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2. Microevolution, reinfection and highly complex genomic diversity in patients with sequential isolates of Mycobacterium abscessus

Author

Buenestado-Serrano, Sergio, Martínez-Lirola, Miguel, Herranz-Martín, Marta, Esteban, Jaime, Broncano-Lavado, Antonio, Molero-Salinas, Andrea, Sanz-Pérez, Amadeo, Blázquez, Jesús, Ruedas-López, Alba, Toro, Carlos, López-Roa, Paula, Domingo, Diego, Zamarrón, Ester, Ruiz Serrano, María Jesús, Muñoz, Patricia, Pérez-Lago, Laura, and García de Viedma, Darío

Published
2024
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3. Genomically-supported Redefinition of an Outbreak in a Pediatric Unit Caused by bla VIM-harboring Klebsiella michiganensis

Author

López-Camacho, Elena, Aguilera-Alonso, David, Buenestado-Serrano, Sergio, Marín, Mercedes, Molero-Salinas, Andrea, López Fresneña, Nieves, Cercenado, Emilia, Vicente, Teresa, Herrera, Laura, Slocker-Barrio, María, Muñoz, Patricia, Saavedra Lozano, Jesús, Navarro Gómez, María Luisa, García de Viedma, Darío, and Pérez-Lago, Laura

Published
2024
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7. First confirmation of importation and transmission in Spain of the newly identified SARS-CoV-2 B.1.1.7 variant

Author

Buenestado-Serrano, Sergio, Recio, Raúl, Sola Campoy, Pedro J., Catalán, Pilar, Folgueira, M. Dolores, Villa, Jennifer, Muñoz Gallego, Irene, de la Cueva, Víctor Manuel, Meléndez, M. Angeles, Andrés Zayas, Cristina, Losa-García, Juan E., Goyanes, M. José, Fraile Torres, Arturo, Von Wermitz, Andres, Fradejas-Villajos, Isabel, del Arco, Carmen, Campelo-Gutiérrez, Carolina, González Bodi, Sara, López-Wolf, Daniel, Iglesias-Franco, Higinio, Pérez-Lago, Laura, Arce Arnaez, Araceli, Rodriguez Baena, Elena, Ordobas Gavin, María, Muñoz, Patricia, Delgado, Rafael, Cardeñoso, Laura, Viedma, Esther, and García de Viedma, Darío

Published
2022
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8. Genomically-supported Redefinition of an Outbreak in a Pediatric Unit Caused by bla VIM -harboring Klebsiella michiganensis.

Author

López-Camacho, Elena, Aguilera-Alonso, David, Buenestado-Serrano, Sergio, Marín, Mercedes, Molero-Salinas, Andrea, López Fresneña, Nieves, Cercenado, Emilia, Vicente, Teresa, Herrera, Laura, Slocker-Barrio, María, Muñoz, Patricia, Saavedra Lozano, Jesús, Navarro Gómez, María Luisa, García de Viedma, Darío, and Pérez-Lago, Laura

Published
2025
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10. Microevolution, reinfection and highly complex genomic diversity in patients with sequential isolates of Mycobacterium abscessus

Author

Instituto de Salud Carlos III, European Commission, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Buenestado-Serrano, Sergio, Martínez-Lirola, Miguel, Herranz-Martín, Marta, Esteban, Jaime, Broncano-Lavado, Antonio, Molero-Salinas, Andrea, Sanz-Pérez, Amadeo, Blázquez Gómez, Jesús, Ruedas-López, Alba, Toro, Carlos, López-Roa, Paula, Domingo, Diego, Zamarrón, Ester, Ruiz Serrano, María Jesús, Muñoz, Patricia, Pérez-Lago, Laura, García de Viedma, Darío, Instituto de Salud Carlos III, European Commission, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Buenestado-Serrano, Sergio, Martínez-Lirola, Miguel, Herranz-Martín, Marta, Esteban, Jaime, Broncano-Lavado, Antonio, Molero-Salinas, Andrea, Sanz-Pérez, Amadeo, Blázquez Gómez, Jesús, Ruedas-López, Alba, Toro, Carlos, López-Roa, Paula, Domingo, Diego, Zamarrón, Ester, Ruiz Serrano, María Jesús, Muñoz, Patricia, Pérez-Lago, Laura, and García de Viedma, Darío

Abstract

Mycobacterium abscessus is an opportunistic, extensively drug-resistant non-tuberculous mycobacterium. Few genomic studies consider its diversity in persistent infections. Our aim was to characterize microevolution/reinfection events in persistent infections. Fifty-three sequential isolates from 14 patients were sequenced to determine SNV-based distances, assign resistance mutations and characterize plasmids. Genomic analysis revealed 12 persistent cases (0-13 differential SNVs), one reinfection (15,956 SNVs) and one very complex case (23 sequential isolates over 192 months), in which a first period of persistence (58 months) involving the same genotype 1 was followed by identification of a genotype 2 (76 SNVs) in 6 additional alternating isolates; additionally, ten transient genotypes (88-243 SNVs) were found. A macrolide resistance mutation was identified from the second isolate. Despite high diversity, the genotypes shared a common phylogenetic ancestor and some coexisted in the same specimens. Genomic analysis is required to access the true intra-patient complexity behind persistent infections involving M. abscessus.

Published
2024

11. Proper assignation of reactivation in a COVID-19 recurrence initially interpreted as a reinfection

Author

Pérez-Lago, laura, primary, Martínez, helena, additional, pajares, Jose Antonio, additional, Gomez, Arantxa Diaz, additional, machado, Marina, additional, Sola-Campoy, Pedro, additional, Herranz, Marta, additional, valerio, Maricela, additional, Olmedo, Maria, additional, Zayas, Cristina Andres, additional, Comas, Iñaki, additional, Candelas, fernando Gonzalez, additional, Bañares, Rafael, additional, Catalán, Pilar, additional, Muñoz, Patricia, additional, and Viedma, Darío García de, additional

Published
2024
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14. Frequent Emergence of Resistance Mutations Following Complex Intra-Host Genomic Dynamics in SARS-CoV-2 Patients Receiving Sotrovimab

Author

Palomino-Cabrera, Rosalía, primary, Tejerina, Francisco, additional, Molero-Salinas, Andrea, additional, Ferris, María, additional, Veintimilla, Cristina, additional, Catalán, Pilar, additional, Rodríguez Macias, Gabriela, additional, Alonso, Roberto, additional, Muñoz, Patricia, additional, García de Viedma, Darío, additional, Pérez-Lago, Laura, additional, Alcalá, Luis, additional, Aldámiz, Teresa, additional, Álvarez-Uría, Ana, additional, Bermúdez, Elena, additional, Bouza, Emilio, additional, Buenestado-Serrano, Sergio, additional, Burillo, Almudena, additional, Carrillo, Raquel, additional, Cercenado, Emilia, additional, Cobos, Alejandro, additional, Díez, Cristina, additional, Escribano, Pilar, additional, Estévez, Agustín, additional, Fanciulli, Chiara, additional, Galar, Alicia, additional, García, Ma Dolores, additional, Gijón, Paloma, additional, Guillén, Helmuth, additional, Guinea, Jesús, additional, Herranz, Marta, additional, Irigoyen, Álvaro, additional, Kestler, Martha, additional, López, Juan Carlos, additional, Machado, Marina, additional, Marín, Mercedes, additional, Martín-Rabadán, Pablo, additional, Montilla, Pedro, additional, Padilla, Belén, additional, Palomino-Cabrera, Rosalía, additional, Palomo, María, additional, Pérez-Granda, María Jesús, additional, Peñas-Utrilla, Daniel, additional, Pérez, Leire, additional, Reigadas, Elena, additional, Rincón, Cristina, additional, Rodríguez, Belén, additional, Rodríguez, Sara, additional, Rodríguez-Grande, Cristina, additional, Rojas, Adriana, additional, Ruiz-Serrano, María Jesús, additional, Sánchez, Carlos, additional, Sánchez, Mar, additional, Sanz-Pérez, Amadeo, additional, Serrano, Julia, additional, Valerio, Maricela, additional, Veintimilla, Ma Cristina, additional, Vesperinas, Lara, additional, Vicente, Teresa, additional, and de la Villa, Sofía, additional

Published
2023
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18. Deciphering the Tangible Spatio-Temporal Spread of a 25-Year Tuberculosis Outbreak Boosted by Social Determinants

Author

European Research Council, Ministerio de Economía, Industria y Competitividad (España), European Commission, Instituto de Salud Carlos III, Gobierno de Aragón, Agencia Estatal de Investigación (España), Comas, Iñaki [0000-0001-5504-9408], López, Mariana G. [0000-0002-2216-9232], López, Mariana G., Campos-Herrero, M. Isolina, Torres-Puente, Manuela, Canas, Fernando, Comin, Jessica, Copado, Rodolfo, Wintringer, Penelope, Iqbal, Zamin, Lagarejos, Eduardo, Moreno-Molina, Miguel, Pérez-Lago, Laura, Pino, Berta, Sante, Laura, García de Viedma, Darío, Samper, Sofia, Comas, Iñaki, European Research Council, Ministerio de Economía, Industria y Competitividad (España), European Commission, Instituto de Salud Carlos III, Gobierno de Aragón, Agencia Estatal de Investigación (España), Comas, Iñaki [0000-0001-5504-9408], López, Mariana G. [0000-0002-2216-9232], López, Mariana G., Campos-Herrero, M. Isolina, Torres-Puente, Manuela, Canas, Fernando, Comin, Jessica, Copado, Rodolfo, Wintringer, Penelope, Iqbal, Zamin, Lagarejos, Eduardo, Moreno-Molina, Miguel, Pérez-Lago, Laura, Pino, Berta, Sante, Laura, García de Viedma, Darío, Samper, Sofia, and Comas, Iñaki

Abstract

Outbreak strains of Mycobacterium tuberculosis are promising candidates as targets in the search for intrinsic determinants of transmissibility, as they are responsible for many cases with sustained transmission; however, the use of low-resolution typing methods and restricted geographical investigations represent flaws in assessing the success of long-lived outbreak strains. We can now address the nature of outbreak strains by combining large genomic data sets and phylodynamic approaches. We retrospectively sequenced the whole genome of representative samples assigned to an outbreak circulating in the Canary Islands (the GC strain) since 1993, which accounts for ~20% of local tuberculosis cases. We selected a panel of specific single nucleotide polymorphism (SNP) markers for an in-silico search for additional outbreak-related sequences within publicly available tuberculosis genomic data. Using this information, we inferred the origin, spread, and epidemiological parameters of the GC strain. Our approach allowed us to accurately trace the historical and more recent dispersion of the GC strain. We provide evidence of a highly successful nature within the Canarian archipelago but limited expansion abroad. Estimation of epidemiological parameters from genomic data disagree with a distinctive biology of the GC strain. With the increasing availability of genomic data allowing for the accurate inference of strain spread and critical epidemiological parameters, we can now revisit the link between Mycobacterium tuberculosis genotypes and transmission, as is routinely carried out for SARS-CoV-2 variants of concern. We demonstrate that social determinants rather than intrinsically higher bacterial transmissibility better explain the success of the GC strain. Importantly, our approach can be used to trace and characterize strains of interest worldwide. IMPORTANCE Infectious disease outbreaks represent a significant problem for public health. Tracing outbreak expansion and unde

Published
2023

19. A One Health approach revealed the long-term role of Mycobacterium caprae as the hidden cause of human tuberculosis in a region of Spain, 2003 to 2022

Author

Martínez-Lirola, Miguel, primary, Herranz, Marta, additional, Buenestado Serrano, Sergio, additional, Rodríguez-Grande, Cristina, additional, Dominguez Inarra, Eva, additional, Garrido-Cárdenas, Jose Antonio, additional, Correa Ruiz, Ana María, additional, Bermúdez, María Pilar, additional, Causse del Río, Manuel, additional, González Galán, Verónica, additional, Liró Armenteros, Julia, additional, Viudez Martínez, Jose María, additional, Vallejo-Godoy, Silvia, additional, Esteban García, Ana Belén, additional, Cabezas Fernández, María Teresa, additional, Muñoz, Patricia, additional, Pérez Lago, Laura, additional, and García de Viedma, Darío, additional

Published
2023
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21. Rapid Identification of Relevant Microbial Strains by Identifying Multiple Marker Single Nucleotide Polymorphisms via Amplicon Sequencing: Epidemic Monkeypox Virus as a Proof of Concept

Author

Buenestado-Serrano, Sergio, primary, Herranz, Marta, additional, Palomino-Cabrera, Rosalía, additional, Rodríguez-Grande, Cristina, additional, Peñas-Utrilla, Daniel, additional, Molero-Salinas, Andrea, additional, Veintimilla, Cristina, additional, Catalán, Pilar, additional, Alonso, Roberto, additional, Muñoz, Patricia, additional, Pérez-Lago, Laura, additional, and García de Viedma, Darío, additional

Published
2023
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22. Deciphering the Tangible Spatio-Temporal Spread of a 25-Year Tuberculosis Outbreak Boosted by Social Determinants

Author

López, Mariana G., primary, Campos-Herrero, Ma Isolina, additional, Torres-Puente, Manuela, additional, Cañas, Fernando, additional, Comín, Jessica, additional, Copado, Rodolfo, additional, Wintringer, Penelope, additional, Iqbal, Zamin, additional, Lagarejos, Eduardo, additional, Moreno-Molina, Miguel, additional, Pérez-Lago, Laura, additional, Pino, Berta, additional, Sante, Laura, additional, García de Viedma, Darío, additional, Samper, Sofía, additional, and Comas, Iñaki, additional

Published
2023
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24. Early SARS-CoV-2 Reinfections Involving the Same or Different Genomic Lineages, Spain.

Author

Rodríguez-Grande, Cristina, Estévez, Agustín, Palomino-Cabrera, Rosalía, Molero-Salinas, Andrea, Peñas-Utrilla, Daniel, Herranz, Marta, Sanz-Pérez, Amadeo, Alcalá, Luis, Veintimilla, Cristina, Catalán, Pilar, Martínez-Laperche, Carolina, Alonso, Roberto, Muñoz, Patricia, Pérez-Lago, Laura, and de Viedma, Darío García

Abstract

Centers for Disease Control and Prevention guidelines consider SARS-CoV-2 reinfection when sequential COVID-19 episodes occur >90 days apart. However, genomic diversity acquired over recent COVID-19 waves could mean previous infection provides insufficient cross-protection. We used genomic analysis to assess the percentage of early reinfections in a sample of 26 patients with 2 COVID-19 episodes separated by 20-45 days. Among sampled patients, 11 (42%) had reinfections involving different SARS-CoV-2 variants or subvariants. Another 4 cases were probable reinfections; 3 involved different strains from the same lineage or sublineage. Host genomic analysis confirmed the 2 sequential specimens belonged to the same patient. Among all reinfections, 36.4% involved non-Omicron, then Omicron lineages. Early reinfections showed no specific clinical patterns; 45% were among unvaccinated or incompletely vaccinated persons, 27% were among persons <18 years of age, and 64% of patients had no risk factors. Time between sequential positive SARS-CoV-2 PCRs to consider reinfection should be re-evaluated. [ABSTRACT FROM AUTHOR]

Published
2023
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26. No emergence of resistance mutations in COVID‐19 patients receiving nirmatrelvir/ritonavir.

Author

Palomino‐Cabrera, Rosalía, Tejerina, Francisco, Molero‐Salinas, Andrea, Veintimilla, Cristina, Catalán, Pilar, Ferris, María, Osorio, Santiago, Alonso, Roberto, Muñoz, Patricia, de García de Viedma, Darío, and Pérez‐Lago, Laura

Subjects
COVID-19, SARS-CoV-2
Abstract

A study published in the Journal of Medical Virology examined the emergence of resistance mutations in COVID-19 patients receiving the antiviral drug nirmatrelvir/ritonavir. The study analyzed 60 patients who received the drug and found that none of the known resistance mutations were identified in the patients. However, low-frequency substitutions and fixed mutations were observed in some patients, particularly those who were immunosuppressed. The study suggests that the emergence of resistance mutations to nirmatrelvir/ritonavir is currently rare. [Extracted from the article]

Published
2024
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27. Deciphering the tangible spatio-temporal spread of a 25 years tuberculosis outbreak boosted by social determinants

Author

Instituto de Salud Carlos III, Gobierno de Aragón, European Research Council, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), López, Mariana G. [0000-0002-2216-9232], Iqbal, Zamin [0000-0001-8466-7547], García de Viedma, Darío [0000-0003-3647-7110], Comas, Iñaki [0000-0001-5504-9408], López, Mariana G., Campos-Herrero, M. Isolina, Torres-Puente, Manuela, Cañas, Fernando, Comín, Jessica, Copado, Rodolfo, Wintringer, Penelope, Iqbal, Zamin, Lagarejos, Eduardo, Moreno-Molina, Miguel, Pérez-Lago, Laura, Pino, Berta, Sante, Laura, García de Viedma, Darío, Samper, Sofía, Comas, Iñaki, Instituto de Salud Carlos III, Gobierno de Aragón, European Research Council, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), López, Mariana G. [0000-0002-2216-9232], Iqbal, Zamin [0000-0001-8466-7547], García de Viedma, Darío [0000-0003-3647-7110], Comas, Iñaki [0000-0001-5504-9408], López, Mariana G., Campos-Herrero, M. Isolina, Torres-Puente, Manuela, Cañas, Fernando, Comín, Jessica, Copado, Rodolfo, Wintringer, Penelope, Iqbal, Zamin, Lagarejos, Eduardo, Moreno-Molina, Miguel, Pérez-Lago, Laura, Pino, Berta, Sante, Laura, García de Viedma, Darío, Samper, Sofía, and Comas, Iñaki

Abstract

Background. Outbreak strains are good candidates to look for intrinsic transmissibility as they are responsible for a large number of cases with sustained transmission. However, assessment of the success of long-lived outbreak strains has been flawed by the use of low-resolution typing methods and restricted geographical investigations. We now have the potential to address the nature of outbreak strains by combining large genomic datasets and phylodynamic approaches. Methods. We retrospectively sequenced the whole genome of representative samples assigned to an outbreak circulating in the Canary Islands (GC) since 1993; accounting for ~20% of local TB cases. We selected a panel of specific SNP markers to in-silico search for additional outbreak related sequences within publicly-available TB genomic data. Using this information we inferred the origin, spread and epidemiological parameters of the GC-outbreak. Findings. Our approach allowed us to accurately trace both the historical and recent dispersion of the strain. We evidenced its high success within the Canarian archipelago but found a limited expansion abroad. Estimation of epidemiological parameters from genomic data contradicts a distinct biology of the GC-strain. Interpretation. With the increasing availability of genomic data allowing for an accurate inference of strain spread and key epidemiological parameters, we can now revisit the link between Mycobacterium tuberculosis genotypes and transmission, as routinely done for SARS-CoV-2 variants of concern. We show that the success of the GC-strain is better explained by social determinants rather than intrinsically higher bacterial transmissibility. Our approach can be used to trace and characterize strains of interest worldwide.

Published
2022

28. Recurrences of multidrug-resistant tuberculosis: Strains involved, within-host diversity, and fine-tuned allocation of reinfections

Author

Instituto de Salud Carlos III, European Research Council, Agencia Nacional de Promoción Científica y Tecnológica (Argentina), Comas, Iñaki [0000-0001-5504-9408], Chiner-Oms, Álvaro [0000-0002-0463-0101], Pérez-Lago, Laura, Monteserin, Johana, Paul, Roxana, Maus, Sandra R., Yokobori, Noemi, Herranz, Marta, Sicilia, Jon, Acosta, Fermín, Fajardo, Sandra, Chiner-Oms, Álvaro, Matteo, Mario, Simboli, Norberto, Comas, Iñaki, Muñoz, Patricia, López, Beatriz, Ritacco, Viviana, Garcia de Viedma, Dario, Instituto de Salud Carlos III, European Research Council, Agencia Nacional de Promoción Científica y Tecnológica (Argentina), Comas, Iñaki [0000-0001-5504-9408], Chiner-Oms, Álvaro [0000-0002-0463-0101], Pérez-Lago, Laura, Monteserin, Johana, Paul, Roxana, Maus, Sandra R., Yokobori, Noemi, Herranz, Marta, Sicilia, Jon, Acosta, Fermín, Fajardo, Sandra, Chiner-Oms, Álvaro, Matteo, Mario, Simboli, Norberto, Comas, Iñaki, Muñoz, Patricia, López, Beatriz, Ritacco, Viviana, and Garcia de Viedma, Dario

Abstract

Recurrent tuberculosis occurs due to exogenous reinfection or reactivation/persistence. We analysed 90 sequential MDR Mtb isolates obtained in Argentina from 27 patients with previously diagnosed MDR-TB that recurred in 2018 (1-10 years, 2-10 isolates per patient). Three long-term predominant strains were responsible for 63% of all MDR-TB recurrences. Most of the remaining patients were infected by strains different from each other. Reactivation/persistence of the same strain caused all but one recurrence, which was due to a reinfection with a predominant strain. One of the prevalent strains showed marked stability in the recurrences, while in another strain higher SNP-based diversity was observed. Comparisons of intra- versus inter-patient SNP distances identified two possible reinfections with closely related variants circulating in the community. Our results show a complex scenario of MDR-TB infections in settings with predominant MDR Mtb strains.

Published
2022

29. Overlapping prison/community tuberculosis outbreaks in Costa Rica revealed by alternative analysis of suboptimal material

Author

Instituto de Salud Carlos III, European Research Council, European Commission, Comas, Iñaki [0000-0001-5504-9408], Chiner-Oms, Álvaro [0000-0002-0463-0101], Jbara, Sarah, Herranz, Marta, Sola-Campoy, Pedro J., Rodríguez-Grande, Cristina, Chiner-Oms, Álvaro, Comas, Iñaki, Muñoz, Patricia, García de Viedma, Darío, Pérez-Lago, Laura, Instituto de Salud Carlos III, European Research Council, European Commission, Comas, Iñaki [0000-0001-5504-9408], Chiner-Oms, Álvaro [0000-0002-0463-0101], Jbara, Sarah, Herranz, Marta, Sola-Campoy, Pedro J., Rodríguez-Grande, Cristina, Chiner-Oms, Álvaro, Comas, Iñaki, Muñoz, Patricia, García de Viedma, Darío, and Pérez-Lago, Laura

Abstract

Costa Rica has a low incidence of tuberculosis. Thus, identifying transmission hotspots is key to implement interventions. A tuberculosis outbreak was suspected in a prison in Costa Rica. Given the suboptimal quality of the samples received in our laboratory in Madrid, we applied alternative schemes for their analysis. In the first scheme, we bypassed the standard approach of applying systematic mycobacterial interspersed repetitive units-variable number of tandem repeats (MIRU-VNTR) and used a strain-specific polymerase chain reaction (PCR) that allowed identifying a cluster involving six cases (C1). The second scheme followed the canonical MIRU-VNTR path coupled with a whole-genomic amplification step, by which a second unsuspected overlapping cluster (C2), was detected in the same prison. These findings justified the implementation of a surveillance programme adapted to local resources based on a tailored multiplex allele-specific oligonucleotide (ASO)-PCR targeting C1 and C2. Presence of the C2 strain at a different prison was determined. ASO-PCR was applied extensively and alerted to the active circulation of one of the strains within and beyond prisons. Our study shows that alternative methodological strategies may provide useful data in settings with lack of resources for performing systematic standard molecular epidemiology programmes and/or with suboptimal material for analysis.

Published
2022

30. Systematic Genomic and Clinical Analysis of Severe Acute Respiratory Syndrome Coronavirus 2 Reinfections and Recurrences Involving the Same Strain

Author

Instituto de Salud Carlos III, Consejo Superior de Investigaciones Científicas (España), Comas, Iñaki [0000-0001-5504-9408], Rodríguez-Grande, Cristina, Alcalá, Luis, Estévez, Agustín, Sola-Campoy, Pedro J., Buenestado-Serrano, Sergio, Martínez-Laperche, Carolina, Cueva, Víctor Manuel de la, Alonso, Roberto, Andrés-Zayas, Cristina, Adán-Jiménez, Javier, Losada, Carmen, Rico-Luna, Carla, Comas, Iñaki, González-Candelas, Fernando, Catalán, Pilar, Muñoz, Patricia, Pérez-Lago, Laura, García de Viedma, Darío, Gregorio Marañón Microbiology-ID COVID 19 Study Group, Instituto de Salud Carlos III, Consejo Superior de Investigaciones Científicas (España), Comas, Iñaki [0000-0001-5504-9408], Rodríguez-Grande, Cristina, Alcalá, Luis, Estévez, Agustín, Sola-Campoy, Pedro J., Buenestado-Serrano, Sergio, Martínez-Laperche, Carolina, Cueva, Víctor Manuel de la, Alonso, Roberto, Andrés-Zayas, Cristina, Adán-Jiménez, Javier, Losada, Carmen, Rico-Luna, Carla, Comas, Iñaki, González-Candelas, Fernando, Catalán, Pilar, Muñoz, Patricia, Pérez-Lago, Laura, García de Viedma, Darío, and Gregorio Marañón Microbiology-ID COVID 19 Study Group

Abstract

Estimates of the burden of severe acute respiratory syndrome coronavirus 2 reinfections are limited by the scarcity of population-level studies incorporating genomic support. We conducted a systematic study of reinfections in Madrid, Spain, supported by genomic viral analysis and host genetic analysis, to cleanse laboratory errors and to discriminate between reinfections and recurrences involving the same strain. Among the 41,195 cases diagnosed (March 2020-March 2021), 93 (0.23%) had 2 positive reverse transcription PCR tests (55-346 days apart). After eliminating cases with specimens not stored, of suboptimal sequence quality, or belonging to different persons, we obtained valid data from 22 cases. Of those, 4 (0.01%) cases were recurrences involving the same strain; case-patients were 39-93 years of age, and 3 were immunosuppressed. Eighteen (0.04%) cases were reinfections; patients were 19-84 years of age, and most had no relevant clinical history. The second episode was more severe in 8 cases.

Published
2022

32. Nosocomial Transmission of SARS-CoV-2 Involving Vaccinated Health Care Workers

Author

Pérez-Lago, Laura, primary, Machado, Marina, additional, Gómez-Ruiz, María de Mar, additional, Sola-Campoy, Pedro J., additional, Buenestado-Serrano, Sergio, additional, de la Cueva-García, Victor Manuel, additional, Herranz, Marta, additional, Andrés Zayas, Cristina, additional, Sánchez-Arcilla, Ignacio, additional, Flores-García, Rubén Francisco, additional, López-Fresneña, Nieves, additional, García de San José, Sonia, additional, Catalán, Pilar, additional, Muñoz, Patricia, additional, and García de Viedma, Darío, additional

Published
2022
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33. Deciphering the tangible spatio-temporal spread of a 25 years tuberculosis outbreak boosted by social determinants

Author

López, Mariana G., primary, Campos-Herrero, Mª Isolina, additional, Torres-Puente, Manuela, additional, Cañas, Fernando, additional, Comín, Jessica, additional, Copado, Rodolfo, additional, Wintringer, Penelope, additional, Iqbal, Zamin, additional, Lagarejos, Eduardo, additional, Moreno-Molina, Miguel, additional, Pérez-Lago, Laura, additional, Pino, Berta, additional, Sante, Laura, additional, de Viedma, Darío García, additional, Samper, Sofía, additional, and Comas, Iñaki, additional

Published
2022
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35. Systematic Genomic and Clinical Analysis of Severe Acute Respiratory Syndrome Coronavirus 2 Reinfections and Recurrences Involving the Same Strain

Author

Rodríguez-Grande, Cristina, Alcalá, Luis, Estévez, Agustín, Sola-Campoy, Pedro J., Buenestado-Serrano, Sergio, Martínez-Laperche, Carolina, Cueva, Víctor Manuel de la, Alonso, Roberto, Andrés-Zayas, Cristina, Adán-Jiménez, Javier, Losada, Carmen, Rico-Luna, Carla, Comas, Iñaki, González-Candelas, Fernando, Catalán, Pilar, Muñoz, Patricia, Pérez-Lago, Laura, García de Viedma, Darío, Gregorio Marañón Microbiology-ID COVID 19 Study Group, Instituto de Salud Carlos III, Consejo Superior de Investigaciones Científicas (España), Comas, Iñaki, and Comas, Iñaki [0000-0001-5504-9408]

Subjects
Microbiology (medical), medicine.medical_specialty, recurrence, Coronavirus disease 2019 (COVID-19), Epidemiology, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Infectious and parasitic diseases, RC109-216, Polymerase Chain Reaction, reinfection, Systematic Genomic and Clinical Analysis of Severe Acute Respiratory Syndrome Coronavirus 2 Reinfections and Recurrences Involving the Same Strain, Variant of concern, respiratory infections, Recurrence, Clinical history, Zoonoses, Internal medicine, Severe acute respiratory syndrome coronavirus 2, Medicine, Humans, viruses, Clinical pathology, business.industry, SARS-CoV-2, Madrid, Strain (biology), Research, Respiratory infections, COVID-19, variant of interest, Genomics, Coronavirus disease, zoonoses, Infectious Diseases, coronavirus disease, Spain, Reinfection, Child, Preschool, Variant of interest, Viruses, business, variant of concern, severe acute respiratory syndrome coronavirus 2
Abstract

10 páginas, 2 figuras, 3 tablas, Estimates of the burden of severe acute respiratory syndrome coronavirus 2 reinfections are limited by the scarcity of population-level studies incorporating genomic support. We conducted a systematic study of reinfections in Madrid, Spain, supported by genomic viral analysis and host genetic analysis, to cleanse laboratory errors and to discriminate between reinfections and recurrences involving the same strain. Among the 41,195 cases diagnosed (March 2020-March 2021), 93 (0.23%) had 2 positive reverse transcription PCR tests (55-346 days apart). After eliminating cases with specimens not stored, of suboptimal sequence quality, or belonging to different persons, we obtained valid data from 22 cases. Of those, 4 (0.01%) cases were recurrences involving the same strain; case-patients were 39-93 years of age, and 3 were immunosuppressed. Eighteen (0.04%) cases were reinfections; patients were 19-84 years of age, and most had no relevant clinical history. The second episode was more severe in 8 cases., This work was supported by the Instituto de Salud Carlos III (Ref COV20/00140: SeqCOVID—Consorcio para la epidemiología genómica de SARS-CoV-2 en España) and by Consejo Superior de Investigaciones Científicas (CSIC) (PTI Salud Global). L.P.L. is the recipient of a Miguel Servet Research contract (CPII20/00001) from the Instituto de Salud Carlos III.

Published
2021

36. SARS-CoV-2 B.1.1.7 Decline Is Not Driven by the Introduction of a More Successful Variant

Author

Rodríguez-Grande, Cristina, primary, Buenestado-Serrano, Sergio, additional, Alcalá, Luis, additional, Sola-Campoy, Pedro J., additional, Molero-Salinas, Andrea, additional, Otero-Sobrino, Álvaro, additional, Rodríguez-Grande, Jorge, additional, de la Cueva García, Víctor Manuel, additional, Adán-Jiménez, Javier, additional, Rico-Luna, Carla, additional, Losada, Carmen, additional, Catalán, Pilar, additional, Muñoz, Patricia, additional, Pérez-Lago, Laura, additional, and García de Viedma, Darío, additional

Published
2021
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37. Detection of Minority Variants and Mixed Infections in Mycobacterium tuberculosis by Direct Whole-Genome Sequencing on Noncultured Specimens Using a Specific-DNA Capture Strategy

Author

Lozano, Nuria, primary, Lanza, Val F., additional, Suárez-González, Julia, additional, Herranz, Marta, additional, Sola-Campoy, Pedro J., additional, Rodríguez-Grande, Cristina, additional, Buenestado-Serrano, Sergio, additional, Ruiz-Serrano, María Jesús, additional, Tudó, Griselda, additional, Alcaide, Fernando, additional, Muñoz, Patricia, additional, García de Viedma, Darío, additional, and Pérez-Lago, Laura, additional

Published
2021
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38. Proper assignation of reactivation in a COVID-19 recurrence initially interpreted as a reinfection

Author

Pérez-Lago, Laura, Martínez Lozano, Helena, Pajares Díaz, José Antonio, Díaz Gómez, Arantxa, Machado, Marina, Sola-Campoy, Pedro J., Herranz, Marta, Buenestado-Serrano, Sergio, Valerio, Maricela, Olmedo, María, Andrés Zayas, Cristina, Comas, Iñaki, González-Candelas, Fernando, Bañares, Rafael, Catalán, Pilar, Muñoz, Patricia, García de Viedma, Darío, Gregorio Marañón Microbiology-ID COVID 19 Study Group, Muñoz, Patricia, Comas, Iñaki, Muñoz, Patricia [0000-0001-5706-5583], and Comas, Iñaki [0000-0001-5504-9408]

Subjects
0301 basic medicine, Male, Pediatrics, medicine.medical_specialty, 2019-20 coronavirus outbreak, Fatal outcome, Coronavirus disease 2019 (COVID-19), Hospitalized patients, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Antibodies, Viral, 03 medical and health sciences, 0302 clinical medicine, Nosocomial transmission, Recurrence, medicine, Immunology and Allergy, Humans, 030212 general & internal medicine, Aged, First episode, Whole Genome Sequencing, business.industry, SARS-CoV-2, Brief Report, COVID-19, Reactivation, 030104 developmental biology, Infectious Diseases, AcademicSubjects/MED00290, Reinfection, business, WGS
Abstract

A 77-year-old-male (Case R) who had had a previous diagnosis of mild COVID-19 episode, was hospitalized 35 days later. On Day 23 post-admission, he developed a second COVID-19 episode, now severe, and finally died. Initially, Case R COVID-19 recurrence was interpreted as a reinfection due to the exposure to a SARS-CoV-2 RT-PCR-positive room-mate. However, whole-genome-sequencing indicated that case R recurrence corresponded to a reactivation of the strain involved in his first episode. Case R reactivation had major consequences, leading to a more severe episode, and causing a subsequent transmission to another two hospitalized patients, one of them with fatal outcome.

Published
2021

39. High SARS-CoV-2 viral load in travellers arriving in Spain with a negative COVID-19 test prior to departure

Author

Molero-Salinas, Andrea, primary, Rico-Luna, Carla, additional, Losada, Carmen, additional, Buenestado-Serrano, Sergio, additional, de la Cueva García, Víctor Manuel, additional, Egido, José, additional, Adán-Jiménez, Javier, additional, Catalán, Pilar, additional, Muñoz, Patricia, additional, Pérez-Lago, Laura, additional, and García de Viedma, Darío, additional

Published
2021
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40. Complete Analysis of the Epidemiological Scenario around a SARS-CoV-2 Reinfection: Previous Infection Events and Subsequent Transmission

Author

Pérez Lago, Laura, primary, Pérez Latorre, Leire, additional, Herranz, Marta, additional, Tejerina, Francisco, additional, Sola-Campoy, Pedro J., additional, Sicilia, Jon, additional, Suárez-González, Julia, additional, Andrés-Zayas, Cristina, additional, Chiner-Oms, Alvaro, additional, Jiménez-Serrano, Santiago, additional, García-González, Neris, additional, Comas, Iñaki, additional, González-Candelas, Fernando, additional, Martínez-Laperche, Carolina, additional, Catalán, Pilar, additional, Muñoz, Patricia, additional, and García de Viedma, Darío, additional

Published
2021
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41. Shared Mutations in Emerging SARS-CoV-2 Circulating Variants May Lead to Reverse Transcription-PCR (RT-PCR)-Based Misidentification of B.1.351 and P.1 Variants of Concern

Author

Losada, Carmen, primary, Rico-Luna, Carla, additional, Otero-Sobrino, Álvaro, additional, Molero-Salinas, Andrea, additional, Buenestado-Serrano, Sergio, additional, Candela, Ana, additional, Pérez-Lago, Laura, additional, Muñoz, Patricia, additional, Catalán, Pilar, additional, and de Viedma, Darío García, additional

Published
2021
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42. High within-host diversity found from direct genotyping on post-mortem tuberculosis specimens in a high-burden setting

Author

Rodríguez-Grande, Cristina, primary, Hurtado, Juan Carlos, additional, Rodríguez-Maus, Sandra, additional, Casas, Isaac, additional, Castillo, Paola, additional, Navarro, Mireia, additional, Rakislova, Natalia, additional, García-Basteiro, Alberto, additional, Carrilho, Carla, additional, Fernandes, Fabiola, additional, Lovane, Lucilia, additional, Jordao, Dercio, additional, Ismail, Mamudo R., additional, Lorenzoni, Cesaltina, additional, Cossa, Anélsio, additional, Mandomando, Inácio, additional, Bassat, Quique, additional, Menéndez, Clara, additional, Ordi, Jaume, additional, Muñoz, Patricia, additional, Pérez-Lago, Laura, additional, García de Viedma, Darío, additional, and Martínez, Miguel J., additional

Published
2021
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43. The first wave of the COVID-19 epidemic in Spain was associated with early introductions and fast spread of a dominating genetic variant

Author

López, Mariana G., Chiner-Oms, Álvaro, García de Viedma, Darío, Ruiz-Rodriguez, Paula, Bracho, Maria Alma, Cancino-Muñoz, Irving, D’Auria, Giuseppe, de Marco, Griselda, García-González, Neris, Goig, Galo Adrian, Gómez-Navarro, Inmaculada, Jiménez-Serrano, Santiago, Martinez-Priego, Llúcia, Ruiz-Hueso, Paula, Ruiz-Roldán, Lidia, Torres-Puente, Manuela, Alberola, Juan, Albert, Eliseo, Aranzamendi Zaldumbide, Maitane, Bea-Escudero, María Pilar, Boga, Jose Antonio, Bordoy, Antoni E., Canut-Blasco, Andrés, Carvajal, Ana, Cilla Eguiluz, Gustavo, Cordón Rodríguez, Maria Luz, Costa-Alcalde, José J., de Toro, María, de Toro Peinado, Inmaculada, del Pozo, Jose Luis, Duchêne, Sebastián, Fernández-Pinero, Jovita, Fuster Escrivá, Begoña, Gimeno Cardona, Concepción, González Galán, Verónica, Gonzalo Jiménez, Nieves, Hernáez Crespo, Silvia, Herranz, Marta, Lepe, José Antonio, López-Causapé, Carla, López-Hontangas, José Luis, Martín, Vicente, Martró, Elisa, Milagro Beamonte, Ana, Montes Ros, Milagrosa, Moreno-Muñoz, Rosario, Navarro, David, Navarro-Marí, José María, Not, Anna, Oliver, Antonio, Palop-Borrás, Begoña, Parra Grande, Mónica, Pedrosa-Corral, Irene, Pérez González, Maria Carmen, Pérez-Lago, Laura, Pérez-Ruiz, Mercedes, Piñeiro Vázquez, Luis, Rabella, Nuria, Rezusta, Antonio, Robles Fonseca, Lorena, Rodríguez-Villodres, Ángel, Sanbonmatsu-Gámez, Sara, Sicilia, Jon, Soriano, Alex, Tirado Balaguer, María Dolores, Torres, Ignacio, Tristancho, Alexander, Marimón, José María, Pérez-Tur, Jordi, Catalán-Alonso, Pilar, Suárez González, Julia, Muñoz, Patricia, Ruiz-Rodríguez, Paula, Bracho, María Alma, Martínez Priego, Llúcia, Galán-Vendrell, Inmaculada, De Marco, Griselda, Ferrús-Abad, María Loreto, Carbó-Ramírez, Sandra, Nogueira, Jose Miguel, Camarena, Juan José, Martínez Expósito, Óscar, Antona Urieta, Nerea, Castelló-Abietar, Cristian, Rojo-Alba, Susana, Álvarez-Argüelles, Marta Elena, Melón, Santiago, Antuori, Adrián, Fernández-Navarro, Anabel, Lecaroz Agara, Maria Concepción, Gómez-González, Carmen, Aguirre-Quiñonero, Amaia, López-Mirones, José Israel, Fernández-Torres, Marina, Almela-Ferrer, Maria Rosario, Fregeneda-Grandes, Juan Miguel, Argüello, Héctor, Sorarrain, Ane, Trastoy, Rocío, Barbeito Castiñeiras, Gema, Coira, Amparo, Pérez del Molino, María Luisa, Aguilera, Antonio, Mediavilla Gradolph, Maria Concepción, Fernández-Alonso, Mirian, González-Recio, Oscar, Gutiérrez-Rivas, Mónica, Jiménez Clavero, Miguel Ángel, Ocete Mochón, María Dolores, Medina-Gonzalez, Rafael, Reina, Jordi, Gómez-Ruiz, Maria Dolores, Gonzalez-Barbera, Eva M., Molina, Antonio J., Fernandez-Villa, Tania, Martínez-Cameo, Nieves Felisa, Gracia-Grataloup, Yolanda, Tirado Balaguer, Maria Dolores, Gómez Alonso, Bárbara, Arjona Zaragozí, Francisco José, Chamizo López, Francisco Javier, Bordes-Benítez, Ana, Rabella, Núria, Navarro, Ferran, Miró, Elisenda, Simarro Córdoba, Encarnación, Lozano-Serra, Julia, Soriano, Álex, Roig Sena, Francisco Javier, Vanaclocha Luna, Hermelinda, Sanmartín, Isabel, García-Souto, Daniel, Pequeño-Valtierra, Ana, Tubio, Jose M. C., Temes, Javier, Rodríguez-Castro, Jorge, Santamarina García, Martín, Rodríguez-Iglesias, Manuel, Galán-Sanchez, Fátima, Rodríguez-Pallares, Salud, Azcona-Gutiérrez, José Manuel, Blasco-Alberdi, Miriam, Mayor, Alfredo, García-Basteiro, Alberto L., Moncunill, Gemma, Dobaño, Carlota, Cisteró, Pau, Mitjà, Oriol, González-Beiras, Camila, Vall-Mayans, Martí, Corbacho-Monné, Marc, Alemany, Andrea, Muñoz-Cuevas, Cristina, Rodríguez-Rodríguez, Guadalupe, Benito, Rafael, Algarate, Sonia, Bueno, Jessica, Vergara-Gómez, Andrea, Martínez, Miguel J., Vila, Jordi, Rubio, Elisa, Peiró-Mestres, Aida, Navero-Castillejos, Jessica, Posada, David, Valverde, Diana, Estévez, Nuria, Fernández-Silva, Iria, de Chiara, Loretta, Gallego-García, Pilar, Varela, Nair, Gómez-Pinedo, Ulises, Gozalo-Margüello, Mónica, Cano García, Maria Eliecer, Méndez-Legaza, José Manuel, Rodríguez-Lozano, Jesus, Siller, María, Pablo-Marcos, Daniel, Ruiz-García, Maria Montserrat, Galiana, Antonio, Sánchez-Almendro, Judith, Gascón Ros, Maria Isabel, Torregrosa-Hetland, Cristina Juana, Pastor Boix, Eva María, Cascales Ramos, Paloma, Garcinuño Enríquez, Pedro Luis, Raga Borja, Salvador, González Cantó, Julia, Martínez Macias, Olalla, de Salazar, Adolfo, Viñuela González, Laura, Chueca, Natalia, García, Federico, Gómez-Camarasa, Cristina, Farga Martí, Amparo, Falcón, Rocío, Domínguez-Márquez, Victoria, Planas, Anna M., Fernández-Cádenas, Israel, Marcos, Maria Ángeles, Ezpeleta, Carmen, Navascués, Ana, Miqueleiz Zapatero, Ana, Segovia, Manuel, Moreno-Docón, Antonio, Viedma, Esther, Recio Martínez, Raúl, Muñoz-Gallego, Irene, Gonzalez-Bodi, Sara, Folgueira, Maria Dolores, Mingorance, Jesús, Dahdouh, Elias, Lázaro-Perona, Fernando, Rodríguez-Tejedor, María, Romero-Gómez, María Pilar, García-Rodríguez, Julio, Galán, Juan Carlos, Rodríguez-Dominguez, Mario, Martínez-García, Laura, Abreu Di Berardino, Melanie, Ponce-Alonso, Manuel, González-Alba, Jose Maria, Sanz-Muñoz, Ivan, Pérez San José, Diana, Gil Fortuño, Maria, Bellido-Blasco, Juan B., Yagüe Muñoz, Alberto, Hernández Pérez, Noelia, Buj Jordá, Helena, Pérez Olaso, Óscar, González Praetorius, Alejandro, Martínez Ramírez, Nora Mariela, Ramírez Marinero, Aida, Padilla León, Eduardo, Vilas Basil, Alba, Canal Aranda, Mireia, Bernet Sánchez, Albert, Bellés Bellés, Alba, López González, Eric, Prats Sánchez, Iván, García-González, Mercè, Martínez-Lirola, Miguel José, Rodríguez Maresca, Manuel Ángel, Cabezas Fernández, Maria Teresa, Carrillo Gil, María Eugenia, Ventero Martín, Maria Paz, Molina Pardines, Carmen, Orta Mira, Nieves, Navarro Cots, María, Vidal Catalá, Inmaculada, García Nava, Isabel, Illescas Fernández-Bermejo, Soledad, Martínez-Alarcón, José, Torres-Narbona, Marta, Colmenarejo, Cristina, García-Agudo, Lidia, Pérez García, Jorge A., Yago López, Martín, Goberna Bravo, María Ángeles, Simón García, Victoria, Llop Furquet, Gonzalo, Iranzo Tatay, Agustín, Moreno-Marro, Sandra, Lozano Rodríguez, Noelia, Broseta Tamarit, Amparo, Badiola Díez, Juan José, Martínez-Ramírez, Amparo, Dopazo, Ana, Callejas, Sergio, Benguría, Alberto, Aguado, Begoña, Alcamí, Antonio, Bermejo Bermejo, Marta, Ramos-Ruíz, Ricardo, Fernández Soria, Víctor Manuel, Simón Soria, Fernando, Roig Cardells, Mercedes, Coscolla, Mireia, González-Candelas, Fernando, Comas, Iñaki, Instituto de Salud Carlos III, Consejo Superior de Investigaciones Científicas (España), Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), European Research Council, European Commission, Generalitat Valenciana, Chiner-Oms, Álvaro [0000-0002-0463-0101], Ruiz-Rodríguez, Paula [0000-0003-0727-5974], D'Auria, Giuseppe [0000-0003-0672-2541], Gómez-Navarro, Inmaculada [0000-0002-5235-7365], Jiménez Serrano, Santiago [0000-0003-2917-6053], Aranzamendi Zaldumbide, Maitane [0000-0003-2432-7078], Boga, José Antonio [0000-0002-5500-9972], Bordoy, Antoni E. [0000-0002-1165-542X], Costa-Alcalde, José J. [0000-0002-1916-2216], Toro Peinado, Inmaculada de [0000-0002-8151-3275], López-Causapé, Carla [0000-0003-2228-2005], Martín, Vicente [0000-0003-0552-2804], Moreno-Muñoz, Rosario [0000-0002-0185-5612], Parra Grande, Mónica [0000-0002-8330-7467], Balaguer, María Dolores [0000-0003-3808-7300], Coscolla, Mireia [0000-0003-0752-0538], González-Candelas, Fernando [0000-0002-0879-5798], Comas, Iñaki [0000-0001-5504-9408], Ministerio de Ciencia (España), Generalitat Valenciana (España), Chiner-Oms, Álvaro, Ruiz-Rodríguez, Paula, D'Auria, Giuseppe, Gómez-Navarro, Inmaculada, Jiménez Serrano, Santiago, Aranzamendi Zaldumbide, Maitane, Boga, José Antonio, Bordoy, Antoni E., Costa-Alcalde, José J., Toro Peinado, Inmaculada de, López-Causapé, Carla, Martín, Vicente, Moreno-Muñoz, Rosario, Parra Grande, Mónica, Balaguer, María Dolores, Coscolla, Mireia, González-Candelas, Fernando, Comas, Iñaki, and Marimon, Jose Maria

Subjects
DYNAMICS, Coronavirus disease 2019 (COVID-19), Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Physical Distancing, Biology, Severity of Illness Index, Article, law.invention, 03 medical and health sciences, 0302 clinical medicine, law, Pandemic, Quarantine, Genetics, Humans, Clade, Phylogeny, 030304 developmental biology, 0303 health sciences, Models, Statistical, SARS-CoV-2, Incidence (epidemiology), Incidence, Genetic variants, COVID-19, Genomics, New variant, Dynamics, Virus, 3. Good health, Spain, Communicable Disease Control, VIRUS, 030217 neurology & neurosurgery, Demography
Abstract

SeqCOVID-Spain consortium: Álvaro Chiner-Oms, Irving Cancino-Muñoz, Mariana G. López, Manuela Torres-Puente, Inmaculada Gómez-Navarro, Santiago Jiménez-Serrano, Jordi Pérez-Tur, Darío García de Viedma, Laura Pérez-Lago, Marta Herranz, Jon Sicilia, Pilar Catalán-Alonso, Julia Suárez González, Patricia Muñoz, Mireia Coscolla, Paula Ruiz-Rodríguez, Fernando González-Candelas, Iñaki Comas, Lidia Ruiz-Roldán, María Alma Bracho, Neris García-González, Llúcia Martínez Priego, Inmaculada Galán-Vendrell, Paula Ruiz-Hueso, Griselda De Marco, María Loreto Ferrús-Abad, Sandra Carbó-Ramírez, Giuseppe D’Auria, Galo Adrian Goig, Juan Alberola, Jose Miguel Nogueira, Juan José Camarena, David Navarro, Eliseo Albert, Ignacio Torres, Maitane Aranzamendi Zaldumbide, Óscar Martínez Expósito, Nerea Antona Urieta, María de Toro, María Pilar Bea-Escudero, Jose Antonio Boga, Cristian Castelló-Abietar, Susana Rojo-Alba, Marta Elena Álvarez-Argüelles, Santiago Melón, Elisa Martró, Antoni E. Bordoy, Anna Not, Adrián Antuori, Anabel Fernández-Navarro, Andrés Canut-Blasco, Silvia Hernáez Crespo, Maria Luz Cordón Rodríguez, Maria Concepción Lecaroz Agara, Carmen Gómez-González, Amaia Aguirre-Quiñonero, José Israel López-Mirones, Marina Fernández-Torres, Maria Rosario Almela-Ferrer, Ana Carvajal, Juan Miguel Fregeneda-Grandes, Héctor Argüello, Gustavo Cilla Eguiluz, Milagrosa Montes Ros, Luis Piñeiro Vázquez, Ane Sorarrain, José María Marimón, José J. Costa-Alcalde, Rocío Trastoy, Gema Barbeito Castiñeiras, Amparo Coira, María Luisa Pérez del Molino, Antonio Aguilera, Begoña Palop-Borrás, Inmaculada de Toro Peinado, Maria Concepción Mediavilla Gradolph, Mercedes Pérez-Ruiz, Mirian Fernández-Alonso, Jose Luis del Pozo, Oscar González-Recio, Mónica Gutiérrez-Rivas, Jovita Fernández-Pinero, Miguel Ángel Jiménez Clavero, Begoña Fuster Escrivá, Concepción Gimeno Cardona, María Dolores Ocete Mochón, Rafael Medina-Gonzalez, José Antonio Lepe, Verónica González Galán, Ángel Rodríguez-Villodres, Nieves Gonzalo Jiménez, Jordi Reina, Carla López-Causapé, Maria Dolores Gómez-Ruiz, Eva M. Gonzalez-Barbera, José Luis López-Hontangas, Vicente Martín, Antonio J. Molina, Tania Fernandez-Villa, Ana Milagro Beamonte, Nieves Felisa Martínez-Cameo, Yolanda Gracia-Grataloup, Rosario Moreno-Muñoz, Maria Dolores Tirado Balaguer, José María Navarro-Marí, Irene Pedrosa-Corral, Sara Sanbonmatsu-Gámez, Antonio Oliver, Mónica Parra Grande, Bárbara Gómez Alonso, Francisco José Arjona Zaragozí, Maria Carmen Pérez González, Francisco Javier Chamizo López, Ana Bordes-Benítez, Núria Rabella, Ferran Navarro, Elisenda Miró, Antonio Rezusta, Alexander Tristancho, Encarnación Simarro Córdoba, Julia Lozano-Serra, Lorena Robles Fonseca, Álex Soriano, Francisco Javier Roig Sena, Hermelinda Vanaclocha Luna, Isabel Sanmartín, Daniel García-Souto, Ana Pequeño-Valtierra, Jose M. C. Tubio, Javier Temes, Jorge Rodríguez-Castro, Martín Santamarina García, Manuel Rodríguez-Iglesias, Fátima Galán-Sanchez, Salud Rodríguez-Pallares, José Manuel Azcona-Gutiérrez, Miriam Blasco-Alberdi, Alfredo Mayor, Alberto L. García-Basteiro, Gemma Moncunill, Carlota Dobaño, Pau Cisteró, Oriol Mitjà, Camila González-Beiras, Martí Vall-Mayans, Marc Corbacho-Monné, Andrea Alemany, Cristina Muñoz-Cuevas, Guadalupe Rodríguez-Rodríguez, Rafael Benito, Sonia Algarate, Jessica Bueno, Andrea Vergara-Gómez, Miguel J. Martínez, Jordi Vila, Elisa Rubio, Aida Peiró-Mestres, Jessica Navero-Castillejos, David Posada, Diana Valverde, Nuria Estévez, Iria Fernández-Silva, Loretta de Chiara, Pilar Gallego-García, Nair Varela, Ulises Gómez-Pinedo, Mónica Gozalo-Margüello, Maria Eliecer Cano García, José Manuel Méndez-Legaza, Jesus Rodríguez-Lozano, María Siller, Daniel Pablo-Marcos, Maria Montserrat Ruiz-García, Antonio Galiana, Judith Sánchez-Almendro, Maria Isabel Gascón Ros, Cristina Juana Torregrosa-Hetland, Eva María Pastor Boix, Paloma Cascales Ramos, Pedro Luis Garcinuño Enríquez, Salvador Raga Borja, Julia González Cantó, Olalla Martínez Macias, Adolfo de Salazar, Laura Viñuela González, Natalia Chueca, Federico García, Cristina Gómez-Camarasa, Amparo Farga Martí, Rocío Falcón, Victoria Domínguez-Márquez, Anna M. Planas, Israel Fernández-Cádenas, Maria Ángeles Marcos, Carmen Ezpeleta, Ana Navascués, Ana Miqueleiz Zapatero, Manuel Segovia, Antonio Moreno-Docón, Esther Viedma, Raúl Recio Martínez, Irene Muñoz-Gallego, Sara Gonzalez-Bodi, Maria Dolores Folgueira, Jesús Mingorance, Elias Dahdouh, Fernando Lázaro-Perona, María Rodríguez-Tejedor, María Pilar Romero-Gómez, Julio García-Rodríguez, Juan Carlos Galán, Mario Rodríguez-Dominguez, Laura Martínez-García, Melanie Abreu Di Berardino, Manuel Ponce-Alonso, Jose Maria González-Alba, Ivan Sanz-Muñoz, Diana Pérez San José, Maria Gil Fortuño, Juan B. Bellido-Blasco, Alberto Yagüe Muñoz, Noelia Hernández Pérez, Helena Buj Jordá, Óscar Pérez Olaso, Alejandro González Praetorius, Nora Mariela Martínez Ramírez, Aida Ramírez Marinero, Eduardo Padilla León, Alba Vilas Basil, Mireia Canal Aranda, Albert Bernet Sánchez, Alba Bellés Bellés, Eric López González, Iván Prats Sánchez, Mercè García-González, Miguel José Martínez-Lirola, Manuel Ángel Rodríguez Maresca, Maria Teresa Cabezas Fernández, María Eugenia Carrillo Gil, Maria Paz Ventero Martín, Carmen Molina Pardines, Nieves Orta Mira, María Navarro Cots, Inmaculada Vidal Catalá, Isabel García Nava, Soledad Illescas Fernández-Bermejo, José Martínez-Alarcón, Marta Torres-Narbona, Cristina Colmenarejo, Lidia García-Agudo, Jorge A. Pérez García, Martín Yago López, María Ángeles Goberna Bravo, Victoria Simón García, Gonzalo Llop Furquet, Agustín Iranzo Tatay, Sandra Moreno-Marro, Noelia Lozano Rodríguez, Amparo Broseta Tamarit, Juan José Badiola Díez, Amparo Martínez-Ramírez, Ana Dopazo, Sergio Callejas, Alberto Benguría, Begoña Aguado, Antonio Alcamí, Marta Bermejo Bermejo, Ricardo Ramos-Ruíz, Víctor Manuel Fernández Soria, Fernando Simón Soria & Mercedes Roig Cardells, 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, This work was mainly funded by the Instituto de Salud Carlos III project COV20/00140, with additional funding by Spanish National Research Council project CSIC-COV19-021, Ministerio de Ciencia project PID2019-104477RB-100, ERC StG 638553 and ERC CoG 101001038 to I.C., and BFU2017-89594R to F.G.C. M.C. is supported by Ramón y Cajal program from Ministerio de Ciencia and grants RTI2018-094399-A-I00 and Generalitat Valenciana (Regional Government) project SEJI/2019/011. We gratefully acknowledge Hospital Universitari Vall d’Hebron, Instituto de Salud Carlos III, IrsiCaixa AIDS Research Lab and all the international researchers and institutions that submitted sequenced SARS-CoV-2 genomes to the GISAID’s EpiCov Database (Supplementary Table 1), as an important part of our analyses has been made possible by the sharing of their work. We also thank Unidad de Bioinformática y Estadística, Centro de Investigación Príncipe Felipe, for allowing us to use the Computer Cluster to perform some of the bioinformatic analysis.

Published
2021

44. Overlapping of Independent SARS-CoV-2 Nosocomial Transmissions in a Complex Outbreak

Author

Pérez-Lago, Laura, primary, Martínez-Lozano, Helena, additional, Pajares-Díaz, Jose Antonio, additional, Díaz-Gómez, Arantxa, additional, Machado, Marina, additional, Sola-Campoy, Pedro J., additional, Herranz, Marta, additional, Valerio, Maricela, additional, Olmedo, María, additional, Suárez-González, Julia, additional, Quesada-Cubo, Víctor, additional, Gómez-Ruiz, Maria del Mar, additional, López-Fresneña, Nieves, additional, Sánchez-Arcilla, Ignacio, additional, Comas, Iñaki, additional, González-Candelas, Fernando, additional, García de San José, Sonia, additional, Bañares, Rafael, additional, Catalán, Pilar, additional, Muñoz, Patricia, additional, and García de Viedma,, Darío, additional

Published
2021
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45. Host genetic analysis should be mandatory for proper classification of COVID-19 reinfections

Author

Pérez Lago, Laura, primary, Machado, Marina, additional, Herranz, Marta, additional, Sola-Campoy, Pedro J, additional, Suárez-González, Julia, additional, Martínez-Laperche, Carolina, additional, Comas, Iñaki, additional, Alcalá, Luis, additional, Catalán, Pilar, additional, Muñoz, Patricia, additional, and García de Viedma, Darío, additional

Published
2021
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46. Proper Assignation of Reactivation in a COVID-19 Recurrence Initially Interpreted as a Reinfection

Author

Pérez-Lago, Laura, primary, Martínez-Lozano, Helena, additional, Pajares Díaz, Jose Antonio, additional, Díaz Gómez, Arantxa, additional, Machado, Marina, additional, Sola-Campoy, Pedro J, additional, Herranz, Marta, additional, Buenestado-Serrano, Sergio, additional, Valerio, Maricela, additional, Olmedo, María, additional, Andrés Zayas, Cristina, additional, Comas, Iñaki, additional, González Candelas, Fernando, additional, Bañares, Rafael, additional, Catalán, Pilar, additional, Muñoz, Patricia, additional, and García de Viedma, Darío, additional

Published
2021
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47. SARS-CoV-2 superinfection and reinfection with three different strains

Author

Viedma, Darío García de, primary, Pérez-Lago, laura, additional, Kestler, Martha, additional, Sola-Campoy, Pedro, additional, Rodríguez-Grande, Cristina, additional, Flores-García, Rubén Francisco, additional, Buenestado-Serrano, Sergio, additional, Herranz, Marta, additional, Alcala, Luis, additional, Martínez-Laperche, Carolina, additional, Suárez-González, Julia, additional, Catalán, Pilar, additional, and Muñoz, Patricia, additional

Published
2021
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48. First importations of SARS-CoV-2 P.1 and P.2 variants from Brazil to Spain and early community transmission

Author

Sola Campoy, Pedro J., primary, Buenestado-Serrano, Sergio, additional, Pérez-Lago, Laura, additional, Rodriguez-Grande, Cristina, additional, Catalán, Pilar, additional, Andrés-Zayas, Cristina, additional, Alcalá, Luis, additional, Losada, Carmen, additional, Rico-Luna, Carla, additional, Muñoz, Patricia, additional, and García de Viedma, Darío, additional

Published
2021
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49. SARS‐CoV‐2 superinfection and reinfection with three different strains.

Author

Pérez‐Lago, Laura, Kestler, Martha, Sola‐Campoy, Pedro J., Rodriguez‐Grande, Cristina, Flores‐García, Rubén Francisco, Buenestado‐Serrano, Sergio, Herranz, Marta, Alcalá, Luis, Martínez‐Laperche, Carolina, Suárez‐González, Julia, Catalán, Pilar, Muñoz, Patricia, and García de Viedma, Darío

Subjects
*SARS-CoV-2, *COVID-19, *SUPERINFECTION, *REINFECTION
Abstract

We report a corona virus disease (COVID‐19) case with unprecedented viral complexity. In the first severe episode, two different severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) strains (superinfection) were identified within a week. Three months after discharge, the patient was readmitted and was infected in a nosocomial outbreak with a different strain, suffering a second milder COVID‐19 episode. [ABSTRACT FROM AUTHOR]

Published
2022
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50. Different Within-Host Viral Evolution Dynamics in Severely Immunosuppressed Cases with Persistent SARS-CoV-2

Author

Pérez Lago, Laura, Aldámiz Echevarría, Teresa, García Martínez, Rita, Pérez Latorre, Leire, Herranz, Marta, Sola Campoy, Pedro, Suárez González, Julia, Martínez Laperche, Carolina, Comas, Iñaki, González Candelas, Fernando, Catalán Alonso, Pilar, Muñoz García, Patricia Carmen, García de Viedma, Darío, Pérez Lago, Laura, Aldámiz Echevarría, Teresa, García Martínez, Rita, Pérez Latorre, Leire, Herranz, Marta, Sola Campoy, Pedro, Suárez González, Julia, Martínez Laperche, Carolina, Comas, Iñaki, González Candelas, Fernando, Catalán Alonso, Pilar, Muñoz García, Patricia Carmen, and García de Viedma, Darío

Abstract

A successful Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variant, B.1.1.7, has recently been reported in the UK, causing global alarm. Most likely, the new variant emerged in a persistently infected patient, justifying a special focus on these cases. Our aim in this study was to explore certain clinical profiles involving severe immunosuppression that may help explain the prolonged persistence of viable viruses. We present three severely immunosuppressed cases (A, B, and C) with a history of lymphoma and prolonged SARS-CoV-2 shedding (2, 4, and 6 months), two of whom finally died. Whole-genome sequencing of 9 and 10 specimens from Cases A and B revealed extensive within-patient acquisition of diversity, 12 and 28 new single nucleotide polymorphisms, respectively, which suggests ongoing SARS-CoV-2 replication. This diversity was not observed for Case C after analysing 5 sequential nasopharyngeal specimens and one plasma specimen, and was only observed in one bronchoaspirate specimen, although viral viability was still considered based on constant low Ct values throughout the disease and recovery of the virus in cell cultures. The acquired viral diversity in Cases A and B followed different dynamics. For Case A, new single nucleotide polymorphisms were quickly fixed (13–15 days) after emerging as minority variants, while for Case B, higher diversity was observed at a slower emergence: fixation pace (1–2 months). Slower SARS-CoV-2 evolutionary pace was observed for Case A following the administration of hyperimmune plasma. This work adds knowledge on SARS-CoV-2 prolonged shedding in severely immunocompromised patients and demonstrates viral viability, noteworthy acquired intra-patient diversity, and different SARS-CoV-2 evolutionary dynamics in persistent cases., Instituto de Salud Carlos III, Consejo Superior de Investigaciones Científicas (España), Depto. de Medicina, Fac. de Medicina, TRUE, pub

Published
2021

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