Accelerating SARS-CoV-2 genomic surveillance in a routine clinical setting with nanopore sequencing

Authors: Buenestado-Serrano, Sergio, Herranz, Marta, Otero-Sobrino, Álvaro, Molero-Salinas, Andrea, Rodríguez-Grande, Cristina, Sanz-Pérez, Amadeo, Durán Galván, María José, Catalán, Pilar, Alonso, Roberto, Muñoz, Patricia, Pérez-Lago, Laura, García de Viedma, Darío

Source: In International Journal of Medical Microbiology March 2024 314

A solution to achieve sequencing from SARS-CoV-2 specimens with low viral loads: concatenation of reads from independent reactions.

Authors: Cerro-Monje, Alba^1,2 (AUTHOR), Buenestado-Serrano, Sergio^1,2,3 (AUTHOR), Palomino-Cabrera, Rosalía^1,2 (AUTHOR), Molero-Salinas, Andrea^1,2 (AUTHOR), Herranz, Marta^1,2 (AUTHOR), Alonso, Roberto^1,2,4 (AUTHOR), Catalán, Pilar^1,2 (AUTHOR), Muñoz, Patricia^1,2,4,5 (AUTHOR), García de Viedma, Darío^1,2,5 (AUTHOR) dgviedma2@gmail.com, Pérez-Lago, Laura^1,2 (AUTHOR) lperezg00@gmail.com

Source: Virology Journal. 5/30/2024, Vol. 21, p1-8. 8p.

Subject Terms: *VIRAL load, *NUCLEOTIDE sequencing, *WHOLE genome sequencing, *SARS-CoV-2, *COVID-19

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

Alternate Title: Primera confirmación de importación y transmisión en España de la variante B.1.1.7 del SARS-CoV-2 recientemente identificada (Spanish; Castilian)

Authors: 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, García de Viedma, Darío

Source: In Enfermedades infecciosas y microbiologia clinica (English ed.) December 2022 40(10):546-549

SARS‐CoV‐2 superinfection and reinfection with three different strains

Authors: 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, García de Viedma, Darío

Source: Transboundary and emerging diseases. 69(5):3084-3089

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100165431133.0x000001&indx=1&recIds=ETOCvdc_100165431133.0x000001

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

Authors: 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, Pérez-Lago, Laura

Source: Pediatric Infectious Disease Journal; Feb2025, Vol. 44 Issue 2, p166-173, 8p

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

Alternate Title: Primeras importaciones de las variantes SARS-CoV-2 P.1 y P.2 de Brasil a Madrid y transmisión comunitaria (Spanish; Castilian)

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

Source: In Enfermedades infecciosas y microbiologia clinica (English ed.) May 2022 40(5):262-265

Different dynamics of mean SARS‐CoV‐2 RT‐PCR Ct values between the first and second COVID‐19 waves in the Madrid population

Authors: Rodríguez‐Grande, Cristina, Catalán, Pilar, Alcalá, Luis, Buenestado‐Serrano, Sergio, Adán‐Jiménez, Javier, Rodríguez‐Maus, Sandra, Herranz, Marta, Sicilia, Jon, Acosta, Fermín, Pérez‐Lago, Laura, Muñoz, Patricia, García de Viedma, Darío

Source: Transboundary and emerging diseases. 68(6):3103-3106

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100134784004.0x000001&indx=1&recIds=ETOCvdc_100134784004.0x000001

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

Authors: Rodríguez-Grande, Cristina^1,2, Alcalá, Luis^1,2,3, Estévez, Agustín^1,2, Sola-Campoy, Pedro J.^1,2, Buenestado-Serrano, Sergio^1,2, Martínez-Laperche, Carolina^1,2, Manuel de la Cueva, Víctor^1,2, Alonso, Roberto^1,2,3, Andrés-Zayas, Cristina^1,2, Adán-Jiménez, Javier^1,2, Losada, Carmen^1,2, Rico-Luna, Carla^1,2, Comas, Iñaki^4,5, González-Candelas, Fernando^5,6, Catalán, Pilar^1,2,3, Muñoz, Patricia^1,2,3,7, Pérez-Lago, Laura^1,2, García de Viedma, Darío^1,2,3, dgviedma2@gmail.com

Source: Emerging Infectious Diseases; Jan2022, Vol. 28 Issue 1, p85-94, 10p, 1 Diagram, 3 Charts, 1 Graph

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

Authors: 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, García de Viedma, Darío

Source: Nature Communications; 3/28/2024, Vol. 15 Issue 1, p1-11, 11p

Subject Terms: MYCOBACTERIUM, GENOMICS, MICROEVOLUTION, REINFECTION, MYCOBACTERIA, SEQUENTIAL analysis

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

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

Source: Journal of travel medicine. 29(3)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100152530891.0x000001&indx=1&recIds=ETOCvdc_100152530891.0x000001

Occult COVID-19 in an immunosuppressed patient with migratory pulmonary infiltrates

Authors: Veintimilla, Cristina ^{1, 2, ⁎}, Miyares, Ana Álvarez-Uría ^{1, 2}, Buenestado-Serrano, Sergio ^{1, 2}, Palomino-Cabrera, Rosalía ^{1, 2}, Centurion, Ignacio Gomez ^{2, 5}, Catalán, Pilar ^{1, 2, 3}, Muñoz, Patricia ^{1, 2, 3, 4}, Pérez-Lago, Laura ^{1, 2, #}, de Viedma, Darío García ^{1, 2, 4, #}

Source: In International Journal of Infectious Diseases February 2025 151

Systematic genomic analysis of SARS-CoV-2 co-infections throughout the pandemic and segregation of the strains involved.

Authors: Peñas-Utrilla, Daniel, Pérez-Lago, Laura, Molero-Salinas, Andrea, Estévez, Agustín, Sanz, Amadeo, Herranz, Marta, Martínez-Laperche, Carolina, Andrés-Zayas, Cristina, Veintimilla, Cristina, Catalán, Pilar, Alonso, Roberto, Muñoz, Patricia, García de Viedma, Darío, on behalf of the Gregorio Marañón Microbiology-ID COVID 19 Study Group, Alcalá, Luis, Aldámiz, Teresa, Álvarez-Uría, Ana, Bermúdez, Elena, Bouza, Emilio, Buenestado-Serrano, Sergio

Source: Genome Medicine; 7/24/2023, Vol. 15 Issue 1, p1-16, 16p

Subject Terms: MIXED infections, GENOMICS, SARS-CoV-2, PANDEMICS, SARS-CoV-2 Omicron variant

A mutation responsible for impaired detection by the Xpert SARS-CoV-2 assay independently emerged in different lineages during the SARS-CoV-2 pandemic.

Authors: Peñas-Utrilla, Daniel, Sanz, Amadeo, Catalán, Pilar, Veintimilla, Cristina, Alcalá, Luis, Alonso, Roberto, Muñoz, Patricia, Pérez-Lago, Laura, García de Viedma, Darío, Aldámiz, Teresa, Álvarez-Uría, Ana, Bermúdez, Elena, Bouza, Emilio, Buenestado-Serrano, Sergio, Burillo, Almudena, Carrillo, Raquel, Cercenado, Emilia, Cobos, Alejandro, Díez, Cristina, Escribano, Pilar

Source: BMC Microbiology; 7/17/2023, Vol. 23 Issue 1, p1-6, 6p

Subject Terms: COVID-19 pandemic, SARS-CoV-2 Omicron variant, SARS-CoV-2, WHOLE genome sequencing, LIE detectors & detection, EXOMES

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.

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

Source: Eurosurveillance (15607917); 3/23/2023, Vol. 28 Issue 12, p40-50, 11p

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

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

Source: Journal of Travel Medicine; Apr2022, Vol. 29 Issue 3, p1-4, 4p

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

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

Source: MSphere; Dec2021, Vol. 6 Issue 6, p1-9, 9p

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

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

Source: Journal of Infectious Diseases; Sep2021, Vol. 224 Issue 5, p788-792, 5p

Subject Terms: COVID-19, REINFECTION, COVID-19 pandemic, SARS-CoV-2, COVID-19 testing

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Epidemiological, clinical and genomic snapshot of the first 100 B.1.1.7 SARS-CoV-2 cases in Madrid.

Authors: Pérez-Lago, Laura, Campoy, Pedro J Sola, Buenestado-Serrano, Sergio, Pharmacy, Pilar Catalán, Estévez, Agustín, Technician, Víctor Manuel de la Cueva, López, Mariana G, Tecnichian, Marta Herranz, Suárez-González, Julia, Alcalá, Luis, Comas, Iñaki, González-Candelas, Fernando, Muñoz, Patricia, Viedma, Darío García de, Sola Campoy, Pedro J, Catalán, Pilar, de la Cueva, Víctor Manuel, Herranz, Marta, Candelas, Fernando González, de Viedma, Darío García

Source: Journal of Travel Medicine; May2021, Vol. 28 Issue 4, p1-4, 4p

Subject Terms: SARS-CoV-2, COUGH, COVID-19 pandemic

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