Rahel-Hirsch-Weg 3, Berlin 10117, Germany; German Centre for Infection Research (DZIF), Partner Site Charité, Charitépl. 1, Berlin 10117, Germany
| | - Terence C Jones
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Virology, Rahel-Hirsch-Weg 3, Berlin 10117, Germany; German Centre for Infection Research (DZIF), Partner Site Charité, Charitépl. 1, Berlin 10117, Germany; Centre for Pathogen Evolution, Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Christian Drosten
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Virology, Rahel-Hirsch-Weg 3, Berlin 10117, Germany; German Centre for Infection Research (DZIF), Partner Site Charité, Charitépl. 1, Berlin 10117, Germany
| | - Claudius Gottschalk
- Division of Infectious Disease and Tropical Medicine, Heidelberg University Hospital, Im Neuenheimer Feld 324, Heidelberg 69120, Germany
| | - Stefan F Weber
- Division of Infectious Disease and Tropical Medicine, Heidelberg University Hospital, Im Neuenheimer Feld 324, Heidelberg 69120, Germany
| | - Stephan Weber
- Acomed Statistik, Fockestraße 57, Leipzig 04275, Germany
| | - Orlando C Ferreira
- Laboratório de Virologia Molecular, Instituto de Biologia - Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Cidade Universitária, Rio de Janeiro, RJ 21941-902, Brazil
| | - Diana Mariani
- Laboratório de Virologia Molecular, Instituto de Biologia - Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Cidade Universitária, Rio de Janeiro, RJ 21941-902, Brazil
| | - Erika Ramos Dos Santos Nascimento
- Laboratório de Virologia Molecular, Instituto de Biologia - Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Cidade Universitária, Rio de Janeiro, RJ 21941-902, Brazil
| | - Terezinha M Pereira Pinto Castineiras
- Departamento de Doenças Infecciosas e Parasitárias, Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Cidade Universitária, Rio de Janeiro, RJ 21941-902, Brazil
| | - Rafael Mello Galliez
- Departamento de Doenças Infecciosas e Parasitárias, Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Cidade Universitária, Rio de Janeiro, RJ 21941-902, Brazil
| | - Debora Souza Faffe
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Cidade Universitária, Rio de Janeiro, RJ 21941-902, Brazil
| | - Isabela de Carvalho Leitão
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Cidade Universitária, Rio de Janeiro, RJ 21941-902, Brazil
| | - Claudia Dos Santos Rodrigues
- Serviço de Atendimento Especializado / Centro de Testagem e Aconselhamento, Avenida Roberto Silveira, 46 - 3° Andar, Maricá, Brazil
| | - Thiago Silva Frauches
- Laboratório Central Dr. Francisco Rímolo Neto, R. Álvares de Castro, n° 346, Maricá, RJ 24900-880, Brazil
| | | | - Natalia Martins Feitosa
- Instituto de Biodiversidade e Sustantabilidade NUPEM, Universidade Federal do Rio de Janeiro, Campus Macaé, Av. São José Barreto, 764 - São José do Barreto, Macaé, RJ 27965-045, Brazil
| | - Sabrina Santana Ribeiro
- Secretaria Municipal de Saúde de Guapimirim, Rua Pastor Francisco Antônio Rosa - S/N, Guapimirim, RJ 25946-253, Brazil
| | - Nira R Pollock
- Department of Laboratory Medicine, Boston Children's Hospital, 300 Longwood Ave, Boston, MA 02115, United States
| | - Britta Knorr
- Department Public Health Rhein Neckar Region, Kurfürsten-Anlage 38-40, Heidelberg 69115, Germany
| | - Andreas Welker
- Department Public Health Rhein Neckar Region, Kurfürsten-Anlage 38-40, Heidelberg 69115, Germany
| | - Margaretha de Vos
- FIND, Campus Biotech, Building B, Level 0, Chemin des Mines 9, Geneva 1202, Switzerland
| | - JilianA Sacks
- FIND, Campus Biotech, Building B, Level 0, Chemin des Mines 9, Geneva 1202, Switzerland
| | - Stefano Ongarello
- FIND, Campus Biotech, Building B, Level 0, Chemin des Mines 9, Geneva 1202, Switzerland
| | - Claudia M Denkinger
- Division of Infectious Disease and Tropical Medicine, Heidelberg University Hospital, Im Neuenheimer Feld 324, Heidelberg 69120, Germany; German Centre for Infection Research (DZIF), Partner Site Heidelberg University Hospital, Im Neuenheimer Feld 672, Heidelberg 69120, Germany.
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12
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Leitão IDC, Calil PT, Galliez RM, Moreira FRR, Mariani D, Castiñeiras ACP, da Silva GPD, Maia RA, Corrêa IA, Monteiro FLL, de Souza MRM, Gonçalves CCA, Higa LM, de Jesus Ribeiro L, Fonseca VWP, Bastos VC, Voloch CM, Faffe DS, da Costa Ferreira O, Tanuri A, Castiñeiras TMPP, da Costa LJ. Prolonged SARS-CoV-2 Positivity in Immunocompetent Patients: Virus Isolation, Genomic Integrity, and Transmission Risk. Microbiol Spectr 2021; 9:e0085521. [PMID: 34787498 PMCID: PMC8597635 DOI: 10.1128/spectrum.00855-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 07/12/2021] [Accepted: 10/21/2021] [Indexed: 12/23/2022] Open
Abstract
Current guidelines for patient isolation in COVID-19 cases recommend a symptom-based approach, averting the use of control real-time reverse transcription PCR (rRT-PCR) testing. However, we hypothesized that patients with persistently positive results by RT-PCR for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) could be potentially infectious for a prolonged time, even if immunocompetent and asymptomatic, which would demand a longer social isolation period than presently recommended. To test this hypothesis, 72 samples from 51 mildly symptomatic immunocompetent patients with long-lasting positive rRT-PCR results for SARS-CoV-2 were tested for their infectiousness in cell culture. The serological response of samples from those patients and virus genomic integrity were also analyzed. Infectious viruses were successfully isolated from 34.38% (22/64) of nasopharynx samples obtained 14 days or longer after symptom onset. Indeed, we observed successful virus isolation up to 128 days. Complete SARS-COV-2 genome integrity was demonstrated, suggesting the presence of replication-competent viruses. No correlation was found between the isolation of infectious viruses and rRT-PCR cycle threshold values or the humoral immune response. These findings call attention to the need to review current isolation guidelines, particularly in scenarios involving high-risk individuals. IMPORTANCE In this study, we evaluated mildly symptomatic immunocompetent patients with long-lasting positive rRT-PCR results for SARS-CoV-2. Infectious viruses were successfully isolated in cell cultures from nasopharynx samples obtained 14 days or longer after symptom onset. Indeed, we observed successful virus isolation for up to 128 days. Moreover, SARS-CoV-2 genome integrity was demonstrated by sequencing, suggesting the presence of replication-competent viruses. These data point out the risk of continuous SARS-CoV-2 transmission from patients with prolonged detection of SARS-CoV-2 in the upper respiratory tract, which has important implications for current precaution guidelines, particularly in settings where vulnerable individuals may be exposed (e.g., nursing homes and hospitals).
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Affiliation(s)
- Isabela de Carvalho Leitão
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Pedro Telles Calil
- Laboratório de Genética e Imunologia das Infecções Virais, Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Rafael Mello Galliez
- Departamento de Doenças Infecciosas e Parasitárias, Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Filipe Romero Rebello Moreira
- Laboratório de Virologia Molecular, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Diana Mariani
- Laboratório de Virologia Molecular, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | | | - Gustavo Peixoto Duarte da Silva
- Laboratório de Genética e Imunologia das Infecções Virais, Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Richard Araújo Maia
- Laboratório de Virologia Molecular, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Isadora Alonso Corrêa
- Laboratório de Genética e Imunologia das Infecções Virais, Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Fábio Luís Lima Monteiro
- Laboratório de Genética e Imunologia das Infecções Virais, Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Marcos Romário Matos de Souza
- Laboratório de Genética e Imunologia das Infecções Virais, Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | | | - Luiza Mendonça Higa
- Laboratório de Virologia Molecular, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Liane de Jesus Ribeiro
- Laboratório de Virologia Molecular, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | | | - Victoria Cortes Bastos
- Departamento de Doenças Infecciosas e Parasitárias, Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Carolina Moreira Voloch
- Laboratório de Virologia Molecular, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Débora Souza Faffe
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Orlando da Costa Ferreira
- Laboratório de Virologia Molecular, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Amilcar Tanuri
- Laboratório de Virologia Molecular, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | | | - Luciana Jesus da Costa
- Laboratório de Genética e Imunologia das Infecções Virais, Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
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13
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Moreira FRR, D'arc M, Mariani D, Herlinger AL, Schiffler FB, Rossi ÁD, Leitão IDC, Miranda TDS, Cosentino MAC, Tôrres MCDP, da Costa RMDSC, Gonçalves CCA, Faffe DS, Galliez RM, Junior ODCF, Aguiar RS, Dos Santos AFA, Voloch CM, Castiñeiras TMPP, Tanuri A. Epidemiological dynamics of SARS-CoV-2 VOC Gamma in Rio de Janeiro, Brazil. Virus Evol 2021; 7:veab087. [PMID: 34725568 PMCID: PMC8522364 DOI: 10.1093/ve/veab087] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [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: 06/23/2021] [Revised: 09/23/2021] [Accepted: 09/29/2021] [Indexed: 12/12/2022] Open
Abstract
The emergence and widespread circulation of severe acute respiratory syndrome coronavirus 2 variants of concern (VOCs) or interest impose an enhanced threat to global public health. In Brazil, one of the countries most severely impacted throughout the pandemic, a complex dynamics involving variants co-circulation and turnover events has been recorded with the emergence and spread of VOC Gamma in Manaus in late 2020. In this context, we present a genomic epidemiology investigation based on samples collected between December 2020 and May 2021 in the second major Brazilian metropolis, Rio de Janeiro. By sequencing 244 novel genomes through all epidemiological weeks in this period, we were able to document the introduction and rapid dissemination of VOC Gamma in the city, driving the rise of the third local epidemic wave. Molecular clock analysis indicates that this variant has circulated locally since the first weeks of 2021 and only 7 weeks were necessary for it to achieve a frequency above 70 per cent, consistent with rates of growth observed in Manaus and other states. Moreover, a Bayesian phylogeographic reconstruction indicates that VOC Gamma spread throughout Brazil between December 2020 and January 2021 and that it was introduced in Rio de Janeiro through at least 13 events coming from nearly all regions of the country. Comparative analysis of reverse transcription-quantitative polymerase chain reaction (RT-qPCR) cycle threshold (Ct) values provides further evidence that VOC Gamma induces higher viral loads (N1 target; mean reduction of Ct: 2.7, 95 per cent confidence interval = ± 0.7). This analysis corroborates the previously proposed mechanistic basis for this variant-enhanced transmissibility and distinguished epidemiological behavior. Our results document the evolution of VOC Gamma and provide independent assessment of scenarios previously studied in Manaus, therefore contributing to the better understanding of the epidemiological dynamics currently being surveyed in other Brazilian regions.
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Affiliation(s)
- Filipe Romero Rebello Moreira
- Departamento de Genética, Laboratório de Virologia Molecular, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, Centro de Ciências da Saúde, Bloco A, lab 121, Cidade Universitária, Rio de Janeiro 21941-902, Brazil
| | - Mirela D'arc
- Departamento de Genética, Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, Centro de Ciências da Saúde, Bloco A, lab 120, Cidade Universitária, Rio de Janeiro 21941-902, Brazil
| | | | - Alice Laschuk Herlinger
- Departamento de Genética, Laboratório de Virologia Molecular, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, Centro de Ciências da Saúde, Bloco A, lab 121, Cidade Universitária, Rio de Janeiro 21941-902, Brazil
| | - Francine Bittencourt Schiffler
- Departamento de Genética, Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, Centro de Ciências da Saúde, Bloco A, lab 120, Cidade Universitária, Rio de Janeiro 21941-902, Brazil
| | - Átila Duque Rossi
- Departamento de Genética, Laboratório de Virologia Molecular, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, Centro de Ciências da Saúde, Bloco A, lab 121, Cidade Universitária, Rio de Janeiro 21941-902, Brazil
| | - Isabela de Carvalho Leitão
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, Centro de Cincias da Saúde, Bloco C, Cidade Universitária, Rio de Janeiro 21941-902, Brazil
| | - Thamiris Dos Santos Miranda
- Departamento de Genética, Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, Centro de Ciências da Saúde, Bloco A, lab 120, Cidade Universitária, Rio de Janeiro 21941-902, Brazil
| | - Matheus Augusto Calvano Cosentino
- Departamento de Genética, Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, Centro de Ciências da Saúde, Bloco A, lab 120, Cidade Universitária, Rio de Janeiro 21941-902, Brazil
| | - Marcelo Calado de Paula Tôrres
- Departamento de Genética, Laboratório de Virologia Molecular, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, Centro de Ciências da Saúde, Bloco A, lab 121, Cidade Universitária, Rio de Janeiro 21941-902, Brazil
| | - Raíssa Mirella Dos Santos Cunha da Costa
- Departamento de Genética, Laboratório de Virologia Molecular, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, Centro de Ciências da Saúde, Bloco A, lab 121, Cidade Universitária, Rio de Janeiro 21941-902, Brazil
| | - Cássia Cristina Alves Gonçalves
- Departamento de Genética, Laboratório de Virologia Molecular, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, Centro de Ciências da Saúde, Bloco A, lab 121, Cidade Universitária, Rio de Janeiro 21941-902, Brazil
| | - Débora Souza Faffe
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, Centro de Cincias da Saúde, Bloco C, Cidade Universitária, Rio de Janeiro 21941-902, Brazil
| | - Rafael Mello Galliez
- Departamento de Doenças Infecciosase Parasitárias, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, Centro de Ciências da Saúde, Bloco K, Cidade Universitária, Rio de Janeiro 21941-902, Brazil
| | - Orlando da Costa Ferreira Junior
- Departamento de Genética, Laboratório de Virologia Molecular, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, Centro de Ciências da Saúde, Bloco A, lab 121, Cidade Universitária, Rio de Janeiro 21941-902, Brazil
| | - Renato Santana Aguiar
- Departamento de Genética, Ecologia e Evolução, Laboratório de Biologia Integrativa, Universidade Federal de Minas Gerais, Belo Horizonte, Av. Antônio Carlos, 6627, Instituto de Ciências Biológicas, G3-60, Pampulha, Belo Horizonte 31270901, Brazil
| | - André Felipe Andrade Dos Santos
- Departamento de Genética, Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, Centro de Ciências da Saúde, Bloco A, lab 120, Cidade Universitária, Rio de Janeiro 21941-902, Brazil
| | - Carolina Moreira Voloch
- Departamento de Genética, Laboratório de Virologia Molecular, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, Centro de Ciências da Saúde, Bloco A, lab 121, Cidade Universitária, Rio de Janeiro 21941-902, Brazil
| | - Terezinha Marta Pereira Pinto Castiñeiras
- Departamento de Doenças Infecciosas e Parasitárias, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, Centro de Ciências da Saúde, Bloco K, Cidade Universitária, Rio de Janeiro 21941-902, Brazil
| | - Amilcar Tanuri
- Departamento de Genética, Laboratório de Virologia Molecular, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, Centro de Ciências da Saúde, Bloco A, lab 121, Cidade Universitária, Rio de Janeiro 21941-902, Brazil
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14
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Voloch CM, da Silva Francisco R, de Almeida LGP, Brustolini OJ, Cardoso CC, Gerber AL, Guimarães APDC, Leitão IDC, Mariani D, Ota VA, Lima CX, Teixeira MM, Dias ACF, Galliez RM, Faffe DS, Pôrto LC, Aguiar RS, Castiñeira TMPP, Ferreira OC, Tanuri A, de Vasconcelos ATR. Intra-host evolution during SARS-CoV-2 prolonged infection. Virus Evol 2021; 7:veab078. [PMID: 34642605 PMCID: PMC8500031 DOI: 10.1093/ve/veab078] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [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: 02/23/2021] [Revised: 09/05/2021] [Accepted: 09/09/2021] [Indexed: 12/23/2022] Open
Abstract
Long-term infection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) represents a challenge to virus dispersion and the control of coronavirus disease 2019 (COVID-19) pandemic. The reason why some people have prolonged infection and how the virus persists for so long are still not fully understood. Recent studies suggested that the accumulation of intra-host single nucleotide variants (iSNVs) over the course of the infection might play an important role in persistence as well as emergence of mutations of concern. For this reason, we aimed to investigate the intra-host evolution of SARS-CoV-2 during prolonged infection. Thirty-three patients who remained reverse transcription polymerase chain reaction (RT-PCR) positive in the nasopharynx for on average 18 days from the symptoms onset were included in this study. Whole-genome sequences were obtained for each patient at two different time points. Phylogenetic, populational, and computational analyses of viral sequences were consistent with prolonged infection without evidence of coinfection in our cohort. We observed an elevated within-host genomic diversity at the second time point samples positively correlated with cycle threshold (Ct) values (lower viral load). Direct transmission was also confirmed in a small cluster of healthcare professionals that shared the same workplace by the presence of common iSNVs. A differential accumulation of missense variants between the time points was detected targeting crucial structural and non-structural proteins such as Spike and helicase. Interestingly, longitudinal acquisition of iSNVs in Spike protein coincided in many cases with SARS-CoV-2 reactive and predicted T cell epitopes. We observed a distinguishing pattern of mutations over the course of the infection mainly driven by increasing A→U and decreasing G→A signatures. G→A mutations may be associated with RNA-editing enzyme activities; therefore, the mutational profiles observed in our analysis were suggestive of innate immune mechanisms of the host cell defense. Therefore, we unveiled a dynamic and complex landscape of host and pathogen interaction during prolonged infection of SARS-CoV-2, suggesting that the host’s innate immunity shapes the increase of intra-host diversity. Our findings may also shed light on possible mechanisms underlying the emergence and spread of new variants resistant to the host immune response as recently observed in COVID-19 pandemic.
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Affiliation(s)
- Carolina M Voloch
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373 - Cidade Universitária da Universidade Federal do Rio de Janeiro - Ilha do Fundão, Rio de Janeiro 21941-902, Brazil
| | - Ronaldo da Silva Francisco
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Av. Getúlio Vargas, 333 - Quitandinha, Petrópolis 25651-076, Brazil
| | - Luiz G P de Almeida
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Av. Getúlio Vargas, 333 - Quitandinha, Petrópolis 25651-076, Brazil
| | - Otavio J Brustolini
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Av. Getúlio Vargas, 333 - Quitandinha, Petrópolis 25651-076, Brazil
| | - Cynthia C Cardoso
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373 - Cidade Universitária da Universidade Federal do Rio de Janeiro - Ilha do Fundão, Rio de Janeiro 21941-902, Brazil
| | - Alexandra L Gerber
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Av. Getúlio Vargas, 333 - Quitandinha, Petrópolis 25651-076, Brazil
| | - Ana Paula de C Guimarães
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Av. Getúlio Vargas, 333 - Quitandinha, Petrópolis 25651-076, Brazil
| | - Isabela de Carvalho Leitão
- Instituto de Biofísica, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373 - Cidade Universitária da Universidade Federal do Rio de Janeiro - Ilha do Fundão, Rio de Janeiro 21941-170, Brazil
| | - Diana Mariani
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373 - Cidade Universitária da Universidade Federal do Rio de Janeiro - Ilha do Fundão, Rio de Janeiro 21941-902, Brazil
| | - Victor Akira Ota
- Departamento de Doenças Infecciosas e Parasitárias, Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Edifício do Centro de Ciências da Saúde, Cidade Universitária da Universidade Federal do Rio de Janeiro - Ilha do Fundão, Rio de Janeiro 21941-902, Brazil
| | - Cristiano X Lima
- Departamento de Cirurgia, Faculdade de Medicina, Universidade Federal de Minas Gerais, Av. Prof. Alfredo Balena, 190 - Santa Efigênia, Belo Horizonte, MG 30130-100, Brazil
| | - Mauro M Teixeira
- Departamento de Bioquimica e Imunologia, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627 - Pampulha, Belo Horizonte 31270-901, Brazil
| | - Ana Carolina F Dias
- Simile Instituto de Imunologia Aplicada Ltda. R. São Paulo, 1932, Belo Horizonte, 30170-132, Brazil
| | - Rafael Mello Galliez
- Departamento de Doenças Infecciosas e Parasitárias, Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Edifício do Centro de Ciências da Saúde, Cidade Universitária da Universidade Federal do Rio de Janeiro - Ilha do Fundão, Rio de Janeiro 21941-902, Brazil
| | - Débora Souza Faffe
- Instituto de Biofísica, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373 - Cidade Universitária da Universidade Federal do Rio de Janeiro - Ilha do Fundão, Rio de Janeiro 21941-170, Brazil
| | - Luís Cristóvão Pôrto
- Instituto de Biologia Roberto Alcântara Gomes, Universidade do Estado do Rio de Janeiro, Boulevard 28 de Setembro, 87, Rio de Janeiro 20511-010, Brazil
| | - Renato S Aguiar
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373 - Cidade Universitária da Universidade Federal do Rio de Janeiro - Ilha do Fundão, Rio de Janeiro 21941-902, Brazil
| | - Terezinha M P P Castiñeira
- Departamento de Doenças Infecciosas e Parasitárias, Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Edifício do Centro de Ciências da Saúde, Cidade Universitária da Universidade Federal do Rio de Janeiro - Ilha do Fundão, Rio de Janeiro 21941-902, Brazil
| | - Orlando C Ferreira
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373 - Cidade Universitária da Universidade Federal do Rio de Janeiro - Ilha do Fundão, Rio de Janeiro 21941-902, Brazil
| | - Amilcar Tanuri
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373 - Cidade Universitária da Universidade Federal do Rio de Janeiro - Ilha do Fundão, Rio de Janeiro 21941-902, Brazil
| | - Ana Tereza R de Vasconcelos
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Av. Getúlio Vargas, 333 - Quitandinha, Petrópolis 25651-076, Brazil
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15
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Lima VC, Bernardi FA, Alves D, Kritski AL, Galliez RM, Rijo RPCL. A Permissioned Blockchain Network for Security and Sharing of De-identified Tuberculosis Research Data in Brazil. Methods Inf Med 2021; 59:205-218. [PMID: 33862661 DOI: 10.1055/s-0041-1727194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
BACKGROUND Tuberculosis (TB) is an infectious disease and is among the top 10 causes of death in the world, and Brazil is part of the top 30 high TB burden countries. Data collection is an essential practice in health studies, and the adoption of electronic data capture (EDC) systems can positively increase the experience of data acquisition and analysis. Also, data-sharing capabilities are crucial to the construction of efficient and effective evidence-based decision-making tools for managerial and operational actions in TB services. Data must be held secure and traceable, as well as available and understandable, for authorized parties. OBJECTIVES In this sense, this work aims to propose a blockchain-based approach to build a reusable, decentralized, and de-identified dataset of TB research data, while increasing transparency, accountability, availability, and integrity of raw data collected in EDC systems. METHODS After identifying challenges and gaps, a solution was proposed to tackle them, considering its relevance for TB studies. Data security issues are being addressed by a blockchain network and a lightweight and practical governance model. Research Electronic Data Capture (REDCap) and KoBoToolbox are used as EDC systems in TB research. Mechanisms to de-identify data and aggregate semantics to data are also available. RESULTS A permissioned blockchain network was built using Kaleido platform. An integration engine integrates the EDC systems with the blockchain network, performing de-identification and aggregating meaning to data. A governance model addresses operational and legal issues for the proper use of data. Finally, a management system facilitates the handling of necessary metadata, and additional applications are available to explore the blockchain and export data. CONCLUSIONS Research data are an important asset not only for the research where it was generated, but also to underpin studies replication and support further investigations. The proposed solution allows the delivery of de-identified databases built in real time by storing data in transactions of a permissioned network, including semantic annotations, as data are being collected in TB research. The governance model promotes the correct use of the solution.
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Affiliation(s)
- Vinícius Costa Lima
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.,Bioengineering Postgraduate Program, University of São Paulo, São Carlos, Brazil
| | - Filipe Andrade Bernardi
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.,Bioengineering Postgraduate Program, University of São Paulo, São Carlos, Brazil
| | - Domingos Alves
- Department of Social Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | | | | | - Rui Pedro Charters Lopes Rijo
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.,School of Technology and Management, Polytechnic Institute of Leiria, Leiria, Portugal.,INESCC - Institute for Systems and Computers Engineering at Coimbra, Coimbra, Portugal.,CINTESIS - Center for Research in Health Technologies and Services, Faculty of Medicine, University of Porto, Porto, Portugal
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16
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Pellison FC, Rijo RPCL, Lima VC, Crepaldi NY, Bernardi FA, Galliez RM, Kritski A, Abhishek K, Alves D. Data Integration in the Brazilian Public Health System for Tuberculosis: Use of the Semantic Web to Establish Interoperability. JMIR Med Inform 2020; 8:e17176. [PMID: 32628611 PMCID: PMC7381074 DOI: 10.2196/17176] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Revised: 02/17/2020] [Accepted: 03/22/2020] [Indexed: 11/13/2022] Open
Abstract
Background Interoperability of health information systems is a challenge due to the heterogeneity of existing systems at both the technological and semantic levels of their data. The lack of existing data about interoperability disrupts intra-unit and inter-unit medical operations as well as creates challenges in conducting studies on existing data. The goal is to exchange data while providing the same meaning for data from different sources. Objective To find ways to solve this challenge, this research paper proposes an interoperability solution for the tuberculosis treatment and follow-up scenario in Brazil using Semantic Web technology supported by an ontology. Methods The entities of the ontology were allocated under the definitions of Basic Formal Ontology. Brazilian tuberculosis applications were tagged with entities from the resulting ontology. Results An interoperability layer was developed to retrieve data with the same meaning and in a structured way enabling semantic and functional interoperability. Conclusions Health professionals could use the data gathered from several data sources to enhance the effectiveness of their actions and decisions, as shown in a practical use case to integrate tuberculosis data in the State of São Paulo.
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Affiliation(s)
- Felipe Carvalho Pellison
- Bioengineering Postgraduate Program of the São Carlos School of Engineering, University of São Paulo, São Carlos, Brazil
| | - Rui Pedro Charters Lopes Rijo
- Polytechnic Institute of Leiria, Leiria, Portugal.,Institute for Systems and Computers Engineering at Coimbra, Coimbra, Portugal.,Center for Health Technology and Services Research, Porto, Portugal.,Department of Social Medicine of Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Vinicius Costa Lima
- Bioengineering Postgraduate Program of the São Carlos School of Engineering, University of São Paulo, São Carlos, Brazil
| | | | - Filipe Andrade Bernardi
- Bioengineering Postgraduate Program of the São Carlos School of Engineering, University of São Paulo, São Carlos, Brazil
| | - Rafael Mello Galliez
- Academic Tuberculosis Program, Medical School of Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Afrânio Kritski
- Academic Tuberculosis Program, Medical School of Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Kumar Abhishek
- Department of Computer Science and Engineering, National Institute of Technology, Patna, India
| | - Domingos Alves
- Department of Social Medicine of Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
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17
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Colombo Filho ME, Mello Galliez R, Andrade Bernardi F, de Oliveira LL, Kritski A, Koenigkam Santos M, Alves D. Preliminary Results on Pulmonary Tuberculosis Detection in Chest X-Ray Using Convolutional Neural Networks. Lecture Notes in Computer Science 2020. [PMCID: PMC7303695 DOI: 10.1007/978-3-030-50423-6_42] [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] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Tuberculosis (TB), is an ancient disease that probably affects humans since pre-hominids. This disease is caused by bacteria belonging to the mycobacterium tuberculosis complex and usually affects the lungs in up to 67% of cases. In 2019, there were estimated to be over 10 million tuberculosis cases in the world, in the same year TB was between the ten leading causes of death, and the deadliest from a single infectious agent. Chest X-ray (CXR) has recently been promoted by the WHO as a tool possibly placed early in screening and triaging algorithms for TB detection. Numerous TB prevalence surveys have demonstrated that CXR is the most sensitive screening tool for pulmonary TB and that a significant proportion of people with TB are asymptomatic in the early stages of the disease. This study presents experimentation of classic convolutional neural network architectures on public CRX databases in order to create a tool applied to the diagnostic aid of TB in chest X-ray images. As result the study has an AUC ranging from 0.78 to 0.84, sensitivity from 0.76 to 0.86 and specificity from 0.58 to 0.74 depending on the network architecture. The observed performance by these metrics alone are within the range of metrics found in the literature, although there is much room for metrics improvement and bias avoiding. Also, the usage of the model in a triage use-case could be used to validate the efficiency of the model in the future.
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18
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Escosteguy CC, Pereira AGL, Marques MRVE, Lima TRDA, Galliez RM, Medronho RDA. Yellow fever: profile of cases and factors associated with death in a hospital in the State of Rio de Janeiro, 2017-2018. Rev Saude Publica 2019; 53:89. [PMID: 31644770 PMCID: PMC6802947 DOI: 10.11606/s1518-8787.2019053001434] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 03/22/2019] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVE Describe the clinical and epidemiological profile of confirmed cases of yellow fever whose patients were hospitalized in a general hospital for infectious diseases in the State of Rio de Janeiro, Brazil, from March 11, 2017 to June 15, 2018, during a recent outbreak and factors associated with death. METHODS This is a retrospective observational study with analysis of secondary databases of local epidemiological surveillance system, and complementary data collection from epidemiological investigation records and clinical records. Study variables included demographic, epidemiological, clinical, and laboratory data. A descriptive statistical analysis and a bivariate and multivariate analysis by logistic regression were performed to analyze factors associated with death. RESULTS Fifty-two patients diagnosed with yellow fever were hospitalized, 86.5% male patients, median age 49.5 years, 40.4% rural workers. The most frequent signs and symptoms were fever (90.4%), jaundice (86.5%), nausea and/or vomiting (69.2%), changes in renal excretion (53.8%), bleeding (50%), and abdominal pain (48.1%), with comorbidity in 38.5% of all cases. The lethality rate was 40.4%. Factors significantly associated with a higher chance of death in the bivariate analysis were: bleeding, changes in renal excretion, and maximum values of direct bilirubin, aspartate aminotransferase (AST), alanine aminotransferase (ALT), urea, and creatinine. In the multivariate analysis by logistic regression, only changes in renal excretion and ALT remained significant predictors of higher chance of death. A threshold effect was also observed for AST. The cutoff points identified as high risk for death were ALT > 4,000 U/L and AST > 6,000 U/L. CONCLUSIONS This study contributed to the knowledge on the profile of confirmed cases of high severity yellow fever. The main factors associated with death were changes in renal excretion and elevated serum transaminases, especially ALT. High lethality emphasizes the need for early diagnosis and treatment, and the importance of increasing vaccination coverage.
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Affiliation(s)
| | - Alessandra Gonçalves Lisbôa Pereira
- Hospital Federal dos Servidores do Estado. Serviço de Epidemiologia. Rio de Janeiro, RJ, Brasil.,Universidade Estácio de Sá. Faculdade de Medicina. Rio de Janeiro, RJ, Brasil
| | | | - Tatiana Rodrigues de Araujo Lima
- Hospital Federal dos Servidores do Estado. Serviço de Epidemiologia. Rio de Janeiro, RJ, Brasil.,Universidade do Estado do Rio de Janeiro. Faculdade de Enfermagem. Rio de Janeiro, RJ, Brasil
| | - Rafael Mello Galliez
- Instituto Estadual de Infectologia São Sebastião. Rio de Janeiro, RJ, Brasil.,Universidade Federal do Rio de Janeiro. Faculdade de Medicina. Rio de Janeiro, RJ, Brasil
| | - Roberto de Andrade Medronho
- Universidade Federal do Rio de Janeiro. Faculdade de Medicina. Rio de Janeiro, RJ, Brasil.,Universidade Federal do Rio de Janeiro. Instituto de Estudos em Saúde Coletiva. Rio de Janeiro, RJ, Brasil
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19
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Bernardi F, Lima V, Pellison F, de Azevedo Marques PM, Rijo R, Galliez RM, Kritski A, Alves D. Blockchain Based Network for Tuberculosis: A Data Sharing Initiative in Brazil. Stud Health Technol Inform 2019; 262:264-267. [PMID: 31349318 DOI: 10.3233/shti190069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Data sharing, information exchange, knowledge acquisition and health intelligence are the basis of an efficient and effective evidence-based decision-making tool. A decentralized blockchain architecture is a flexible solution that can be adapted to institutional and managerial culture of organizations and services. Blockchain can play a fundamental role in enabling data sharing within a network and, to achieve that, this work defines the high-level resources necessary to apply this technology to Tuberculosis related issues. Thus, relying in open-source tools and in a collaborative development approach, we present a proposal of a blockchain based network, the TB Network, to underpin an initiative of sharing of Tuberculosis scientific, operational and epidemiologic data between several stakeholders across Brazilian cities.
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Affiliation(s)
- Filipe Bernardi
- Bioengineering Postgraduate Program, University of São Paulo, Brazil
| | - Vinicius Lima
- Bioengineering Postgraduate Program, University of São Paulo, Brazil
| | - Felipe Pellison
- Bioengineering Postgraduate Program, University of São Paulo, Brazil
| | | | - Rui Rijo
- School of Technology and Management, Polytechnic Institute of Leiria, Portugal.,CINTESIS - Center for Health Technology and Services Research, Portugal.,INESCC - Institute for Systems and Computers Engineering at Coimbra, Portugal
| | - Rafael Mello Galliez
- Center of Scientific and Technological Information, Oswaldo Cruz Foundation, Brazil
| | - Afrânio Kritski
- Faculty of Medicine, Federal University of Rio de Janeiro, Brazil
| | - Domingos Alves
- Ribeirão Preto Medical School, University of São Paulo, Brazil.,CINTESIS - Center for Health Technology and Services Research, Portugal
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20
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Kritski A, Andrade KB, Galliez RM, Maciel ELN, Cordeiro-Santos M, Miranda SS, Villa TS, Ruffino Netto A, Arakaki-Sanchéz D, Croda J. Tuberculosis: renewed challenge in Brazil. Rev Soc Bras Med Trop 2018. [PMID: 29513837 DOI: 10.1590/0037-8682-0349-2017] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
This article reviews tuberculosis control actions performed over the last decade, at a global level. The perspectives for the fulfillment of the goals of the new Global Tuberculosis Elimination Plan are described, where the insertion of social protection (Pillar 2) and research (Pillar 3) will play an innovative and strategic role, especially in high-burden countries, like Brazil.
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Affiliation(s)
- Afranio Kritski
- Rede Brasileira de Pesquisa em Tuberculose, Rede Tuberculose, Rio de Janeiro, RJ, Brasil.,Programa Acadêmico de Tuberculose, Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | - Kleydson Bonfim Andrade
- Programa Nacional de Controle de Tuberculose, Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília, DF, Brasil
| | - Rafael Mello Galliez
- Rede Brasileira de Pesquisa em Tuberculose, Rede Tuberculose, Rio de Janeiro, RJ, Brasil.,Instituto Estadual São Sebastião, Secretaria Estadual de Saúde do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | - Ethel Leonor Noia Maciel
- Rede Brasileira de Pesquisa em Tuberculose, Rede Tuberculose, Rio de Janeiro, RJ, Brasil.,Programa de Pós-Graduação em Saúde Coletiva, Universidade Federal do Espírito Santo, Vitória, ES, Brasil
| | - Marcelo Cordeiro-Santos
- Rede Brasileira de Pesquisa em Tuberculose, Rede Tuberculose, Rio de Janeiro, RJ, Brasil.,Fundação de Medicina Tropical Doutor Heitor Vieira Dourado, Secretaria Estadual de Estado da Saúde do Amazonas, Manaus, AM, Brasil
| | - Silvana Spindola Miranda
- Rede Brasileira de Pesquisa em Tuberculose, Rede Tuberculose, Rio de Janeiro, RJ, Brasil.,Departamento de Clínica Médica, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil
| | - Teresa Scatena Villa
- Rede Brasileira de Pesquisa em Tuberculose, Rede Tuberculose, Rio de Janeiro, RJ, Brasil.,Escola de Enfermagem de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brasil
| | - Antonio Ruffino Netto
- Rede Brasileira de Pesquisa em Tuberculose, Rede Tuberculose, Rio de Janeiro, RJ, Brasil.,Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brasil
| | - Denise Arakaki-Sanchéz
- Programa Nacional de Controle de Tuberculose, Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília, DF, Brasil
| | - Julio Croda
- Rede Brasileira de Pesquisa em Tuberculose, Rede Tuberculose, Rio de Janeiro, RJ, Brasil.,Faculdade de Medicina, Universidade Federal de Mato Grosso do Sul/Fundação Oswaldo Cruz, Campo Grande, MS, Brasil
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21
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Galliez RM, Spitz M, Rafful PP, Cagy M, Escosteguy C, Germano CSB, Sasse E, Gonçalves AL, Silveira PP, Pezzuto P, Ornelas AMDM, Tanuri A, Aguiar RS, Moll FT. Zika Virus Causing Encephalomyelitis Associated With Immunoactivation. Open Forum Infect Dis 2016; 3:ofw203. [PMID: 28053996 PMCID: PMC5193179 DOI: 10.1093/ofid/ofw203] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [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: 06/16/2016] [Accepted: 09/29/2016] [Indexed: 11/29/2022] Open
Abstract
Brazil has experienced a Zika virus (ZIKV) outbreak with increased incidence of congenital malformations and neurological manifestations. We describe a case of a 26-year-old Brazilian Caucasian man infected with ZIKV and diagnosed with encephalomyelitis. Brain and spinal cord images showed hyperintense lesions on T2 and fluid-attenuated inversion recovery (FLAIR), and levels of proinflammatory cytokines in the cerebrospinal fluid showed a remarkable increase of interleukin (IL)-6 and IL-8. The observed pattern suggests immune activation during the acute phase, along with the neurological impairment, with normalization in the recovery phase. This is the first longitudinal report of ZIKV infection causing encephalomyelitis with documented immune activation.
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Affiliation(s)
- Rafael Mello Galliez
- Instituto Estadual de Infectologia São Sebastião, Rio de Janeiro, Brazil;; Programa de Pós-Graduação em Clínica Médica da Faculdade de Medicina da Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Mariana Spitz
- University of the State of Rio de Janeiro, Brazil;; Neurology Service and
| | - Patricia Piazza Rafful
- Epidemiology Service, Hospital Federal dos Servidores do Estado, Rio de Janeiro, Brazil;; D'Or Institute for Research and Education, Rio de Janeiro, Brazil
| | - Marcelo Cagy
- University of the State of Rio de Janeiro, Brazil;; Neurology Service and
| | - Claudia Escosteguy
- Epidemiology Service, Hospital Federal dos Servidores do Estado , Rio de Janeiro , Brazil
| | | | - Elisa Sasse
- University of the State of Rio de Janeiro, Brazil;; Neurology Service and
| | | | | | | | | | | | | | - Fernanda Tovar Moll
- Epidemiology Service, Hospital Federal dos Servidores do Estado, Rio de Janeiro, Brazil;; Radiology Department, and
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