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Forato J, Meira CA, Claro IM, Amorim MR, de Souza GF, Muraro SP, Toledo-Teixeira DA, Dias MF, Meneses CAR, Angerami RN, Lalwani P, Weaver SC, Sabino EC, Faria NR, de Souza WM, Granja F, Proenca-Modena JL. Molecular Epidemiology of Mayaro Virus among Febrile Patients, Roraima State, Brazil, 2018-2021. Emerg Infect Dis 2024; 30:1013-1016. [PMID: 38666638 PMCID: PMC11060474 DOI: 10.3201/eid3005.231406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024] Open
Abstract
We detected Mayaro virus (MAYV) in 3.4% (28/822) of febrile patients tested during 2018-2021 from Roraima State, Brazil. We also isolated MAYV strains and confirmed that these cases were caused by genotype D. Improved surveillance is needed to better determine the burden of MAYV in the Amazon Region.
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de Souza WM, Fumagalli MJ, de Lima STS, Parise PL, Carvalho DCM, Hernandez C, de Jesus R, Delafiori J, Candido DS, Carregari VC, Muraro SP, Souza GF, Simões Mello LM, Claro IM, Díaz Y, Kato RB, Trentin LN, Costa CHS, Maximo ACBM, Cavalcante KF, Fiuza TS, Viana VAF, Melo MEL, Ferraz CPM, Silva DB, Duarte LMF, Barbosa PP, Amorim MR, Judice CC, Toledo-Teixeira DA, Ramundo MS, Aguilar PV, Araújo ELL, Costa FTM, Cerqueira-Silva T, Khouri R, Boaventura VS, Figueiredo LTM, Fang R, Moreno B, López-Vergès S, Mello LP, Skaf MS, Catharino RR, Granja F, Martins-de-Souza D, Plante JA, Plante KS, Sabino EC, Diamond MS, Eugenin E, Proença-Módena JL, Faria NR, Weaver SC. Pathophysiology of chikungunya virus infection associated with fatal outcomes. Cell Host Microbe 2024; 32:606-622.e8. [PMID: 38479396 PMCID: PMC11018361 DOI: 10.1016/j.chom.2024.02.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 12/08/2023] [Accepted: 02/16/2024] [Indexed: 03/28/2024]
Abstract
Chikungunya virus (CHIKV) is a mosquito-borne alphavirus that causes acute, subacute, and chronic human arthritogenic diseases and, in rare instances, can lead to neurological complications and death. Here, we combined epidemiological, virological, histopathological, cytokine, molecular dynamics, metabolomic, proteomic, and genomic analyses to investigate viral and host factors that contribute to chikungunya-associated (CHIK) death. Our results indicate that CHIK deaths are associated with multi-organ infection, central nervous system damage, and elevated serum levels of pro-inflammatory cytokines and chemokines compared with survivors. The histopathologic, metabolite, and proteomic signatures of CHIK deaths reveal hemodynamic disorders and dysregulated immune responses. The CHIKV East-Central-South-African lineage infecting our study population causes both fatal and survival cases. Additionally, CHIKV infection impairs the integrity of the blood-brain barrier, as evidenced by an increase in permeability and altered tight junction protein expression. Overall, our findings improve the understanding of CHIK pathophysiology and the causes of fatal infections.
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Affiliation(s)
- William M de Souza
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky, College of Medicine, Lexington, KY, USA; Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA; Global Virus Network, Baltimore, MD, USA.
| | - Marcilio J Fumagalli
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Shirlene T S de Lima
- Laboratório Central de Saúde Pública do Ceará, Fortaleza, Ceará, Brazil; Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Pierina L Parise
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil; Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Deyse C M Carvalho
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; Laboratory of Immunobiotechnology, Biotechnology Center, Federal University of Paraíba, João Pessoa, Paraíba, Brazil
| | - Cristian Hernandez
- Department of Neurobiology, University of Texas Medical Branch, Galveston, TX, USA
| | - Ronaldo de Jesus
- Coordenação Geral dos Laboratórios de Saúde Pública, Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília, Brazil; Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Jeany Delafiori
- Innovare Biomarkers Laboratory, School of Pharmaceutical Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Darlan S Candido
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK; Department of Zoology, University of Oxford, Oxford, UK; Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Victor C Carregari
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Stefanie P Muraro
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Gabriela F Souza
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | | | - Ingra M Claro
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK; Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil; Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Yamilka Díaz
- Department of Research in Virology and Biotechnology, Gorgas Memorial Institute of Health Studies, Panama, Panama
| | - Rodrigo B Kato
- Coordenação Geral dos Laboratórios de Saúde Pública, Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília, Brazil; Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Lucas N Trentin
- Institute of Chemistry and Center for Computing in Engineering and Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Clauber H S Costa
- Institute of Chemistry and Center for Computing in Engineering and Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | | | | | - Tayna S Fiuza
- Laboratório Central de Saúde Pública do Ceará, Fortaleza, Ceará, Brazil; Programa de Pós Graduação em Bioinformática, Instituto Metrópole Digital, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Vânia A F Viana
- Laboratório Central de Saúde Pública do Ceará, Fortaleza, Ceará, Brazil
| | | | | | - Débora B Silva
- Laboratório Central de Saúde Pública do Ceará, Fortaleza, Ceará, Brazil
| | | | - Priscilla P Barbosa
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Mariene R Amorim
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Carla C Judice
- Laboratory of Tropical Diseases, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Daniel A Toledo-Teixeira
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Mariana S Ramundo
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil; Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Patricia V Aguilar
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA; Center for Tropical Diseases, Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Emerson L L Araújo
- Coordenação Geral de Atenção às Doenças Transmissíveis na Atenção Primária, Departamento de Gestão ao cuidado Integral, Secretaria de Atenção Primária à Saúde, Ministério da Saúde, Brasília, Brazil
| | - Fabio T M Costa
- Laboratory of Tropical Diseases, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Thiago Cerqueira-Silva
- Universidade Federal da Bahia, Faculdade de Medicina, Salvador, Bahia, Brazil; Fundação Oswaldo Cruz, Instituto Gonçalo Muniz, Laboratório de Medicina e Saúde Pública de Precisão, Salvador, Bahia, Brazil
| | - Ricardo Khouri
- Universidade Federal da Bahia, Faculdade de Medicina, Salvador, Bahia, Brazil; Fundação Oswaldo Cruz, Instituto Gonçalo Muniz, Laboratório de Medicina e Saúde Pública de Precisão, Salvador, Bahia, Brazil
| | - Viviane S Boaventura
- Universidade Federal da Bahia, Faculdade de Medicina, Salvador, Bahia, Brazil; Fundação Oswaldo Cruz, Instituto Gonçalo Muniz, Laboratório de Medicina e Saúde Pública de Precisão, Salvador, Bahia, Brazil; Hospital Santa Izabel, Santa Casa de Misericórdia da Bahia, Serviço de Otorrinolaringologia, Salvador, Bahia, Brazil
| | - Luiz Tadeu M Figueiredo
- Virology Research Centre, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Rong Fang
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Brechla Moreno
- Department of Research in Virology and Biotechnology, Gorgas Memorial Institute of Health Studies, Panama, Panama
| | - Sandra López-Vergès
- Department of Research in Virology and Biotechnology, Gorgas Memorial Institute of Health Studies, Panama, Panama; Sistema Nacional de Investigación from SENACYT, Panama, Panama
| | | | - Munir S Skaf
- Institute of Chemistry and Center for Computing in Engineering and Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Rodrigo R Catharino
- Innovare Biomarkers Laboratory, School of Pharmaceutical Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Fabiana Granja
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil; Biodiversity Research Centre, Federal University of Roraima, Boa Vista, Roraima, Brazil
| | - Daniel Martins-de-Souza
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil; D'Or Institute for Research and Education, São Paulo, São Paulo, Brazil; Experimental Medicine Research Cluster, University of Campinas, Campinas, São Paulo, Brazil
| | - Jessica A Plante
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
| | - Kenneth S Plante
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
| | - Ester C Sabino
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil; Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Michael S Diamond
- Departments of Medicine, Molecular Microbiology, Pathology & Immunology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Eliseo Eugenin
- Department of Neurobiology, University of Texas Medical Branch, Galveston, TX, USA
| | - José Luiz Proença-Módena
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Nuno R Faria
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK; Department of Zoology, University of Oxford, Oxford, UK; Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Scott C Weaver
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA; Global Virus Network, Baltimore, MD, USA; Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX, USA
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Mercy K, Tibebu B, Fallah M, Faria NR, Ndembi N, Tebeje YK. Mpox continues to spread in Africa and threatens global health security. Nat Med 2024:10.1038/s41591-024-02862-6. [PMID: 38472296 DOI: 10.1038/s41591-024-02862-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2024]
Affiliation(s)
- Kyeng Mercy
- Africa Centres for Disease Control and Prevention, Addis Ababa, Ethiopia
| | - Bethelhem Tibebu
- Africa Centres for Disease Control and Prevention, Addis Ababa, Ethiopia
| | - Mosoka Fallah
- Africa Centres for Disease Control and Prevention, Addis Ababa, Ethiopia
| | - Nuno R Faria
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
| | - Nicaise Ndembi
- Africa Centres for Disease Control and Prevention, Addis Ababa, Ethiopia.
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Rivera LF, Lezcano-Coba C, Galué J, Rodriguez X, Juarez Y, de Souza WM, Capitan-Barrios Z, Valderrama A, Abrego L, Cedeño H, Jackman C, Waggoner JJ, Aguilar PV, Guzman H, Weaver SC, Tesh RB, López-Vèrges S, Donnelly CA, Estofolete CF, Nogueira ML, Faria NR, Vasilakis N, Vittor AY, Smith DR, Carrera JP. Clinical and epidemiological characteristics of Madariaga and Venezuelan equine encephalitis virus infections. medRxiv 2024:2024.02.02.24302220. [PMID: 38352566 PMCID: PMC10863014 DOI: 10.1101/2024.02.02.24302220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/19/2024]
Abstract
Madariaga virus (MADV) and Venezuelan equine encephalitis virus (VEEV) are emerging arboviruses affecting rural and remote areas of Latin America. However, there are limited clinical and epidemiological reports available, and outbreaks are occurring at an increasing frequency. We addressed this gap by analyzing all the available clinical and epidemiological data of MADV and VEEV infections recorded since 1961 in Panama. A total of 168 of human alphavirus encephalitis cases were detected in Panama from 1961 to 2023. Here we describe the clinical signs and symptoms and epidemiological characteristics of these cases, and also explored signs and symptoms as potential predictors of encephalitic alphavirus infection when compared to those of other arbovirus infections occurring in the region. Our results highlight the challenges clinical diagnosis of alphavirus disease in endemic regions with overlapping circulation of multiple arboviruses.
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Affiliation(s)
- Luis Felipe Rivera
- Instituto Conmemorativo Gorgas de Estudios de la Salud, Panama City, Panama
- Carson Centre for Research in Environment and Emerging Infectious Diseases, La Peñita, Darién, Panama
| | - Carlos Lezcano-Coba
- Instituto Conmemorativo Gorgas de Estudios de la Salud, Panama City, Panama
- Carson Centre for Research in Environment and Emerging Infectious Diseases, La Peñita, Darién, Panama
| | - Josefrancisco Galué
- Instituto Conmemorativo Gorgas de Estudios de la Salud, Panama City, Panama
- Carson Centre for Research in Environment and Emerging Infectious Diseases, La Peñita, Darién, Panama
| | - Xacdiel Rodriguez
- Instituto Conmemorativo Gorgas de Estudios de la Salud, Panama City, Panama
- Carson Centre for Research in Environment and Emerging Infectious Diseases, La Peñita, Darién, Panama
| | - Yelissa Juarez
- Instituto Conmemorativo Gorgas de Estudios de la Salud, Panama City, Panama
- Carson Centre for Research in Environment and Emerging Infectious Diseases, La Peñita, Darién, Panama
| | | | - Zeuz Capitan-Barrios
- Carson Centre for Research in Environment and Emerging Infectious Diseases, La Peñita, Darién, Panama
- Universidad de Panamá, Ciudad de Panamá
| | - Anayansi Valderrama
- Instituto Conmemorativo Gorgas de Estudios de la Salud, Panama City, Panama
- Carson Centre for Research in Environment and Emerging Infectious Diseases, La Peñita, Darién, Panama
| | - Leyda Abrego
- Instituto Conmemorativo Gorgas de Estudios de la Salud, Panama City, Panama
- Carson Centre for Research in Environment and Emerging Infectious Diseases, La Peñita, Darién, Panama
- Universidad de Panamá, Ciudad de Panamá
| | | | | | | | | | - Hilda Guzman
- The University of Texas Medical Branch, Galveston, TX, USA
| | | | - Robert B. Tesh
- The University of Texas Medical Branch, Galveston, TX, USA
| | | | | | - Cassia F. Estofolete
- Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, São Paulo Brazil
| | - Mauricio L. Nogueira
- The University of Texas Medical Branch, Galveston, TX, USA
- Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, São Paulo Brazil
| | - Nuno R. Faria
- Imperial College London, London, United Kingdom
- Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | | | | | | | - Jean-Paul Carrera
- Instituto Conmemorativo Gorgas de Estudios de la Salud, Panama City, Panama
- Carson Centre for Research in Environment and Emerging Infectious Diseases, La Peñita, Darién, Panama
- University of Oxford, Oxford, United Kingdom
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de Souza WM, Ribeiro GS, de Lima ST, de Jesus R, Moreira FR, Whittaker C, Sallum MAM, Carrington CV, Sabino EC, Kitron U, Faria NR, Weaver SC. Chikungunya: a decade of burden in the Americas. Lancet Reg Health Am 2024; 30:100673. [PMID: 38283942 PMCID: PMC10820659 DOI: 10.1016/j.lana.2023.100673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/24/2023] [Accepted: 12/29/2023] [Indexed: 01/30/2024]
Abstract
In the Americas, one decade following its emergence in 2013, chikungunya virus (CHIKV) continues to spread and cause epidemics across the region. To date, 3.7 million suspected and laboratory-confirmed chikungunya cases have been reported in 50 countries or territories in the Americas. Here, we outline the current status and epidemiological aspects of chikungunya in the Americas and discuss prospects for future research and public health strategies to combat CHIKV in the region.
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Affiliation(s)
- William M. de Souza
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky, College of Medicine, Lexington, KY, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
- Global Virus Network, Baltimore, MD, USA
| | - Guilherme S. Ribeiro
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Bahia, Brazil
- Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Salvador, Bahia, Brazil
| | - Shirlene T.S. de Lima
- Laboratório Central de Saúde Pública do Ceará, Fortaleza, Ceará, Brazil
- Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Ronaldo de Jesus
- Coordenação Geral dos Laboratórios de Saúde Pública, Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília, Brazil
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Filipe R.R. Moreira
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK
| | - Maria Anice M. Sallum
- Departamento de Epidemiologia, Faculdade de Saúde Pública, Universidade de São Paulo, Brazil
| | - Christine V.F. Carrington
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Republic of Trinidad and Tobago
| | - Ester C. Sabino
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Uriel Kitron
- Department of Environmental Sciences, Emory University, Atlanta, GA, USA
| | - Nuno R. Faria
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Department of Biology, University of Oxford, Oxford, UK
| | - Scott C. Weaver
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
- Global Virus Network, Baltimore, MD, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
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6
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Mirza JD, de Oliveira Guimarães L, Wilkinson S, Rocha EC, Bertanhe M, Helfstein VC, de-Deus JT, Claro IM, Cumley N, Quick J, Faria NR, Sabino EC, Kirchgatter K, Loman NJ. Tracking arboviruses, their transmission vectors and potential hosts by nanopore sequencing of mosquitoes. Microb Genom 2024; 10:001184. [PMID: 38240642 PMCID: PMC10868619 DOI: 10.1099/mgen.0.001184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 01/08/2024] [Indexed: 01/23/2024] Open
Abstract
The risk to human health from mosquito-borne viruses such as dengue, chikungunya and yellow fever is increasing due to increased human expansion, deforestation and climate change. To anticipate and predict the spread and transmission of mosquito-borne viruses, a better understanding of the transmission cycle in mosquito populations is needed. We present a pathogen-agnostic combined sequencing protocol for identifying vectors, viral pathogens and their hosts or reservoirs using portable Oxford Nanopore sequencing. Using mosquitoes collected in São Paulo, Brazil, we extracted RNA for virus identification and DNA for blood meal and mosquito identification. Mosquitoes and blood meals were identified by comparing cytochrome c oxidase I (COI) sequences against a curated Barcode of Life Data System (BOLD). Viruses were identified using the SMART-9N protocol, which allows amplified DNA to be prepared with native barcoding for nanopore sequencing. Kraken 2 was employed to detect viral pathogens and Minimap2 and BOLD identified the contents of the blood meal. Due to the high similarity of some species, mosquito identification was conducted using blast after generation of consensus COI sequences using RACON polishing. This protocol can simultaneously uncover viral diversity, mosquito species and mosquito feeding habits. It also has the potential to increase understanding of mosquito genetic diversity and transmission dynamics of zoonotic mosquito-borne viruses.
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Affiliation(s)
- Jeremy D. Mirza
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK
- Department of Biosciences, University of Birmingham, Birmingham, UK
| | | | - Sam Wilkinson
- Department of Biosciences, University of Birmingham, Birmingham, UK
| | - Esmenia C. Rocha
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Mayara Bertanhe
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | | | | | - Ingra M. Claro
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, Imperial College London, London, UK
| | - Nicola Cumley
- Department of Biosciences, University of Birmingham, Birmingham, UK
| | - Joshua Quick
- Department of Biosciences, University of Birmingham, Birmingham, UK
| | - Nuno R. Faria
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, Imperial College London, London, UK
| | - Ester C. Sabino
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Karin Kirchgatter
- Instituto Pasteur, São Paulo, Brazil
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
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7
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Carrera JP, Araúz D, Rojas A, Cardozo F, Stittleburg V, Morales Claro I, Galue J, Lezcano-Coba C, Romero Rebello Moreira F, -Rivera LF, Chen-Germán M, Moreno B, Capitan-Barrios Z, López-Vergès S, Pascale JM, Sabino EC, Valderrama A, Hanley KA, Donnelly CA, Vasilakis N, Faria NR, Waggoner JJ. Real-time RT-PCR for Venezuelan equine encephalitis complex, Madariaga, and Eastern equine encephalitis viruses: application in human and mosquito public health surveillance in Panama. J Clin Microbiol 2023; 61:e0015223. [PMID: 37982611 PMCID: PMC10729654 DOI: 10.1128/jcm.00152-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 09/08/2023] [Indexed: 11/21/2023] Open
Abstract
Eastern equine encephalitis virus (EEEV), Madariaga virus (MADV), and Venezuelan equine encephalitis virus complex (VEEV) are New World alphaviruses transmitted by mosquitoes. They cause febrile and sometimes severe neurological diseases in human and equine hosts. Detecting them during the acute phase is hindered by non-specific symptoms and limited diagnostic tools. We designed and clinically assessed real-time reverse transcription polymerase chain reaction assays (rRT-PCRs) for VEEV complex, MADV, and EEEV using whole-genome sequences. Validation involved 15 retrospective serum samples from 2015 to 2017 outbreaks, 150 mosquito pools from 2015, and 118 prospective samples from 2021 to 2022 surveillance in Panama. The rRT-PCRs detected VEEV complex RNA in 10 samples (66.7%) from outbreaks, with one having both VEEV complex and MADV RNAs. VEEV complex RNA was found in five suspected dengue cases from disease surveillance. The rRT-PCR assays identified VEEV complex RNA in three Culex (Melanoconion) vomerifer pools, leading to VEEV isolates in two. Phylogenetic analysis revealed the VEEV ID subtype in positive samples. Notably, 11.9% of dengue-like disease patients showed VEEV infections. Together, our rRT-PCR validation in human and mosquito samples suggests that this method can be incorporated into mosquito and human encephalitic alphavirus surveillance programs in endemic regions.
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Affiliation(s)
- Jean-Paul Carrera
- Department of Biology, University of Oxford, Oxford, United Kingdom
- Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Department of Research in Virology and Biotechnology, Gorgas Memorial Institute of Health Studies, Panama City, Panama
- Viral Emerging Disease Dynamics Group, Gorgas Memorial Institute of Health Studies, Panama City, Panama
| | - Dimelza Araúz
- Department of Research in Virology and Biotechnology, Gorgas Memorial Institute of Health Studies, Panama City, Panama
| | - Alejandra Rojas
- Departamento de Producción, Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, San Lorenzo, Paraguay
| | - Fátima Cardozo
- Departamento de Producción, Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, San Lorenzo, Paraguay
| | - Victoria Stittleburg
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
| | - Ingra Morales Claro
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- MRC Centre for Global Infectious Disease Analysis (MRC-GIDA), Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Josefrancisco Galue
- Department of Research in Virology and Biotechnology, Gorgas Memorial Institute of Health Studies, Panama City, Panama
- Viral Emerging Disease Dynamics Group, Gorgas Memorial Institute of Health Studies, Panama City, Panama
| | - Carlos Lezcano-Coba
- Department of Research in Virology and Biotechnology, Gorgas Memorial Institute of Health Studies, Panama City, Panama
- Viral Emerging Disease Dynamics Group, Gorgas Memorial Institute of Health Studies, Panama City, Panama
| | - Filipe Romero Rebello Moreira
- MRC Centre for Global Infectious Disease Analysis (MRC-GIDA), Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Luis Felipe -Rivera
- Department of Research in Virology and Biotechnology, Gorgas Memorial Institute of Health Studies, Panama City, Panama
- Viral Emerging Disease Dynamics Group, Gorgas Memorial Institute of Health Studies, Panama City, Panama
| | - Maria Chen-Germán
- Department of Research in Virology and Biotechnology, Gorgas Memorial Institute of Health Studies, Panama City, Panama
| | - Brechla Moreno
- Department of Research in Virology and Biotechnology, Gorgas Memorial Institute of Health Studies, Panama City, Panama
| | - Zeuz Capitan-Barrios
- Department of Research in Virology and Biotechnology, Gorgas Memorial Institute of Health Studies, Panama City, Panama
- Viral Emerging Disease Dynamics Group, Gorgas Memorial Institute of Health Studies, Panama City, Panama
- Departamento de Microbiología y Parasitología, Facultad de Ciencias Naturales, Exactas y Tecnología, Universidad de Panamá, Ciudad de Panamá, Panama
| | - Sandra López-Vergès
- Department of Research in Virology and Biotechnology, Gorgas Memorial Institute of Health Studies, Panama City, Panama
| | - Juan Miguel Pascale
- Clinical of Tropical Diseases and Research Unit, Gorgas Memorial Institute of Health Studies, Panama City, Panama
| | - Ester C. Sabino
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Anayansi Valderrama
- Viral Emerging Disease Dynamics Group, Gorgas Memorial Institute of Health Studies, Panama City, Panama
- Department of Medical Entomology, Gorgas Memorial Institute of Health Studies, Panama City, Panama
| | - Kathryn A. Hanley
- Department of Biology, New Mexico State University, Las Cruces, New Mexico, USA
| | - Christl A. Donnelly
- Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- MRC Centre for Global Infectious Disease Analysis (MRC-GIDA), Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Nikos Vasilakis
- Department of Pathology, The University of Texas Medical Branch, Galveston, Texas, USA
- Department of Preventive Medicine and Population Health, The University of Texas Medical Branch, Galveston, Texas, USA
- Center for Biodefense and Emerging Infectious Diseases, The University of Texas Medical Branch, Galveston, Texas, USA
- Center for Vector-Borne and Zoonotic Diseases, The University of Texas Medical Branch, Galveston, Texas, USA
- Center for Tropical Diseases, The University of Texas Medical Branch, Galveston, Texas, USA
- Institute for Human Infection and Immunity, The University of Texas Medical Branch, Galveston, Texas, USA
| | - Nuno R. Faria
- Department of Biology, University of Oxford, Oxford, United Kingdom
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- MRC Centre for Global Infectious Disease Analysis (MRC-GIDA), Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Jesse J. Waggoner
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
- Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
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8
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Duarte-Neto AN, Gonçalves AM, Eliodoro RHDA, Martins WD, Claro IM, Valença IN, Paes VR, Teixeira R, Sztajnbok J, França E Silva ILA, Leite LAF, Malaque CMS, Borges LMS, Gonzalez MP, Barra LAC, Junior LCP, Mello CF, Queiroz W, Atomya AN, Fernezlian SDM, Alves VAF, Leite KRM, Ferreira CR, Saldiva PHN, Mauad T, da Silva LFF, Faria NR, Mendes Corrêa MCJ, Sabino EC, Sotto MN, Dolhnikoff M. Main autopsy findings of visceral involvement by fatal mpox in patients with AIDS: necrotising nodular pneumonia, nodular ulcerative colitis, and diffuse vasculopathy. Lancet Infect Dis 2023; 23:1218-1222. [PMID: 37827188 DOI: 10.1016/s1473-3099(23)00574-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 09/09/2023] [Accepted: 09/11/2023] [Indexed: 10/14/2023]
Affiliation(s)
- Amaro Nunes Duarte-Neto
- Departamento de Patologia, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brazil.
| | - Ana Maria Gonçalves
- Departamento de Patologia, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brazil
| | | | - Wilker Dias Martins
- Departamento de Patologia, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Ingra Morales Claro
- Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brazil; Imperial College London, MRC Centre for Global Infectious Disease Analysis, London, UK
| | - Ian Nunes Valença
- Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brazil; Imperial College London, MRC Centre for Global Infectious Disease Analysis, London, UK
| | - Vitor Ribeiro Paes
- Departamento de Patologia, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brazil
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Thais Mauad
- Departamento de Patologia, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Luiz Fernando Ferraz da Silva
- Departamento de Patologia, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brazil; and Serviço de Verificação de Óbitos da Capital, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Nuno R Faria
- Imperial College London, MRC Centre for Global Infectious Disease Analysis, London, UK; University of Oxford, Department of Zoology, Oxford, UK
| | - Maria Cássia Jacinto Mendes Corrêa
- Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brazil; Departamento de Doenças Infecciosas e Parasitárias, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Ester Cerdeira Sabino
- Departamento de Patologia, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brazil; Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Mirian Nacagami Sotto
- Departamento de Patologia, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Marisa Dolhnikoff
- Departamento de Patologia, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brazil
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9
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Sahadeo NSD, Nicholls S, Moreira FRR, O'Toole Á, Ramkissoon V, Whittaker C, Hill V, McCrone JT, Mohammed N, Ramjag A, Jordan AB, Hill SC, Singh R, Nathaniel-Girdharrie SM, Hinds A, Ramkissoon N, Parag KV, Nandram N, Parasram R, Khan-Mohammed Z, Edghill L, Indar L, Andrewin A, Sealey-Thomas R, McMillan P, Oyinloye A, George K, Potter I, Lee J, Johnson D, Charles S, Singh N, Bisesor-McKenzie J, Laws H, Belmar-George S, Keizer-Beache S, Greenaway-Duberry S, Ashwood N, Foster JE, Georges K, Naidu R, Ivey M, Giddings S, Haraksingh R, Ramsubhag A, Jayaraman J, Chinnadurai C, Oura C, Pybus OG, St John J, Gonzalez-Escobar G, Faria NR, Carrington CVF. Correction: Implementation of Genomic Surveillance of SARS-CoV-2 in the Caribbean: Lessons learned for sustainability in resource-limited settings. PLOS Glob Public Health 2023; 3:e0002393. [PMID: 37695757 PMCID: PMC10495005 DOI: 10.1371/journal.pgph.0002393] [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] [Subscribe] [Scholar Register] [Indexed: 09/13/2023]
Abstract
[This corrects the article DOI: 10.1371/journal.pgph.0001455.].
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10
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Policarpo JMP, Ramos AAGF, Dye C, Faria NR, Leal FE, Moraes OJS, Parag KV, Peixoto PS, Buss L, Sabino EC, Nascimento VH, Deppman A. Scale-free dynamics of COVID-19 in a Brazilian city. Appl Math Model 2023; 121:166-184. [PMID: 37151217 PMCID: PMC10154131 DOI: 10.1016/j.apm.2023.03.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 03/13/2023] [Accepted: 03/29/2023] [Indexed: 05/09/2023]
Abstract
A common basis to address the dynamics of directly transmitted infectious diseases, such as COVID-19, are compartmental (or SIR) models. SIR models typically assume homogenous population mixing, a simplification that is convenient but unrealistic. Here we validate an existing model of a scale-free fractal infection process using high-resolution data on COVID-19 spread in São Caetano, Brazil. We find that transmission can be described by a network in which each infectious individual has a small number of susceptible contacts, of the order of 2-5. This model parameter correlated tightly with physical distancing measured by mobile phone data, such that in periods of greater distancing the model recovered a lower average number of contacts, and vice versa. We show that the SIR model is a special case of our scale-free fractal process model in which the parameter that reflects population structure is set at unity, indicating homogeneous mixing. Our more general framework better explained the dynamics of COVID-19 in São Caetano, used fewer parameters than a standard SIR model and accounted for geographically localized clusters of disease. Our model requires further validation in other locations and with other directly transmitted infectious agents.
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Affiliation(s)
| | - A A G F Ramos
- Instituto de Física - Universidade de São Paulo, Brazil
| | - C Dye
- Department of Biology, University of Oxford, UK
| | - N R Faria
- Department of Biology, University of Oxford, UK
- Imperial Coll London, MRC Ctr Global Infect Dis Anal, Sch Publ Helth, London, England, UK
- Faculdade de Medicina - Universidade de São Paulo, Brazil
| | - F E Leal
- Universidade de São Caetano do Sul, São Caetano do Sul and Programa de Oncovirologia - Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - O J S Moraes
- Instituto de Física - Universidade de São Paulo, Brazil
| | - K V Parag
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London W2 1PG, UK
| | - P S Peixoto
- Instituto de Matemática e Estatística, Universidade de São Paulo, Brazil
| | - L Buss
- Faculdade de Medicina - Universidade de São Paulo, Brazil
| | - E C Sabino
- Faculdade de Medicina - Universidade de São Paulo, Brazil
| | | | - A Deppman
- Instituto de Física - Universidade de São Paulo, Brazil
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11
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Gutierrez B, da Silva Candido D, Bajaj S, Rodriguez Maldonado AP, Ayala FG, Rodriguez MDLLT, Rodriguez AA, Arámbula CW, González ER, Martínez IL, Díaz-Quiñónez JA, Pichardo MV, Hill SC, Thézé J, Faria NR, Pybus OG, Preciado-Llanes L, Reyes-Sandoval A, Kraemer MUG, Escalera-Zamudio M. Convergent trends and spatiotemporal patterns of Aedes-borne arboviruses in Mexico and Central America. PLoS Negl Trop Dis 2023; 17:e0011169. [PMID: 37672514 PMCID: PMC10506721 DOI: 10.1371/journal.pntd.0011169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 09/18/2023] [Accepted: 08/21/2023] [Indexed: 09/08/2023] Open
Abstract
BACKGROUND Aedes-borne arboviruses cause both seasonal epidemics and emerging outbreaks with a significant impact on global health. These viruses share mosquito vector species, often infecting the same host population within overlapping geographic regions. Thus, comparative analyses of the virus evolutionary and epidemiological dynamics across spatial and temporal scales could reveal convergent trends. METHODOLOGY/PRINCIPAL FINDINGS Focusing on Mexico as a case study, we generated novel chikungunya and dengue (CHIKV, DENV-1 and DENV-2) virus genomes from an epidemiological surveillance-derived historical sample collection, and analysed them together with longitudinally-collected genome and epidemiological data from the Americas. Aedes-borne arboviruses endemically circulating within the country were found to be introduced multiple times from lineages predominantly sampled from the Caribbean and Central America. For CHIKV, at least thirteen introductions were inferred over a year, with six of these leading to persistent transmission chains. For both DENV-1 and DENV-2, at least seven introductions were inferred over a decade. CONCLUSIONS/SIGNIFICANCE Our results suggest that CHIKV, DENV-1 and DENV-2 in Mexico share evolutionary and epidemiological trajectories. The southwest region of the country was determined to be the most likely location for viral introductions from abroad, with a subsequent spread into the Pacific coast towards the north of Mexico. Virus diffusion patterns observed across the country are likely driven by multiple factors, including mobility linked to human migration from Central towards North America. Considering Mexico's geographic positioning displaying a high human mobility across borders, our results prompt the need to better understand the role of anthropogenic factors in the transmission dynamics of Aedes-borne arboviruses, particularly linked to land-based human migration.
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Affiliation(s)
- Bernardo Gutierrez
- Department of Biology, University of Oxford, Oxford, United Kingdom
- Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Darlan da Silva Candido
- Department of Biology, University of Oxford, Oxford, United Kingdom
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Sumali Bajaj
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | | | - Fabiola Garces Ayala
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE) "Dr. Manuel Martínez Báez", Secretaría de Salud, Mexico City, México
| | - María de la Luz Torre Rodriguez
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE) "Dr. Manuel Martínez Báez", Secretaría de Salud, Mexico City, México
| | - Adnan Araiza Rodriguez
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE) "Dr. Manuel Martínez Báez", Secretaría de Salud, Mexico City, México
| | - Claudia Wong Arámbula
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE) "Dr. Manuel Martínez Báez", Secretaría de Salud, Mexico City, México
| | - Ernesto Ramírez González
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE) "Dr. Manuel Martínez Báez", Secretaría de Salud, Mexico City, México
| | - Irma López Martínez
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE) "Dr. Manuel Martínez Báez", Secretaría de Salud, Mexico City, México
| | - José Alberto Díaz-Quiñónez
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE) "Dr. Manuel Martínez Báez", Secretaría de Salud, Mexico City, México
- Instituto de Ciencias de la Salud, Universidad Autónoma del Estado de Hidalgo, Pachuca de Soto, Mexico
| | - Mauricio Vázquez Pichardo
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE) "Dr. Manuel Martínez Báez", Secretaría de Salud, Mexico City, México
| | - Sarah C. Hill
- Department of Pathobiology and Population Sciences, Royal Veterinary College, London, United Kingdom
| | - Julien Thézé
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR EPIA, Saint-Genès-Champanelle, France
| | - Nuno R. Faria
- Department of Biology, University of Oxford, Oxford, United Kingdom
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics, School of Public Health, Imperial College London, London, United Kingdom
| | - Oliver G. Pybus
- Department of Biology, University of Oxford, Oxford, United Kingdom
- Department of Pathobiology and Population Sciences, Royal Veterinary College, London, United Kingdom
| | - Lorena Preciado-Llanes
- Nuffield Department of Medicine/Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Arturo Reyes-Sandoval
- Nuffield Department of Medicine/Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Instituto Politécnico Nacional (IPN), Av. Luis Enrique Erro s/n., Unidad Adolfo López Mateos, Mexico City, Mexico
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12
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Carrera JP, Galué J, de Souza WM, Torres-Cosme R, Lezcano-Coba C, Cumbrera A, Vasilakis N, Tesh RB, Guzman H, Weaver SC, Vittor AY, Samudio R, Miguel Pascale J, Valderrama A, Cáceres Carrera L, Donnelly CA, Faria NR. Madariaga and Venezuelan equine encephalitis virus seroprevalence in rodent enzootic hosts in Eastern and Western Panama. bioRxiv 2023:2023.08.28.555226. [PMID: 37693579 PMCID: PMC10491141 DOI: 10.1101/2023.08.28.555226] [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] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
While rodents are primary reservoirs of Venezuelan equine encephalitis virus (VEEV), their role in Madariaga virus (MADV) transmission remains uncertain, particularly given their overlapping geographic distribution. This study explores the interplay of alphavirus prevalence, rodent diversity, and land use within Darien and Western Panama provinces. A total of three locations were selected for rodent sampling in Darien province: Los Pavitos, El Real de Santa Maria and Santa Librada. Two sites were selected in Western Panama province: El Cacao and Cirí Grande. We used plaque reduction neutralization tests to assess MADV and VEEV seroprevalences in 599 rodents of 16 species across five study sites. MADV seroprevalence was observed at higher rates in Los Pavitos (Darien province), 9.0%, 95% CI: 3.6-17.6, while VEEV seroprevalence was elevated in El Cacao (Western Panama province), 27.3%, 95% CI: 16.1-40.9, and El Real de Santa María (Darien province), 20.4%, 95% CI: 12.6-29.7. Species like Oryzomys coesi, 23.1%, 95% CI: 5.0-53.8, and Transandinomys bolivaris, 20.0%, 95% CI: 0.5-71.6 displayed higher MADV seroprevalences than other species, whereas Transandinomys bolivaris, 80.0%, 95% CI: 28.3-99.4, and Proechimys semispinosus, 27.3%, 95% CI: 17.0-39.6, exhibited higher VEEV seroprevalences. Our findings provide support to the notion that rodents are vertebrate reservoirs of MADV and reveal spatial variations in alphavirus seropositivity among rodent species, with different provinces exhibiting distinct rates for MADV and VEEV. Moreover, specific rodent species are linked to unique seroprevalence patterns for these viruses, suggesting that rodent diversity and environmental conditions might play a significant role in shaping alphavirus distribution.
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Affiliation(s)
- Jean-Paul Carrera
- Department of Biology, University of Oxford, Oxford, United Kingdom
- Pandemic Sciences Institute, University of Oxford, Oxford United Kingdom
- Department of Research in Virology and Biotechnology, Gorgas Memorial Institute of Health Studies, Panama City, Panama
- Viral Emerging Disease Dynamics Group, Gorgas Memorial Institute of Health Studies, Panama City, Panama
- Carson Centre for Research in Environment and Emerging Infectious Diseases, La Peñita, Darien, Panama
| | - Josefrancisco Galué
- Department of Research in Virology and Biotechnology, Gorgas Memorial Institute of Health Studies, Panama City, Panama
- Viral Emerging Disease Dynamics Group, Gorgas Memorial Institute of Health Studies, Panama City, Panama
- Carson Centre for Research in Environment and Emerging Infectious Diseases, La Peñita, Darien, Panama
| | - William M. de Souza
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky, College of Medicine, Lexington, Kentucky, USA
| | - Rolando Torres-Cosme
- Department of Medical Entomology, Gorgas Memorial Institute of Health Studies, Panama City, Panama
| | - Carlos Lezcano-Coba
- Department of Research in Virology and Biotechnology, Gorgas Memorial Institute of Health Studies, Panama City, Panama
- Viral Emerging Disease Dynamics Group, Gorgas Memorial Institute of Health Studies, Panama City, Panama
- Carson Centre for Research in Environment and Emerging Infectious Diseases, La Peñita, Darien, Panama
| | - Alberto Cumbrera
- Department of Medical Entomology, Gorgas Memorial Institute of Health Studies, Panama City, Panama
| | - Nikos Vasilakis
- Institute for Human infection and Immunity, University of Texas Medical Branch, Texas, USA
- Geographic System Information Unit, Gorgas Memorial Institute of Health Studies, Panama City, Panama
- Department of Pathology, University of Texas Medical Branch, Galveston Texas, USA
- Center for Vector-Borne and Zoonotic Diseases, University of Texas Medical Branch, Galveston, Texas, USA
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, Texas, USA
- Center for Tropical Diseases, University of Texas Medical Branch, Galveston, Texas, USA
| | - Robert B. Tesh
- Geographic System Information Unit, Gorgas Memorial Institute of Health Studies, Panama City, Panama
- Department of Pathology, University of Texas Medical Branch, Galveston Texas, USA
- Center for Vector-Borne and Zoonotic Diseases, University of Texas Medical Branch, Galveston, Texas, USA
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, Texas, USA
- Center for Tropical Diseases, University of Texas Medical Branch, Galveston, Texas, USA
| | - Hilda Guzman
- Geographic System Information Unit, Gorgas Memorial Institute of Health Studies, Panama City, Panama
| | - Scott C. Weaver
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- Institute for Human infection and Immunity, University of Texas Medical Branch, Texas, USA
- Department of Pathology, University of Texas Medical Branch, Galveston Texas, USA
- Center for Vector-Borne and Zoonotic Diseases, University of Texas Medical Branch, Galveston, Texas, USA
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, Texas, USA
- Center for Tropical Diseases, University of Texas Medical Branch, Galveston, Texas, USA
| | - Amy Y. Vittor
- Department of Medicine, Division of Infectious Disease and Global Medicine, University of Florida, Gainesville, Florida, USA
| | | | - Juan Miguel Pascale
- Clinical Research Unit, Gorgas Memorial Institute of health Studies, Panama City, Panama
| | - Anayansi Valderrama
- Carson Centre for Research in Environment and Emerging Infectious Diseases, La Peñita, Darien, Panama
- Department of Medical Entomology, Gorgas Memorial Institute of Health Studies, Panama City, Panama
| | - Lorenzo Cáceres Carrera
- Department of Medical Entomology, Gorgas Memorial Institute of Health Studies, Panama City, Panama
| | - Christl A. Donnelly
- Pandemic Sciences Institute, University of Oxford, Oxford United Kingdom
- Department of Statistics, University of Oxford, Oxford United Kingdom
- Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, UK
| | - Nuno R. Faria
- Department of Biology, University of Oxford, Oxford, United Kingdom
- Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, UK
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13
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Tegally H, Wilkinson E, Tsui JLH, Moir M, Martin D, Brito AF, Giovanetti M, Khan K, Huber C, Bogoch II, San JE, Poongavanan J, Xavier JS, Candido DDS, Romero F, Baxter C, Pybus OG, Lessells RJ, Faria NR, Kraemer MUG, de Oliveira T. Dispersal patterns and influence of air travel during the global expansion of SARS-CoV-2 variants of concern. Cell 2023; 186:3277-3290.e16. [PMID: 37413988 PMCID: PMC10247138 DOI: 10.1016/j.cell.2023.06.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 05/31/2023] [Accepted: 06/02/2023] [Indexed: 07/08/2023]
Abstract
The Alpha, Beta, and Gamma SARS-CoV-2 variants of concern (VOCs) co-circulated globally during 2020 and 2021, fueling waves of infections. They were displaced by Delta during a third wave worldwide in 2021, which, in turn, was displaced by Omicron in late 2021. In this study, we use phylogenetic and phylogeographic methods to reconstruct the dispersal patterns of VOCs worldwide. We find that source-sink dynamics varied substantially by VOC and identify countries that acted as global and regional hubs of dissemination. We demonstrate the declining role of presumed origin countries of VOCs in their global dispersal, estimating that India contributed <15% of Delta exports and South Africa <1%-2% of Omicron dispersal. We estimate that >80 countries had received introductions of Omicron within 100 days of its emergence, associated with accelerated passenger air travel and higher transmissibility. Our study highlights the rapid dispersal of highly transmissible variants, with implications for genomic surveillance along the hierarchical airline network.
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Affiliation(s)
- Houriiyah Tegally
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.
| | - Eduan Wilkinson
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | | | - Monika Moir
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Darren Martin
- Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Cape Town, South Africa; Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | | | - Marta Giovanetti
- Laboratorio de Flavivirus, Fundacao Oswaldo Cruz, Rio de Janeiro, Brazil; Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil; Department of Science and Technology for Humans and the Environment, University of Campus Bio-Medico di Roma, Rome, Italy
| | - Kamran Khan
- BlueDot, Toronto, ON, Canada; Department of Medicine, Division of Infectious Diseases, University of Toronto, Toronto, ON, Canada
| | | | - Isaac I Bogoch
- Department of Medicine, Division of Infectious Diseases, University of Toronto, Toronto, ON, Canada
| | - James Emmanuel San
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Jenicca Poongavanan
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Joicymara S Xavier
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa; Universidade Federal de Minas Gerais, Belo Horizonte, Brazil; Institute of Agricultural Sciences, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Unaí, Brazil
| | - Darlan da S Candido
- MRC Centre for Global Infectious Disease Analysis and Department of Infectious Disease Epidemiology, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Filipe Romero
- MRC Centre for Global Infectious Disease Analysis and Department of Infectious Disease Epidemiology, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Cheryl Baxter
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Oliver G Pybus
- Department of Biology, University of Oxford, Oxford, UK; Pandemic Sciences Institute, University of Oxford, Oxford, UK; Department of Pathobiology and Population Sciences, Royal Veterinary College London, London, UK
| | - Richard J Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Nuno R Faria
- Department of Biology, University of Oxford, Oxford, UK; MRC Centre for Global Infectious Disease Analysis and Department of Infectious Disease Epidemiology, Jameel Institute, School of Public Health, Imperial College London, London, UK; Departamento de Moléstias Infecciosas e Parasitárias e Instituto de Medicina Tropical da Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Moritz U G Kraemer
- Department of Biology, University of Oxford, Oxford, UK; Pandemic Sciences Institute, University of Oxford, Oxford, UK.
| | - Tulio de Oliveira
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa; Department of Global Health, University of Washington, Seattle, WA, USA.
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14
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de Souza WM, de Lima STS, Simões Mello LM, Candido DS, Buss L, Whittaker C, Claro IM, Chandradeva N, Granja F, de Jesus R, Lemos PS, Toledo-Teixeira DA, Barbosa PP, Firmino ACL, Amorim MR, Duarte LMF, Pessoa IB, Forato J, Vasconcelos IL, Maximo ACBM, Araújo ELL, Perdigão Mello L, Sabino EC, Proença-Módena JL, Faria NR, Weaver SC. Spatiotemporal dynamics and recurrence of chikungunya virus in Brazil: an epidemiological study. Lancet Microbe 2023; 4:e319-e329. [PMID: 37031687 PMCID: PMC10281060 DOI: 10.1016/s2666-5247(23)00033-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 12/13/2022] [Accepted: 01/27/2023] [Indexed: 04/09/2023]
Abstract
BACKGROUND Chikungunya virus (CHIKV) is an Aedes mosquito-borne virus that has caused large epidemics linked to acute, chronic, and severe clinical outcomes. Currently, Brazil has the highest number of chikungunya cases in the Americas. We aimed to investigate the spatiotemporal dynamics and recurrence pattern of chikungunya in Brazil since its introduction in 2013. METHODS In this epidemiological study, we used CHIKV genomic sequencing data, CHIKV vector information, and aggregate clinical data on chikungunya cases from Brazil. The genomic data comprised 241 Brazilian CHIKV genome sequences from GenBank (n=180) and the 2022 CHIKV outbreak in Ceará state (n=61). The vector data (Breteau index and House index) were obtained from the Brazilian Ministry of Health for all 184 municipalities in Ceará state and 116 municipalities in Tocantins state in 2022. Epidemiological data on laboratory-confirmed cases of chikungunya between 2013 and 2022 were obtained from the Brazilian Ministry of Health and Laboratory of Public Health of Ceará. We assessed the spatiotemporal dynamics of chikungunya in Brazil via time series, mapping, age-sex distribution, cumulative case-fatality, linear correlation, logistic regression, and phylogenetic analyses. FINDINGS Between March 3, 2013, and June 4, 2022, 253 545 laboratory-confirmed chikungunya cases were reported in 3316 (59·5%) of 5570 municipalities, mainly distributed in seven epidemic waves from 2016 to 2022. To date, Ceará in the northeast has been the most affected state, with 77 418 cases during the two largest epidemic waves in 2016 and 2017 and the third wave in 2022. From 2016 to 2022 in Ceará, the odds of being CHIKV-positive were higher in females than in males (odds ratio 0·87, 95% CI 0·85-0·89, p<0·0001), and the cumulative case-fatality ratio was 1·3 deaths per 1000 cases. Chikungunya recurrences in the states of Ceará, Tocantins (recurrence in 2022), and Pernambuco (recurrence in 2021) were limited to municipalities with few or no previously reported cases in the previous epidemic waves. The recurrence of chikungunya in Ceará in 2022 was associated with a new East-Central-South-African lineage. Population density metrics of the main CHIKV vector in Brazil, Aedes aegypti, were not correlated spatially with locations of chikungunya recurrence in Ceará and Tocantins. INTERPRETATION Spatial heterogeneity of CHIKV spread and population immunity might explain the recurrence pattern of chikungunya in Brazil. These results can be used to inform public health interventions to prevent future chikungunya epidemic waves in urban settings. FUNDING Global Virus Network, Burroughs Wellcome Fund, Wellcome Trust, US National Institutes of Health, São Paulo Research Foundation, Brazil Ministry of Education, UK Medical Research Council, Brazilian National Council for Scientific and Technological Development, and UK Royal Society. TRANSLATION For the Portuguese translation of the abstract see Supplementary Materials section.
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Affiliation(s)
- William M de Souza
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA.
| | - Shirlene T S de Lima
- Laboratório Central de Saúde Pública do Ceará, Fortaleza, Brazil; Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
| | | | - Darlan S Candido
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK; Department of Zoology, University of Oxford, Oxford, UK; Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Lewis Buss
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK
| | - Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK; The Abdul Latif Jameel Institute for Disease and Emergency Analytics, School of Public Health, Imperial College London, London, UK
| | - Ingra M Claro
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK; Department of Zoology, University of Oxford, Oxford, UK; Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Nilani Chandradeva
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK
| | - Fabiana Granja
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil; Biodiversity Research Centre, Federal University of Roraima, Boa Vista, Brazil
| | - Ronaldo de Jesus
- Ministério da Saúde, Departamento de Articulação Estratégica de Vigilância em Saúde, Brasilia, Brazil; Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Poliana S Lemos
- Ministério da Saúde, Departamento de Articulação Estratégica de Vigilância em Saúde, Brasilia, Brazil
| | - Daniel A Toledo-Teixeira
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Priscilla P Barbosa
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
| | | | - Mariene R Amorim
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
| | | | - Ivan B Pessoa
- Laboratório Central de Saúde Pública do Ceará, Fortaleza, Brazil
| | - Julia Forato
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
| | | | | | - Emerson L L Araújo
- Ministério da Saúde, Departamento de Articulação Estratégica de Vigilância em Saúde, Brasilia, Brazil
| | | | - Ester C Sabino
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil; Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - José Luiz Proença-Módena
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil; Hub of Global Health, University of Campinas, Campinas, Brazil
| | - Nuno R Faria
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK; Department of Zoology, University of Oxford, Oxford, UK; Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Scott C Weaver
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
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15
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Sahadeo NSD, Nicholls S, Moreira FRR, O’Toole Á, Ramkissoon V, Whittaker C, Hill V, McCrone JT, Mohammed N, Ramjag A, Brown Jordan A, Hill SC, Singh R, Nathaniel-Girdharrie SM, Hinds A, Ramkissoon N, Parag KV, Nandram N, Parasram R, Khan-Mohammed Z, Edghill L, Indar L, Andrewin A, Sealey-Thomas R, McMillan P, Oyinloye A, George K, Potter I, Lee J, Johnson D, Charles S, Singh N, Bisesor-McKenzie J, Laws H, Belmar-George S, Keizer-Beache S, Greenaway-Duberry S, Ashwood N, Foster JE, Georges K, Naidu R, Ivey M, Giddings S, Haraksingh R, Ramsubhag A, Jayaraman J, Chinnadurai C, Oura C, Pybus OG, St. John J, Gonzalez-Escobar G, Faria NR, Carrington CVF. Implementation of genomic surveillance of SARS-CoV-2 in the Caribbean: Lessons learned for sustainability in resource-limited settings. PLOS Glob Public Health 2023; 3:e0001455. [PMID: 36963002 PMCID: PMC10022082 DOI: 10.1371/journal.pgph.0001455] [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] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 01/26/2023] [Indexed: 02/24/2023]
Abstract
The COVID-19 pandemic highlighted the importance of global genomic surveillance to monitor the emergence and spread of SARS-CoV-2 variants and inform public health decision-making. Until December 2020 there was minimal capacity for viral genomic surveillance in most Caribbean countries. To overcome this constraint, the COVID-19: Infectious disease Molecular epidemiology for PAthogen Control & Tracking (COVID-19 IMPACT) project was implemented to establish rapid SARS-CoV-2 whole genome nanopore sequencing at The University of the West Indies (UWI) in Trinidad and Tobago (T&T) and provide needed SARS-CoV-2 sequencing services for T&T and other Caribbean Public Health Agency Member States (CMS). Using the Oxford Nanopore Technologies MinION sequencing platform and ARTIC network sequencing protocols and bioinformatics pipeline, a total of 3610 SARS-CoV-2 positive RNA samples, received from 17 CMS, were sequenced in-situ during the period December 5th 2020 to December 31st 2021. Ninety-one Pango lineages, including those of five variants of concern (VOC), were identified. Genetic analysis revealed at least 260 introductions to the CMS from other global regions. For each of the 17 CMS, the percentage of reported COVID-19 cases sequenced by the COVID-19 IMPACT laboratory ranged from 0·02% to 3·80% (median = 1·12%). Sequences submitted to GISAID by our study represented 73·3% of all SARS-CoV-2 sequences from the 17 CMS available on the database up to December 31st 2021. Increased staffing, process and infrastructural improvement over the course of the project helped reduce turnaround times for reporting to originating institutions and sequence uploads to GISAID. Insights from our genomic surveillance network in the Caribbean region directly influenced non-pharmaceutical countermeasures in the CMS countries. However, limited availability of associated surveillance and clinical data made it challenging to contextualise the observed SARS-CoV-2 diversity and evolution, highlighting the need for development of infrastructure for collecting and integrating genomic sequencing data and sample-associated metadata.
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Affiliation(s)
- Nikita S. D. Sahadeo
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Republic of Trinidad and Tobago
| | - Soren Nicholls
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Republic of Trinidad and Tobago
| | - Filipe R. R. Moreira
- MRC Centre for Global Infectious Disease Analysis, Department for Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Áine O’Toole
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Vernie Ramkissoon
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Republic of Trinidad and Tobago
| | - Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis, Department for Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Verity Hill
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - John T. McCrone
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Nicholas Mohammed
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Republic of Trinidad and Tobago
| | - Anushka Ramjag
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Republic of Trinidad and Tobago
| | - Arianne Brown Jordan
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Republic of Trinidad and Tobago
| | - Sarah C. Hill
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, London, United Kingdom
| | - Risha Singh
- Caribbean Public Health Agency (CARPHA), Headquartered in Port of Spain, Republic of Trinidad and Tobago
| | | | - Avery Hinds
- Ministry of Health, Port of Spain, Republic of Trinidad and Tobago
| | - Nuala Ramkissoon
- Ministry of Health, Port of Spain, Republic of Trinidad and Tobago
| | - Kris V. Parag
- MRC Centre for Global Infectious Disease Analysis, Department for Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Naresh Nandram
- Ministry of Health, Port of Spain, Republic of Trinidad and Tobago
| | - Roshan Parasram
- Ministry of Health, Port of Spain, Republic of Trinidad and Tobago
| | | | - Lisa Edghill
- Caribbean Public Health Agency (CARPHA), Headquartered in Port of Spain, Republic of Trinidad and Tobago
| | - Lisa Indar
- Caribbean Public Health Agency (CARPHA), Headquartered in Port of Spain, Republic of Trinidad and Tobago
| | | | | | | | | | | | - Irad Potter
- Ministry of Health and Social Development, Road Town, Tortola, British Virgin Islands
| | - John Lee
- Ministry of Health and Wellness, George Town, Grand Cayman, Cayman Islands
| | - David Johnson
- Ministry of Health, Wellness and New Health Investment, Roseau, Dominica
| | | | | | | | - Hazel Laws
- Ministry of Health, Basseterre, Saint Kitts and Nevis
| | | | - Simone Keizer-Beache
- Ministry of Health, Wellness and the Environment, Kingstown, Saint Vincent and the Grenadines
| | | | - Nadia Ashwood
- Ministry of Health, Agriculture, Sports and Human Services, Grand Turk, Turks and Caicos Islands
| | - Jerome E. Foster
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Republic of Trinidad and Tobago
| | - Karla Georges
- School of Veterinary Medicine, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Republic of Trinidad and Tobago
| | - Rahul Naidu
- School of Dentistry, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Republic of Trinidad and Tobago
| | - Marsha Ivey
- Department of Clinical Medical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Republic of Trinidad and Tobago
| | - Stanley Giddings
- Department of Clinical Medical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Republic of Trinidad and Tobago
| | - Rajini Haraksingh
- Department of Life Sciences, Faculty of Sciences of Technology, The University of the West Indies, St. Augustine, Republic of Trinidad and Tobago
| | - Adesh Ramsubhag
- Department of Life Sciences, Faculty of Sciences of Technology, The University of the West Indies, St. Augustine, Republic of Trinidad and Tobago
| | - Jayaraj Jayaraman
- Department of Life Sciences, Faculty of Sciences of Technology, The University of the West Indies, St. Augustine, Republic of Trinidad and Tobago
| | - Chinnaraja Chinnadurai
- Department of Life Sciences, Faculty of Sciences of Technology, The University of the West Indies, St. Augustine, Republic of Trinidad and Tobago
| | - Christopher Oura
- School of Veterinary Medicine, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Republic of Trinidad and Tobago
| | - Oliver G. Pybus
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, London, United Kingdom
| | - Joy St. John
- Caribbean Public Health Agency (CARPHA), Headquartered in Port of Spain, Republic of Trinidad and Tobago
| | - Gabriel Gonzalez-Escobar
- Caribbean Public Health Agency (CARPHA), Headquartered in Port of Spain, Republic of Trinidad and Tobago
| | - Nuno R. Faria
- MRC Centre for Global Infectious Disease Analysis, Department for Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
- Departamento de Moléstias Infecciosas e Parasitárias e Instituto de Medicina Tropical da Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Christine V. F. Carrington
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Republic of Trinidad and Tobago
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16
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Tegally H, Wilkinson E, Martin D, Moir M, Brito A, Giovanetti M, Khan K, Huber C, Bogoch II, San JE, Tsui JLH, Poongavanan J, Xavier JS, Candido DDS, Romero F, Baxter C, Pybus OG, Lessells R, Faria NR, Kraemer MUG, de Oliveira T. Global Expansion of SARS-CoV-2 Variants of Concern: Dispersal Patterns and Influence of Air Travel. medRxiv 2022:2022.11.22.22282629. [PMID: 36451885 PMCID: PMC9709793 DOI: 10.1101/2022.11.22.22282629] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
In many regions of the world, the Alpha, Beta and Gamma SARS-CoV-2 Variants of Concern (VOCs) co-circulated during 2020-21 and fueled waves of infections. During 2021, these variants were almost completely displaced by the Delta variant, causing a third wave of infections worldwide. This phenomenon of global viral lineage displacement was observed again in late 2021, when the Omicron variant disseminated globally. In this study, we use phylogenetic and phylogeographic methods to reconstruct the dispersal patterns of SARS-CoV-2 VOCs worldwide. We find that the source-sink dynamics of SARS-CoV-2 varied substantially by VOC, and identify countries that acted as global hubs of variant dissemination, while other countries became regional contributors to the export of specific variants. We demonstrate a declining role of presumed origin countries of VOCs to their global dispersal: we estimate that India contributed <15% of all global exports of Delta to other countries and South Africa <1-2% of all global Omicron exports globally. We further estimate that >80 countries had received introductions of Omicron BA.1 100 days after its inferred date of emergence, compared to just over 25 countries for the Alpha variant. This increased speed of global dissemination was associated with a rebound in air travel volume prior to Omicron emergence in addition to the higher transmissibility of Omicron relative to Alpha. Our study highlights the importance of global and regional hubs in VOC dispersal, and the speed at which highly transmissible variants disseminate through these hubs, even before their detection and characterization through genomic surveillance. Highlights Global phylogenetic analysis reveals relationship between air travel and speed of dispersal of SARS-CoV-2 variants of concern (VOCs)Omicron VOC spread to 5x more countries within 100 days of its emergence compared to all other VOCsOnward transmission and dissemination of VOCs Delta and Omicron was primarily from secondary hubs rather than initial country of detection during a time of increased global air travelAnalysis highlights highly connected countries identified as major global and regional exporters of VOCs.
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Affiliation(s)
- Houriiyah Tegally
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Eduan Wilkinson
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Darren Martin
- Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Monika Moir
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Anderson Brito
- Instituto Todos pela Saúde, São Paulo, São Paulo, Brazil
| | - Marta Giovanetti
- Laboratorio de Flavivirus, Fundacao Oswaldo Cruz, Rio de Janeiro, Brazil
- Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Department of Science and Technology for Humans and the Environment, University of Campus Bio-Medico di Roma, Rome, Italy
| | - Kamran Khan
- BlueDot, Toronto, Canada
- Department of Medicine, Division of Infectious Diseases, University of Toronto, Toronto, Canada
| | | | - Isaac I Bogoch
- Department of Medicine, Division of Infectious Diseases, University of Toronto, Toronto, Canada
| | - James Emmanuel San
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | | | - Jenicca Poongavanan
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Joicymara S Xavier
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Institute of Agricultural Sciences, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Unaí, Brazil
| | - Darlan da S Candido
- MRC Centre for Global Infectious Disease Analysis and Department of Infectious Disease Epidemiology, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Filipe Romero
- MRC Centre for Global Infectious Disease Analysis and Department of Infectious Disease Epidemiology, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Cheryl Baxter
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Oliver G Pybus
- Department of Biology, University of Oxford, Oxford, UK
- Pandemic Sciences Institute, University of Oxford, Oxford, UK
- Department of Pathobiology and Population Sciences, Royal Veterinary College London, London, UK
| | - Richard Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Nuno R Faria
- MRC Centre for Global Infectious Disease Analysis and Department of Infectious Disease Epidemiology, Jameel Institute, School of Public Health, Imperial College London, London, UK
- Departamento de Moléstias Infecciosas e Parasitárias e Instituto de Medicina Tropical da Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
- Department of Biology, University of Oxford, Oxford, UK
| | - Moritz U G Kraemer
- Department of Biology, University of Oxford, Oxford, UK
- Pandemic Sciences Institute, University of Oxford, Oxford, UK
| | - Tulio de Oliveira
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Department of Global Health, University of Washington, Seattle, WA, USA
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17
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Brito AF, Semenova E, Dudas G, Hassler GW, Kalinich CC, Kraemer MUG, Ho J, Tegally H, Githinji G, Agoti CN, Matkin LE, Whittaker C, Howden BP, Sintchenko V, Zuckerman NS, Mor O, Blankenship HM, de Oliveira T, Lin RTP, Siqueira MM, Resende PC, Vasconcelos ATR, Spilki FR, Aguiar RS, Alexiev I, Ivanov IN, Philipova I, Carrington CVF, Sahadeo NSD, Branda B, Gurry C, Maurer-Stroh S, Naidoo D, von Eije KJ, Perkins MD, van Kerkhove M, Hill SC, Sabino EC, Pybus OG, Dye C, Bhatt S, Flaxman S, Suchard MA, Grubaugh ND, Baele G, Faria NR. Global disparities in SARS-CoV-2 genomic surveillance. Nat Commun 2022; 13:7003. [PMID: 36385137 PMCID: PMC9667854 DOI: 10.1038/s41467-022-33713-y] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 09/29/2022] [Indexed: 11/17/2022] Open
Abstract
Genomic sequencing is essential to track the evolution and spread of SARS-CoV-2, optimize molecular tests, treatments, vaccines, and guide public health responses. To investigate the global SARS-CoV-2 genomic surveillance, we used sequences shared via GISAID to estimate the impact of sequencing intensity and turnaround times on variant detection in 189 countries. In the first two years of the pandemic, 78% of high-income countries sequenced >0.5% of their COVID-19 cases, while 42% of low- and middle-income countries reached that mark. Around 25% of the genomes from high income countries were submitted within 21 days, a pattern observed in 5% of the genomes from low- and middle-income countries. We found that sequencing around 0.5% of the cases, with a turnaround time <21 days, could provide a benchmark for SARS-CoV-2 genomic surveillance. Socioeconomic inequalities undermine the global pandemic preparedness, and efforts must be made to support low- and middle-income countries improve their local sequencing capacity.
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Affiliation(s)
- Anderson F Brito
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.
- Instituto Todos pela Saúde, São Paulo, SP, Brazil.
| | | | - Gytis Dudas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Gabriel W Hassler
- Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Chaney C Kalinich
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- Yale School of Medicine, Yale University, New Haven, CT, USA
| | | | - Joses Ho
- GISAID Global Data Science Initiative, Munich, Germany
- Bioinformatics Institute & ID Labs, Agency for Science Technology and Research, Singapore, Singapore
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - George Githinji
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya
| | - Charles N Agoti
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- School of Health and Human Sciences, Pwani University, Kilifi, Kenya
| | - Lucy E Matkin
- Department of Biology, University of Oxford, Oxford, UK
| | - Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK
| | | | | | | | | | | | | | | | | | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Vitali Sintchenko
- Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW, Australia
- Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
| | - Neta S Zuckerman
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
| | - Orna Mor
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
| | - Heather M Blankenship
- Michigan Department of Health and Human Services, Bureau of Laboratories, Lansing, MI, USA
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Raymond T P Lin
- National Centre for Infectious Diseases, Singapore, Singapore
| | - Marilda Mendonça Siqueira
- Laboratory of Respiratory Viruses and Measles, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Paola Cristina Resende
- Laboratory of Respiratory Viruses and Measles, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Ana Tereza R Vasconcelos
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | - Fernando R Spilki
- Feevale University, Institute of Health Sciences, Novo Hamburgo, RS, Brazil
| | - Renato Santana Aguiar
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Instituto D'Or de Pesquisa e Ensino (IDOR), Rio de Janeiro, Brazil
| | - Ivailo Alexiev
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Ivan N Ivanov
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Ivva Philipova
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Christine V F Carrington
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Nikita S D Sahadeo
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Ben Branda
- GISAID Global Data Science Initiative, Munich, Germany
| | - Céline Gurry
- GISAID Global Data Science Initiative, Munich, Germany
| | - Sebastian Maurer-Stroh
- GISAID Global Data Science Initiative, Munich, Germany
- Bioinformatics Institute & ID Labs, Agency for Science Technology and Research, Singapore, Singapore
- National Centre for Infectious Diseases, Singapore, Singapore
| | - Dhamari Naidoo
- Health Emergencies Programme, World Health Organization Regional Office for South-East Asia, New Delhi, India
| | - Karin J von Eije
- Department of Medical Microbiology and Infection Prevention, Division of Clinical Virology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Emerging Diseases and Zoonoses Unit, Health Emergencies Programme, World Health Organization, Geneva, Switzerland
| | - Mark D Perkins
- Emerging Diseases and Zoonoses Unit, Health Emergencies Programme, World Health Organization, Geneva, Switzerland
| | - Maria van Kerkhove
- Emerging Diseases and Zoonoses Unit, Health Emergencies Programme, World Health Organization, Geneva, Switzerland
| | | | - Ester C Sabino
- Instituto Todos pela Saúde, São Paulo, SP, Brazil
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Oliver G Pybus
- Department of Biology, University of Oxford, Oxford, UK
- Royal Veterinary College, Hawkshead, UK
| | | | - Samir Bhatt
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Seth Flaxman
- Department of Computer Science, University of Oxford, Oxford, UK
| | - Marc A Suchard
- Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Nuno R Faria
- Department of Biology, University of Oxford, Oxford, UK.
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK.
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK.
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.
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18
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Andrade PS, Valença IN, Heinisch MRS, Rocha EC, Fernandes LN, Faria NR, Sabino EC, Lima-Camara TN. First Report of Wenzhou sobemo-like virus 4 in Aedes albopictus (Diptera: Culicidae) in Latin America. Viruses 2022; 14:v14112341. [PMID: 36366436 PMCID: PMC9696862 DOI: 10.3390/v14112341] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/21/2022] [Accepted: 10/22/2022] [Indexed: 02/01/2023] Open
Abstract
Insect-specific viruses (ISVs) are viruses that replicate exclusively in arthropod cells. Many ISVs have been studied in mosquitoes as many of them act as vectors for human etiological agents, such as arboviruses. Aedes (Stegomyia) albopictus is an important potential vector of several arboviruses in Brazil, such as dengue (DENV), Zika (ZIKV) and chikungunya (CHIKV). The development of next-generation sequencing metagenomics has enabled the discovery and characterization of new ISVs. Ae. albopictus eggs were collected using oviposition traps placed in two urban parks in the city of São Paulo, Brazil. The Aedes albopictus females were divided into pools and the genetic material was extracted and processed for sequencing by metagenomics. Complete genomes of ISV Wenzhou sobemo-like virus 4 (WSLV4) were obtained in three of the four pools tested. This is the first detection of ISV WSLV4 in Ae. albopictus females in Latin America. Further studies on ISVs in Ae. albopictus are needed to better understand the role of this species in the dynamics of arbovirus transmission in the Americas.
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Affiliation(s)
- Pâmela S. Andrade
- Department of Epidemiology, Faculdade de Saúde Pública, Universidade de São Paulo, São Paulo 01246-904, Brazil
- Institute of Tropical Medicine, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
- Correspondence:
| | - Ian N. Valença
- Institute of Tropical Medicine, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
- Department of Infectious and Parasitic Diseases, Faculdade de Medicina, Universidade de São Paulo, São Paulo 01246-903, Brazil
| | - Marta R. S. Heinisch
- Department of Epidemiology, Faculdade de Saúde Pública, Universidade de São Paulo, São Paulo 01246-904, Brazil
| | - Esmenia C. Rocha
- Institute of Tropical Medicine, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Lícia N. Fernandes
- Medical Research Laboratory 49, Institute of Tropical Medicine, Faculdade de Medicina, Universidade de São Paulo, São Paulo 01246-903, Brazil
| | - Nuno R. Faria
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London W2 1PG, UK
| | - Ester C. Sabino
- Institute of Tropical Medicine, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
- Department of Infectious and Parasitic Diseases, Faculdade de Medicina, Universidade de São Paulo, São Paulo 01246-903, Brazil
| | - Tamara N. Lima-Camara
- Department of Epidemiology, Faculdade de Saúde Pública, Universidade de São Paulo, São Paulo 01246-904, Brazil
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19
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McCrone JT, Hill V, Bajaj S, Pena RE, Lambert BC, Inward R, Bhatt S, Volz E, Ruis C, Dellicour S, Baele G, Zarebski AE, Sadilek A, Wu N, Schneider A, Ji X, Raghwani J, Jackson B, Colquhoun R, O'Toole Á, Peacock TP, Twohig K, Thelwall S, Dabrera G, Myers R, Faria NR, Huber C, Bogoch II, Khan K, du Plessis L, Barrett JC, Aanensen DM, Barclay WS, Chand M, Connor T, Loman NJ, Suchard MA, Pybus OG, Rambaut A, Kraemer MUG. Context-specific emergence and growth of the SARS-CoV-2 Delta variant. Nature 2022; 610:154-160. [PMID: 35952712 PMCID: PMC9534748 DOI: 10.1038/s41586-022-05200-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [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: 12/10/2021] [Accepted: 08/05/2022] [Indexed: 02/01/2023]
Abstract
The SARS-CoV-2 Delta (Pango lineage B.1.617.2) variant of concern spread globally, causing resurgences of COVID-19 worldwide1,2. The emergence of the Delta variant in the UK occurred on the background of a heterogeneous landscape of immunity and relaxation of non-pharmaceutical interventions. Here we analyse 52,992 SARS-CoV-2 genomes from England together with 93,649 genomes from the rest of the world to reconstruct the emergence of Delta and quantify its introduction to and regional dissemination across England in the context of changing travel and social restrictions. Using analysis of human movement, contact tracing and virus genomic data, we find that the geographic focus of the expansion of Delta shifted from India to a more global pattern in early May 2021. In England, Delta lineages were introduced more than 1,000 times and spread nationally as non-pharmaceutical interventions were relaxed. We find that hotel quarantine for travellers reduced onward transmission from importations; however, the transmission chains that later dominated the Delta wave in England were seeded before travel restrictions were introduced. Increasing inter-regional travel within England drove the nationwide dissemination of Delta, with some cities receiving more than 2,000 observable lineage introductions from elsewhere. Subsequently, increased levels of local population mixing-and not the number of importations-were associated with the faster relative spread of Delta. The invasion dynamics of Delta depended on spatial heterogeneity in contact patterns, and our findings will inform optimal spatial interventions to reduce the transmission of current and future variants of concern, such as Omicron (Pango lineage B.1.1.529).
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Affiliation(s)
- John T McCrone
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Verity Hill
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Sumali Bajaj
- Department of Zoology, University of Oxford, Oxford, UK
| | | | - Ben C Lambert
- College of Engineering, Mathematics and Physical Sciences, University of Exeter, Exeter, UK
| | - Rhys Inward
- Department of Zoology, University of Oxford, Oxford, UK
- MRC Centre of Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Samir Bhatt
- MRC Centre of Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Erik Volz
- MRC Centre of Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Christopher Ruis
- Molecular Immunity Unit, Department of Medicine, Cambridge University, Cambridge, UK
| | - Simon Dellicour
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Bruxelles, Belgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | | | | | - Neo Wu
- Google, Mountain View, CA, USA
| | | | - Xiang Ji
- Department of Mathematics, School of Science and Engineering, Tulane University, New Orleans, LA, USA
| | | | - Ben Jackson
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Rachel Colquhoun
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Áine O'Toole
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Thomas P Peacock
- Department of Infectious Disease, Imperial College London, London, UK
- UK Health Security Agency, London, UK
| | | | | | | | | | - Nuno R Faria
- Department of Zoology, University of Oxford, Oxford, UK
- MRC Centre of Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil
| | | | - Isaac I Bogoch
- Divisions of Internal Medicine and Infectious Diseases, Toronto General Hospital, University Health Network, Toronto, Ontario, Canada
- Department of Medicine, Division of Infectious Diseases, University of Toronto, Toronto, Ontario, Canada
| | - Kamran Khan
- BlueDot, Toronto, Ontario, Canada
- Department of Medicine, Division of Infectious Diseases, University of Toronto, Toronto, Ontario, Canada
- Li Ka Shing Knowledge Institute, St Michael's Hospital, Toronto, Ontario, Canada
| | - Louis du Plessis
- Department of Zoology, University of Oxford, Oxford, UK
- Department of Biosystems Science and Engineering, ETH Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | - David M Aanensen
- Centre for Genomic Pathogen Surveillance, Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Wendy S Barclay
- Department of Infectious Disease, Imperial College London, London, UK
| | | | - Thomas Connor
- Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff, UK
- School of Biosciences, The Sir Martin Evans Building, Cardiff University, Cardiff, UK
- Quadram Institute, Norwich, UK
| | - Nicholas J Loman
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Marc A Suchard
- Departments of Biostatistics, Biomathematics and Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, UK.
- Department of Pathobiology and Population Sciences, Royal Veterinary College London, London, UK.
- Pandemic Sciences Institute, University of Oxford, Oxford, UK.
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
| | - Moritz U G Kraemer
- Department of Zoology, University of Oxford, Oxford, UK.
- Pandemic Sciences Institute, University of Oxford, Oxford, UK.
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20
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Inward RPD, Parag KV, Faria NR. Using multiple sampling strategies to estimate SARS-CoV-2 epidemiological parameters from genomic sequencing data. Nat Commun 2022; 13:5587. [PMID: 36151084 PMCID: PMC9508174 DOI: 10.1038/s41467-022-32812-0] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 08/16/2022] [Indexed: 11/09/2022] Open
Abstract
The choice of viral sequences used in genetic and epidemiological analysis is important as it can induce biases that detract from the value of these rich datasets. This raises questions about how a set of sequences should be chosen for analysis. We provide insights on these largely understudied problems using SARS-CoV-2 genomic sequences from Hong Kong, China, and the Amazonas State, Brazil. We consider multiple sampling schemes which were used to estimate Rt and rt as well as related R0 and date of origin parameters. We find that both Rt and rt are sensitive to changes in sampling whilst R0 and the date of origin are relatively robust. Moreover, we find that analysis using unsampled datasets result in the most biased Rt and rt estimates for both our Hong Kong and Amazonas case studies. We highlight that sampling strategy choices may be an influential yet neglected component of sequencing analysis pipelines.
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Affiliation(s)
| | - Kris V Parag
- MRC Centre of Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK.
- NIHR Health Protection Research Unit in Behavioural Science and Evaluation, University of Bristol, Bristol, UK.
| | - Nuno R Faria
- Department of Zoology, University of Oxford, Oxford, UK.
- MRC Centre of Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK.
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil.
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21
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Prete CA, Buss LF, Whittaker C, Salomon T, Oikawa MK, Pereira RHM, Moura ICG, Delerino L, Barral-Netto M, Tavares NM, Franca RFO, Boaventura VS, Miyajima F, Mendrone-Junior A, de Almeida-Neto C, Salles NA, Ferreira SC, Fladzinski KA, de Souza LM, Schier LK, Inoue PM, Xabregas LA, Crispim MAE, Fraiji N, Araujo FLV, Carlos LMB, Pessoa V, Ribeiro MA, de Souza RE, da Silva SMN, Cavalcante AF, Valença MIB, da Silva MV, Lopes E, Filho LA, Mateos SOG, Nunes GT, Silva-Junior AL, Busch MP, Castro MC, Dye C, Ratmann O, Faria NR, Nascimento VH, Sabino EC. SARS-CoV-2 antibody dynamics in blood donors and COVID-19 epidemiology in eight Brazilian state capitals: A serial cross-sectional study. eLife 2022; 11:e78233. [PMID: 36135358 PMCID: PMC9545556 DOI: 10.7554/elife.78233] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 09/17/2022] [Indexed: 11/13/2022] Open
Abstract
Background The COVID-19 situation in Brazil is complex due to large differences in the shape and size of regional epidemics. Understanding these patterns is crucial to understand future outbreaks of SARS-CoV-2 or other respiratory pathogens in the country. Methods We tested 97,950 blood donation samples for IgG antibodies from March 2020 to March 2021 in 8 of Brazil's most populous cities. Residential postal codes were used to obtain representative samples. Weekly age- and sex-specific seroprevalence were estimated by correcting the crude seroprevalence by test sensitivity, specificity, and antibody waning. Results The inferred attack rate of SARS-CoV-2 in December 2020, before the Gamma variant of concern (VOC) was dominant, ranged from 19.3% (95% credible interval [CrI] 17.5-21.2%) in Curitiba to 75.0% (95% CrI 70.8-80.3%) in Manaus. Seroprevalence was consistently smaller in women and donors older than 55 years. The age-specific infection fatality rate (IFR) differed between cities and consistently increased with age. The infection hospitalisation rate increased significantly during the Gamma-dominated second wave in Manaus, suggesting increased morbidity of the Gamma VOC compared to previous variants circulating in Manaus. The higher disease penetrance associated with the health system's collapse increased the overall IFR by a minimum factor of 2.91 (95% CrI 2.43-3.53). Conclusions These results highlight the utility of blood donor serosurveillance to track epidemic maturity and demonstrate demographic and spatial heterogeneity in SARS-CoV-2 spread. Funding This work was supported by Itaú Unibanco 'Todos pela Saude' program; FAPESP (grants 18/14389-0, 2019/21585-0); Wellcome Trust and Royal Society Sir Henry Dale Fellowship 204311/Z/16/Z; the Gates Foundation (INV- 034540 and INV-034652); REDS-IV-P (grant HHSN268201100007I); the UK Medical Research Council (MR/S0195/1, MR/V038109/1); CAPES; CNPq (304714/2018-6); Fundação Faculdade de Medicina; Programa Inova Fiocruz-CE/Funcap - Edital 01/2020 Number: FIO-0167-00065.01.00/20 SPU N°06531047/2020; JBS - Fazer o bem faz bem.
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Affiliation(s)
- Carlos A Prete
- Department of Electronic Systems Engineering, University of São PauloSão PauloBrazil
| | | | - Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis, Imperial College LondonLondonUnited Kingdom
- Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College LondonLondonUnited Kingdom
| | - Tassila Salomon
- Faculdade Ciências Médicas de Minas GeraisBelo HorizonteBrazil
| | | | | | - Isabel CG Moura
- Faculdade Ciências Médicas de Minas GeraisBelo HorizonteBrazil
| | | | | | | | | | | | - Fabio Miyajima
- Fundação Oswaldo CruzManguinhosBrazil
- Universidade Federal do CearáFortalezaBrazil
| | | | | | - Nanci A Salles
- Fundação Pró Sangue Hemocentro de São Paulo (FPS)São PauloBrazil
| | | | | | - Luana M de Souza
- Centro de Hematologia e Hemoterapia do Paraná (HEMEPAR)CuritibaBrazil
| | - Luciane K Schier
- Centro de Hematologia e Hemoterapia do Paraná (HEMEPAR)CuritibaBrazil
| | - Patricia M Inoue
- Centro de Hematologia e Hemoterapia do Paraná (HEMEPAR)CuritibaBrazil
| | - Lilyane A Xabregas
- Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas (HEMOAM)ManausBrazil
| | - Myuki AE Crispim
- Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas (HEMOAM)ManausBrazil
| | - Nelson Fraiji
- Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas (HEMOAM)ManausBrazil
| | | | - Luciana MB Carlos
- Centro de Hematologia e Hemoterapia do Ceará (HEMOCE)FortalezaBrazil
| | - Veridiana Pessoa
- Centro de Hematologia e Hemoterapia do Ceará (HEMOCE)FortalezaBrazil
| | | | | | | | - Anna F Cavalcante
- Fundação de Hematologia e Hemoterapia de Pernambuco (HEMOPE)RecifeBrazil
| | - Maria IB Valença
- Fundação de Hematologia e Hemoterapia de Pernambuco (HEMOPE)RecifeBrazil
| | - Maria V da Silva
- Fundação de Hematologia e Hemoterapia de Pernambuco (HEMOPE)RecifeBrazil
| | - Esther Lopes
- Instituto Estadual de Hematologia Arthur de Siqueira Cavalcanti (HEMORIO)Rio de JaneiroBrazil
| | - Luiz A Filho
- Instituto Estadual de Hematologia Arthur de Siqueira Cavalcanti (HEMORIO)Rio de JaneiroBrazil
| | - Sheila OG Mateos
- Instituto Estadual de Hematologia Arthur de Siqueira Cavalcanti (HEMORIO)Rio de JaneiroBrazil
| | - Gabrielle T Nunes
- Fundação Oswaldo CruzManguinhosBrazil
- Instituto Estadual de Hematologia Arthur de Siqueira Cavalcanti (HEMORIO)Rio de JaneiroBrazil
| | - Alexander L Silva-Junior
- Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas (HEMOAM)ManausBrazil
- Universidade Federal do AmazonasManausBrazil
- Centro Universitário do NorteManausBrazil
| | - Michael P Busch
- Vitalant Research InstituteSan FranscicoUnited States
- University of California, San FranciscoSan FranciscoUnited States
| | | | - Christopher Dye
- Department of Zoology, University of OxfordOxfordUnited Kingdom
| | | | - Nuno R Faria
- MRC Centre for Global Infectious Disease Analysis, Imperial College LondonLondonUnited Kingdom
- Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College LondonLondonUnited Kingdom
- Department of Zoology, University of OxfordOxfordUnited Kingdom
- Instituto de Medicina Tropical, University of São PauloSão PauloBrazil
| | - Vítor H Nascimento
- Department of Electronic Systems Engineering, University of São PauloSão PauloBrazil
| | - Ester C Sabino
- Instituto de Medicina Tropical, University of São PauloSão PauloBrazil
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22
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Buss L, Prete CA, Whittaker C, Salomon T, Oikawa MK, Pereira RHM, Moura ICG, Delerino L, Franca RFO, Miyajima F, Mendrone Jr. A, Almeida-Neto C, Salles NA, Ferreira SC, Fladzinski KA, de Souza LM, Schier LK, Inoue PM, Xabregas LA, Crispim MAE, Fraiji N, Carlos LMB, Pessoa V, Ribeiro MA, de Souza RE, Cavalcante AF, Valença MIB, da Silva MV, Lopes E, Filho LA, Mateos SOG, Nunes GT, Schlesinger D, da Silva SMN, Silva-Junior AL, Castro MC, Nascimento VH, Dye C, Busch MP, Faria NR, Sabino EC. Predicting SARS-CoV-2 Variant Spread in a Completely Seropositive Population Using Semi-Quantitative Antibody Measurements in Blood Donors. Vaccines (Basel) 2022; 10:vaccines10091437. [PMID: 36146515 PMCID: PMC9501043 DOI: 10.3390/vaccines10091437] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/21/2022] [Accepted: 08/24/2022] [Indexed: 11/16/2022] Open
Abstract
SARS-CoV-2 serologic surveys estimate the proportion of the population with antibodies against historical variants, which nears 100% in many settings. New approaches are required to fully exploit serosurvey data. Using a SARS-CoV-2 anti-Spike (S) protein chemiluminescent microparticle assay, we attained a semi-quantitative measurement of population IgG titers in serial cross-sectional monthly samples of blood donations across seven Brazilian state capitals (March 2021−November 2021). Using an ecological analysis, we assessed the contributions of prior attack rate and vaccination to antibody titer. We compared anti-S titer across the seven cities during the growth phase of the Delta variant and used this to predict the resulting age-standardized incidence of severe COVID-19 cases. We tested ~780 samples per month, per location. Seroprevalence rose to >95% across all seven capitals by November 2021. Driven by vaccination, mean antibody titer increased 16-fold over the study, with the greatest increases occurring in cities with the highest prior attack rates. Mean anti-S IgG was strongly correlated (adjusted R2 = 0.89) with the number of severe cases caused by Delta. Semi-quantitative anti-S antibody titers are informative about prior exposure and vaccination coverage and may also indicate the potential impact of future SARS-CoV-2 variants.
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Affiliation(s)
- Lewis Buss
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London SW7 2BX, UK
- Correspondence: (L.B.); (E.C.S.)
| | - Carlos A. Prete
- Department of Electronic Systems Engineering, University of São Paulo, São Paulo 05508-010, Brazil
| | - Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London SW7 2BX, UK
| | - Tassila Salomon
- Faculdade Ciências Médicas de Minas Gerais, Belo Horizonte 30130-110, Brazil
| | - Marcio K. Oikawa
- Center of Mathematics, Computing and Cognition, Universidade Federal do ABC, Santo André 09210-170, Brazil
| | | | - Isabel C. G. Moura
- Faculdade Ciências Médicas de Minas Gerais, Belo Horizonte 30130-110, Brazil
| | | | | | - Fabio Miyajima
- Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, Brazil
- Universidade Federal do Ceará, Fortaleza 60455-760, Brazil
| | | | - Cesar Almeida-Neto
- Fundação Pró Sangue Hemocentro de São Paulo (FPS), Sao Paulo 05403-000, Brazil
| | - Nanci A. Salles
- Fundação Pró Sangue Hemocentro de São Paulo (FPS), Sao Paulo 05403-000, Brazil
| | - Suzete C. Ferreira
- Fundação Pró Sangue Hemocentro de São Paulo (FPS), Sao Paulo 05403-000, Brazil
| | - Karine A. Fladzinski
- Centro de Hematologia e Hemoterapia do Paraná (HEMEPAR), Curitiba 80045-145, Brazil
| | - Luana M. de Souza
- Centro de Hematologia e Hemoterapia do Paraná (HEMEPAR), Curitiba 80045-145, Brazil
| | - Luciane K. Schier
- Centro de Hematologia e Hemoterapia do Paraná (HEMEPAR), Curitiba 80045-145, Brazil
| | - Patricia M. Inoue
- Centro de Hematologia e Hemoterapia do Paraná (HEMEPAR), Curitiba 80045-145, Brazil
| | - Lilyane A. Xabregas
- Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas (HEMOAM), Manaus 69050-001, Brazil
| | - Myuki A. E. Crispim
- Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas (HEMOAM), Manaus 69050-001, Brazil
| | - Nelson Fraiji
- Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas (HEMOAM), Manaus 69050-001, Brazil
| | - Luciana M. B. Carlos
- Centro de Hematologia e Hemoterapia do Ceará (HEMOCE), Fortaleza 60140-200, Brazil
| | - Veridiana Pessoa
- Centro de Hematologia e Hemoterapia do Ceará (HEMOCE), Fortaleza 60140-200, Brazil
| | | | | | - Anna F. Cavalcante
- Fundação de Hematologia e Hemoterapia de Pernambuco (HEMOPE), Recife 52011-000, Brazil
| | - Maria I. B. Valença
- Fundação de Hematologia e Hemoterapia de Pernambuco (HEMOPE), Recife 52011-000, Brazil
| | - Maria V. da Silva
- Fundação de Hematologia e Hemoterapia de Pernambuco (HEMOPE), Recife 52011-000, Brazil
| | - Esther Lopes
- Instituto Estadual de Hematologia Arthur de Siqueira Cavalcanti (HEMORIO), Rio de Janeiro 20211-030, Brazil
| | - Luiz A. Filho
- Instituto Estadual de Hematologia Arthur de Siqueira Cavalcanti (HEMORIO), Rio de Janeiro 20211-030, Brazil
| | - Sheila O. G. Mateos
- Instituto Estadual de Hematologia Arthur de Siqueira Cavalcanti (HEMORIO), Rio de Janeiro 20211-030, Brazil
| | - Gabrielle T. Nunes
- Instituto Estadual de Hematologia Arthur de Siqueira Cavalcanti (HEMORIO), Rio de Janeiro 20211-030, Brazil
| | | | | | - Alexander L. Silva-Junior
- Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas (HEMOAM), Manaus 69050-001, Brazil
- Universidade Federal do Amazonas, Manaus 69067-005, Brazil
| | - Marcia C. Castro
- Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Vítor H. Nascimento
- Department of Electronic Systems Engineering, University of São Paulo, São Paulo 05508-010, Brazil
| | - Christopher Dye
- Department of Zoology, University of Oxford, Oxford OX1 3SZ, UK
| | - Michael P. Busch
- Vitalant Research Institute, Denver, CO 80230, USA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94158, USA
| | - Nuno R. Faria
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London SW7 2BX, UK
- Department of Zoology, University of Oxford, Oxford OX1 3SZ, UK
- Departamento de Moléstias Infecciosas e Parasitárias e Instituto de Medicina Tropical da Faculdade de Medicina, Universidade de São Paulo, São Paulo 05508-010, Brazil
- Department of Infectious Disease Epidemiology, Imperial College London, London SW7 2BX, UK
| | - Ester C. Sabino
- Departamento de Moléstias Infecciosas e Parasitárias e Instituto de Medicina Tropical da Faculdade de Medicina, Universidade de São Paulo, São Paulo 05508-010, Brazil
- Correspondence: (L.B.); (E.C.S.)
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23
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Whittaker C, Watson OJ, Alvarez-Moreno C, Angkasekwinai N, Boonyasiri A, Carlos Triana L, Chanda D, Charoenpong L, Chayakulkeeree M, Cooke GS, Croda J, Cucunubá ZM, Djaafara BA, Estofolete CF, Grillet ME, Faria NR, Figueiredo Costa S, Forero-Peña DA, Gibb DM, Gordon AC, Hamers RL, Hamlet A, Irawany V, Jitmuang A, Keurueangkul N, Kimani TN, Lampo M, Levin AS, Lopardo G, Mustafa R, Nayagam S, Ngamprasertchai T, Njeri NIH, Nogueira ML, Ortiz-Prado E, Perroud MW, Phillips AN, Promsin P, Qavi A, Rodger AJ, Sabino EC, Sangkaew S, Sari D, Sirijatuphat R, Sposito AC, Srisangthong P, Thompson HA, Udwadia Z, Valderrama-Beltrán S, Winskill P, Ghani AC, Walker PGT, Hallett TB. Understanding the Potential Impact of Different Drug Properties on Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Transmission and Disease Burden: A Modelling Analysis. Clin Infect Dis 2022; 75:e224-e233. [PMID: 34549260 PMCID: PMC9402649 DOI: 10.1093/cid/ciab837] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The public health impact of the coronavirus disease 2019 (COVID-19) pandemic has motivated a rapid search for potential therapeutics, with some key successes. However, the potential impact of different treatments, and consequently research and procurement priorities, have not been clear. METHODS Using a mathematical model of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission, COVID-19 disease and clinical care, we explore the public-health impact of different potential therapeutics, under a range of scenarios varying healthcare capacity, epidemic trajectories; and drug efficacy in the absence of supportive care. RESULTS The impact of drugs like dexamethasone (delivered to the most critically-ill in hospital and whose therapeutic benefit is expected to depend on the availability of supportive care such as oxygen and mechanical ventilation) is likely to be limited in settings where healthcare capacity is lowest or where uncontrolled epidemics result in hospitals being overwhelmed. As such, it may avert 22% of deaths in high-income countries but only 8% in low-income countries (assuming R = 1.35). Therapeutics for different patient populations (those not in hospital, early in the course of infection) and types of benefit (reducing disease severity or infectiousness, preventing hospitalization) could have much greater benefits, particularly in resource-poor settings facing large epidemics. CONCLUSIONS Advances in the treatment of COVID-19 to date have been focused on hospitalized-patients and predicated on an assumption of adequate access to supportive care. Therapeutics delivered earlier in the course of infection that reduce the need for healthcare or reduce infectiousness could have significant impact, and research into their efficacy and means of delivery should be a priority.
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Affiliation(s)
- Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Oliver J Watson
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Carlos Alvarez-Moreno
- Clínica Universitaria Colombia, Clínica Colsanitas, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Nasikarn Angkasekwinai
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | | | - Luis Carlos Triana
- Hospital Universitario San Ignacio -Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Duncan Chanda
- Adult Infectious Diseases Centre, University Teaching Hospital, Lusaka, Zambia
- Department of Internal Medicine, University of Zambia School of Medicine, Lusaka, Zambia
| | - Lantharita Charoenpong
- Bamrasnaradura Infectious Diseases Institute, Department of Diseases Control, Ministry of Public Health, Nonthaburi, Thailand
| | - Methee Chayakulkeeree
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Graham S Cooke
- Department of Infectious Diseases, Imperial College London, London, UK
- NIHR Biomedical Research Centre, Imperial College NHS Trust, London, UK
| | - Julio Croda
- Oswaldo Cruz Foudantion, Mato Grosso do Sul, Campo Grande, Brazil
- School of Medicine, Federal University of Mato Grosso do Sul, Campo Grande, Brazil
- Yale School of Public Health, New Haven, Connecticut, USA
| | - Zulma M Cucunubá
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
- Departamento de Epidemiología Clínica y Bioestadística. Facultad de Medicina, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Bimandra A Djaafara
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
- Eijkman-Oxford Clinical Research Unit, Jakarta, Indonesia
| | - Cassia F Estofolete
- Faculdade de Medicina de São José do Rio Preto (FAMERP), São José do Rio Preto, Brazil
| | - Maria Eugenia Grillet
- Instituto de Zoologia y Ecologia Tropical, Facultad de Ciencias, Universidad Central de Venezuela, Caracas, Venezuela
| | - Nuno R Faria
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
- Departamento de Molestias Infecciosas e Parasitarias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Department of Zoology, University of Oxford, Oxford, UK
| | - Silvia Figueiredo Costa
- Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - David A Forero-Peña
- Biomedical Research and Therapeutic Vaccines Institute, Ciudad Bolívar, Venezuela
| | - Diana M Gibb
- MRC Clinical Trials Unit at University College London, London, UK
| | - Anthony C Gordon
- Division of Anaesthetics, Pain Medicine and Intensive Care, Imperial College London, London, UK
| | - Raph L Hamers
- Eijkman-Oxford Clinical Research Unit, Jakarta, Indonesia
- Centre for Tropical Medicine and Global Health, Nuffield Dept of Medicine, University of Oxford, Oxford, UK
| | - Arran Hamlet
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Vera Irawany
- Fatmawati General Hospital, Faculty of Medicine University of Indonesia, Jakarta, Indonesia
| | - Anupop Jitmuang
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | | | | | - Margarita Lampo
- Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela
| | - Anna S Levin
- Department of Infectious Diseases, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | | | - Rima Mustafa
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
| | - Shevanthi Nayagam
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Thundon Ngamprasertchai
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | | | - Mauricio L Nogueira
- Faculdade de Medicina de São José do Rio Preto (FAMERP), São José do Rio Preto, Brazil
| | - Esteban Ortiz-Prado
- OneHealth Global Research Group, Universidad de las Américas, Quito, Ecuador
| | | | | | - Panuwat Promsin
- Critical Care Division, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Ambar Qavi
- School of Public Health, Imperial College London, London, UK
| | - Alison J Rodger
- Institute for Global Health, University College London, London, UK
| | - Ester C Sabino
- Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Sorawat Sangkaew
- Section of Adult Infectious Disease, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Djayanti Sari
- Department of Anesthesiology and Intensive Theraphy, Faculty of Medicine, Public Health and Nursing Universitas Gadjah Mada. Public Hospital Dr. Sardjito, Yogyakarta, Indonesia
| | - Rujipas Sirijatuphat
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Andrei C Sposito
- Atherosclerosis and Vascular Biology Laboratory, State University of Campinas, Campinas, Brazil
| | | | - Hayley A Thompson
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | | | - Sandra Valderrama-Beltrán
- Division of Infectious Diseases. School of Medicine. Pontificia Universidad Javeriana, Hospital Universitario San Ignacio, Bogotá, Colombia
| | - Peter Winskill
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Azra C Ghani
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Patrick G T Walker
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Timothy B Hallett
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
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24
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Gutierrez B, Castelán Sánchez HG, Candido DDS, Jackson B, Fleishon S, Houzet R, Ruis C, Delaye L, Faria NR, Rambaut A, Pybus OG, Escalera-Zamudio M. Emergence and widespread circulation of a recombinant SARS-CoV-2 lineage in North America. Cell Host Microbe 2022; 30:1112-1123.e3. [PMID: 35853454 PMCID: PMC9212848 DOI: 10.1016/j.chom.2022.06.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 03/18/2022] [Accepted: 06/16/2022] [Indexed: 02/09/2023]
Abstract
Although recombination is a feature of coronavirus evolution, previously detected recombinant lineages of SARS-CoV-2 have shown limited circulation thus far. Here, we present a detailed phylogenetic analysis of four SARS-CoV-2 lineages to investigate the possibility of virus recombination among them. Our analyses reveal well-supported phylogenetic differences between the Orf1ab region encoding viral non-structural proteins and the rest of the genome, including Spike (S) protein and remaining reading frames. By accounting for several deletions in NSP6, Orf3a, and S, we conclude that the B.1.628 major cluster, now designated as lineage XB, originated from a recombination event between viruses of B.1.631 and B.1.634 lineages. This scenario is supported by the spatiotemporal distribution of these lineages across the USA and Mexico during 2021, suggesting that the recombination event originated in this geographical region. This event raises important questions regarding the role and potential effects of recombination on SARS-CoV-2 evolution.
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Affiliation(s)
- Bernardo Gutierrez
- Department of Zoology, University of Oxford, Oxford, UK; Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex), México; Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito USFQ, Quito, Ecuador.
| | - Hugo G Castelán Sánchez
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex), México; Consejo Nacional de Ciencia y Tecnología, Ciudad de México, México
| | - Darlan da Silva Candido
- Department of Zoology, University of Oxford, Oxford, UK; Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Ben Jackson
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | | | | | - Christopher Ruis
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK; Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Luis Delaye
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex), México; Departamento de Ingeniería Genética, Unidad Irapuato, CINVESTAV, Irapuato, Mexico
| | - Nuno R Faria
- Department of Zoology, University of Oxford, Oxford, UK; Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil; MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK; The Abdul Latif Jameel Institute for Disease and Emergency Analytics, School of Public Health, Imperial College London, London, UK
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, UK; Department of Pathobiology, Royal Veterinary College, London, UK.
| | - Marina Escalera-Zamudio
- Department of Zoology, University of Oxford, Oxford, UK; Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex), México.
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25
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Nastri AC, Duarte-Neto AN, Casadio LVB, Souza WMD, Claro IM, Manuli ER, Selegatto G, Salomão MC, Fialkovitz G, Taborda M, Almeida BLD, Magri MC, Guedes AR, Perdigão Neto LV, Sataki FM, Guimarães T, Mendes-Correa MC, Tozetto-Mendoza TR, Fumagalli MJ, Ho YL, Maia da Silva CA, Coletti TM, Goes de Jesus J, Romano CM, Hill SC, Pybus O, Rebello Pinho JR, Ledesma FL, Casal YR, Kanamura CT, Tadeu de Araújo LJ, Ferreira CSDS, Guerra JM, Figueiredo LTM, Dolhnikoff M, Faria NR, Sabino EC, Alves VAF, Levin AS. Understanding Sabiá virus infections (Brazilian mammarenavirus). Travel Med Infect Dis 2022; 48:102351. [PMID: 35537676 DOI: 10.1016/j.tmaid.2022.102351] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/27/2022] [Accepted: 04/28/2022] [Indexed: 02/09/2023]
Abstract
BACKGROUND Only two naturally occurring human Sabiá virus (SABV) infections have been reported, and those occurred over 20 years ago. METHODS We diagnosed two new cases of SABV infection using metagenomics in patients thought to have severe yellow fever and described new features of histopathological findings. RESULTS We characterized clinical manifestations, histopathology and analyzed possible nosocomial transmission. Patients presented with hepatitis, bleeding, neurological alterations and died. We traced twenty-nine hospital contacts and evaluated them clinically and by RT-PCR and neutralizing antibodies. Autopsies uncovered unique features on electron microscopy, such as hepatocyte "pinewood knot" lesions. Although previous reports with similar New-World arenavirus had nosocomial transmission, our data did not find any case in contact tracing. CONCLUSIONS Although an apparent by rare, Brazilian mammarenavirus infection is an etiology for acute hemorrhagic fever syndrome. The two fatal cases had peculiar histopathological findings not previously described. The virological diagnosis was possible only by contemporary techniques such as metagenomic assays. We found no subsequent infections when we used serological and molecular tests to evaluate close contacts.
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Affiliation(s)
- Ana Catharina Nastri
- Division of Infectious Diseases, Hospital das Clínicas, Faculdade de Medicina, Universidade de Sao Paulo, Brazil.
| | - Amaro Nunes Duarte-Neto
- Department of Pathology, Faculdade de Medicina, Universidade de Sao Paulo, Brazil; Núcleo de Anatomia Patológica, Instituto Adolfo Lutz, Sao Paulo, Brazil.
| | - Luciana Vilas Boas Casadio
- Division of Infectious Diseases, Hospital das Clínicas, Faculdade de Medicina, Universidade de Sao Paulo, Brazil.
| | - William Marciel de Souza
- World Reference Center for Emerging Viruses and Arboviruses and Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston, Galveston, TX, USA.
| | - Ingra M Claro
- Department of Infectious Diseases, Faculdade de Medicina, Universidade de Sao Paulo, Brazil; Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de Sao Paulo, Brazil.
| | - Erika R Manuli
- Department of Infectious Diseases, Faculdade de Medicina, Universidade de Sao Paulo, Brazil; Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de Sao Paulo, Brazil.
| | - Gloria Selegatto
- Division of Infectious Diseases, Hospital das Clínicas, Faculdade de Medicina, Universidade de Sao Paulo, Brazil.
| | - Matias C Salomão
- Infection Control Department, Hospital das Clínicas, Faculdade de Medicina, Universidade de Sao Paulo, Brazil.
| | - Gabriel Fialkovitz
- Division of Infectious Diseases, Hospital das Clínicas, Faculdade de Medicina, Universidade de Sao Paulo, Brazil.
| | - Mariane Taborda
- Division of Infectious Diseases, Hospital das Clínicas, Faculdade de Medicina, Universidade de Sao Paulo, Brazil.
| | - Bianca Leal de Almeida
- Division of Infectious Diseases, Hospital das Clínicas, Faculdade de Medicina, Universidade de Sao Paulo, Brazil; Infection Control Department, Hospital das Clínicas, Faculdade de Medicina, Universidade de Sao Paulo, Brazil.
| | - Marcello C Magri
- Division of Infectious Diseases, Hospital das Clínicas, Faculdade de Medicina, Universidade de Sao Paulo, Brazil.
| | - Ana Rúbia Guedes
- Infection Control Department, Hospital das Clínicas, Faculdade de Medicina, Universidade de Sao Paulo, Brazil.
| | - Lauro Vieira Perdigão Neto
- Infection Control Department, Hospital das Clínicas, Faculdade de Medicina, Universidade de Sao Paulo, Brazil.
| | - Fatima Mitie Sataki
- Division of Infectious Diseases, Hospital das Clínicas, Faculdade de Medicina, Universidade de Sao Paulo, Brazil.
| | - Thais Guimarães
- Infection Control Department, Hospital das Clínicas, Faculdade de Medicina, Universidade de Sao Paulo, Brazil.
| | - Maria Cassia Mendes-Correa
- Department of Infectious Diseases, Faculdade de Medicina, Universidade de Sao Paulo, Brazil; Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de Sao Paulo, Brazil.
| | | | - Marcilio Jorge Fumagalli
- Centro de Pesquisa em Virologia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil.
| | - Yeh-Li Ho
- Division of Infectious Diseases, Hospital das Clínicas, Faculdade de Medicina, Universidade de Sao Paulo, Brazil.
| | - Camila Alves Maia da Silva
- Department of Infectious Diseases, Faculdade de Medicina, Universidade de Sao Paulo, Brazil; Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de Sao Paulo, Brazil.
| | - Thaís M Coletti
- Department of Infectious Diseases, Faculdade de Medicina, Universidade de Sao Paulo, Brazil; Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de Sao Paulo, Brazil.
| | - Jaqueline Goes de Jesus
- Department of Infectious Diseases, Faculdade de Medicina, Universidade de Sao Paulo, Brazil; Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de Sao Paulo, Brazil.
| | - Camila M Romano
- Department of Infectious Diseases, Faculdade de Medicina, Universidade de Sao Paulo, Brazil; Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de Sao Paulo, Brazil.
| | - Sarah C Hill
- Department of Zoology, University of Oxford, United Kingdom Department of Pathobiology and Population Sciences, The Royal Veterinary College, United Kingdom; Department of Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, United Kingdom.
| | - Oliver Pybus
- Department of Zoology, University of Oxford, United Kingdom.
| | - João Renato Rebello Pinho
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de Sao Paulo, Brazil; Hospital Israelita Albert Einstein, São Paulo, SP, Brazil.
| | | | - Yuri R Casal
- Department of Pathology, Faculdade de Medicina, Universidade de Sao Paulo, Brazil.
| | | | | | | | | | - Luiz Tadeu Moraes Figueiredo
- Centro de Pesquisa em Virologia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil.
| | - Marisa Dolhnikoff
- Department of Pathology, Faculdade de Medicina, Universidade de Sao Paulo, Brazil.
| | - Nuno R Faria
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de Sao Paulo, Brazil; Department of Zoology, University of Oxford, United Kingdom; MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, United Kingdom.
| | - Ester C Sabino
- Department of Infectious Diseases, Faculdade de Medicina, Universidade de Sao Paulo, Brazil; Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de Sao Paulo, Brazil.
| | | | - Anna S Levin
- Division of Infectious Diseases, Hospital das Clínicas, Faculdade de Medicina, Universidade de Sao Paulo, Brazil; Department of Infectious Diseases, Faculdade de Medicina, Universidade de Sao Paulo, Brazil; Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de Sao Paulo, Brazil; Infection Control Department, Hospital das Clínicas, Faculdade de Medicina, Universidade de Sao Paulo, Brazil.
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26
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Brizzi A, Whittaker C, Servo LMS, Hawryluk I, Prete CA, de Souza WM, Aguiar RS, Araujo LJT, Bastos LS, Blenkinsop A, Buss LF, Candido D, Castro MC, Costa SF, Croda J, de Souza Santos AA, Dye C, Flaxman S, Fonseca PLC, Geddes VEV, Gutierrez B, Lemey P, Levin AS, Mellan T, Bonfim DM, Miscouridou X, Mishra S, Monod M, Moreira FRR, Nelson B, Pereira RHM, Ranzani O, Schnekenberg RP, Semenova E, Sonabend R, Souza RP, Xi X, Sabino EC, Faria NR, Bhatt S, Ratmann O. Spatial and temporal fluctuations in COVID-19 fatality rates in Brazilian hospitals. Nat Med 2022; 28:1476-1485. [PMID: 35538260 PMCID: PMC9307484 DOI: 10.1038/s41591-022-01807-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 03/31/2022] [Indexed: 02/07/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Gamma variant of concern has spread rapidly across Brazil since late 2020, causing substantial infection and death waves. Here we used individual-level patient records after hospitalization with suspected or confirmed coronavirus disease 2019 (COVID-19) between 20 January 2020 and 26 July 2021 to document temporary, sweeping shocks in hospital fatality rates that followed the spread of Gamma across 14 state capitals, during which typically more than half of hospitalized patients aged 70 years and older died. We show that such extensive shocks in COVID-19 in-hospital fatality rates also existed before the detection of Gamma. Using a Bayesian fatality rate model, we found that the geographic and temporal fluctuations in Brazil's COVID-19 in-hospital fatality rates were primarily associated with geographic inequities and shortages in healthcare capacity. We estimate that approximately half of the COVID-19 deaths in hospitals in the 14 cities could have been avoided without pre-pandemic geographic inequities and without pandemic healthcare pressure. Our results suggest that investments in healthcare resources, healthcare optimization and pandemic preparedness are critical to minimize population-wide mortality and morbidity caused by highly transmissible and deadly pathogens such as SARS-CoV-2, especially in low- and middle-income countries.
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Affiliation(s)
- Andrea Brizzi
- Department of Mathematics, Imperial College London, London, UK
| | - Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | | | - Iwona Hawryluk
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Carlos A Prete
- Departamento de Engenharia de Sistemas Eletrônicos, Escola Politécnica, Universidade de São Paulo, São Paulo, Brazil
| | - William M de Souza
- World Reference Center for Emerging Viruses and Arboviruses and Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston TX, USA
| | - Renato S Aguiar
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Instituto D'Or de Pesquisa e Ensino (IDOR), Rio de Janeiro, Brazil
| | - Leonardo J T Araujo
- Laboratory of Quantitative Pathology, Center of Pathology, Adolfo Lutz Institute, São Paulo, Brazil
| | - Leonardo S Bastos
- Programa de Computação Científica, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | | | - Lewis F Buss
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
- Departamento de Moléstias Infecciosas e Parasitárias e Instituto de Medicina Tropical da Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | | | - Marcia C Castro
- Department of Global Health and Population, Harvard T. H. Chan School of Public Health, Boston MA, USA
| | - Silvia F Costa
- Departamento de Moléstias Infecciosas e Parasitárias e Instituto de Medicina Tropical da Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Julio Croda
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven CT, USA
| | | | | | - Seth Flaxman
- Department of Computer Science, University of Oxford, Oxford, UK
| | - Paula L C Fonseca
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Victor E V Geddes
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven - University of Leuven, Leuven, Belgium
| | - Anna S Levin
- Departamento de Moléstias Infecciosas e Parasitárias e Instituto de Medicina Tropical da Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Thomas Mellan
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Diego M Bonfim
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Swapnil Mishra
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
- Section of Epidemiology, School of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Mélodie Monod
- Department of Mathematics, Imperial College London, London, UK
| | - Filipe R R Moreira
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Bruce Nelson
- Environmental Dynamics, INPA, National Institute for Amazon Research, Manaus, Brazil
| | | | - Otavio Ranzani
- Barcelona Institute for Global Health, ISGlobal, Barcelona, Spain
| | | | | | - Raphael Sonabend
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Renan P Souza
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Xiaoyue Xi
- Department of Mathematics, Imperial College London, London, UK
| | - Ester C Sabino
- Departamento de Moléstias Infecciosas e Parasitárias e Instituto de Medicina Tropical da Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil.
| | - Nuno R Faria
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK.
- Departamento de Moléstias Infecciosas e Parasitárias e Instituto de Medicina Tropical da Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil.
- Department of Zoology, University of Oxford, Oxford, UK.
- Department of Infectious Disease Epidemiology, Imperial College London, London, UK.
| | - Samir Bhatt
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK.
- Section of Epidemiology, School of Public Health, University of Copenhagen, Copenhagen, Denmark.
| | - Oliver Ratmann
- Department of Mathematics, Imperial College London, London, UK.
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27
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Fonseca PLC, Moreira FRR, de Souza RM, Guimarães NR, Carvalho NO, Adelino TER, Alves HJ, Alvim LB, Candido DS, Coelho HP, Costa AVB, Costa WC, de Carvalho AF, de Faria BWF, de Lima AB, de Oliveira ES, de Souza CSA, de Souza FG, Dias RC, Geddes VEV, Godinho IP, Gonçalves AL, Lourenço KL, Magalhães RDM, Malta FSV, Medeiros ELA, Mendes FS, Mendes PHBDP, Mendonça CPTB, Menezes AL, Menezes D, Menezes MT, Miguita L, Moreira RG, Peixoto RB, Queiroz DC, Ribeiro AA, Ribeiro APDB, Saliba JW, Sato HI, Silva JDP, Silva NP, Faria NR, Teixeira SMR, da Fonseca FG, Fernandes APSM, Zauli DAG, Januario JN, de Oliveira JS, Iani FCDM, de Aguiar RS, de Souza RP. Tracking the turnover of SARS-CoV-2 VOCs Gamma to Delta in a Brazilian state (Minas Gerais) with a high-vaccination status. Virus Evol 2022; 8:veac064. [PMID: 35996592 PMCID: PMC9384558 DOI: 10.1093/ve/veac064] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 06/24/2022] [Accepted: 07/26/2022] [Indexed: 11/24/2022] Open
Abstract
The emergence and global dissemination of Severe Acute Respiratory Syndrome virus 2 (SARS-CoV-2) variants of concern (VOCs) have been described as the main factor driving the Coronavirus Disease 2019 pandemic. In Brazil, the Gamma variant dominated the epidemiological scenario during the first period of 2021. Many Brazilian regions detected the Delta variant after its first description and documented its spread. To monitor the introduction and spread of VOC Delta, we performed Polymerase Chain Reaction (PCR) genotyping and genome sequencing in ten regional sentinel units from June to October 2021 in the State of Minas Gerais (MG). We documented the introduction and spread of Delta, comprising 70 per cent of the cases 8 weeks later. Comparing the viral loads of the Gamma and Delta dominance periods, we provide additional evidence that the latter is more transmissible. The spread and dominance of Delta did not culminate in the increase in cases and deaths, suggesting that the vaccination may have restrained the epidemic growth. Analysis of 224 novel Delta genomes revealed that Rio de Janeiro state was the primary source for disseminating this variant in the state of MG. We present the establishment of Delta, providing evidence of its enhanced transmissibility and showing that this variant shift did not aggravate the epidemiological scenario in a high immunity setting.
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Affiliation(s)
- Paula L C Fonseca
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte 31270901, Minas Gerais, Brazil
| | - Filipe R R Moreira
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, Exhibition Rd, South Kensington, London SW7 2BX, UK
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Av. Carlos Chagas Filho 373, Cidade Universitaria, Rio de Janeiro 21941-902, Rio de Janeiro, Brazil
| | - Rafael M de Souza
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte 31270901, Minas Gerais, Brazil
| | - Natália R Guimarães
- Fundacao Ezequiel Dias, Rua Conde Pereira Carneiro 80, Gameleira, Belo Horizonte 30510-010, Minas Gerais, Brazil
| | - Nara O Carvalho
- Núcleo de Ações e Pesquisa em Apoio Diagnóstico-Nupad/Faculdade de Medicina/Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Av. Prof. Alfredo Balena 189, Centro, Belo Horizonte 30130-100, Minas Gerais, Brazil
| | - Talita E R Adelino
- Fundacao Ezequiel Dias, Rua Conde Pereira Carneiro 80, Gameleira, Belo Horizonte 30510-010, Minas Gerais, Brazil
| | - Hugo J Alves
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte 31270901, Minas Gerais, Brazil
| | - Luige B Alvim
- Instituto Hermes Pardini, Av. das Nações 2448, Distrito Industrial, Vespasiano 33201003, Minas Gerais, Brazil
| | - Darlan S Candido
- Department of Zoology, University of Oxford, 11a Mansfield Rd, Oxford OX13SZ, UK
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Av. Dr. Enéas Carvalho de Aguiar 470, Jardim América, São Paulo 05403000, São Paulo, Brazil
| | - Helena P Coelho
- Centro de Tecnologia de Vacinas, Universidade Federal de Minas Gerais, Rua Professor José Vieira de Mendonça 770, Engenho Nogueira, Belo Horizonte 31310260, Minas Gerais, Brazil
| | - Alana V B Costa
- Fundacao Ezequiel Dias, Rua Conde Pereira Carneiro 80, Gameleira, Belo Horizonte 30510-010, Minas Gerais, Brazil
| | - Walyson C Costa
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte 31270901, Minas Gerais, Brazil
| | - Alex F de Carvalho
- Centro de Tecnologia de Vacinas, Universidade Federal de Minas Gerais, Rua Professor José Vieira de Mendonça 770, Engenho Nogueira, Belo Horizonte 31310260, Minas Gerais, Brazil
| | - Bruna W F de Faria
- Secretaria Municipal de Saúde de Belo Horizonte, Av. Afonso Pena 2336, Funcionários, Belo Horizonte 30130-040, Minas Gerais, Brazil
| | - Aline B de Lima
- Instituto Hermes Pardini, Av. das Nações 2448, Distrito Industrial, Vespasiano 33201003, Minas Gerais, Brazil
| | - Eneida S de Oliveira
- Secretaria Municipal de Saúde de Belo Horizonte, Av. Afonso Pena 2336, Funcionários, Belo Horizonte 30130-040, Minas Gerais, Brazil
| | - Carolina S A de Souza
- Pan American Health Organization—PAHO, Av. Das Nações SEN, Asa Norte, Brasilia 70312970, Brazil
| | - Fernanda G de Souza
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte 31270901, Minas Gerais, Brazil
| | - Rillery C Dias
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte 31270901, Minas Gerais, Brazil
| | - Victor E V Geddes
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte 31270901, Minas Gerais, Brazil
| | - Igor P Godinho
- Centro de Tecnologia de Vacinas, Universidade Federal de Minas Gerais, Rua Professor José Vieira de Mendonça 770, Engenho Nogueira, Belo Horizonte 31310260, Minas Gerais, Brazil
| | - Alessandro L Gonçalves
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte 31270901, Minas Gerais, Brazil
| | - Karine L Lourenço
- Centro de Tecnologia de Vacinas, Universidade Federal de Minas Gerais, Rua Professor José Vieira de Mendonça 770, Engenho Nogueira, Belo Horizonte 31310260, Minas Gerais, Brazil
| | - Rubens D M Magalhães
- Centro de Tecnologia de Vacinas, Universidade Federal de Minas Gerais, Rua Professor José Vieira de Mendonça 770, Engenho Nogueira, Belo Horizonte 31310260, Minas Gerais, Brazil
| | - Frederico S V Malta
- Instituto Hermes Pardini, Av. das Nações 2448, Distrito Industrial, Vespasiano 33201003, Minas Gerais, Brazil
| | - Eva L A Medeiros
- Subsecretaria de Vigilância em Saúde, Secretaria de Estado de Saúde de Minas Gerais, Rodovia Papa João Paulo II 4143. Edifício Minas Gerais, Cidade Administrativa, Serra verde, Belo Horizonte 31630900, Minas Gerais, Brazil
| | - Fernanda S Mendes
- Núcleo de Ações e Pesquisa em Apoio Diagnóstico-Nupad/Faculdade de Medicina/Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Av. Prof. Alfredo Balena 189, Centro, Belo Horizonte 30130-100, Minas Gerais, Brazil
| | - Pedro H B de P Mendes
- Fundacao Ezequiel Dias, Rua Conde Pereira Carneiro 80, Gameleira, Belo Horizonte 30510-010, Minas Gerais, Brazil
| | - Cristiane P T B Mendonça
- Instituto Hermes Pardini, Av. das Nações 2448, Distrito Industrial, Vespasiano 33201003, Minas Gerais, Brazil
| | - Andre L Menezes
- Secretaria Municipal de Saúde de Belo Horizonte, Av. Afonso Pena 2336, Funcionários, Belo Horizonte 30130-040, Minas Gerais, Brazil
| | - Diego Menezes
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte 31270901, Minas Gerais, Brazil
| | - Mariane T Menezes
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, Exhibition Rd, South Kensington, London SW7 2BX, UK
| | - Lucyene Miguita
- Departamento de Patologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte 31270901, Minas Gerais, Brazil
| | - Rennan G Moreira
- Centro de Laboratórios Multiusuários, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte 31270901, Minas Gerais, Brazil
| | - Renata B Peixoto
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte 31270901, Minas Gerais, Brazil
| | - Daniel C Queiroz
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte 31270901, Minas Gerais, Brazil
| | - Adriana A Ribeiro
- Fundacao Ezequiel Dias, Rua Conde Pereira Carneiro 80, Gameleira, Belo Horizonte 30510-010, Minas Gerais, Brazil
| | - Ana Paula de B Ribeiro
- Fundacao Ezequiel Dias, Rua Conde Pereira Carneiro 80, Gameleira, Belo Horizonte 30510-010, Minas Gerais, Brazil
| | - Juliana W Saliba
- Pan American Health Organization—PAHO, Av. Das Nações SEN, Asa Norte, Brasilia 70312970, Brazil
| | - Hugo I Sato
- Centro de Tecnologia de Vacinas, Universidade Federal de Minas Gerais, Rua Professor José Vieira de Mendonça 770, Engenho Nogueira, Belo Horizonte 31310260, Minas Gerais, Brazil
| | - Joice do P Silva
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte 31270901, Minas Gerais, Brazil
- Instituto Hermes Pardini, Av. das Nações 2448, Distrito Industrial, Vespasiano 33201003, Minas Gerais, Brazil
| | - Natiely P Silva
- Núcleo de Ações e Pesquisa em Apoio Diagnóstico-Nupad/Faculdade de Medicina/Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Av. Prof. Alfredo Balena 189, Centro, Belo Horizonte 30130-100, Minas Gerais, Brazil
| | - Nuno R Faria
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, Exhibition Rd, South Kensington, London SW7 2BX, UK
- Department of Zoology, University of Oxford, 11a Mansfield Rd, Oxford OX13SZ, UK
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Av. Dr. Enéas Carvalho de Aguiar 470, Jardim América, São Paulo 05403000, São Paulo, Brazil
| | - Santuza M R Teixeira
- Centro de Tecnologia de Vacinas, Universidade Federal de Minas Gerais, Rua Professor José Vieira de Mendonça 770, Engenho Nogueira, Belo Horizonte 31310260, Minas Gerais, Brazil
| | - Flávio G da Fonseca
- Centro de Tecnologia de Vacinas, Universidade Federal de Minas Gerais, Rua Professor José Vieira de Mendonça 770, Engenho Nogueira, Belo Horizonte 31310260, Minas Gerais, Brazil
| | - Ana Paula S M Fernandes
- Centro de Tecnologia de Vacinas, Universidade Federal de Minas Gerais, Rua Professor José Vieira de Mendonça 770, Engenho Nogueira, Belo Horizonte 31310260, Minas Gerais, Brazil
| | - Danielle A G Zauli
- Instituto Hermes Pardini, Av. das Nações 2448, Distrito Industrial, Vespasiano 33201003, Minas Gerais, Brazil
| | - José Nélio Januario
- Núcleo de Ações e Pesquisa em Apoio Diagnóstico-Nupad/Faculdade de Medicina/Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Av. Prof. Alfredo Balena 189, Centro, Belo Horizonte 30130-100, Minas Gerais, Brazil
| | - Jaqueline S de Oliveira
- Subsecretaria de Vigilância em Saúde, Secretaria de Estado de Saúde de Minas Gerais, Rodovia Papa João Paulo II 4143. Edifício Minas Gerais, Cidade Administrativa, Serra verde, Belo Horizonte 31630900, Minas Gerais, Brazil
| | - Felipe C de M Iani
- Fundacao Ezequiel Dias, Rua Conde Pereira Carneiro 80, Gameleira, Belo Horizonte 30510-010, Minas Gerais, Brazil
| | - Renato S de Aguiar
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte 31270901, Minas Gerais, Brazil
- Instituto D’OR de Pesquisa e Ensino, Rio de Janeiro 22281100, Rio de Janeiro, Brazil
| | - Renan P de Souza
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte 31270901, Minas Gerais, Brazil
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28
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Claro IM, Romano CM, Candido DDS, de Lima EL, Lindoso JAL, Ramundo MS, Moreira FRR, Barra LAC, Borges LMS, Medeiros LA, Tomishige MYS, Moutinho T, da Silva AJD, Rodrigues CCM, de Azevedo LCF, Villas-Boas LS, da Silva CAM, Coletti TM, Manuli ER, O’Toole A, Quick J, Loman N, Rambaut A, Faria NR, Figueiredo-Mello C, Sabino EC. Shotgun metagenomic sequencing of the first case of monkeypox virus in Brazil, 2022. Rev Inst Med Trop Sao Paulo 2022; 64:e48. [PMID: 35749419 PMCID: PMC9217064 DOI: 10.1590/s1678-9946202264048] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 06/20/2022] [Indexed: 11/21/2022] Open
Abstract
Monkeypox virus (MPXV), a zoonotic virus endemic to the African continent, has been reported in 33 non-endemic countries since May 2022. We report an almost complete genome of the first confirmed case of MPXV in Brazil. Shotgun metagenomic sequencing was completed in 18 hours, from DNA extraction to consensus sequence generation.
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Affiliation(s)
- Ingra Morales Claro
- Universidade de São Paulo, Faculdade de Medicina, Instituto de Medicina Tropical de São Paulo, São Paulo, São Paulo, Brazil
- Imperial College London, MRC Centre for Global Infectious Disease Analysis, London, United Kingdom
| | - Camila Malta Romano
- Universidade de São Paulo, Faculdade de Medicina, Instituto de Medicina Tropical de São Paulo, São Paulo, São Paulo, Brazil
| | - Darlan da Silva Candido
- Universidade de São Paulo, Faculdade de Medicina, Instituto de Medicina Tropical de São Paulo, São Paulo, São Paulo, Brazil
- Imperial College London, MRC Centre for Global Infectious Disease Analysis, London, United Kingdom
- University of Oxford, Department of Zoology, Oxford, United Kingdom
| | | | - José Angelo Lauletta Lindoso
- Universidade de São Paulo, Faculdade de Medicina, Instituto de Medicina Tropical de São Paulo, São Paulo, São Paulo, Brazil
- Instituto de Infectologia Emílio Ribas, São Paulo, São Paulo, Brazil
- Universidade de São Paulo, Faculdade de Medicina, Departamento de Moléstias Infecciosas e Parasitárias, São Paulo, São Paulo, Brazil
| | - Mariana Severo Ramundo
- Universidade de São Paulo, Faculdade de Medicina, Instituto de Medicina Tropical de São Paulo, São Paulo, São Paulo, Brazil
| | - Filipe Romero Rebello Moreira
- Imperial College London, MRC Centre for Global Infectious Disease Analysis, London, United Kingdom
- Universidade Federal do Rio de Janeiro, Instituto de Biologia, Departamento de Genética, Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | | | | | - Tomas Moutinho
- Universidade de São Paulo, Faculdade de Medicina, Departamento de Moléstias Infecciosas e Parasitárias, São Paulo, São Paulo, Brazil
| | | | | | | | - Lucy Santos Villas-Boas
- Universidade de São Paulo, Faculdade de Medicina, Instituto de Medicina Tropical de São Paulo, São Paulo, São Paulo, Brazil
| | - Camila Alves Maia da Silva
- Universidade de São Paulo, Faculdade de Medicina, Instituto de Medicina Tropical de São Paulo, São Paulo, São Paulo, Brazil
| | - Thaís Moura Coletti
- Universidade de São Paulo, Faculdade de Medicina, Instituto de Medicina Tropical de São Paulo, São Paulo, São Paulo, Brazil
| | - Erika R. Manuli
- Universidade de São Paulo, Faculdade de Medicina, Instituto de Medicina Tropical de São Paulo, São Paulo, São Paulo, Brazil
| | - Aine O’Toole
- University of Edinburgh, Institute of Ecology and Evolution, Edinburgh, United Kingdom
| | - Joshua Quick
- University of Birmingham, School of Biosciences, Birmingham, United Kingdom
| | - Nicholas Loman
- University of Birmingham, School of Biosciences, Birmingham, United Kingdom
| | - Andrew Rambaut
- University of Edinburgh, Institute of Ecology and Evolution, Edinburgh, United Kingdom
| | - Nuno R. Faria
- Universidade de São Paulo, Faculdade de Medicina, Instituto de Medicina Tropical de São Paulo, São Paulo, São Paulo, Brazil
- Imperial College London, MRC Centre for Global Infectious Disease Analysis, London, United Kingdom
- University of Oxford, Department of Zoology, Oxford, United Kingdom
| | | | - Ester Cerdeira Sabino
- Universidade de São Paulo, Faculdade de Medicina, Instituto de Medicina Tropical de São Paulo, São Paulo, São Paulo, Brazil
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Sabino JS, Amorim MR, de Souza WM, Marega LF, Mofatto LS, Toledo-Teixeira DA, Forato J, Stabeli RG, Costa ML, Spilki FR, Sabino EC, Faria NR, Benites BD, Addas-Carvalho M, Stucchi RSB, Vasconcelos DM, Weaver SC, Granja F, Proenca-Modena JL, Vilela MMDS. Clearance of Persistent SARS-CoV-2 RNA Detection in a NFκB-Deficient Patient in Association with the Ingestion of Human Breast Milk: A Case Report. Viruses 2022; 14:1042. [PMID: 35632784 PMCID: PMC9143223 DOI: 10.3390/v14051042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 02/01/2023] Open
Abstract
Currently, there are no evidence-based treatment options for long COVID-19, and it is known that SARS-CoV-2 can persist in part of the infected patients, especially those with immunosuppression. Since there is a robust secretion of SARS-CoV-2-specific highly-neutralizing IgA antibodies in breast milk, and because this immunoglobulin plays an essential role against respiratory virus infection in mucosa cells, being, in addition, more potent in neutralizing SARS-CoV-2 than IgG, here we report the clinical course of an NFκB-deficient patient chronically infected with the SARS-CoV-2 Gamma variant, who, after a non-full effective treatment with plasma infusion, received breast milk from a vaccinated mother by oral route as treatment for COVID-19. After such treatment, the symptoms improved, and the patient was systematically tested negative for SARS-CoV-2. Thus, we hypothesize that IgA and IgG secreted antibodies present in breast milk could be useful to treat persistent SARS-CoV-2 infection in immunodeficient patients.
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Affiliation(s)
- Janine S. Sabino
- Laboratory of Pediatric Immunology, Center for Investigation in Pediatrics, Faculty of Medical Sciences, University of Campinas, Campinas 13083-887, Brazil; (J.S.S.); (L.F.M.)
| | - Mariene R. Amorim
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas 13083-862, Brazil; (M.R.A.); (L.S.M.); (D.A.T.-T.); (J.F.); (F.G.)
| | - William M. de Souza
- World Reference Center for Emerging Viruses, Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA; (W.M.d.S.); (S.C.W.)
| | - Lia F. Marega
- Laboratory of Pediatric Immunology, Center for Investigation in Pediatrics, Faculty of Medical Sciences, University of Campinas, Campinas 13083-887, Brazil; (J.S.S.); (L.F.M.)
| | - Luciana S. Mofatto
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas 13083-862, Brazil; (M.R.A.); (L.S.M.); (D.A.T.-T.); (J.F.); (F.G.)
| | - Daniel A. Toledo-Teixeira
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas 13083-862, Brazil; (M.R.A.); (L.S.M.); (D.A.T.-T.); (J.F.); (F.G.)
| | - Julia Forato
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas 13083-862, Brazil; (M.R.A.); (L.S.M.); (D.A.T.-T.); (J.F.); (F.G.)
| | - Rodrigo G. Stabeli
- Oswaldo Cruz Foundation (Fiocruz-SP), Ribeirão Preto 14049-900, Brazil;
- Department of Public Health Emergency, Preparedness and Disaster, PAHO/WHO, Brasilia 70312-970, Brazil
| | - Maria Laura Costa
- Department of Obstetrics and Gynecology, Faculty of Medical Sciences, University of Campinas, Campinas 13083-887, Brazil;
| | - Fernando R. Spilki
- One Health Laboratory, Feevale University, Novo Hamburgo 93510-235, Brazil;
| | - Ester C. Sabino
- Tropical Medicine Institute, Medical School, University of São Paulo, São Paulo 5403-907, Brazil;
- Department of Infectious and Parasitic Disease, Medical School, University of São Paulo, São Paulo 05403-000, Brazil;
| | - Nuno R. Faria
- Department of Infectious and Parasitic Disease, Medical School, University of São Paulo, São Paulo 05403-000, Brazil;
- Department of Zoology, University of Oxford, Oxford OX1 2JD, UK
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London SW7 2AZ, UK
| | - Bruno D. Benites
- Hematology and Transfusion Medicine Center, University of Campinas, Campinas 13083-878, Brazil; (B.D.B.); (M.A.-C.)
| | - Marcelo Addas-Carvalho
- Hematology and Transfusion Medicine Center, University of Campinas, Campinas 13083-878, Brazil; (B.D.B.); (M.A.-C.)
| | - Raquel S. B. Stucchi
- Division of Infectious Diseases, University of Campinas, Campinas 13083-887, Brazil;
| | - Dewton M. Vasconcelos
- Laboratory of Investigation in Dermatology and Immunodeficiencies, Department of Dermatology, Medical School, University of São Paulo, São Paulo 05403-000, Brazil;
| | - Scott C. Weaver
- World Reference Center for Emerging Viruses, Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA; (W.M.d.S.); (S.C.W.)
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Fabiana Granja
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas 13083-862, Brazil; (M.R.A.); (L.S.M.); (D.A.T.-T.); (J.F.); (F.G.)
- Biodiversity Research Centre, Federal University of Roraima, Boa Vista 72000-000, Brazil
| | - José Luiz Proenca-Modena
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas 13083-862, Brazil; (M.R.A.); (L.S.M.); (D.A.T.-T.); (J.F.); (F.G.)
- Experimental Medicine Research Cluster (EMRC), University of Campinas, Campinas 13083-862, Brazil
- Hub of Global Health (HGH), University of Campinas, Campinas 13083-862, Brazil
| | - Maria Marluce dos S. Vilela
- Laboratory of Pediatric Immunology, Center for Investigation in Pediatrics, Faculty of Medical Sciences, University of Campinas, Campinas 13083-887, Brazil; (J.S.S.); (L.F.M.)
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30
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Nicolete VC, Rodrigues PT, Fernandes ARJ, Corder RM, Tonini J, Buss LF, Sales FC, Faria NR, Sabino EC, Castro MC, Ferreira MU. Epidemiology of COVID-19 after Emergence of SARS-CoV-2 Gamma Variant, Brazilian Amazon, 2020-2021. Emerg Infect Dis 2022; 28:709-712. [PMID: 34963505 PMCID: PMC8888227 DOI: 10.3201/eid2803.211993] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Gamma variant has been hypothesized to cause more severe illness than previous variants, especially in children. Successive SARS-CoV-2 IgG serosurveys in the Brazilian Amazon showed that age-specific attack rates and proportions of symptomatic SARS-CoV-2 infections were similar before and after Gamma variant emergence.
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31
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Prete CA, Buss LF, Buccheri R, Abrahim CMM, Salomon T, Crispim MAE, Oikawa MK, Grebe E, da Costa AG, Fraiji NA, do P S S Carvalho M, Whittaker C, Alexander N, Faria NR, Dye C, Nascimento VH, Busch MP, Sabino EC. Reinfection by the SARS-CoV-2 Gamma variant in blood donors in Manaus, Brazil. BMC Infect Dis 2022; 22:127. [PMID: 35123418 PMCID: PMC8817641 DOI: 10.1186/s12879-022-07094-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 01/18/2022] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND The city of Manaus, north Brazil, was stricken by a second epidemic wave of SARS-CoV-2 despite high seroprevalence estimates, coinciding with the emergence of the Gamma (P.1) variant. Reinfections were postulated as a partial explanation for the second surge. However, accurate calculation of reinfection rates is difficult when stringent criteria as two time-separated RT-PCR tests and/or genome sequencing are required. To estimate the proportion of reinfections caused by Gamma during the second wave in Manaus and the protection conferred by previous infection, we identified anti-SARS-CoV-2 antibody boosting in repeat blood donors as a mean to infer reinfection. METHODS We tested serial blood samples from unvaccinated repeat blood donors in Manaus for the presence of anti-SARS-CoV-2 IgG antibodies using two assays that display waning in early convalescence, enabling the detection of reinfection-induced boosting. Donors were required to have three or more donations, being at least one during each epidemic wave. We propose a strict serological definition of reinfection (reactivity boosting following waning like a V-shaped curve in both assays or three spaced boostings), probable (two separate boosting events) and possible (reinfection detected by only one assay) reinfections. The serial samples were used to divide donors into six groups defined based on the inferred sequence of infection and reinfection with non-Gamma and Gamma variants. RESULTS From 3655 repeat blood donors, 238 met all inclusion criteria, and 223 had enough residual sample volume to perform both serological assays. We found 13.6% (95% CI 7.0-24.5%) of all presumed Gamma infections that were observed in 2021 were reinfections. If we also include cases of probable or possible reinfections, these percentages increase respectively to 22.7% (95% CI 14.3-34.2%) and 39.3% (95% CI 29.5-50.0%). Previous infection conferred a protection against reinfection of 85.3% (95% CI 71.3-92.7%), decreasing to respectively 72.5% (95% CI 54.7-83.6%) and 39.5% (95% CI 14.1-57.8%) if probable and possible reinfections are included. CONCLUSIONS Reinfection by Gamma is common and may play a significant role in epidemics where Gamma is prevalent, highlighting the continued threat variants of concern pose even to settings previously hit by substantial epidemics.
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Affiliation(s)
- Carlos A Prete
- Department of Electronic Systems Engineering, University of São Paulo, Av. Professor Luciano Gualberto, Travessa 3, São Paulo, 158, Brazil
| | - Lewis F Buss
- Departamento de Moléstias Infecciosas e Parasitarias, Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, Av Dr Eneas de Carvalho 470, 1º andar, São Paulo, 05403-000, Brazil
| | - Renata Buccheri
- Vitalant Research Institute, 270 Masonic Avenue, San Francisco, CA, USA
| | - Claudia M M Abrahim
- Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas, Av. Constantino Nery, Manaus, 4397, Brazil
| | - Tassila Salomon
- Faculdade de Ciências Médicas de Minas Gerais, Alameda Ezequiel Dias, Belo Horizonte, 275, Brazil
| | - Myuki A E Crispim
- Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas, Av. Constantino Nery, Manaus, 4397, Brazil
| | - Marcio K Oikawa
- Center of Mathematics, Computing and Cognition, Universidade Federal do ABC, Rua Arcturus, 03, São Bernardo do Campo, Brasil
| | - Eduard Grebe
- Vitalant Research Institute, 270 Masonic Avenue, San Francisco, CA, USA
- University of California San Francisco, 1001 Potrero Ave, San Francisco, CA, USA
- SACEMA, Stellenbosch University, 19 Jonkershoek Rd, Stellenbosch, South Africa
| | - Allyson G da Costa
- Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas, Av. Constantino Nery, Manaus, 4397, Brazil
| | - Nelson A Fraiji
- Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas, Av. Constantino Nery, Manaus, 4397, Brazil
| | - Maria do P S S Carvalho
- Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas, Av. Constantino Nery, Manaus, 4397, Brazil
| | - Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis, and the Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Neal Alexander
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, LSHTM, Keppel Street, London, WC1E 7HT, UK
| | - Nuno R Faria
- Departamento de Moléstias Infecciosas e Parasitarias, Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, Av Dr Eneas de Carvalho 470, 1º andar, São Paulo, 05403-000, Brazil
- MRC Centre for Global Infectious Disease Analysis, and the Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3SZ, UK
| | - Christopher Dye
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3SZ, UK
| | - Vítor H Nascimento
- Department of Electronic Systems Engineering, University of São Paulo, Av. Professor Luciano Gualberto, Travessa 3, São Paulo, 158, Brazil
| | - Michael P Busch
- Vitalant Research Institute, 270 Masonic Avenue, San Francisco, CA, USA
- University of California San Francisco, 1001 Potrero Ave, San Francisco, CA, USA
| | - Ester Cerdeira Sabino
- Departamento de Moléstias Infecciosas e Parasitarias, Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, Av Dr Eneas de Carvalho 470, 1º andar, São Paulo, 05403-000, Brazil.
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32
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Li SL, Acosta AL, Hill SC, Brady OJ, de Almeida MAB, Cardoso JDC, Hamlet A, Mucci LF, Telles de Deus J, Iani FCM, Alexander NS, Wint GRW, Pybus OG, Kraemer MUG, Faria NR, Messina JP. Mapping environmental suitability of Haemagogus and Sabethes spp. mosquitoes to understand sylvatic transmission risk of yellow fever virus in Brazil. PLoS Negl Trop Dis 2022; 16:e0010019. [PMID: 34995277 PMCID: PMC8797211 DOI: 10.1371/journal.pntd.0010019] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 01/28/2022] [Accepted: 11/23/2021] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Yellow fever (YF) is an arboviral disease which is endemic to Brazil due to a sylvatic transmission cycle maintained by infected mosquito vectors, non-human primate (NHP) hosts, and humans. Despite the existence of an effective vaccine, recent sporadic YF epidemics have underscored concerns about sylvatic vector surveillance, as very little is known about their spatial distribution. Here, we model and map the environmental suitability of YF's main vectors in Brazil, Haemagogus spp. and Sabethes spp., and use human population and NHP data to identify locations prone to transmission and spillover risk. METHODOLOGY/PRINCIPAL FINDINGS We compiled a comprehensive set of occurrence records on Hg. janthinomys, Hg. leucocelaenus, and Sabethes spp. from 1991-2019 using primary and secondary data sources. Linking these data with selected environmental and land-cover variables, we adopted a stacked regression ensemble modelling approach (elastic-net regularized GLM, extreme gradient boosted regression trees, and random forest) to predict the environmental suitability of these species across Brazil at a 1 km x 1 km resolution. We show that while suitability for each species varies spatially, high suitability for all species was predicted in the Southeastern region where recent outbreaks have occurred. By integrating data on NHP host reservoirs and human populations, our risk maps further highlight municipalities within the region that are prone to transmission and spillover. CONCLUSIONS/SIGNIFICANCE Our maps of sylvatic vector suitability can help elucidate potential locations of sylvatic reservoirs and be used as a tool to help mitigate risk of future YF outbreaks and assist in vector surveillance. Furthermore, at-risk regions identified from our work could help disease control and elucidate gaps in vaccination coverage and NHP host surveillance.
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Affiliation(s)
- Sabrina L. Li
- School of Geography and the Environment, University of Oxford, Oxford, United Kingdom
- * E-mail: (SLL); (JPM)
| | - André L. Acosta
- Departamento de Ecologia, Instituto de Biociências, Laboratório de Ecologia de Paisagens e Conservação—LEPAC, Universidade de São Paulo, São Paulo, Brazil
| | - Sarah C. Hill
- Department of Pathobiology and Population Sciences, Royal Veterinary College London, London, United Kingdom
| | - Oliver J. Brady
- Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Marco A. B. de Almeida
- State Centre of Health Surveillance, Rio Grande do Sul State Health Secretariat, Rio Grande do Sul, Brazil
| | - Jader da C. Cardoso
- State Centre of Health Surveillance, Rio Grande do Sul State Health Secretariat, Rio Grande do Sul, Brazil
| | - Arran Hamlet
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Luis F. Mucci
- Superintendence for Endemic Diseases Control, São Paulo State Health Secretariat, São Paulo, Brazil
| | - Juliana Telles de Deus
- Superintendence for Endemic Diseases Control, São Paulo State Health Secretariat, São Paulo, Brazil
| | | | - Neil S. Alexander
- Environmental Research Group Oxford, c/o Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - G. R. William Wint
- Environmental Research Group Oxford, c/o Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Oliver G. Pybus
- Department of Pathobiology and Population Sciences, Royal Veterinary College London, London, United Kingdom
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | | | - Nuno R. Faria
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Departamento de Molestias Infecciosas e Parasitarias & Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Jane P. Messina
- School of Geography and the Environment, University of Oxford, Oxford, United Kingdom
- Oxford School of Global and Area Studies, University of Oxford, Oxford, United Kingdom
- * E-mail: (SLL); (JPM)
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Brizzi A, Whittaker C, Servo LMS, Hawryluk I, Prete CA, de Souza WM, Aguiar RS, Araujo LJT, Bastos LS, Blenkinsop A, Buss LF, Candido D, Castro MC, Costa SF, Croda J, de Souza Santos AA, Dye C, Flaxman S, Fonseca PLC, Geddes VEV, Gutierrez B, Lemey P, Levin AS, Mellan T, Bonfim DM, Miscouridou X, Mishra S, Monod M, Moreira FRR, Nelson B, Pereira RHM, Ranzani O, Schnekenberg RP, Semenova E, Sonabend R, Souza RP, Xi X, Sabino EC, Faria NR, Bhatt S, Ratmann O. Author Correction: Spatial and temporal fluctuations in COVID-19 fatality rates in Brazilian hospitals. Nat Med 2022; 28:1509. [PMID: 35835884 PMCID: PMC9282140 DOI: 10.1038/s41591-022-01939-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Andrea Brizzi
- grid.7445.20000 0001 2113 8111Department of Mathematics, Imperial College London, London, UK
| | - Charles Whittaker
- grid.7445.20000 0001 2113 8111MRC Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Luciana M. S. Servo
- grid.457041.30000 0001 2324 8955Institute for Applied Economic Research, IPEA, Brasília, Brazil
| | - Iwona Hawryluk
- grid.7445.20000 0001 2113 8111MRC Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Carlos A. Prete
- grid.11899.380000 0004 1937 0722Departamento de Engenharia de Sistemas Eletrônicos, Escola Politécnica, Universidade de São Paulo, São Paulo, Brazil
| | - William M. de Souza
- grid.176731.50000 0001 1547 9964World Reference Center for Emerging Viruses and Arboviruses and Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston TX, USA
| | - Renato S. Aguiar
- grid.8430.f0000 0001 2181 4888Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil ,grid.472984.4Instituto D’Or de Pesquisa e Ensino (IDOR), Rio de Janeiro, Brazil
| | - Leonardo J. T. Araujo
- grid.414596.b0000 0004 0602 9808Laboratory of Quantitative Pathology, Center of Pathology, Adolfo Lutz Institute, São Paulo, Brazil
| | - Leonardo S. Bastos
- grid.418068.30000 0001 0723 0931Programa de Computação Científica, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Alexandra Blenkinsop
- grid.7445.20000 0001 2113 8111Department of Mathematics, Imperial College London, London, UK
| | - Lewis F. Buss
- grid.7445.20000 0001 2113 8111MRC Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK ,grid.11899.380000 0004 1937 0722Departamento de Moléstias Infecciosas e Parasitárias e Instituto de Medicina Tropical da Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Darlan Candido
- grid.4991.50000 0004 1936 8948Department of Zoology, University of Oxford, Oxford, UK
| | - Marcia C. Castro
- grid.38142.3c000000041936754XDepartment of Global Health and Population, Harvard T. H. Chan School of Public Health, Boston MA, USA
| | - Silvia F. Costa
- grid.11899.380000 0004 1937 0722Departamento de Moléstias Infecciosas e Parasitárias e Instituto de Medicina Tropical da Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Julio Croda
- grid.47100.320000000419368710Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven CT, USA
| | | | - Christopher Dye
- grid.4991.50000 0004 1936 8948Department of Zoology, University of Oxford, Oxford, UK
| | - Seth Flaxman
- grid.4991.50000 0004 1936 8948Department of Computer Science, University of Oxford, Oxford, UK
| | - Paula L. C. Fonseca
- grid.8430.f0000 0001 2181 4888Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Victor E. V. Geddes
- grid.8430.f0000 0001 2181 4888Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Bernardo Gutierrez
- grid.4991.50000 0004 1936 8948Department of Zoology, University of Oxford, Oxford, UK
| | - Philippe Lemey
- grid.5596.f0000 0001 0668 7884Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven – University of Leuven, Leuven, Belgium
| | - Anna S. Levin
- grid.11899.380000 0004 1937 0722Departamento de Moléstias Infecciosas e Parasitárias e Instituto de Medicina Tropical da Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Thomas Mellan
- grid.7445.20000 0001 2113 8111MRC Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Diego M. Bonfim
- grid.8430.f0000 0001 2181 4888Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Xenia Miscouridou
- grid.7445.20000 0001 2113 8111Department of Mathematics, Imperial College London, London, UK
| | - Swapnil Mishra
- grid.7445.20000 0001 2113 8111MRC Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK ,grid.5254.60000 0001 0674 042XSection of Epidemiology, School of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Mélodie Monod
- grid.7445.20000 0001 2113 8111Department of Mathematics, Imperial College London, London, UK
| | - Filipe R. R. Moreira
- grid.8536.80000 0001 2294 473XDepartamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Bruce Nelson
- grid.419220.c0000 0004 0427 0577Environmental Dynamics, INPA, National Institute for Amazon Research, Manaus, Brazil
| | - Rafael H. M. Pereira
- grid.457041.30000 0001 2324 8955Institute for Applied Economic Research, IPEA, Brasília, Brazil
| | - Otavio Ranzani
- grid.434607.20000 0004 1763 3517Barcelona Institute for Global Health, ISGlobal, Barcelona, Spain
| | - Ricardo P. Schnekenberg
- grid.4991.50000 0004 1936 8948Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Elizaveta Semenova
- grid.7445.20000 0001 2113 8111Department of Mathematics, Imperial College London, London, UK
| | - Raphael Sonabend
- grid.7445.20000 0001 2113 8111MRC Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Renan P. Souza
- grid.8430.f0000 0001 2181 4888Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Xiaoyue Xi
- grid.7445.20000 0001 2113 8111Department of Mathematics, Imperial College London, London, UK
| | - Ester C. Sabino
- grid.11899.380000 0004 1937 0722Departamento de Moléstias Infecciosas e Parasitárias e Instituto de Medicina Tropical da Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Nuno R. Faria
- grid.7445.20000 0001 2113 8111MRC Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK ,grid.11899.380000 0004 1937 0722Departamento de Moléstias Infecciosas e Parasitárias e Instituto de Medicina Tropical da Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil ,grid.4991.50000 0004 1936 8948Department of Zoology, University of Oxford, Oxford, UK ,grid.7445.20000 0001 2113 8111Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Samir Bhatt
- grid.7445.20000 0001 2113 8111MRC Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK ,grid.5254.60000 0001 0674 042XSection of Epidemiology, School of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Oliver Ratmann
- grid.7445.20000 0001 2113 8111Department of Mathematics, Imperial College London, London, UK
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Mee P, Alexander N, Mayaud P, González FDJC, Abbott S, Santos AADS, Acosta AL, Parag KV, Pereira RH, Prete CA, Sabino EC, Faria NR, Brady OJ. Tracking the emergence of disparities in the subnational spread of COVID-19 in Brazil using an online application for real-time data visualisation: A longitudinal analysis. Lancet Reg Health Am 2022; 5:None. [PMID: 35098203 PMCID: PMC8782271 DOI: 10.1016/j.lana.2021.100119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BACKGROUND Brazil is one of the countries worst affected by the COVID-19 pandemic with over 20 million cases and 557,000 deaths reported by August 2021. Comparison of real-time local COVID-19 data between areas is essential for understanding transmission, measuring the effects of interventions, and predicting the course of the epidemic, but are often challenging due to different population sizes and structures. METHODS We describe the development of a new app for the real-time visualisation of COVID-19 data in Brazil at the municipality level. In the CLIC-Brazil app, daily updates of case and death data are downloaded, age standardised and used to estimate the effective reproduction number (Rt ). We show how such platforms can perform real-time regression analyses to identify factors associated with the rate of initial spread and early reproduction number. We also use survival methods to predict the likelihood of occurrence of a new peak of COVID-19 incidence. FINDINGS After an initial introduction in São Paulo and Rio de Janeiro states in early March 2020, the epidemic spread to northern states and then to highly populated coastal regions and the Central-West. Municipalities with higher metrics of social development experienced earlier arrival of COVID-19 (decrease of 11·1 days [95% CI:8.9,13.2] in the time to arrival for each 10% increase in the social development index). Differences in the initial epidemic intensity (mean Rt ) were largely driven by geographic location and the date of local onset. INTERPRETATION This study demonstrates that platforms that monitor, standardise and analyse the epidemiological data at a local level can give useful real-time insights into outbreak dynamics that can be used to better adapt responses to the current and future pandemics. FUNDING This project was supported by a Medical Research Council UK (MRC-UK) -São Paulo Research Foundation (FAPESP) CADDE partnership award (MR/S0195/1 and FAPESP 18/14389-0).
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Affiliation(s)
- Paul Mee
- Faculty of Epidemiology and Public Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- International Statistics and Epidemiology Group, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Neal Alexander
- Faculty of Epidemiology and Public Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
- International Statistics and Epidemiology Group, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Philippe Mayaud
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Felipe de Jesus Colón González
- Faculty of Epidemiology and Public Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Sam Abbott
- Faculty of Epidemiology and Public Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | | - André Luís Acosta
- Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Kris V. Parag
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, United Kingdom
| | | | - Carlos A. Prete
- Department of Electronic Systems Engineering, University of São Paulo, São Paulo, Brazil
| | - Ester C. Sabino
- Departamento de Molestias Infecciosas e Parasitarias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, Brazil
| | - Nuno R. Faria
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, United Kingdom
- Departamento de Molestias Infecciosas e Parasitarias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, Brazil
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | | | - Oliver J Brady
- Faculty of Epidemiology and Public Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
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McCrone JT, Hill V, Bajaj S, Pena RE, Lambert BC, Inward R, Bhatt S, Volz E, Ruis C, Dellicour S, Baele G, Zarebski AE, Sadilek A, Wu N, Schneider A, Ji X, Raghwani J, Jackson B, Colquhoun R, O'Toole Á, Peacock TP, Twohig K, Thelwall S, Dabrera G, Myers R, Faria NR, Huber C, Bogoch II, Khan K, du Plessis L, Barrett JC, Aanensen DM, Barclay WS, Chand M, Connor T, Loman NJ, Suchard MA, Pybus OG, Rambaut A, Kraemer MUG. Context-specific emergence and growth of the SARS-CoV-2 Delta variant. medRxiv 2021:2021.12.14.21267606. [PMID: 34981069 PMCID: PMC8722612 DOI: 10.1101/2021.12.14.21267606] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The Delta variant of concern of SARS-CoV-2 has spread globally causing large outbreaks and resurgences of COVID-19 cases 1-3 . The emergence of Delta in the UK occurred on the background of a heterogeneous landscape of immunity and relaxation of non-pharmaceutical interventions 4,5 . Here we analyse 52,992 Delta genomes from England in combination with 93,649 global genomes to reconstruct the emergence of Delta, and quantify its introduction to and regional dissemination across England, in the context of changing travel and social restrictions. Through analysis of human movement, contact tracing, and virus genomic data, we find that the focus of geographic expansion of Delta shifted from India to a more global pattern in early May 2021. In England, Delta lineages were introduced >1,000 times and spread nationally as non-pharmaceutical interventions were relaxed. We find that hotel quarantine for travellers from India reduced onward transmission from importations; however the transmission chains that later dominated the Delta wave in England had been already seeded before restrictions were introduced. In England, increasing inter-regional travel drove Delta's nationwide dissemination, with some cities receiving >2,000 observable lineage introductions from other regions. Subsequently, increased levels of local population mixing, not the number of importations, was associated with faster relative growth of Delta. Among US states, we find that regions that previously experienced large waves also had faster Delta growth rates, and a model including interactions between immunity and human behaviour could accurately predict the rise of Delta there. Delta's invasion dynamics depended on fine scale spatial heterogeneity in immunity and contact patterns and our findings will inform optimal spatial interventions to reduce transmission of current and future VOCs such as Omicron.
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Affiliation(s)
- John T McCrone
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- contributed equally as first authors
| | - Verity Hill
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- contributed equally as first authors
| | - Sumali Bajaj
- Department of Zoology, University of Oxford, Oxford, UK
- contributed equally as first authors
| | - Rosario Evans Pena
- Department of Zoology, University of Oxford, Oxford, UK
- contributed equally as first authors
| | - Ben C Lambert
- Department of Computer Science, University of Oxford, Oxford, UK
| | - Rhys Inward
- Department of Zoology, University of Oxford, Oxford, UK
- MRC Centre of Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Samir Bhatt
- MRC Centre of Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Erik Volz
- MRC Centre of Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Christopher Ruis
- Molecular Immunity Unit, Department of Medicine, Cambridge University, Cambridge, UK
| | - Simon Dellicour
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Bruxelles, Belgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | | | | | - Neo Wu
- Google, Mountain View, CA, USA
| | | | - Xiang Ji
- Department of Mathematics, School of Science & Engineering, Tulane University, New Orleans, LA, USA
| | | | - Ben Jackson
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Rachel Colquhoun
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Áine O'Toole
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Thomas P Peacock
- Department of Infectious Disease, Imperial College London, London, UK
- UK Health Security Agency, London, UK
| | | | | | | | | | - Nuno R Faria
- Department of Zoology, University of Oxford, Oxford, UK
- MRC Centre of Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil
| | | | - Isaac I Bogoch
- Divisions of Internal Medicine & Infectious Diseases, Toronto General Hospital, University Health Network, Toronto, Canada
- Department of Medicine, Division of Infectious Diseases, University of Toronto, ON, Canada
| | - Kamran Khan
- BlueDot, Toronto, Canada
- Department of Medicine, Division of Infectious Diseases, University of Toronto, ON, Canada
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON, Canada
| | | | | | - David M Aanensen
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Wendy S Barclay
- Department of Infectious Disease, Imperial College London, London, UK
| | | | - Thomas Connor
- Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff, UK
- School of Biosciences, The Sir Martin Evans Building, Cardiff University, Cardiff, UK
- Quadram Institute, Norwich, UK
| | - Nicholas J Loman
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Marc A Suchard
- Departments of Biostatistics, Biomathematics and Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, UK
- Department of Pathobiology and Population Sciences, Royal Veterinary College London, London, UK
- jointly supervised this work
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- jointly supervised this work
| | - Moritz U G Kraemer
- Department of Zoology, University of Oxford, Oxford, UK
- jointly supervised this work
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McCrone JT, Hill V, Bajaj S, Pena RE, Lambert BC, Inward R, Bhatt S, Volz E, Ruis C, Dellicour S, Baele G, Zarebski AE, Sadilek A, Wu N, Schneider A, Ji X, Raghwani J, Jackson B, Colquhoun R, O'Toole Á, Peacock TP, Twohig K, Thelwall S, Dabrera G, Myers R, Faria NR, Huber C, Bogoch II, Khan K, du Plessis L, Barrett JC, Aanensen DM, Barclay WS, Chand M, Connor T, Loman NJ, Suchard MA, Pybus OG, Rambaut A, Kraemer MUG. Context-specific emergence and growth of the SARS-CoV-2 Delta variant. Res Sq 2021:rs.3.rs-1159614. [PMID: 34981043 PMCID: PMC8722606 DOI: 10.21203/rs.3.rs-1159614/v1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
The Delta variant of concern of SARS-CoV-2 has spread globally causing large outbreaks and resurgences of COVID-19 cases. The emergence of Delta in the UK occurred on the background of a heterogeneous landscape of immunity and relaxation of non-pharmaceutical interventions. Here we analyse 52,992 Delta genomes from England in combination with 93,649 global genomes to reconstruct the emergence of Delta, and quantify its introduction to and regional dissemination across England, in the context of changing travel and social restrictions. Through analysis of human movement, contact tracing, and virus genomic data, we find that the focus of geographic expansion of Delta shifted from India to a more global pattern in early May 2021. In England, Delta lineages were introduced >1,000 times and spread nationally as non-pharmaceutical interventions were relaxed. We find that hotel quarantine for travellers from India reduced onward transmission from importations; however the transmission chains that later dominated the Delta wave in England had been already seeded before restrictions were introduced. In England, increasing inter-regional travel drove Delta's nationwide dissemination, with some cities receiving >2,000 observable lineage introductions from other regions. Subsequently, increased levels of local population mixing, not the number of importations, was associated with faster relative growth of Delta. Among US states, we find that regions that previously experienced large waves also had faster Delta growth rates, and a model including interactions between immunity and human behaviour could accurately predict the rise of Delta there. Delta’s invasion dynamics depended on fine scale spatial heterogeneity in immunity and contact patterns and our findings will inform optimal spatial interventions to reduce transmission of current and future VOCs such as Omicron.
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Affiliation(s)
- John T McCrone
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Verity Hill
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Sumali Bajaj
- Department of Zoology, University of Oxford, Oxford, UK
| | | | - Ben C Lambert
- Department of Computer Science, University of Oxford, Oxford, UK
| | - Rhys Inward
- Department of Zoology, University of Oxford, Oxford, UK
- MRC Centre of Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Samir Bhatt
- MRC Centre of Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Erik Volz
- MRC Centre of Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Christopher Ruis
- Molecular Immunity Unit, Department of Medicine, Cambridge University, Cambridge, UK
| | - Simon Dellicour
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Bruxelles, Belgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | | | | | - Neo Wu
- Google, Mountain View, CA, USA
| | | | - Xiang Ji
- Department of Mathematics, School of Science & Engineering, Tulane University, New Orleans, LA, USA
| | | | - Ben Jackson
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Rachel Colquhoun
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Áine O'Toole
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Thomas P Peacock
- Department of Infectious Disease, Imperial College London, London, UK
- UK Health Security Agency, London, UK
| | | | | | | | | | - Nuno R Faria
- Department of Zoology, University of Oxford, Oxford, UK
- MRC Centre of Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil
| | | | - Isaac I Bogoch
- Divisions of Internal Medicine & Infectious Diseases, Toronto General Hospital, University Health Network, Toronto, Canada
- Department of Medicine, Division of Infectious Diseases, University of Toronto, ON, Canada
| | - Kamran Khan
- BlueDot, Toronto, Canada
- Department of Medicine, Division of Infectious Diseases, University of Toronto, ON, Canada
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON, Canada
| | | | | | - David M Aanensen
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Wendy S Barclay
- Department of Infectious Disease, Imperial College London, London, UK
| | | | - Thomas Connor
- Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff, UK
- School of Biosciences, The Sir Martin Evans Building, Cardiff University, Cardiff, UK
- Quadram Institute, Norwich, UK
| | - Nicholas J Loman
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Marc A Suchard
- Departments of Biostatistics, Biomathematics and Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, UK
- Department of Pathobiology and Population Sciences, Royal Veterinary College London, London, UK
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
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Scott L, Hsiao NY, Moyo S, Singh L, Tegally H, Dor G, Maes P, Pybus OG, Kraemer MUG, Semenova E, Bhatt S, Flaxman S, Faria NR, de Oliveira T. Track Omicron's spread with molecular data. Science 2021; 374:1454-1455. [PMID: 34882437 DOI: 10.1126/science.abn4543] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Lesley Scott
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa
| | - Nei-Yuan Hsiao
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.,National Health Laboratory Service, Cape Town, South Africa
| | - Sikhuline Moyo
- Botswana Harvard AIDS Institute Partnership and Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
| | - Lavanya Singh
- Centre for Epidemic Response and Innovation, Stellenbosch University, Stellenbosch, South Africa.,KwaZulu-Natal Research Innovation and Sequencing Platform, University of KwaZulu-Natal, Durban, South Africa
| | - Houriiyah Tegally
- Centre for Epidemic Response and Innovation, Stellenbosch University, Stellenbosch, South Africa.,KwaZulu-Natal Research Innovation and Sequencing Platform, University of KwaZulu-Natal, Durban, South Africa
| | - Graeme Dor
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa
| | - Piet Maes
- Laboratory of Clinical and Epidemiological Virology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, UK.,Royal Veterinary College, London, UK
| | | | | | - Samir Bhatt
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark.,MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK.,The Abdul Latif Jameel Institute for Disease and Emergency Analytics, School of Public Health, Imperial College London, London, UK
| | - Seth Flaxman
- Department of Computer Science, University of Oxford, Oxford, UK
| | - Nuno R Faria
- Department of Zoology, University of Oxford, Oxford, UK.,MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK.,The Abdul Latif Jameel Institute for Disease and Emergency Analytics, School of Public Health, Imperial College London, London, UK.,Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Tulio de Oliveira
- Centre for Epidemic Response and Innovation, Stellenbosch University, Stellenbosch, South Africa.,KwaZulu-Natal Research Innovation and Sequencing Platform, University of KwaZulu-Natal, Durban, South Africa
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38
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Brito AF, Semenova E, Dudas G, Hassler GW, Kalinich CC, Kraemer MU, Ho J, Tegally H, Githinji G, Agoti CN, Matkin LE, Whittaker C, Howden BP, Sintchenko V, Zuckerman NS, Mor O, Blankenship HM, de Oliveira T, Lin RTP, Siqueira MM, Resende PC, Vasconcelos ATR, Spilki FR, Aguiar RS, Alexiev I, Ivanov IN, Philipova I, Carrington CVF, Sahadeo NSD, Gurry C, Maurer-Stroh S, Naidoo D, von Eije KJ, Perkins MD, van Kerkhove M, Hill SC, Sabino EC, Pybus OG, Dye C, Bhatt S, Flaxman S, Suchard MA, Grubaugh ND, Baele G, Faria NR. Global disparities in SARS-CoV-2 genomic surveillance. medRxiv 2021:2021.08.21.21262393. [PMID: 34462754 PMCID: PMC8404891 DOI: 10.1101/2021.08.21.21262393] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Genomic sequencing provides critical information to track the evolution and spread of SARS-CoV-2, optimize molecular tests, treatments and vaccines, and guide public health responses. To investigate the spatiotemporal heterogeneity in the global SARS-CoV-2 genomic surveillance, we estimated the impact of sequencing intensity and turnaround times (TAT) on variant detection in 167 countries. Most countries submit genomes >21 days after sample collection, and 77% of low and middle income countries sequenced <0.5% of their cases. We found that sequencing at least 0.5% of the cases, with a TAT <21 days, could be a benchmark for SARS-CoV-2 genomic surveillance efforts. Socioeconomic inequalities substantially impact our ability to quickly detect SARS-CoV-2 variants, and undermine the global pandemic preparedness.
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Affiliation(s)
- Anderson F. Brito
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
- Instituto Todos pela Saúde, São Paulo, São Paulo, Brazil
| | - Elizaveta Semenova
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
- Department of Mathematics, Imperial College London, London, UK
| | - Gytis Dudas
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Gabriel W. Hassler
- Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Chaney C. Kalinich
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
- Yale School of Medicine, Yale University, New Haven, Connecticut, USA
| | | | - Joses Ho
- GISAID Global Data Science Initiative, Munich, Germany
- Bioinformatics Institute & ID Labs, Agency for Science Technology and Research, Singapore, Singapore
| | - Houriiyah Tegally
- KwaZulu–Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu–Natal, Durban, South Africa
| | - George Githinji
- KEMRI-Wellcome Trust Research Programme, Kenya
- Department of Biochemistry and Biotechnology, Pwani University, Kenya
| | | | - Lucy E. Matkin
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, United Kingdom
| | | | | | | | | | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Vitali Sintchenko
- Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, New South Wales, Australia
- Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, New South Wales 2145, Australia
| | - Neta S. Zuckerman
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Israel
| | - Orna Mor
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Israel
| | - Heather M Blankenship
- Michigan Department of Health and Human Services, Bureau of Laboratories, Lansing, Michigan, USA
| | - Tulio de Oliveira
- KwaZulu–Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu–Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | | | | | | | | | - Fernando R. Spilki
- Feevale University, Institute of Health Sciences, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Renato Santana Aguiar
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Instituto D’Or de Pesquisa e Ensino (IDOR), Rio de Janeiro, Brazil
| | - Ivailo Alexiev
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Ivan N. Ivanov
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Ivva Philipova
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Christine V. F. Carrington
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Nikita S. D. Sahadeo
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Céline Gurry
- GISAID Global Data Science Initiative, Munich, Germany
| | - Sebastian Maurer-Stroh
- GISAID Global Data Science Initiative, Munich, Germany
- Bioinformatics Institute & ID Labs, Agency for Science Technology and Research, Singapore, Singapore
- National Centre for Infectious Diseases, Singapore
| | - Dhamari Naidoo
- Health Emergencies Programme, World Health Organization Regional Office for South-East Asia, New Delhi, India
| | - Karin J von Eije
- Department of Medical Microbiology and Infection Prevention, Division of Clinical Virology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Emerging Diseases and Zoonoses Unit, Health Emergencies Programme, World Health Organization, Geneva, Switzerland
| | - Mark D. Perkins
- Emerging Diseases and Zoonoses Unit, Health Emergencies Programme, World Health Organization, Geneva, Switzerland
| | - Maria van Kerkhove
- Emerging Diseases and Zoonoses Unit, Health Emergencies Programme, World Health Organization, Geneva, Switzerland
| | | | - Ester C. Sabino
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Oliver G. Pybus
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Royal Veterinary College, Hawkshead, United Kingdom
| | - Christopher Dye
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Samir Bhatt
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, United Kingdom
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Seth Flaxman
- Department of Computer Science, University of Oxford, Oxford, United Kingdom
| | - Marc A. Suchard
- Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, California, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Nuno R. Faria
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom
- Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, New South Wales, Australia
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
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Nicolete VC, Rodrigues PT, Johansen IC, Corder RM, Tonini J, Cardoso MA, de Jesus JG, Claro IM, Faria NR, Sabino EC, Castro MC, Ferreira MU. Interacting Epidemics in Amazonian Brazil: Prior Dengue Infection Associated With Increased Coronavirus Disease 2019 (COVID-19) Risk in a Population-Based Cohort Study. Clin Infect Dis 2021; 73:2045-2054. [PMID: 33956939 PMCID: PMC8135953 DOI: 10.1093/cid/ciab410] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Immunity after dengue virus (DENV) infection has been suggested to cross-protect from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and mortality. METHODS We tested whether serologically proven prior DENV infection diagnosed in September-October 2019, before the coronavirus disease 2019 (COVID-19) pandemic, reduced the risk of SARS-CoV-2 infection and clinically apparent COVID-19 over the next 13 months in a population-based cohort in Amazonian Brazil. Mixed-effects multiple logistic regression analysis was used to identify predictors of infection and disease, adjusting for potential individual and household-level confounders. Virus genomes from 14 local SARS-CoV-2 isolates were obtained using whole-genome sequencing. RESULTS Anti-DENV immunoglobulin G (IgG) was found in 37.0% of 1285 cohort participants (95% confidence interval [CI]: 34.3% to 39.7%) in 2019, with 10.4 (95% CI: 6.7-15.5) seroconversion events per 100 person-years during the follow-up. In 2020, 35.2% of the participants (95% CI: 32.6% to 37.8%) had anti-SARS-CoV-2 IgG and 57.1% of the 448 SARS-CoV-2 seropositives (95% CI: 52.4% to 61.8%) reported clinical manifestations at the time of infection. Participants aged >60 years were twice more likely to have symptomatic COVID-19 than children under 5 years. Locally circulating SARS-CoV-2 isolates were assigned to the B.1.1.33 lineage. Contrary to the cross-protection hypothesis, prior DENV infection was associated with twice the risk of clinically apparent COVID-19 upon SARS-CoV-2 infection, with P values between .025 and .039 after adjustment for identified confounders. CONCLUSIONS Higher risk of clinically apparent COVID-19 among individuals with prior dengue has important public health implications for communities sequentially exposed to DENV and SARS-CoV-2 epidemics.
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Affiliation(s)
- Vanessa C Nicolete
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Priscila T Rodrigues
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Igor C Johansen
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Rodrigo M Corder
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Juliana Tonini
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Marly A Cardoso
- Department of Nutrition, School of Public Health, University of São Paulo, São Paulo, Brazil
| | - Jaqueline G de Jesus
- Institute of Tropical Medicine and Department of Infectious and Parasitic Diseases, Medical School, University of São Paulo, São Paulo, Brazil
| | - Ingra M Claro
- Institute of Tropical Medicine and Department of Infectious and Parasitic Diseases, Medical School, University of São Paulo, São Paulo, Brazil
| | - Nuno R Faria
- Institute of Tropical Medicine and Department of Infectious and Parasitic Diseases, Medical School, University of São Paulo, São Paulo, Brazil.,Department of Infectious Disease Epidemiology, Imperial College London, ,London, UK.,Department of Zoology, University of Oxford, Oxford, UK
| | - Ester C Sabino
- Institute of Tropical Medicine and Department of Infectious and Parasitic Diseases, Medical School, University of São Paulo, São Paulo, Brazil
| | - Marcia C Castro
- Department of Global Health and Population, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Marcelo U Ferreira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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Brizzi A, Whittaker C, Servo LMS, Hawryluk I, Prete CA, de Souza WM, Aguiar RS, Araujo LJT, Bastos LS, Blenkinsop A, Buss LF, Candido D, Castro MC, Costa SF, Croda J, de Souza Santos AA, Dye C, Flaxman S, Fonseca PLC, Geddes VEV, Gutierrez B, Lemey P, Levin AS, Mellan T, Bonfim DM, Miscouridou X, Mishra S, Monod M, Moreira FRR, Nelson B, Pereira RHM, Ranzani O, Schnekenberg RP, Semenova E, Sonnabend R, Souza RP, Xi X, Sabino EC, Faria NR, Bhatt S, Ratmann O. Report 46: Factors driving extensive spatial and temporal fluctuations in COVID-19 fatality rates in Brazilian hospitals. medRxiv 2021:2021.11.01.21265731. [PMID: 34751273 PMCID: PMC8575144 DOI: 10.1101/2021.11.01.21265731] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The SARS-CoV-2 Gamma variant spread rapidly across Brazil, causing substantial infection and death waves. We use individual-level patient records following hospitalisation with suspected or confirmed COVID-19 to document the extensive shocks in hospital fatality rates that followed Gamma's spread across 14 state capitals, and in which more than half of hospitalised patients died over sustained time periods. We show that extensive fluctuations in COVID-19 in-hospital fatality rates also existed prior to Gamma's detection, and were largely transient after Gamma's detection, subsiding with hospital demand. Using a Bayesian fatality rate model, we find that the geographic and temporal fluctuations in Brazil's COVID-19 in-hospital fatality rates are primarily associated with geographic inequities and shortages in healthcare capacity. We project that approximately half of Brazil's COVID-19 deaths in hospitals could have been avoided without pre-pandemic geographic inequities and without pandemic healthcare pressure. Our results suggest that investments in healthcare resources, healthcare optimization, and pandemic preparedness are critical to minimize population wide mortality and morbidity caused by highly transmissible and deadly pathogens such as SARS-CoV-2, especially in low- and middle-income countries. NOTE The following manuscript has appeared as 'Report 46 - Factors driving extensive spatial and temporal fluctuations in COVID-19 fatality rates in Brazilian hospitals' at https://spiral.imperial.ac.uk:8443/handle/10044/1/91875 . ONE SENTENCE SUMMARY COVID-19 in-hospital fatality rates fluctuate dramatically in Brazil, and these fluctuations are primarily associated with geographic inequities and shortages in healthcare capacity.
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Affiliation(s)
- Andrea Brizzi
- Department of Mathematics, Imperial College London, London, United Kingdom
| | - Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, United Kingdom
| | | | - Iwona Hawryluk
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, United Kingdom
| | - Carlos A Prete
- Departamento de Engenharia de Sistemas Eletrônicos, Escola Politécnica da Universidade de São Paulo, São Paulo, Brazil
| | - William M de Souza
- World Reference Center for Emerging Viruses and Arboviruses and Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Renato S Aguiar
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Instituto D'Or de Pesquisa e Ensino (IDOR), Rio de Janeiro, Brazil
| | - Leonardo J T Araujo
- Laboratory of Quantitative Pathology, Center of Pathology, Adolfo Lutz Institute, São Paulo, Brazil
| | - Leonardo S Bastos
- Programa de Computação Científica, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | | | - Lewis F Buss
- Departamento de Moléstias Infecciosas e Parasitárias e Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brasil
| | - Darlan Candido
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Marcia C Castro
- Department of Global Health and Population, Harvard T.H. Chan School of Public Health, Boston, United States
| | - Silvia F Costa
- Departamento de Moléstias Infecciosas e Parasitárias e Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brasil
| | - Julio Croda
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, United States
| | | | - Christopher Dye
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Seth Flaxman
- Department of Computer Science, University of Oxford, Oxford, United Kingdom
| | - Paula L C Fonseca
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Victor E V Geddes
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, KU Leuven - University of Leuven, Leuven, Belgium
| | - Anna S Levin
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Thomas Mellan
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, United Kingdom
| | - Diego M Bonfim
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Xenia Miscouridou
- Department of Mathematics, Imperial College London, London, United Kingdom
| | - Swapnil Mishra
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, United Kingdom
- Section of Epidemiology, School of Public Health, University of Copenhagen, Denmark, Copenhagen
| | - Mélodie Monod
- Department of Mathematics, Imperial College London, London, United Kingdom
| | - Filipe R R Moreira
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Bruce Nelson
- Environmental Dynamics, INPA, National Institute for Amazon Research, Bairro Petropolis, Brazil
| | | | - Otavio Ranzani
- Barcelona Institute for Global Health, ISGlobal, Barcelona, Spain
| | - Ricardo P Schnekenberg
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Elizaveta Semenova
- Department of Mathematics, Imperial College London, London, United Kingdom
| | - Raphael Sonnabend
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, United Kingdom
| | - Renan P Souza
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Xiaoyue Xi
- Department of Mathematics, Imperial College London, London, United Kingdom
| | - Ester C Sabino
- Programa de Computação Científica, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Nuno R Faria
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, United Kingdom
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Samir Bhatt
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, United Kingdom
- Section of Epidemiology, School of Public Health, University of Copenhagen
| | - Oliver Ratmann
- Department of Mathematics, Imperial College London, London, United Kingdom
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Souza WM, Amorim MR, Sesti-Costa R, Coimbra LD, Brunetti NS, Toledo-Teixeira DA, de Souza GF, Muraro SP, Parise PL, Barbosa PP, Bispo-dos-Santos K, Mofatto LS, Simeoni CL, Claro IM, Duarte ASS, Coletti TM, Zangirolami AB, Costa-Lima C, Gomes ABSP, Buscaratti LI, Sales FC, Costa VA, Franco LAM, Candido DS, Pybus OG, de Jesus JG, Silva CAM, Ramundo MS, Ferreira GM, Pinho MC, Souza LM, Rocha EC, Andrade PS, Crispim MAE, Maktura GC, Manuli ER, Santos MNN, Camilo CC, Angerami RN, Moretti ML, Spilki FR, Arns CW, Addas-Carvalho M, Benites BD, Vinolo MAR, Mori MAS, Gaburo N, Dye C, Marques-Souza H, Marques RE, Farias AS, Diamond MS, Faria NR, Sabino EC, Granja F, Proença-Módena JL. Neutralisation of SARS-CoV-2 lineage P.1 by antibodies elicited through natural SARS-CoV-2 infection or vaccination with an inactivated SARS-CoV-2 vaccine: an immunological study. Lancet Microbe 2021; 2:e527-e535. [PMID: 34258603 PMCID: PMC8266272 DOI: 10.1016/s2666-5247(21)00129-4] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
BACKGROUND Mutations accrued by SARS-CoV-2 lineage P.1-first detected in Brazil in early January, 2021-include amino acid changes in the receptor-binding domain of the viral spike protein that also are reported in other variants of concern, including B.1.1.7 and B.1.351. We aimed to investigate whether isolates of wild-type P.1 lineage SARS-CoV-2 can escape from neutralising antibodies generated by a polyclonal immune response. METHODS We did an immunological study to assess the neutralising effects of antibodies on lineage P.1 and lineage B isolates of SARS-CoV-2, using plasma samples from patients previously infected with or vaccinated against SARS-CoV-2. Two specimens (P.1/28 and P.1/30) containing SARS-CoV-2 lineage P.1 (as confirmed by viral genome sequencing) were obtained from nasopharyngeal and bronchoalveolar lavage samples collected from patients in Manaus, Brazil, and compared against an isolate of SARS-CoV-2 lineage B (SARS.CoV2/SP02.2020) recovered from a patient in Brazil in February, 2020. Isolates were incubated with plasma samples from 21 blood donors who had previously had COVID-19 and from a total of 53 recipients of the chemically inactivated SARS-CoV-2 vaccine CoronaVac: 18 individuals after receipt of a single dose and an additional 20 individuals (38 in total) after receipt of two doses (collected 17-38 days after the most recent dose); and 15 individuals who received two doses during the phase 3 trial of the vaccine (collected 134-230 days after the second dose). Antibody neutralisation of P.1/28, P.1/30, and B isolates by plasma samples were compared in terms of median virus neutralisation titre (VNT50, defined as the reciprocal value of the sample dilution that showed 50% protection against cytopathic effects). FINDINGS In terms of VNT50, plasma from individuals previously infected with SARS-CoV-2 had an 8·6 times lower neutralising capacity against the P.1 isolates (median VNT50 30 [IQR <20-45] for P.1/28 and 30 [<20-40] for P.1/30) than against the lineage B isolate (260 [160-400]), with a binominal model showing significant reductions in lineage P.1 isolates compared with the lineage B isolate (p≤0·0001). Efficient neutralisation of P.1 isolates was not seen with plasma samples collected from individuals vaccinated with a first dose of CoronaVac 20-23 days earlier (VNT50s below the limit of detection [<20] for most plasma samples), a second dose 17-38 days earlier (median VNT50 24 [IQR <20-25] for P.1/28 and 28 [<20-25] for P.1/30), or a second dose 134-260 days earlier (all VNT50s below limit of detection). Median VNT50s against the lineage B isolate were 20 (IQR 20-30) after a first dose of CoronaVac 20-23 days earlier, 75 (<20-263) after a second dose 17-38 days earlier, and 20 (<20-30) after a second dose 134-260 days earlier. In plasma collected 17-38 days after a second dose of CoronaVac, neutralising capacity against both P.1 isolates was significantly decreased (p=0·0051 for P.1/28 and p=0·0336 for P.1/30) compared with that against the lineage B isolate. All data were corroborated by results obtained through plaque reduction neutralisation tests. INTERPRETATION SARS-CoV-2 lineage P.1 might escape neutralisation by antibodies generated in response to polyclonal stimulation against previously circulating variants of SARS-CoV-2. Continuous genomic surveillance of SARS-CoV-2 combined with antibody neutralisation assays could help to guide national immunisation programmes. FUNDING São Paulo Research Foundation, Brazilian Ministry of Science, Technology and Innovation and Funding Authority for Studies, Medical Research Council, National Council for Scientific and Technological Development, National Institutes of Health. TRANSLATION For the Portuguese translation of the abstract see Supplementary Materials section.
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Affiliation(s)
- William M Souza
- Virology Research Centre, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Mariene R Amorim
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Renata Sesti-Costa
- Brazilian Biosciences National Laboratory, Brazilian Centre for Research in Energy and Materials, Campinas, Brazil
- Hematology and Hemotherapy Center, University of Campinas, Campinas, Brazil
| | - Lais D Coimbra
- Brazilian Biosciences National Laboratory, Brazilian Centre for Research in Energy and Materials, Campinas, Brazil
| | - Natalia S Brunetti
- Autoimmune Research Laboratory, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Daniel A Toledo-Teixeira
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Gabriela F de Souza
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Stefanie P Muraro
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Pierina L Parise
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Priscilla P Barbosa
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Karina Bispo-dos-Santos
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Luciana S Mofatto
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Camila L Simeoni
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Ingra M Claro
- Tropical Medicine Institute, Medical School, University of São Paulo, São Paulo, Brazil
- Department of Infectious and Parasitic Disease, Medical School, University of São Paulo, São Paulo, Brazil
| | - Adriana S S Duarte
- Hematology and Hemotherapy Center, University of Campinas, Campinas, Brazil
| | - Thais M Coletti
- Tropical Medicine Institute, Medical School, University of São Paulo, São Paulo, Brazil
| | | | | | - Arilson B S P Gomes
- Laboratory of Immunoinflammation, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Lucas I Buscaratti
- Brazilian Laboratory on Silencing Technologies, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Flavia C Sales
- Tropical Medicine Institute, Medical School, University of São Paulo, São Paulo, Brazil
- Department of Infectious and Parasitic Disease, Medical School, University of São Paulo, São Paulo, Brazil
| | - Vitor A Costa
- Hematology and Transfusion Medicine Center, University of Campinas, Campinas, Brazil
| | - Lucas A M Franco
- Tropical Medicine Institute, Medical School, University of São Paulo, São Paulo, Brazil
| | | | | | - Jaqueline G de Jesus
- Tropical Medicine Institute, Medical School, University of São Paulo, São Paulo, Brazil
| | - Camila A M Silva
- Tropical Medicine Institute, Medical School, University of São Paulo, São Paulo, Brazil
| | - Mariana S Ramundo
- Tropical Medicine Institute, Medical School, University of São Paulo, São Paulo, Brazil
| | - Giulia M Ferreira
- Hematology and Transfusion Medicine Center, University of Campinas, Campinas, Brazil
- Tropical Medicine Institute, Medical School, University of São Paulo, São Paulo, Brazil
- Laboratory of Virology, Institute of Biomedical Sciences, Federal University of Uberlândia, Uberlândia, Brazil
| | - Mariana C Pinho
- Tropical Medicine Institute, Medical School, University of São Paulo, São Paulo, Brazil
| | - Leandro M Souza
- Tropical Medicine Institute, Medical School, University of São Paulo, São Paulo, Brazil
| | - Esmenia C Rocha
- Tropical Medicine Institute, Medical School, University of São Paulo, São Paulo, Brazil
| | - Pamela S Andrade
- Tropical Medicine Institute, Medical School, University of São Paulo, São Paulo, Brazil
- School of Public Health, University of São Paulo, São Paulo, Brazil
| | - Myuki A E Crispim
- Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas, Manaus, Brazil
| | - Grazielle C Maktura
- Brazilian Laboratory on Silencing Technologies, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Erika R Manuli
- Tropical Medicine Institute, Medical School, University of São Paulo, São Paulo, Brazil
- Department of Infectious and Parasitic Disease, Medical School, University of São Paulo, São Paulo, Brazil
| | - Magnun N N Santos
- Department of Clinical Pathology, School of Medical Sciences, University of Campinas, Campinas, Brazil
| | | | - Rodrigo N Angerami
- Department of Internal Medicine, School of Medical Sciences, University of Campinas, Campinas, Brazil
- Campinas Department of Public Health Surveillance, Campinas, Brazil
| | - Maria L Moretti
- Department of Internal Medicine, School of Medical Sciences, University of Campinas, Campinas, Brazil
| | | | - Clarice W Arns
- Animal Virology Laboratory, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
| | | | - Bruno D Benites
- Hematology and Transfusion Medicine Center, University of Campinas, Campinas, Brazil
| | - Marco A R Vinolo
- Laboratory of Immunoinflammation, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Marcelo A S Mori
- Experimental Medicine Research Cluster, University of Campinas, Campinas, Brazil
- Obesity and Comorbidities Research Center, University of Campinas, Campinas, Brazil
- Laboratory of Aging Biology, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, Brazil
| | | | | | - Henrique Marques-Souza
- Brazilian Laboratory on Silencing Technologies, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Rafael E Marques
- Brazilian Biosciences National Laboratory, Brazilian Centre for Research in Energy and Materials, Campinas, Brazil
| | - Alessandro S Farias
- Autoimmune Research Laboratory, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
- Experimental Medicine Research Cluster, University of Campinas, Campinas, Brazil
- Obesity and Comorbidities Research Center, University of Campinas, Campinas, Brazil
| | - Michael S Diamond
- Departments of Medicine, Molecular Microbiology, Pathology, and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Nuno R Faria
- Tropical Medicine Institute, Medical School, University of São Paulo, São Paulo, Brazil
- Department of Zoology, University of Oxford, UK
- Medical Research Council Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Ester C Sabino
- Tropical Medicine Institute, Medical School, University of São Paulo, São Paulo, Brazil
- Department of Infectious and Parasitic Disease, Medical School, University of São Paulo, São Paulo, Brazil
| | - Fabiana Granja
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
- Biodiversity Research Centre, Federal University of Roraima, Boa Vista, Brazil
| | - Jose Luiz Proença-Módena
- Laboratory of Emerging Viruses, Department of Genetics, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
- Experimental Medicine Research Cluster, University of Campinas, Campinas, Brazil
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Kraemer MUG, Hill V, Ruis C, Dellicour S, Bajaj S, McCrone JT, Baele G, Parag KV, Battle AL, Gutierrez B, Jackson B, Colquhoun R, O'Toole Á, Klein B, Vespignani A, Volz E, Faria NR, Aanensen DM, Loman NJ, du Plessis L, Cauchemez S, Rambaut A, Scarpino SV, Pybus OG. Spatiotemporal invasion dynamics of SARS-CoV-2 lineage B.1.1.7 emergence. Science 2021; 373:889-895. [PMID: 34301854 PMCID: PMC9269003 DOI: 10.1126/science.abj0113] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 07/12/2021] [Indexed: 12/24/2022]
Abstract
Understanding the causes and consequences of the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern is crucial to pandemic control yet difficult to achieve because they arise in the context of variable human behavior and immunity. We investigated the spatial invasion dynamics of lineage B.1.1.7 by jointly analyzing UK human mobility, virus genomes, and community-based polymerase chain reaction data. We identified a multistage spatial invasion process in which early B.1.1.7 growth rates were associated with mobility and asymmetric lineage export from a dominant source location, enhancing the effects of B.1.1.7's increased intrinsic transmissibility. We further explored how B.1.1.7 spread was shaped by nonpharmaceutical interventions and spatial variation in previous attack rates. Our findings show that careful accounting of the behavioral and epidemiological context within which variants of concern emerge is necessary to interpret correctly their observed relative growth rates.
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Affiliation(s)
- Moritz U G Kraemer
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil.
- Department of Zoology, University of Oxford, Oxford, UK
| | - Verity Hill
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Christopher Ruis
- Department of Zoology, University of Oxford, Oxford, UK
- Molecular Immunity Unit, Department of Medicine, Cambridge University, Cambridge, UK
| | - Simon Dellicour
- Network Science Institute, Northeastern University, Boston, USA
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Bruxelles, Belgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Sumali Bajaj
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil
- Department of Zoology, University of Oxford, Oxford, UK
| | - John T McCrone
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Guy Baele
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, UK
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Kris V Parag
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Anya Lindström Battle
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Bernardo Gutierrez
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil
- Department of Plant Sciences, University of Oxford, Oxford, UK
- Department of Zoology, University of Oxford, Oxford, UK
| | - Ben Jackson
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Rachel Colquhoun
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Áine O'Toole
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Brennan Klein
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
- Network Science Institute, Northeastern University, Boston, USA
| | - Alessandro Vespignani
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
- Network Science Institute, Northeastern University, Boston, USA
| | - Erik Volz
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Nuno R Faria
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil
| | - David M Aanensen
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Bruxelles, Belgium
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Nicholas J Loman
- Molecular Immunity Unit, Department of Medicine, Cambridge University, Cambridge, UK
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Louis du Plessis
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil
- Department of Zoology, University of Oxford, Oxford, UK
| | - Simon Cauchemez
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
| | - Andrew Rambaut
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, CNRS, Paris, France.
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Samuel V Scarpino
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium.
- Network Science Institute, Northeastern University, Boston, USA
- Vermont Complex Systems Center, University of Vermont, Burlington, USA
- Santa Fe Institute, Santa Fe, USA
| | - Oliver G Pybus
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil.
- Department of Zoology, University of Oxford, Oxford, UK
- Department of Pathobiology and Population Sciences, Royal Veterinary College London, London, UK
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Dellicour S, Gill MS, Faria NR, Rambaut A, Pybus OG, Suchard MA, Lemey P. Relax, Keep Walking - A Practical Guide to Continuous Phylogeographic Inference with BEAST. Mol Biol Evol 2021; 38:3486-3493. [PMID: 33528560 PMCID: PMC8321535 DOI: 10.1093/molbev/msab031] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Spatially explicit phylogeographic analyses can be performed with an inference framework that employs relaxed random walks to reconstruct phylogenetic dispersal histories in continuous space. This core model was first implemented 10 years ago and has opened up new opportunities in the field of phylodynamics, allowing researchers to map and analyze the spatial dissemination of rapidly evolving pathogens. We here provide a detailed and step-by-step guide on how to set up, run, and interpret continuous phylogeographic analyses using the programs BEAUti, BEAST, Tracer, and TreeAnnotator.
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Affiliation(s)
- Simon Dellicour
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Bruxelles, Belgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Mandev S Gill
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Nuno R Faria
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, United Kingdom
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Marc A Suchard
- Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
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Amorim MR, Souza WM, Barros ACG, Toledo-Teixeira DA, Dos-Santos KB, Simeoni CL, Parise PL, Vieira A, Forato J, Claro IM, Mofatto LS, Barbosa PP, Brunetti NS, França ESS, Pedroso GA, Carvalho BFN, Zaccariotto TR, Krywacz KCS, Vieira AS, Mori MA, Farias AS, Pavan MHP, Bachur LF, Cardoso LGO, Spilki FR, Sabino EC, Faria NR, Santos MNN, Angerami R, Leme PAF, Schreiber A, Moretti ML, Granja F, Proenca-Modena JL. Respiratory Viral Shedding in Healthcare Workers Reinfected with SARS-CoV-2, Brazil, 2020. Emerg Infect Dis 2021; 27:1737-1740. [PMID: 33871331 PMCID: PMC8153890 DOI: 10.3201/eid2706.210558] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
We documented 4 cases of severe acute respiratory syndrome coronavirus 2 reinfection by non-variant of concern strains among healthcare workers in Campinas, Brazil. We isolated infectious particles from nasopharyngeal secretions during both infection episodes. Improved and continued protection measures are necessary to mitigate the risk for reinfection among healthcare workers.
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Faria NR, Mellan TA, Whittaker C, Claro IM, Candido DDS, Mishra S, Crispim MAE, Sales FCS, Hawryluk I, McCrone JT, Hulswit RJG, Franco LAM, Ramundo MS, de Jesus JG, Andrade PS, Coletti TM, Ferreira GM, Silva CAM, Manuli ER, Pereira RHM, Peixoto PS, Kraemer MUG, Gaburo N, Camilo CDC, Hoeltgebaum H, Souza WM, Rocha EC, de Souza LM, de Pinho MC, Araujo LJT, Malta FSV, de Lima AB, Silva JDP, Zauli DAG, Ferreira ACDS, Schnekenberg RP, Laydon DJ, Walker PGT, Schlüter HM, Dos Santos ALP, Vidal MS, Del Caro VS, Filho RMF, Dos Santos HM, Aguiar RS, Proença-Modena JL, Nelson B, Hay JA, Monod M, Miscouridou X, Coupland H, Sonabend R, Vollmer M, Gandy A, Prete CA, Nascimento VH, Suchard MA, Bowden TA, Pond SLK, Wu CH, Ratmann O, Ferguson NM, Dye C, Loman NJ, Lemey P, Rambaut A, Fraiji NA, Carvalho MDPSS, Pybus OG, Flaxman S, Bhatt S, Sabino EC. Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil. Science 2021; 372:815-821. [PMID: 33853970 PMCID: PMC8139423 DOI: 10.1126/science.abh2644] [Citation(s) in RCA: 872] [Impact Index Per Article: 290.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 04/11/2021] [Indexed: 12/17/2022]
Abstract
Cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in Manaus, Brazil, resurged in late 2020 despite previously high levels of infection. Genome sequencing of viruses sampled in Manaus between November 2020 and January 2021 revealed the emergence and circulation of a novel SARS-CoV-2 variant of concern. Lineage P.1 acquired 17 mutations, including a trio in the spike protein (K417T, E484K, and N501Y) associated with increased binding to the human ACE2 (angiotensin-converting enzyme 2) receptor. Molecular clock analysis shows that P.1 emergence occurred around mid-November 2020 and was preceded by a period of faster molecular evolution. Using a two-category dynamical model that integrates genomic and mortality data, we estimate that P.1 may be 1.7- to 2.4-fold more transmissible and that previous (non-P.1) infection provides 54 to 79% of the protection against infection with P.1 that it provides against non-P.1 lineages. Enhanced global genomic surveillance of variants of concern, which may exhibit increased transmissibility and/or immune evasion, is critical to accelerate pandemic responsiveness.
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Affiliation(s)
- Nuno R Faria
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK.
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Department of Zoology, University of Oxford, Oxford, UK
| | - Thomas A Mellan
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK
| | - Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK
| | - Ingra M Claro
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Darlan da S Candido
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Department of Zoology, University of Oxford, Oxford, UK
| | - Swapnil Mishra
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK
| | - Myuki A E Crispim
- Fundação Hospitalar de Hematologia e Hemoterapia, Manaus, Brazil
- Diretoria de Ensino e Pesquisa, Fundação Hospitalar de Hematologia e Hemoterapia, Manaus, Brazil
| | - Flavia C S Sales
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Iwona Hawryluk
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK
| | - John T McCrone
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Ruben J G Hulswit
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Lucas A M Franco
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Mariana S Ramundo
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Jaqueline G de Jesus
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Pamela S Andrade
- Departamento de Epidemiologia, Faculdade de Saúde Pública da Universidade de São Paulo, Sao Paulo, Brazil
| | - Thais M Coletti
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Giulia M Ferreira
- Laboratório de Virologia, Instituto de Ciências Biomédicas, Universidade Federal de Uberlândia, Uberlândia, Brazil
| | - Camila A M Silva
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Erika R Manuli
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | | | - Pedro S Peixoto
- Institute of Mathematics and Statistics, University of São Paulo, São Paulo, Brazil
| | | | | | | | | | - William M Souza
- Virology Research Centre, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Esmenia C Rocha
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Leandro M de Souza
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Mariana C de Pinho
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Leonardo J T Araujo
- Laboratory of Quantitative Pathology, Center of Pathology, Adolfo Lutz Institute, São Paulo, Brazil
| | | | | | | | | | | | | | - Daniel J Laydon
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK
| | - Patrick G T Walker
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK
| | | | | | | | | | | | | | - Renato S Aguiar
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - José L Proença-Modena
- Laboratory of Emerging Viruses, Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas (UNICAMP), São Paulo, Brazil
| | - Bruce Nelson
- Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
| | - James A Hay
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Center for Communicable Disease Dynamics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Mélodie Monod
- Department of Mathematics, Imperial College London, London, UK
| | | | - Helen Coupland
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK
| | - Raphael Sonabend
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK
| | - Michaela Vollmer
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK
| | - Axel Gandy
- Department of Mathematics, Imperial College London, London, UK
| | - Carlos A Prete
- Departamento de Engenharia de Sistemas Eletrônicos, Escola Politécnica da Universidade de São Paulo, São Paulo, Brazil
| | - Vitor H Nascimento
- Departamento de Engenharia de Sistemas Eletrônicos, Escola Politécnica da Universidade de São Paulo, São Paulo, Brazil
| | - Marc A Suchard
- Department of Biomathematics, Department of Biostatistics, and Department of Human Genetics, University of California, Los Angeles, CA, USA
| | - Thomas A Bowden
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Sergei L K Pond
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA
| | - Chieh-Hsi Wu
- Mathematical Sciences, University of Southampton, Southampton, UK
| | - Oliver Ratmann
- Department of Mathematics, Imperial College London, London, UK
| | - Neil M Ferguson
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK
| | | | - Nick J Loman
- Institute for Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Nelson A Fraiji
- Fundação Hospitalar de Hematologia e Hemoterapia, Manaus, Brazil
- Diretoria Clínica, Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas, Manaus, Brazil
| | - Maria do P S S Carvalho
- Fundação Hospitalar de Hematologia e Hemoterapia, Manaus, Brazil
- Diretoria da Presidência, Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas, Manaus, Brazil
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, UK
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, London, UK
| | - Seth Flaxman
- Department of Mathematics, Imperial College London, London, UK
| | - Samir Bhatt
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK.
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Ester C Sabino
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
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Vogels CBF, Breban MI, Ott IM, Alpert T, Petrone ME, Watkins AE, Kalinich CC, Earnest R, Rothman JE, Goes de Jesus J, Morales Claro I, Magalhães Ferreira G, Crispim MAE, Singh L, Tegally H, Anyaneji UJ, Hodcroft EB, Mason CE, Khullar G, Metti J, Dudley JT, MacKay MJ, Nash M, Wang J, Liu C, Hui P, Murphy S, Neal C, Laszlo E, Landry ML, Muyombwe A, Downing R, Razeq J, de Oliveira T, Faria NR, Sabino EC, Neher RA, Fauver JR, Grubaugh ND. Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2. PLoS Biol 2021; 19:e3001236. [PMID: 33961632 PMCID: PMC8133773 DOI: 10.1371/journal.pbio.3001236] [Citation(s) in RCA: 156] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/19/2021] [Accepted: 04/16/2021] [Indexed: 12/25/2022] Open
Abstract
With the emergence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants that may increase transmissibility and/or cause escape from immune responses, there is an urgent need for the targeted surveillance of circulating lineages. It was found that the B.1.1.7 (also 501Y.V1) variant, first detected in the United Kingdom, could be serendipitously detected by the Thermo Fisher TaqPath COVID-19 PCR assay because a key deletion in these viruses, spike Δ69-70, would cause a "spike gene target failure" (SGTF) result. However, a SGTF result is not definitive for B.1.1.7, and this assay cannot detect other variants of concern (VOC) that lack spike Δ69-70, such as B.1.351 (also 501Y.V2), detected in South Africa, and P.1 (also 501Y.V3), recently detected in Brazil. We identified a deletion in the ORF1a gene (ORF1a Δ3675-3677) in all 3 variants, which has not yet been widely detected in other SARS-CoV-2 lineages. Using ORF1a Δ3675-3677 as the primary target and spike Δ69-70 to differentiate, we designed and validated an open-source PCR assay to detect SARS-CoV-2 VOC. Our assay can be rapidly deployed in laboratories around the world to enhance surveillance for the local emergence and spread of B.1.1.7, B.1.351, and P.1.
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Affiliation(s)
- Chantal B. F. Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Mallery I. Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Isabel M. Ott
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Tara Alpert
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Mary E. Petrone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Anne E. Watkins
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Chaney C. Kalinich
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Rebecca Earnest
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Jessica E. Rothman
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Jaqueline Goes de Jesus
- Departamento de Molestias Infecciosas e Parasitarias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Ingra Morales Claro
- Departamento de Molestias Infecciosas e Parasitarias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Giulia Magalhães Ferreira
- Departamento de Molestias Infecciosas e Parasitarias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Laboratório de Virologia, Instituto de Ciências Biomédicas, Universidade Federal de Uberlândia, Uberlândia, Minas Gerais, Brazil
| | - Myuki A. E. Crispim
- Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas, Manaus, Brazil
| | | | - Lavanya Singh
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Ugochukwu J. Anyaneji
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | | | - Emma B. Hodcroft
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | | | - Gaurav Khullar
- Tempus Labs, Chicago, Illinois, United States of America
| | - Jessica Metti
- Tempus Labs, Chicago, Illinois, United States of America
| | - Joel T. Dudley
- Tempus Labs, Chicago, Illinois, United States of America
| | | | - Megan Nash
- Tempus Labs, Chicago, Illinois, United States of America
| | - Jianhui Wang
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Chen Liu
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Pei Hui
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Steven Murphy
- Murphy Medical Associates, Greenwich, Connecticut, United States of America
| | - Caleb Neal
- Murphy Medical Associates, Greenwich, Connecticut, United States of America
| | - Eva Laszlo
- Murphy Medical Associates, Greenwich, Connecticut, United States of America
| | - Marie L. Landry
- Departments of Laboratory Medicine and Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Anthony Muyombwe
- Connecticut State Department of Public Health, Rocky Hill, Connecticut, United States of America
| | - Randy Downing
- Connecticut State Department of Public Health, Rocky Hill, Connecticut, United States of America
| | - Jafar Razeq
- Connecticut State Department of Public Health, Rocky Hill, Connecticut, United States of America
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Nuno R. Faria
- Departamento de Molestias Infecciosas e Parasitarias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, United Kingdom
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Ester C. Sabino
- Departamento de Molestias Infecciosas e Parasitarias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Richard A. Neher
- Biozentrum, University of Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Joseph R. Fauver
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
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Dellicour S, Durkin K, Hong SL, Vanmechelen B, Martí-Carreras J, Gill MS, Meex C, Bontems S, André E, Gilbert M, Walker C, Maio ND, Faria NR, Hadfield J, Hayette MP, Bours V, Wawina-Bokalanga T, Artesi M, Baele G, Maes P. A Phylodynamic Workflow to Rapidly Gain Insights into the Dispersal History and Dynamics of SARS-CoV-2 Lineages. Mol Biol Evol 2021; 38:1608-1613. [PMID: 33316043 PMCID: PMC7665608 DOI: 10.1093/molbev/msaa284] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Since the start of the COVID-19 pandemic, an unprecedented number of genomic sequences of SARS-CoV-2 have been generated and shared with the scientific community. The unparalleled volume of available genetic data presents a unique opportunity to gain real-time insights into the virus transmission during the pandemic, but also a daunting computational hurdle if analyzed with gold-standard phylogeographic approaches. To tackle this practical limitation, we here describe and apply a rapid analytical pipeline to analyze the spatiotemporal dispersal history and dynamics of SARS-CoV-2 lineages. As a proof of concept, we focus on the Belgian epidemic, which has had one of the highest spatial densities of available SARS-CoV-2 genomes. Our pipeline has the potential to be quickly applied to other countries or regions, with key benefits in complementing epidemiological analyses in assessing the impact of intervention measures or their progressive easement.
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Affiliation(s)
- Simon Dellicour
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Bruxelles, Belgium.,Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Keith Durkin
- Department of Human Genetics, CHU Liège, and Medical Genomics, GIGA Research Center, University of Liège, Liège, Belgium
| | - Samuel L Hong
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Bert Vanmechelen
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Joan Martí-Carreras
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Mandev S Gill
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Cécile Meex
- Department of Clinical Microbiology, University of Liège, Liège, Belgium
| | - Sébastien Bontems
- Department of Clinical Microbiology, University of Liège, Liège, Belgium
| | - Emmanuel André
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Marius Gilbert
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Bruxelles, Belgium
| | - Conor Walker
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Nicola De Maio
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Nuno R Faria
- Department of Zoology, University of Oxford, Oxford, United Kingdom.,MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, United Kingdom
| | - James Hadfield
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | - Vincent Bours
- Department of Human Genetics, CHU Liège, and Medical Genomics, GIGA Research Center, University of Liège, Liège, Belgium
| | - Tony Wawina-Bokalanga
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Maria Artesi
- Department of Human Genetics, CHU Liège, and Medical Genomics, GIGA Research Center, University of Liège, Liège, Belgium
| | - Guy Baele
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Piet Maes
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
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Gutierrez B, Márquez S, Prado-Vivar B, Becerra-Wong M, Guadalupe JJ, da Silva Candido D, Fernandez-Cadena JC, Morey-Leon G, Armas-Gonzalez R, Andrade-Molina DM, Bruno A, de Mora D, Olmedo M, Portugal D, Gonzalez M, Orlando A, Drexler JF, Moreira-Soto A, Sander AL, Brünink S, Kühne A, Patiño L, Carrazco-Montalvo A, Mestanza O, Zurita J, Sevillano G, du Plessis L, McCrone JT, Coloma J, Trueba G, Barragán V, Rojas-Silva P, Grunauer M, Kraemer MU, Faria NR, Escalera-Zamudio M, Pybus OG, Cárdenas P. Genomic epidemiology of SARS-CoV-2 transmission lineages in Ecuador. medRxiv 2021:2021.03.31.21254685. [PMID: 33851177 PMCID: PMC8043474 DOI: 10.1101/2021.03.31.21254685] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Characterisation of SARS-CoV-2 genetic diversity through space and time can reveal trends in virus importation and domestic circulation, and permit the exploration of questions regarding the early transmission dynamics. Here we present a detailed description of SARS-CoV-2 genomic epidemiology in Ecuador, one of the hardest hit countries during the early stages of the COVID-19 pandemic. We generate and analyse 160 whole genome sequences sampled from all provinces of Ecuador in 2020. Molecular clock and phylgeographic analysis of these sequences in the context of global SARS-CoV-2 diversity enable us to identify and characterise individual transmission lineages within Ecuador, explore their spatiotemporal distributions, and consider their introduction and domestic circulation. Our results reveal a pattern of multiple international importations across the country, with apparent differences between key provinces. Transmission lineages were mostly introduced before the implementation of non-pharmaceutical interventions (NPIs), with differential degrees of persistence and national dissemination.
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Affiliation(s)
- Bernardo Gutierrez
- Department of Zoology, University of Oxford, Oxford, UK
- Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador
| | - Sully Márquez
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito, Ecuador
| | - Belén Prado-Vivar
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito, Ecuador
| | - Mónica Becerra-Wong
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito, Ecuador
| | - Juan José Guadalupe
- Laboratorio de Biotecnología Vegetal, Universidad San Francisco de Quito, Quito, Ecuador
| | | | - Juan Carlos Fernandez-Cadena
- Omics Sciences Laboratory, Faculty of Medical Sciences, Universidad de Especialidades Espíritu Santo, Samborondón, Ecuador
| | - Gabriel Morey-Leon
- Faculty of Medical Sciences, Universidad de Guayaquil, Guayaquil, Ecuador
| | - Rubén Armas-Gonzalez
- Faculty of Sciences, Escuela Superior Politécnica del Litoral, Guayaquil, Ecuador
| | - Derly Madeleiny Andrade-Molina
- Omics Sciences Laboratory, Faculty of Medical Sciences, Universidad de Especialidades Espíritu Santo, Samborondón, Ecuador
| | - Alfredo Bruno
- Instituto Nacional de Investigación en Salud Pública, Guayaquil, Ecuador
- Universidad Agraria del Ecuador
| | - Domenica de Mora
- Instituto Nacional de Investigación en Salud Pública, Guayaquil, Ecuador
| | - Maritza Olmedo
- Instituto Nacional de Investigación en Salud Pública, Guayaquil, Ecuador
| | - Denisse Portugal
- Instituto Nacional de Investigación en Salud Pública, Guayaquil, Ecuador
| | - Manuel Gonzalez
- Instituto Nacional de Investigación en Salud Pública, Guayaquil, Ecuador
| | - Alberto Orlando
- Instituto Nacional de Investigación en Salud Pública, Guayaquil, Ecuador
| | - Jan Felix Drexler
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin, Germany
| | - Andres Moreira-Soto
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin, Germany
| | - Anna-Lena Sander
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin, Germany
| | - Sebastian Brünink
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin, Germany
| | - Arne Kühne
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin, Germany
| | - Leandro Patiño
- Instituto Nacional de Investigación en Salud Pública, Guayaquil, Ecuador
| | | | - Orson Mestanza
- Instituto Nacional de Investigación en Salud Pública, Guayaquil, Ecuador
| | - Jeannete Zurita
- Facultad de Medicina, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
- Unidad de Investigaciones en Biomedicina, Zurita & Zurita Laboratorios, Quito, Ecuador
| | - Gabriela Sevillano
- Unidad de Investigaciones en Biomedicina, Zurita & Zurita Laboratorios, Quito, Ecuador
| | | | - John T. McCrone
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Josefina Coloma
- School of Public Health, University of California, Berkeley, USA
| | - Gabriel Trueba
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito, Ecuador
| | - Verónica Barragán
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito, Ecuador
| | | | - Michelle Grunauer
- Escuela de Medicina, Universidad San Francisco de Quito, Quito, Ecuador
| | | | - Nuno R. Faria
- Department of Zoology, University of Oxford, Oxford, UK
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, UK
| | | | - Oliver G. Pybus
- Department of Zoology, University of Oxford, Oxford, UK
- Department of Pathobiology and Population Sciences, Royal Veterinary College London, London, UK
| | - Paúl Cárdenas
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito, Ecuador
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49
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Li SL, Pereira RHM, Prete CA, Zarebski AE, Emanuel L, Alves PJH, Peixoto PS, Braga CKV, de Souza Santos AA, de Souza WM, Barbosa RJ, Buss LF, Mendrone A, de Almeida-Neto C, Ferreira SC, Salles NA, Marcilio I, Wu CH, Gouveia N, Nascimento VH, Sabino EC, Faria NR, Messina JP. Higher risk of death from COVID-19 in low-income and non-White populations of São Paulo, Brazil. BMJ Glob Health 2021; 6:e004959. [PMID: 33926892 PMCID: PMC8094342 DOI: 10.1136/bmjgh-2021-004959] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 03/08/2021] [Accepted: 04/06/2021] [Indexed: 12/23/2022] Open
Abstract
INTRODUCTION Little evidence exists on the differential health effects of COVID-19 on disadvantaged population groups. Here we characterise the differential risk of hospitalisation and death in São Paulo state, Brazil, and show how vulnerability to COVID-19 is shaped by socioeconomic inequalities. METHODS We conducted a cross-sectional study using hospitalised severe acute respiratory infections notified from March to August 2020 in the Sistema de Monitoramento Inteligente de São Paulo database. We examined the risk of hospitalisation and death by race and socioeconomic status using multiple data sets for individual-level and spatiotemporal analyses. We explained these inequalities according to differences in daily mobility from mobile phone data, teleworking behaviour and comorbidities. RESULTS Throughout the study period, patients living in the 40% poorest areas were more likely to die when compared with patients living in the 5% wealthiest areas (OR: 1.60, 95% CI 1.48 to 1.74) and were more likely to be hospitalised between April and July 2020 (OR: 1.08, 95% CI 1.04 to 1.12). Black and Pardo individuals were more likely to be hospitalised when compared with White individuals (OR: 1.41, 95% CI 1.37 to 1.46; OR: 1.26, 95% CI 1.23 to 1.28, respectively), and were more likely to die (OR: 1.13, 95% CI 1.07 to 1.19; 1.07, 95% CI 1.04 to 1.10, respectively) between April and July 2020. Once hospitalised, patients treated in public hospitals were more likely to die than patients in private hospitals (OR: 1.40%, 95% CI 1.34% to 1.46%). Black individuals and those with low education attainment were more likely to have one or more comorbidities, respectively (OR: 1.29, 95% CI 1.19 to 1.39; 1.36, 95% CI 1.27 to 1.45). CONCLUSIONS Low-income and Black and Pardo communities are more likely to die with COVID-19. This is associated with differential access to quality healthcare, ability to self-isolate and the higher prevalence of comorbidities.
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Affiliation(s)
- Sabrina L Li
- School of Geography and the Environment, University of Oxford, Oxford, UK
| | | | - Carlos A Prete
- Department of Electronic Systems Engineering, University of São Paulo, São Paulo, Brazil
| | | | - Lucas Emanuel
- Institute of Applied Economic Research, Brasília, Brazil
| | | | - Pedro S Peixoto
- Department of Applied Mathematics, Institute of Mathematics and Statistics, University of São Paulo, São Paulo, Brazil
| | | | | | - William M de Souza
- Department of Zoology, University of Oxford, Oxford, UK
- Virology Research Center, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Rogerio J Barbosa
- Institute of Social and Political Studies (IESP), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Lewis F Buss
- Departamento de Molestias Infecciosas e Parasitarias andInstituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | | | - Cesar de Almeida-Neto
- Fundação Pró-Sangue Hemocentro de São Paulo, São Paulo, Brazil
- Disciplina de Ciências Médicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Suzete C Ferreira
- Fundação Pró-Sangue Hemocentro de São Paulo, São Paulo, Brazil
- Laboratory of Medical Investigation in Pathogenesis and Directed Therapy in Onco - Immuno - Hematology (LIM-31) HCFMUSP, University of São Paulo Medical School, São Paulo, Brazil
| | - Nanci A Salles
- Fundação Pró-Sangue Hemocentro de São Paulo, São Paulo, Brazil
- Laboratory of Medical Investigation in Pathogenesis and Directed Therapy in Onco - Immuno - Hematology (LIM-31) HCFMUSP, University of São Paulo Medical School, São Paulo, Brazil
| | - Izabel Marcilio
- Hospital das Clinicas da Faculdade de Medicina da Universidade de São Paulo, University of São Paulo, São Paulo, Brazil
| | - Chieh-Hsi Wu
- Mathematical Sciences, University of Southampton, Southampton, UK
| | - Nelson Gouveia
- Department of Preventive Medicine, University of São Paulo Medical School, São Paulo, Brazil
| | - Vitor H Nascimento
- Department of Electronic Systems Engineering, University of São Paulo, São Paulo, Brazil
| | - Ester C Sabino
- Departamento de Molestias Infecciosas e Parasitarias andInstituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Nuno R Faria
- Department of Zoology, University of Oxford, Oxford, UK
- Departamento de Molestias Infecciosas e Parasitarias andInstituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- MRC Centre for Global Infectious Disease Analysis; and the Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK
| | - Jane P Messina
- School of Geography and the Environment, University of Oxford, Oxford, UK
- Oxford School of Global and Area Studies, University of Oxford, Oxford, UK
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50
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Vogels CB, Breban MI, Alpert T, Petrone ME, Watkins AE, Ott IM, de Jesus JG, Claro IM, Ferreira GM, Crispim MA, Singh L, Tegally H, Anyaneji UJ, Hodcroft EB, Mason CE, Khullar G, Metti J, Dudley JT, MacKay MJ, Nash M, Wang J, Liu C, Hui P, Murphy S, Neal C, Laszlo E, Landry ML, Muyombwe A, Downing R, Razeq J, de Oliveira T, Faria NR, Sabino EC, Neher RA, Fauver JR, Grubaugh ND. PCR assay to enhance global surveillance for SARS-CoV-2 variants of concern. medRxiv 2021:2021.01.28.21250486. [PMID: 33758901 PMCID: PMC7987060 DOI: 10.1101/2021.01.28.21250486] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
With the emergence of SARS-CoV-2 variants that may increase transmissibility and/or cause escape from immune responses 1-3 , there is an urgent need for the targeted surveillance of circulating lineages. It was found that the B.1.1.7 (also 501Y.V1) variant first detected in the UK 4,5 could be serendipitously detected by the ThermoFisher TaqPath COVID-19 PCR assay because a key deletion in these viruses, spike Δ69-70, would cause a "spike gene target failure" (SGTF) result. However, a SGTF result is not definitive for B.1.1.7, and this assay cannot detect other variants of concern that lack spike Δ69-70, such as B.1.351 (also 501Y.V2) detected in South Africa 6 and P.1 (also 501Y.V3) recently detected in Brazil 7 . We identified a deletion in the ORF1a gene (ORF1a Δ3675-3677) in all three variants, which has not yet been widely detected in other SARS-CoV-2 lineages. Using ORF1a Δ3675-3677 as the primary target and spike Δ69-70 to differentiate, we designed and validated an open source PCR assay to detect SARS-CoV-2 variants of concern 8 . Our assay can be rapidly deployed in laboratories around the world to enhance surveillance for the local emergence spread of B.1.1.7, B.1.351, and P.1.
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Affiliation(s)
- Chantal B.F. Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Mallery I. Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Tara Alpert
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Mary E. Petrone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Anne E. Watkins
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Isabel M. Ott
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Jaqueline Goes de Jesus
- Departamento de Molestias Infecciosas e Parasitarias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP 05403–000, Brazil
| | - Ingra Morales Claro
- Departamento de Molestias Infecciosas e Parasitarias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP 05403–000, Brazil
| | - Giulia Magalhães Ferreira
- Departamento de Molestias Infecciosas e Parasitarias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP 05403–000, Brazil
- Laboratório de Virologia, Instituto de Ciências Biomédicas, Universidade Federal de Uberlândia, Uberlândia, MG, Brazil
| | - Myuki A.E. Crispim
- Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas, Manaus, Brazil
| | | | - Lavanya Singh
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Ugochukwu J. Anyaneji
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | | | - Emma B. Hodcroft
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | | | | | | | | | | | | | - Jianhui Wang
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Chen Liu
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Pei Hui
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06510, USA
| | | | - Caleb Neal
- Murphy Medical Associates, Greenwich, CT 06614, USA
| | - Eva Laszlo
- Murphy Medical Associates, Greenwich, CT 06614, USA
| | - Marie L. Landry
- Departments of Laboratory Medicine and Medicine, Yale School of Medicine, New Haven, CT 06510, USA
| | - Anthony Muyombwe
- Connecticut State Department of Public Health, Rocky Hill, CT 06067, USA
| | - Randy Downing
- Connecticut State Department of Public Health, Rocky Hill, CT 06067, USA
| | - Jafar Razeq
- Connecticut State Department of Public Health, Rocky Hill, CT 06067, USA
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Nuno R. Faria
- Departamento de Molestias Infecciosas e Parasitarias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP 05403–000, Brazil
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, UK
- Department of Zoology, University of Oxford, Oxford, UK
| | - Ester C. Sabino
- Departamento de Molestias Infecciosas e Parasitarias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP 05403–000, Brazil
| | - Richard A. Neher
- Biozentrum, University of Basel, 4056 Basel, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Joseph R. Fauver
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06510, USA
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