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Martínez-Martínez FJ, Massinga AJ, De Jesus Á, Ernesto RM, Cano-Jiménez P, Chiner-Oms Á, Gómez-Navarro I, Guillot-Fernández M, Guinovart C, Sitoe A, Vubil D, Bila R, Gujamo R, Enosse S, Jiménez-Serrano S, Torres-Puente M, Comas I, Mandomando I, López MG, Mayor A. Tracking SARS-CoV-2 introductions in Mozambique using pandemic-scale phylogenies: a retrospective observational study. Lancet Glob Health 2023; 11:e933-e941. [PMID: 37202028 DOI: 10.1016/s2214-109x(23)00169-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 03/09/2023] [Accepted: 03/23/2023] [Indexed: 05/20/2023]
Abstract
BACKGROUND From the start of the SARS-CoV-2 outbreak, global sequencing efforts have generated an unprecedented amount of genomic data. Nonetheless, unequal sampling between high-income and low-income countries hinders the implementation of genomic surveillance systems at the global and local level. Filling the knowledge gaps of genomic information and understanding pandemic dynamics in low-income countries is essential for public health decision making and to prepare for future pandemics. In this context, we aimed to discover the timing and origin of SARS-CoV-2 variant introductions in Mozambique, taking advantage of pandemic-scale phylogenies. METHODS We did a retrospective, observational study in southern Mozambique. Patients from Manhiça presenting with respiratory symptoms were recruited, and those enrolled in clinical trials were excluded. Data were included from three sources: (1) a prospective hospital-based surveillance study (MozCOVID), recruiting patients living in Manhiça, attending the Manhiça district hospital, and fulfilling the criteria of suspected COVID-19 case according to WHO; (2) symptomatic and asymptomatic individuals with SARS-CoV-2 infection recruited by the National Surveillance system; and (3) sequences from SARS-CoV-2-infected Mozambican cases deposited on the Global Initiative on Sharing Avian Influenza Data database. Positive samples amenable for sequencing were analysed. We used Ultrafast Sample placement on Existing tRees to understand the dynamics of beta and delta waves, using available genomic data. This tool can reconstruct a phylogeny with millions of sequences by efficient sample placement in a tree. We reconstructed a phylogeny (~7·6 million sequences) adding new and publicly available beta and delta sequences. FINDINGS A total of 5793 patients were recruited between Nov 1, 2020, and Aug 31, 2021. During this time, 133 328 COVID-19 cases were reported in Mozambique. 280 good quality new SARS-CoV-2 sequences were obtained after the inclusion criteria were applied and an additional 652 beta (B.1.351) and delta (B.1.617.2) public sequences were included from Mozambique. We evaluated 373 beta and 559 delta sequences. We identified 187 beta introductions (including 295 sequences), divided in 42 transmission groups and 145 unique introductions, mostly from South Africa, between August, 2020 and July, 2021. For delta, we identified 220 introductions (including 494 sequences), with 49 transmission groups and 171 unique introductions, mostly from the UK, India, and South Africa, between April and November, 2021. INTERPRETATION The timing and origin of introductions suggests that movement restrictions effectively avoided introductions from non-African countries, but not from surrounding countries. Our results raise questions about the imbalance between the consequences of restrictions and health benefits. This new understanding of pandemic dynamics in Mozambique can be used to inform public health interventions to control the spread of new variants. FUNDING European and Developing Countries Clinical Trials, European Research Council, Bill & Melinda Gates Foundation, and Agència de Gestió d'Ajuts Universitaris i de Recerca.
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Affiliation(s)
- Francisco José Martínez-Martínez
- Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | | | - Áuria De Jesus
- Centro de Investigação em Saúde de Manhiça, Maputo, Mozambique
| | - Rita M Ernesto
- Centro de Investigação em Saúde de Manhiça, Maputo, Mozambique
| | - Pablo Cano-Jiménez
- Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Álvaro Chiner-Oms
- Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Inmaculada Gómez-Navarro
- Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Marina Guillot-Fernández
- Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | | | - António Sitoe
- Centro de Investigação em Saúde de Manhiça, Maputo, Mozambique
| | - Delfino Vubil
- Centro de Investigação em Saúde de Manhiça, Maputo, Mozambique
| | - Rubão Bila
- Hospital Distrital da Manhiça, Marracuene, Mozambique
| | | | - Sónia Enosse
- Instituto Nacional de Saúde, Marracuene, Mozambique
| | - Santiago Jiménez-Serrano
- Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Manuela Torres-Puente
- Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Iñaki Comas
- Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, Valencia, Spain; Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Inácio Mandomando
- Centro de Investigação em Saúde de Manhiça, Maputo, Mozambique; Instituto Nacional de Saúde, Marracuene, Mozambique
| | - Mariana G López
- Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, Valencia, Spain.
| | - Alfredo Mayor
- Centro de Investigação em Saúde de Manhiça, Maputo, Mozambique; ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain; Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain; Department of Physiologic Sciences, Faculty of Medicine, Universidade Eduardo Mondlane, Maputo, Mozambique
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Jiménez-Serrano S, Rodrigo M, Calvo C, Millet J, Castells F. From 12 to 1 ECG lead: multiple cardiac condition detection mixing a hybrid machine learning approach with a one-vs-rest classification strategy. Physiol Meas 2022; 43. [PMID: 35609610 DOI: 10.1088/1361-6579/ac72f5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 05/24/2022] [Indexed: 11/11/2022]
Abstract
OBJECTIVE Detecting different cardiac diseases using a single or reduced number of leads is still challenging. This work aims to provide and validate an automated method able to classify ECG recordings. Performance using complete 12-lead systems, reduced lead sets, and single-lead ECGs is evaluated and compared. APPROACH Seven different databases with 12-lead ECGs were provided during the PhysioNet/Computing in Cardiology Challenge 2021, where 88,253 annotated samples associated with none, one, or several cardiac conditions among 26 different classes were released for training, whereas 42,896 hidden samples were used for testing. After signal preprocessing, 81 features per ECG-lead were extracted, mainly based on heart rate variability, QRST patterns and spectral domain. Next, a One-vs-Rest classification approach made of independent binary classifiers for each cardiac condition was trained. This strategy allowed each ECG to be classified as belonging to none, one or several classes. For each class, a classification model among two binary Supervised Classifiers and one Hybrid Unsupervised-Supervised classification system was selected. Finally, we performed a 3-fold cross-validation to assess the system's performance. MAIN RESULTS Our classifiers received scores of 0.39, 0.38, 0.39, 0.38, and 0.37 for the 12, 6, 4, 3 and 2-lead versions of the hidden test set with the Challenge evaluation metric (CM). Also, we obtained a mean G-score of 0.80, 0.78, 0.79, 0.79, 0.77 and 0.74 for the 12, 6, 4, 3, 2 and 1-lead subsets with the public training set during our 3-fold cross-validation. SIGNIFICANCE We proposed and tested a machine learning approach focused on flexibility for identifying multiple cardiac conditions using one or more ECG leads. Our minimal-lead approach may be beneficial for novel portable or wearable ECG devices used as screening tools, as it can also detect multiple and concurrent cardiac conditions.
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Affiliation(s)
- Santiago Jiménez-Serrano
- Instituto ITACA, Universitat Politècnica de València, Camino de Vera s/n, Valencia, Comunitat Valenciana, 46022, SPAIN
| | - Miguel Rodrigo
- CoMMLab, Universitat de València, Av. de Blasco Ibáñez, 13, Valencia, Comunitat Valenciana, 46010, SPAIN
| | - Conrado Calvo
- Universitat Politècnica de València, Camino de Vera s/n, Valencia, Comunitat Valenciana, 46022, SPAIN
| | - José Millet
- Instituto ITACA, Universitat Politecnica de Valencia, Camino de Vera s/n, Valencia, Comunitat Valenciana, 46022, SPAIN
| | - Francisco Castells
- Instituto ITACA, Universitat Politecnica de Valencia, Camino de Vera s/n, Valencia, Comunitat Valenciana, 46022, SPAIN
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3
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López-Causapé C, Fraile-Ribot PA, Jiménez-Serrano S, Cabot G, Del Barrio-Tofiño E, Prado MC, Linares JM, López A, Hurtado A, Riera E, Serra A, Roselló E, Carbó L, Fernández-Baca MV, Gallegos C, Saurina J, Arteaga E, Salom MM, Salvá A, Nicolau A, González-Candelas F, Comas I, Oliver A. A Genomic Snapshot of the SARS-CoV-2 Pandemic in the Balearic Islands. Front Microbiol 2022; 12:803827. [PMID: 35095814 PMCID: PMC8790175 DOI: 10.3389/fmicb.2021.803827] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 12/15/2021] [Indexed: 11/29/2022] Open
Abstract
Objective: To analyze the SARS-CoV-2 genomic epidemiology in the Balearic Islands, a unique setting in which the course of the pandemic has been influenced by a complex interplay between insularity, severe social restrictions and tourism travels. Methods: Since the onset of the pandemic, more than 2,700 SARS-CoV-2 positive respiratory samples have been randomly selected and sequenced in the Balearic Islands. Genetic diversity of circulating variants was assessed by lineage assignment of consensus whole genome sequences with PANGOLIN and investigation of additional spike mutations. Results: Consensus sequences were assigned to 46 different PANGO lineages and 75% of genomes were classified within a VOC, VUI, or VUM variant according to the WHO definitions. Highest genetic diversity was documented in the island of Majorca (42 different lineages detected). Globally, lineages B.1.1.7 and B.1.617.2/AY.X were identified as the 2 major lineages circulating in the Balearic Islands during the pandemic, distantly followed by lineages B.1.177/B.1.177.X. However, in Ibiza/Formentera lineage distribution was slightly different and lineage B.1.221 was the third most prevalent. Temporal distribution analysis showed that B.1 and B.1.5 lineages dominated the first epidemic wave, lineage B.1.177 dominated the second and third, and lineage B.1.617.2 the fourth. Of note, lineage B.1.1.7 became the most prevalent circulating lineage during first half of 2021; however, it was not associated with an increased in COVID-19 cases likely due to severe social restrictions and limited travels. Additional spike mutations were rarely documented with the exception of mutation S:Q613H which has been detected in several genomes (n = 25) since July 2021. Conclusion: Virus evolution, mainly driven by the acquisition and selection of spike substitutions conferring biological advantages, social restrictions, and size population are apparently key factors for explaining the epidemic patterns registered in the Balearic Islands.
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Affiliation(s)
- Carla López-Causapé
- Servicio de Microbiología y Unidad de Investigación, Hospital Universitario Son Espases, Instituto de Investigación Sanitaria de las Islas Baleares, Palma, Spain.,CIBER en Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Pablo A Fraile-Ribot
- Servicio de Microbiología y Unidad de Investigación, Hospital Universitario Son Espases, Instituto de Investigación Sanitaria de las Islas Baleares, Palma, Spain.,CIBER en Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | | | - Gabriel Cabot
- Servicio de Microbiología y Unidad de Investigación, Hospital Universitario Son Espases, Instituto de Investigación Sanitaria de las Islas Baleares, Palma, Spain.,CIBER en Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Ester Del Barrio-Tofiño
- Servicio de Microbiología y Unidad de Investigación, Hospital Universitario Son Espases, Instituto de Investigación Sanitaria de las Islas Baleares, Palma, Spain.,CIBER en Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - M Carmen Prado
- Servicio de Microbiología y Unidad de Investigación, Hospital Universitario Son Espases, Instituto de Investigación Sanitaria de las Islas Baleares, Palma, Spain
| | - Juana María Linares
- Servicio de Microbiología y Unidad de Investigación, Hospital Universitario Son Espases, Instituto de Investigación Sanitaria de las Islas Baleares, Palma, Spain
| | - Aranzazu López
- Servicio de Microbiología, Hospital Can Misses, Ibiza, Spain
| | | | - Elena Riera
- Servicio de Microbiología, Hospital de Manacor, Manacor, Spain
| | - Antoni Serra
- Servicio de Microbiología, Hospital de Manacor, Manacor, Spain
| | - Eva Roselló
- Servicio de Microbiología, Hospital Mateu Orfila, Mahón, Spain
| | - Lluis Carbó
- Servicio de Microbiología, Hospital Mateu Orfila, Mahón, Spain
| | | | - Carmen Gallegos
- Servicio de Microbiología, Hospital Universitari Son Llàtzer, Palma, Spain
| | - Juan Saurina
- Servicio de Microbiología, Hospital Comarcal de Inca, Inca, Spain
| | - Emilio Arteaga
- Servicio de Microbiología, Hospital Comarcal de Inca, Inca, Spain
| | | | - Antonia Salvá
- Gabinete Técnico-Asistencial, Servicio de Salud de las Islas Baleares, Palma, Spain
| | - Antoni Nicolau
- Servicio de Epidemiología de las Islas Baleares, Palma, Spain
| | - Fernando González-Candelas
- Unidad Mixta de Investigación "Infección y Salud Pública" FISABIO-Universidad de Valencia, Instituto de Biología Integrativa de Sistemas (I2SysBIO, CSIC-UV), Valencia, Spain.,CIBER en Epidemiología y Salud Publica (CIBERESP), Madrid, Spain
| | - Iñaki Comas
- Instituto de Biomedicina de Valencia, Valencia, Spain.,CIBER en Epidemiología y Salud Publica (CIBERESP), Madrid, Spain
| | - Antonio Oliver
- Servicio de Microbiología y Unidad de Investigación, Hospital Universitario Son Espases, Instituto de Investigación Sanitaria de las Islas Baleares, Palma, Spain.,CIBER en Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
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Pérez Lago L, Pérez Latorre L, Herranz M, Tejerina F, Sola-Campoy PJ, Sicilia J, Suárez-González J, Andrés-Zayas C, Chiner-Oms A, Jiménez-Serrano S, García-González N, Comas I, González-Candelas F, Martínez-Laperche C, Catalán P, Muñoz P, García de Viedma D. Complete Analysis of the Epidemiological Scenario around a SARS-CoV-2 Reinfection: Previous Infection Events and Subsequent Transmission. mSphere 2021; 6:e0059621. [PMID: 34494886 PMCID: PMC8550076 DOI: 10.1128/msphere.00596-21] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/12/2021] [Indexed: 11/20/2022] Open
Abstract
The first descriptions of reinfection by SARS-CoV-2 have been recently reported. However, these studies focus exclusively on the reinfected case, without considering the epidemiological context of the event. Our objectives were to perform a complete analysis of the sequential infections and community transmission events around a SARS-CoV-2 reinfection, including the infection events preceding it, the exposure, and subsequent transmissions. Our analysis was supported by host genetics, viral whole-genome sequencing, phylogenomic viral population analysis, and refined epidemiological data obtained from interviews with the involved subjects. The reinfection involved a 53-year-old woman with asthma (Case A), with a first COVID-19 episode in April 2020 and a much more severe second episode 4-1/2 months later, with SARS-CoV-2 seroconversion in August, that required hospital admission. An extended genomic analysis allowed us to demonstrate that the strain involved in Case A's reinfection was circulating in the epidemiological context of Case A and was also transmitted subsequently from Case A to her family context. The reinfection was also supported by a phylogenetic analysis, including 348 strains from Madrid, which revealed that the strain involved in the reinfection was circulating by the time Case A suffered the second episode, August-September 2020, but absent at the time range corresponding to Case A's first episode. IMPORTANCE We present the first complete analysis of the epidemiological scenario around a reinfection by SARS-CoV-2, more severe than the first episode, including three cases preceding the reinfection, the reinfected case per se, and the subsequent transmission to another seven cases.
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Affiliation(s)
- Laura Pérez Lago
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Gregorio Marañón General University Hospital, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Leire Pérez Latorre
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Gregorio Marañón General University Hospital, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Marta Herranz
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Gregorio Marañón General University Hospital, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- CIBER Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Francisco Tejerina
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Gregorio Marañón General University Hospital, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Pedro J. Sola-Campoy
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Gregorio Marañón General University Hospital, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Jon Sicilia
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Gregorio Marañón General University Hospital, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Julia Suárez-González
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- Genomics Unit, Gregorio Marañón General University Hospital, Madrid, Spain
| | - Cristina Andrés-Zayas
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- Genomics Unit, Gregorio Marañón General University Hospital, Madrid, Spain
| | | | | | - Neris García-González
- Joint Research Unit Infection and Public Health FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain
| | - Iñaki Comas
- Instituto de Biomedicina de Valencia-CSIC, Valencia, Spain
- CIBER Salud Pública (CIBERESP), Madrid, Spain
| | - Fernando González-Candelas
- Joint Research Unit Infection and Public Health FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain
- CIBER Salud Pública (CIBERESP), Madrid, Spain
| | - Carolina Martínez-Laperche
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- Servicio de Oncohematología, Gregorio Marañón General University Hospital, Madrid, Spain
| | - Pilar Catalán
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Gregorio Marañón General University Hospital, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- CIBER Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Patricia Muñoz
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Gregorio Marañón General University Hospital, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- CIBER Enfermedades Respiratorias (CIBERES), Madrid, Spain
- Departamento de Medicina, Universidad Complutense, Madrid, Spain
| | - Darío García de Viedma
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Gregorio Marañón General University Hospital, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- CIBER Enfermedades Respiratorias (CIBERES), Madrid, Spain
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5
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Pérez Lago L, Pérez Latorre L, Herranz M, Tejerina F, Sola-Campoy PJ, Sicilia J, Suárez-González J, Andrés-Zayas C, Chiner-Oms A, Jiménez-Serrano S, García-González N, Comas I, González-Candelas F, Martínez-Laperche C, Catalán P, Muñoz P, García de Viedma D. Complete Analysis of the Epidemiological Scenario around a SARS-CoV-2 Reinfection: Previous Infection Events and Subsequent Transmission. mSphere 2021; 6:e0059621. [PMID: 34494886 DOI: 10.21203/rs.3.rs-106167/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023] Open
Abstract
The first descriptions of reinfection by SARS-CoV-2 have been recently reported. However, these studies focus exclusively on the reinfected case, without considering the epidemiological context of the event. Our objectives were to perform a complete analysis of the sequential infections and community transmission events around a SARS-CoV-2 reinfection, including the infection events preceding it, the exposure, and subsequent transmissions. Our analysis was supported by host genetics, viral whole-genome sequencing, phylogenomic viral population analysis, and refined epidemiological data obtained from interviews with the involved subjects. The reinfection involved a 53-year-old woman with asthma (Case A), with a first COVID-19 episode in April 2020 and a much more severe second episode 4-1/2 months later, with SARS-CoV-2 seroconversion in August, that required hospital admission. An extended genomic analysis allowed us to demonstrate that the strain involved in Case A's reinfection was circulating in the epidemiological context of Case A and was also transmitted subsequently from Case A to her family context. The reinfection was also supported by a phylogenetic analysis, including 348 strains from Madrid, which revealed that the strain involved in the reinfection was circulating by the time Case A suffered the second episode, August-September 2020, but absent at the time range corresponding to Case A's first episode. IMPORTANCE We present the first complete analysis of the epidemiological scenario around a reinfection by SARS-CoV-2, more severe than the first episode, including three cases preceding the reinfection, the reinfected case per se, and the subsequent transmission to another seven cases.
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Affiliation(s)
- Laura Pérez Lago
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Gregorio Marañón General University Hospital, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Leire Pérez Latorre
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Gregorio Marañón General University Hospital, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Marta Herranz
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Gregorio Marañón General University Hospital, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- CIBER Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Francisco Tejerina
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Gregorio Marañón General University Hospital, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Pedro J Sola-Campoy
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Gregorio Marañón General University Hospital, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Jon Sicilia
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Gregorio Marañón General University Hospital, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Julia Suárez-González
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- Genomics Unit, Gregorio Marañón General University Hospital, Madrid, Spain
| | - Cristina Andrés-Zayas
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- Genomics Unit, Gregorio Marañón General University Hospital, Madrid, Spain
| | | | | | - Neris García-González
- Joint Research Unit Infection and Public Health FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain
| | - Iñaki Comas
- Instituto de Biomedicina de Valencia-CSIC, Valencia, Spain
- CIBER Salud Pública (CIBERESP), Madrid, Spain
| | - Fernando González-Candelas
- Joint Research Unit Infection and Public Health FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain
- CIBER Salud Pública (CIBERESP), Madrid, Spain
| | - Carolina Martínez-Laperche
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- Servicio de Oncohematología, Gregorio Marañón General University Hospital, Madrid, Spain
| | - Pilar Catalán
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Gregorio Marañón General University Hospital, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- CIBER Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Patricia Muñoz
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Gregorio Marañón General University Hospital, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- CIBER Enfermedades Respiratorias (CIBERES), Madrid, Spain
- Departamento de Medicina, Universidad Complutense, Madrid, Spain
| | - Darío García de Viedma
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Gregorio Marañón General University Hospital, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- CIBER Enfermedades Respiratorias (CIBERES), Madrid, Spain
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López MG, Chiner-Oms Á, García de Viedma D, Ruiz-Rodriguez P, Bracho MA, Cancino-Muñoz I, D’Auria G, de Marco G, García-González N, Goig GA, Gómez-Navarro I, Jiménez-Serrano S, Martinez-Priego L, Ruiz-Hueso P, Ruiz-Roldán L, Torres-Puente M, Alberola J, Albert E, Aranzamendi Zaldumbide M, Bea-Escudero MP, Boga JA, Bordoy AE, Canut-Blasco A, Carvajal A, Cilla Eguiluz G, Cordón Rodríguez ML, Costa-Alcalde JJ, de Toro M, de Toro Peinado I, del Pozo JL, Duchêne S, Fernández-Pinero J, Fuster Escrivá B, Gimeno Cardona C, González Galán V, Gonzalo Jiménez N, Hernáez Crespo S, Herranz M, Lepe JA, López-Causapé C, López-Hontangas JL, Martín V, Martró E, Milagro Beamonte A, Montes Ros M, Moreno-Muñoz R, Navarro D, Navarro-Marí JM, Not A, Oliver A, Palop-Borrás B, Parra Grande M, Pedrosa-Corral I, Pérez González MC, Pérez-Lago L, Pérez-Ruiz M, Piñeiro Vázquez L, Rabella N, Rezusta A, Robles Fonseca L, Rodríguez-Villodres Á, Sanbonmatsu-Gámez S, Sicilia J, Soriano A, Tirado Balaguer MD, Torres I, Tristancho A, Marimón JM, Coscolla M, González-Candelas F, Comas I. The first wave of the COVID-19 epidemic in Spain was associated with early introductions and fast spread of a dominating genetic variant. Nat Genet 2021; 53:1405-1414. [PMID: 34594042 PMCID: PMC8481935 DOI: 10.1038/s41588-021-00936-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 08/11/2021] [Indexed: 02/08/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has affected the world radically since 2020. Spain was one of the European countries with the highest incidence during the first wave. As a part of a consortium to monitor and study the evolution of the epidemic, we sequenced 2,170 samples, diagnosed mostly before lockdown measures. Here, we identified at least 500 introductions from multiple international sources and documented the early rise of two dominant Spanish epidemic clades (SECs), probably amplified by superspreading events. Both SECs were related closely to the initial Asian variants of SARS-CoV-2 and spread widely across Spain. We inferred a substantial reduction in the effective reproductive number of both SECs due to public-health interventions (Re < 1), also reflected in the replacement of SECs by a new variant over the summer of 2020. In summary, we reveal a notable difference in the initial genetic makeup of SARS-CoV-2 in Spain compared with other European countries and show evidence to support the effectiveness of lockdown measures in controlling virus spread, even for the most successful genetic variants.
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Affiliation(s)
- Mariana G. López
- grid.466828.60000 0004 1793 8484Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain
| | - Álvaro Chiner-Oms
- grid.466828.60000 0004 1793 8484Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain
| | - Darío García de Viedma
- grid.410526.40000 0001 0277 7938Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain ,grid.410526.40000 0001 0277 7938Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain ,grid.413448.e0000 0000 9314 1427CIBER Enfermedades Respiratorias (CIBERES), Bunyola, Spain
| | - Paula Ruiz-Rodriguez
- grid.5338.d0000 0001 2173 938XInstituto de Biología Integrativa de Sistemas, I2SysBio (CSIC-Universitat de València), Valencia, Spain
| | - Maria Alma Bracho
- grid.5338.d0000 0001 2173 938XJoint Research Unit Infection and Public Health FISABIO-University of Valencia I2SysBio, Valencia, Spain ,grid.413448.e0000 0000 9314 1427Ciber en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Irving Cancino-Muñoz
- grid.466828.60000 0004 1793 8484Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain
| | - Giuseppe D’Auria
- grid.413448.e0000 0000 9314 1427Ciber en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain ,grid.428862.2FISABIO, Servicio de Secuenciación, València, Spain
| | | | - Neris García-González
- grid.5338.d0000 0001 2173 938XJoint Research Unit Infection and Public Health FISABIO-University of Valencia I2SysBio, Valencia, Spain
| | - Galo Adrian Goig
- grid.416786.a0000 0004 0587 0574Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Inmaculada Gómez-Navarro
- grid.466828.60000 0004 1793 8484Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain
| | - Santiago Jiménez-Serrano
- grid.466828.60000 0004 1793 8484Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain
| | | | - Paula Ruiz-Hueso
- grid.428862.2FISABIO, Servicio de Secuenciación, València, Spain
| | - Lidia Ruiz-Roldán
- grid.5338.d0000 0001 2173 938XJoint Research Unit Infection and Public Health FISABIO-University of Valencia I2SysBio, Valencia, Spain
| | - Manuela Torres-Puente
- grid.466828.60000 0004 1793 8484Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain
| | - Juan Alberola
- grid.411289.70000 0004 1770 9825Servicio de Microbiología. Hospital Dr Peset, Valencia, Spain ,grid.424970.c0000 0001 2353 2112Conselleria de Sanitat i Consum, Generalitat Valenciana, Valencia, Spain ,grid.5338.d0000 0001 2173 938XDepartamento Microbiología, Facultad de Medicina, Universitat de València, Valencia, Spain
| | - Eliseo Albert
- grid.411308.fMicrobiology Service, Hospital Clínico Universitario, INCLIVA Research Institute, Valencia, Spain
| | - Maitane Aranzamendi Zaldumbide
- grid.411232.70000 0004 1767 5135Servicio de Microbiología, Hospital Universitario Cruces, Bilbao, Spain ,Grupo de Microbiología y Control de Infección, Instituto de Investigación Sanitaria Biocruces Bizkaia, Barakaldo, Spain
| | - María Pilar Bea-Escudero
- grid.460738.ePlataforma de Genómica y Bioinformática, Centro de Investigación Biomédica de La Rioja (CIBIR), Logroño, Spain
| | - Jose Antonio Boga
- grid.411052.30000 0001 2176 9028Servicio de Microbiología, Hospital Universitario Central de Asturias, Oviedo, Spain ,grid.511562.4Grupo de Microbiología Traslacional, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Asturias, Spain
| | - Antoni E. Bordoy
- grid.411438.b0000 0004 1767 6330Servicio de Microbiología, Laboratori Clínic Metropolitana Nord, Hospital Universitari Germans Trias i Pujol, Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Badalona, Barcelona, Spain
| | - Andrés Canut-Blasco
- grid.426049.d0000 0004 1793 9479Servicio de Microbiología, Hospital Universitario de Álava, Osakidetza-Servicio Vasco de Salud, Vitoria-Gasteiz (Álava), Spain
| | - Ana Carvajal
- grid.4807.b0000 0001 2187 3167Animal Health Department, Universidad de León, León, Spain
| | - Gustavo Cilla Eguiluz
- grid.414651.3Servicio de MicrobiologíaBiodonostia, Osakidetza, Hospital Universitario Donostia, San Sebastián, Spain
| | - Maria Luz Cordón Rodríguez
- grid.426049.d0000 0004 1793 9479Servicio de Microbiología, Hospital Universitario de Álava, Osakidetza-Servicio Vasco de Salud, Vitoria-Gasteiz (Álava), Spain
| | - José J. Costa-Alcalde
- grid.411048.80000 0000 8816 6945Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - María de Toro
- grid.460738.ePlataforma de Genómica y Bioinformática, Centro de Investigación Biomédica de La Rioja (CIBIR), Logroño, Spain
| | | | - Jose Luis del Pozo
- grid.411730.00000 0001 2191 685XServicio de Enfermedades Infecciosas y Microbiología clínica, Clínica Universidad de Navarra, Pamplona, Spain
| | - Sebastián Duchêne
- grid.1008.90000 0001 2179 088XDepartment of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria Australia
| | - Jovita Fernández-Pinero
- grid.419190.40000 0001 2300 669XInstituto Nacional de Investigación y Tecnología Agraria y Alimentaria, O.A., M.P. – INIA, Madrid, Spain
| | - Begoña Fuster Escrivá
- grid.5338.d0000 0001 2173 938XDepartamento Microbiología, Facultad de Medicina, Universitat de València, Valencia, Spain ,grid.106023.60000 0004 1770 977XServicio de Microbiología, Consorcio Hospital General Universitario de Valencia, Valencia, Spain
| | - Concepción Gimeno Cardona
- grid.106023.60000 0004 1770 977XServicio de Microbiología, Consorcio Hospital General Universitario de Valencia, Valencia, Spain
| | - Verónica González Galán
- grid.411109.c0000 0000 9542 1158Servicio de Microbiología UCEIMP, Hospital Universitario Virgen del Rocío, Sevilla, Spain
| | - Nieves Gonzalo Jiménez
- grid.411093.e0000 0004 0399 7977Servicio Microbiología, Departamento de Salud de Elche-Hospital General, Elche, Alicante, Spain
| | - Silvia Hernáez Crespo
- grid.426049.d0000 0004 1793 9479Servicio de Microbiología, Hospital Universitario de Álava, Osakidetza-Servicio Vasco de Salud, Vitoria-Gasteiz (Álava), Spain
| | - Marta Herranz
- grid.410526.40000 0001 0277 7938Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain ,grid.410526.40000 0001 0277 7938Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain ,grid.413448.e0000 0000 9314 1427CIBER Enfermedades Respiratorias (CIBERES), Bunyola, Spain
| | - José Antonio Lepe
- grid.411109.c0000 0000 9542 1158Servicio de Microbiología UCEIMP, Hospital Universitario Virgen del Rocío, Sevilla, Spain
| | - Carla López-Causapé
- grid.411164.70000 0004 1796 5984Servicio de Microbiología, Hospital Universitario Son Espases, Palma de Mallorca, Spain
| | - José Luis López-Hontangas
- grid.84393.350000 0001 0360 9602Hospital Universitario y Politécnico La Fe, Servicio de Microbiología, Valencia, Spain
| | - Vicente Martín
- grid.413448.e0000 0000 9314 1427Ciber en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain ,grid.4807.b0000 0001 2187 3167Research Group on Gene-Environment Interactions and Health. Institute of Biomedicine (IBIOMED), Universidad de León, León, Spain
| | - Elisa Martró
- grid.413448.e0000 0000 9314 1427Ciber en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain ,grid.411438.b0000 0004 1767 6330Servicio de Microbiología, Laboratori Clínic Metropolitana Nord, Hospital Universitari Germans Trias i Pujol, Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Badalona, Barcelona, Spain
| | - Ana Milagro Beamonte
- grid.411106.30000 0000 9854 2756Servicio de Microbiología Clínica, Hospital Universitario Miguel Servet, Zaragoza, Spain
| | - Milagrosa Montes Ros
- grid.414651.3Servicio de MicrobiologíaBiodonostia, Osakidetza, Hospital Universitario Donostia, San Sebastián, Spain
| | | | - David Navarro
- grid.5338.d0000 0001 2173 938XDepartamento Microbiología, Facultad de Medicina, Universitat de València, Valencia, Spain ,grid.411308.fMicrobiology Service, Hospital Clínico Universitario, INCLIVA Research Institute, Valencia, Spain
| | - José María Navarro-Marí
- grid.411380.f0000 0000 8771 3783Servicio de Microbiología, Hospital Universitario Virgen de las Nieves, Granada, Spain ,grid.411380.f0000 0000 8771 3783Hospital Universitario Virgen de las Nieves, Instituto de Investigación Biosanitaria ibs, Granada, Spain
| | - Anna Not
- grid.411438.b0000 0004 1767 6330Servicio de Microbiología, Laboratori Clínic Metropolitana Nord, Hospital Universitari Germans Trias i Pujol, Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Badalona, Barcelona, Spain
| | - Antonio Oliver
- grid.411164.70000 0004 1796 5984Servicio de Microbiología, Hospital Universitario Son Espases, Palma de Mallorca, Spain ,Instituto de Investigación Sanitaria de las Islas Baleares, Palma, Spain
| | - Begoña Palop-Borrás
- grid.411457.2Servicio de Microbiologia, Hospital Regional Universitario de Málaga, Málaga, Spain
| | - Mónica Parra Grande
- grid.507938.0Laboratorio de Microbiología, Hospital Marina Baixa, Villajoyosa, Spain
| | - Irene Pedrosa-Corral
- grid.411380.f0000 0000 8771 3783Servicio de Microbiología, Hospital Universitario Virgen de las Nieves, Granada, Spain ,grid.411380.f0000 0000 8771 3783Hospital Universitario Virgen de las Nieves, Instituto de Investigación Biosanitaria ibs, Granada, Spain
| | - Maria Carmen Pérez González
- grid.411250.30000 0004 0399 7109Hospital Universitario de Gran Canaria Dr. Negrin, Las Palmas de Gran Canaria, Spain
| | - Laura Pérez-Lago
- grid.410526.40000 0001 0277 7938Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain ,grid.410526.40000 0001 0277 7938Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Mercedes Pérez-Ruiz
- grid.411457.2Servicio de Microbiologia, Hospital Regional Universitario de Málaga, Málaga, Spain
| | - Luis Piñeiro Vázquez
- grid.414651.3Servicio de MicrobiologíaBiodonostia, Osakidetza, Hospital Universitario Donostia, San Sebastián, Spain
| | - Nuria Rabella
- grid.413396.a0000 0004 1768 8905Servei de Microbiologia, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain ,CREPIMC, Institut d’Investigació Biomèdica Sant Pau, Barcelona, Spain ,grid.7080.fDepartament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola, Spain
| | - Antonio Rezusta
- grid.411106.30000 0000 9854 2756Servicio de Microbiología Clínica, Hospital Universitario Miguel Servet, Zaragoza, Spain ,grid.488737.70000000463436020Instituto de Investigación Sanitaria de Aragón, Centro de Investigación Biomédica de Aragón (CIBA), Zaragoza, Spain ,grid.11205.370000 0001 2152 8769Facultad de Medicina, Universidad de Zaragoza, Zaragoza, Spain
| | - Lorena Robles Fonseca
- grid.411094.90000 0004 0506 8127Hospital General Universitario de Albacete, Albacete, Spain
| | - Ángel Rodríguez-Villodres
- grid.411109.c0000 0000 9542 1158Servicio de Microbiología UCEIMP, Hospital Universitario Virgen del Rocío, Sevilla, Spain
| | - Sara Sanbonmatsu-Gámez
- grid.411380.f0000 0000 8771 3783Servicio de Microbiología, Hospital Universitario Virgen de las Nieves, Granada, Spain ,grid.411380.f0000 0000 8771 3783Hospital Universitario Virgen de las Nieves, Instituto de Investigación Biosanitaria ibs, Granada, Spain
| | - Jon Sicilia
- grid.410526.40000 0001 0277 7938Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain ,grid.410526.40000 0001 0277 7938Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Alex Soriano
- grid.410458.c0000 0000 9635 9413Servicio de Enfermedades Infecciosas, Hospital Clínic de Barcelona, Barcelona, Spain
| | | | - Ignacio Torres
- grid.411308.fMicrobiology Service, Hospital Clínico Universitario, INCLIVA Research Institute, Valencia, Spain
| | - Alexander Tristancho
- grid.411106.30000 0000 9854 2756Servicio de Microbiología Clínica, Hospital Universitario Miguel Servet, Zaragoza, Spain ,grid.488737.70000000463436020Instituto de Investigación Sanitaria de Aragón, Centro de Investigación Biomédica de Aragón (CIBA), Zaragoza, Spain
| | - José María Marimón
- grid.414651.3Servicio de MicrobiologíaBiodonostia, Osakidetza, Hospital Universitario Donostia, San Sebastián, Spain
| | | | - Mireia Coscolla
- grid.5338.d0000 0001 2173 938XInstituto de Biología Integrativa de Sistemas, I2SysBio (CSIC-Universitat de València), Valencia, Spain
| | - Fernando González-Candelas
- grid.5338.d0000 0001 2173 938XJoint Research Unit Infection and Public Health FISABIO-University of Valencia I2SysBio, Valencia, Spain ,grid.413448.e0000 0000 9314 1427Ciber en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Iñaki Comas
- grid.466828.60000 0004 1793 8484Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain ,grid.413448.e0000 0000 9314 1427Ciber en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
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Gisbert V, Jiménez-Serrano S, Roses-Albert E, Rodrigo M. Atrial location optimization by electrical measures for Electrocardiographic Imaging. Comput Biol Med 2020; 127:104031. [PMID: 33096296 DOI: 10.1016/j.compbiomed.2020.104031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 09/07/2020] [Accepted: 10/01/2020] [Indexed: 12/18/2022]
Abstract
BACKGROUND The Electrocardiographic Imaging (ECGI) technique, used to non-invasively reconstruct the epicardial electrical activity, requires an accurate model of the atria and torso anatomy. Here we evaluate a new automatic methodology able to locate the atrial anatomy within the torso based on an intrinsic electrical parameter of the ECGI solution. METHODS In 28 realistic simulations of the atrial electrical activity, we randomly displaced the atrial anatomy for ±2.5 cm and ±30° on each axis. An automatic optimization method based on the L-curve curvature was used to estimate the original position using exclusively non-invasive data. RESULTS The automatic optimization algorithm located the atrial anatomy with a deviation of 0.5 ± 0.5 cm in position and 16.0 ± 10.7° in orientation. With these approximate locations, the obtained electrophysiological maps reduced the average error in atrial rate measures from 1.1 ± 1.1 Hz to 0.5 ± 1.0 Hz and in the phase singularity position from 7.2 ± 4.0 cm to 1.6 ± 1.7 cm (p < 0.01). CONCLUSIONS This proposed automatic optimization may help to solve spatial inaccuracies provoked by cardiac motion or respiration, as well as to use ECGI on torso and atrial anatomies from different medical image systems.
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Affiliation(s)
- Víctor Gisbert
- ITACA Institute, Universitat Politècnica de València, Valencia, Spain
| | - Santiago Jiménez-Serrano
- ITACA Institute, Universitat Politècnica de València, Valencia, Spain; Proteu Tecnologia Aplicada Coop V, Spain
| | - Eduardo Roses-Albert
- ITACA Institute, Universitat Politècnica de València, Valencia, Spain; Proteu Tecnologia Aplicada Coop V, Spain
| | - Miguel Rodrigo
- ITACA Institute, Universitat Politècnica de València, Valencia, Spain.
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Abstract
BACKGROUND Postpartum depression (PPD) is a disorder that often goes undiagnosed. The development of a screening program requires considerable and careful effort, where evidence-based decisions have to be taken in order to obtain an effective test with a high level of sensitivity and an acceptable specificity that is quick to perform, easy to interpret, culturally sensitive, and cost-effective. The purpose of this article is twofold: first, to develop classification models for detecting the risk of PPD during the first week after childbirth, thus enabling early intervention; and second, to develop a mobile health (m-health) application (app) for the Android(®) (Google, Mountain View, CA) platform based on the model with best performance for both mothers who have just given birth and clinicians who want to monitor their patient's test. MATERIALS AND METHODS A set of predictive models for estimating the risk of PPD was trained using machine learning techniques and data about postpartum women collected from seven Spanish hospitals. An internal evaluation was carried out using a hold-out strategy. An easy flowchart and architecture for designing the graphical user interface of the m-health app was followed. RESULTS Naive Bayes showed the best balance between sensitivity and specificity as a predictive model for PPD during the first week after delivery. It was integrated into the clinical decision support system for Android mobile apps. CONCLUSIONS This approach can enable the early prediction and detection of PPD because it fulfills the conditions of an effective screening test with a high level of sensitivity and specificity that is quick to perform, easy to interpret, culturally sensitive, and cost-effective.
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Affiliation(s)
- Santiago Jiménez-Serrano
- 1 Biomedical Informatics Group, Institute for the Applications of Advanced Information and Communication Technologies (ITACA), Polytechnic University of Valencia , Valencia, Spain
| | - Salvador Tortajada
- 1 Biomedical Informatics Group, Institute for the Applications of Advanced Information and Communication Technologies (ITACA), Polytechnic University of Valencia , Valencia, Spain
- 2 Joint Research Unit in Biomedical Engineering-eRPSS (ICT Applied to Healthcare Process Re-engineering), Health Research Institute Hospital La Fe, Valencia , Spain
| | - Juan Miguel García-Gómez
- 1 Biomedical Informatics Group, Institute for the Applications of Advanced Information and Communication Technologies (ITACA), Polytechnic University of Valencia , Valencia, Spain
- 2 Joint Research Unit in Biomedical Engineering-eRPSS (ICT Applied to Healthcare Process Re-engineering), Health Research Institute Hospital La Fe, Valencia , Spain
- 3 Biomedical Imaging Research Group (GIBI230), Health Research Institute Hospital La Fe, Valencia , Spain
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