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2. Spread of a SARS-CoV-2 variant through Europe in the summer of 2020

Author

Hodcroft E.B., Zuber M., Nadeau S., Vaughan T.G., Crawford K.H.D., Althaus C.L., Reichmuth M.L., Bowen J.E., Walls A.C., Corti D., Bloom J.D., Veesler D., Mateo D., Hernando A., Comas I., González-Candelas F., Goig G.A., Chiner-Oms Á., Cancino-Muñoz I., López M.G., Torres-Puente M., Gomez-Navarro I., Jiménez-Serrano S., Ruiz-Roldán L., Bracho M.A., García-González N., Martínez-Priego L., Galán-Vendrell I., Ruiz-Hueso P., De Marco G., Ferrús M.L., Carbó-Ramírez S., D’Auria G., Coscollá M., Ruiz-Rodríguez P., Roig-Sena F.J., Sanmartín I., Garcia-Souto D., Pequeno-Valtierra A., Tubio J.M.C., Rodríguez-Castro J., Rabella N., Navarro F., Miró E., Rodríguez-Iglesias M., Galán-Sanchez F., Rodriguez-Pallares S., de Toro M., Escudero M.B., Azcona-Gutiérrez J.M., Alberdi M.B., Mayor A., García-Basteiro A.L., Moncunill G., Dobaño C., Cisteró P., García-de-Viedma D., Pérez-Lago L., Herranz M., Sicilia J., Catalán-Alonso P., Muñoz P., Muñoz-Cuevas C., Rodríguez-Rodríguez G., Alberola-Enguidanos J., Nogueira J.M., Camarena J.J., Rezusta A., Tristancho-Baró A., Milagro A., Martínez-Cameo N.F., Gracia-Grataloup Y., Martró E., Bordoy A.E., Not A., Antuori-Torres A., Benito R., Algarate S., Bueno J., del Pozo J.L., Boga J.A., Castelló-Abietar C., Rojo-Alba S., Alvarez-Argüelles M.E., Melon S., Aranzamendi-Zaldumbide M., Vergara-Gómez A., Fernández-Pinero J., Martínez M.J., Vila J., Rubio E., Peiró-Mestres A., Navero-Castillejos J., Posada D., Valverde D., Estévez-Gómez N., Fernandez-Silva I., de Chiara L., Gallego-García P., Varela N., Moreno R., Tirado M.D., Gomez-Pinedo U., Gozalo-Margüello M., Eliecer-Cano M., Méndez-Legaza J.M., Rodríguez-Lozano J., Siller M., Pablo-Marcos D., Oliver A., Reina J., López-Causapé C., Canut-Blasco A., Hernáez-Crespo S., Cordón M.L.A., Lecároz-Agara M.-C., Gómez-González C., Aguirre-Quiñonero A., López-Mirones J.I., Fernández-Torres M., Almela-Ferrer M.R., Gonzalo-Jiménez N., Ruiz-García M.M., Galiana A., Sanchez-Almendro J., Cilla G., Montes M., Piñeiro L., Sorarrain A., Marimón J.M., Gomez-Ruiz M.D., López-Hontangas J.L., González Barberá E.M., Navarro-Marí J.M., Pedrosa-Corral I., Sanbonmatsu-Gámez S., Pérez-González C., Chamizo-López F., Bordes-Benítez A., Navarro D., Albert E., Torres I., Gascón I., Torregrosa-Hetland C.J., Pastor-Boix E., Cascales-Ramos P., Fuster-Escrivá B., Gimeno-Cardona C., Ocete M.D., Medina-Gonzalez R., González-Cantó J., Martínez-Macias O., Palop-Borrás B., de Toro I., Mediavilla-Gradolph M.C., Pérez-Ruiz M., González-Recio Ó., Gutiérrez-Rivas M., Simarro-Córdoba E., Lozano-Serra J., Robles-Fonseca L., de Salazar A., Viñuela-González L., Chueca N., García F., Gómez-Camarasa C., Carvajal A., de la Puente R., Martín-Sánchez V., Fregeneda-Grandes J.-M., Molina A.J., Argüello H., Fernández-Villa T., Farga-Martí M.A., Domínguez-Márquez V., Costa-Alcalde J.J., Trastoy R., Barbeito-Castiñeiras G., Coira A., Pérez-del-Molino M.L., Aguilera A., Planas A.M., Soriano A., Fernandez-Cádenas I., Pérez-Tur J., Marcos M.Á., Moreno-Docón A., Viedma E., Mingorance J., Galán-Montemayor J.C., Parra-Grande M., Stadler T., Neher R.A., Swiss National Science Foundation, European Commission, University of Basel, ETH Zurich, National Institute of General Medical Sciences (US), National Institute of Allergy and Infectious Diseases (US), Burroughs Wellcome Fund, Instituto de Salud Carlos III, Consejo Superior de Investigaciones Científicas (España), European Research Council, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Howard Hughes Medical Institute, Hodcroft, Emma B. [0000-0002-0078-2212], Zuber, Moira [0000-0002-4275-8739], Nadeau, Sarah [0000-0003-1008-8918], Vaughan, Timothy G. [0000-0001-6220-2239], Crawford, Katharine H. D. [0000-0002-6223-4019], Althaus, Christian L. [0000-0002-5230-6760], Reichmuth, Martina L. [0000-0001-9345-851X], Bowen, John E. [0000-0003-3590-9727], Walls, Alexandra C. [0000-0002-9636-8330], Corti, Davide [0000-0002-5797-1364], Bloom, Jesse D. [0000-0003-1267-3408], Veesler, David [0000-0002-6019-8675], Mateo, David [0000-0002-1590-4163], Hernando de Castro, Alberto [0000-0003-1180-1068], Comas, Iñaki [0000-0001-5504-9408], González-Candelas, Fernando [0000-0002-0879-5798], Stadler, Tanja [0000-0001-6431-535X], Neher, Richard A. [0000-0003-2525-1407], Hodcroft, Emma B., Zuber, Moira, Nadeau, Sarah, Vaughan, Timothy G., Crawford, Katharine H. D., Althaus, Christian L., Reichmuth, Martina L., Bowen, John E., Walls, Alexandra C., Corti, Davide, Bloom, Jesse D., Veesler, David, Mateo, David, Hernando de Castro, Alberto, Comas, Iñaki, González-Candelas, Fernando, Stadler, Tanja, and Neher, Richard A.

Subjects
Phylogenetics, Sars-Cov-2, Viral infection, 0303 health sciences, 2019-20 coronavirus outbreak, Multidisciplinary, Coronavirus disease 2019 (COVID-19), SARS-CoV-2, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), 610 Medicine & health, 3. Good health, law.invention, 03 medical and health sciences, 0302 clinical medicine, Transmission (mechanics), Geography, 360 Social problems & social services, law, Development economics, 030217 neurology & neurosurgery, 030304 developmental biology
Abstract

Following its emergence in late 2019, the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)1,2 has been tracked via phylogenetic analysis of viral genome sequences in unprecedented detail3–5. While the virus spread globally in early 2020 before borders closed, intercontinental travel has since been greatly reduced. However, within Europe travel resumed in the summer of 2020. Here we report on a novel SARS-CoV-2 variant, 20E (EU1), that emerged in Spain in early summer, and subsequently spread across Europe. We find no evidence of increased transmissibility, but instead demonstrate how rising incidence in Spain, resumption of travel, and lack of effective screening and containment may explain the variant’s success. Despite travel restrictions, we estimate 20E (EU1) was introduced hundreds of times to European countries by summertime travelers, likely undermining local efforts to keep SARS-CoV-2 cases low. Our results demonstrate how a variant can rapidly become dominant even in absence of a substantial transmission advantage in favorable epidemiological settings. Genomic surveillance is critical to understanding how travel can impact SARS-CoV-2 transmission, and thus for informing future containment strategies as travel resumes., This work was supported by the Swiss National Science Foundation (SNSF) through grant numbers 31CA30 196046 (to RAN, EBH, CLA), 31CA30 196267 (to TS), European Union’s Horizon 2020 research and innovation programme - project EpiPose (No 101003688) (MLR, CLA), core funding by the University of Basel and ETH Zürich, the National Institute of General Medical Sciences (R01GM120553 to DV), the National Institute of Allergy and Infectious Diseases (DP1AI158186 and HHSN272201700059C to DV), a Pew Biomedical Scholars Award (DV), an Investigators in the Pathogenesis of Infectious Disease Awards from the Burroughs Wellcome Fund (DV and JDB), a Fast Grants (DV), and NIAID grants R01AI141707 (JDB) and F30AI149928 (KHDC). SeqCOVID-SPAIN is funded by the Instituto de Salud Carlos III project COV20/00140, Spanish National Research Council and ERC StG 638553 to IC and BFU2017-89594R from MICIN to FGC. JDB is an Investigator of the Howard Hughes Medical Institute.

Published
2021
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4. Azole and Amphotericin B MIC Values against Aspergillus fumigatus: High Agreement between Spectrophotometric and Visual Readings Using the EUCAST EDef 9.3.2 Procedure

Author

Serrano-Lobo, J., Gómez, A., Sánchez-Yebra, W., Fajardo, M., Lorenzo, B., Sánchez-Reus, F., Vidal, I., Fernández-Torres, M., Sánchez-Romero, I., de Alegría-Puig, C.R., del Pozo, J.L., Muñoz, P., Escribano, P., Guinea, J., Sánchez-Gómez, J., Lozano, I., Marfil, E., de la Rosa, M.M., García, R.T., Cobo, F., Castro, C., López, C., Rezusta, A., Peláez, T., Castelló-Abietar, C., Cos-Tales, I., Serra, J.L., Jiménez, R., Echeverría, C.L., Pérez, C.L., Megías-Lobón, G., Ayats, J., Martín, M.T., Sánchez-Hellín, V., Ibáñez, E., Pemán, J., Pazos, C., Rodríguez-Mayo, M., Pérez-Ayala, A., Gómez, E., Serrano, J., Reigadas, E., Rodríguez, B., Zvezdanova, E., Díaz-García, J., González Leiva, J., Machado, M., García-Rodríguez, J., Vallejo, M.R., López-Soria, L., Marimón, J.M., Vicente, D., and Hernáez-Crespo, S.

Subjects
Azoles, Posaconazole, Antifungal Agents, Itraconazole, Microbial Sensitivity Tests, azoles, Microbiology, Aspergillus fumigatus, 03 medical and health sciences, 0302 clinical medicine, EUCAST, Drug Resistance, Fungal, Amphotericin B, parasitic diseases, medicine, Pharmacology (medical), spectrophotometric, 030212 general & internal medicine, Pharmacology, chemistry.chemical_classification, Voriconazole, 0303 health sciences, Aspergillus, biology, 030306 microbiology, biology.organism_classification, bacterial infections and mycoses, Infectious Diseases, chemistry, amphotericin B, Mic values, Azole, medicine.drug
Abstract

The EUCAST EDef 9.3.2 procedure recommends visual readings of azole and amphotericin B MICs against Aspergillus spp. Visual determination of MICs may be challenging. In this work, we aim to obtain and compare visual and spectrophotometric MIC readings of azoles and amphotericin B against Aspergillus fumigatus sensu lato isolates. A total of 847 A. fumigatus sensu lato isolates (A. fumigatus sensu stricto [n = 828] and cryptic species [n = 19]) were tested against amphotericin B, itraconazole, voriconazole, posaconazole, and isavuconazole using the EUCAST EDef 9.3.2 procedure. Isolates were classified as susceptible or resistant/non-wild type according to the 2020 updated breakpoints. The area of technical uncertainty for the azoles was defined in the updated breakpoints. Visual and spectrophotometric (fungal growth reduction of >95% compared to the control, read at 540 nm) MICs were compared. Essential (±1 2-fold dilution) and categorical agreements were calculated. Overall, high essential (97.1%) and categorical (99.6%) agreements were found. We obtained 100% categorical agreements for amphotericin B, itraconazole, and posaconazole, and consequently, no errors were found. Categorical agreements were 98.7 and 99.3% for voriconazole and isavuconazole, respectively. Most of the misclassifications for voriconazole and isavuconazole were found to be associated with MIC results falling either in the area of technical uncertainty or within one 2-fold dilution above the breakpoint. The resistance rate was slightly lower when the MICs were obtained by spectrophotometric readings. However, all relevant cyp51A mutants were correctly classified as resistant. Spectrophotometric determination of azole and amphotericin B MICs against A. fumigatus sensu lato isolates may be a convenient alternative to visual endpoint readings.

Published
2020

5. The Burden of Neglected HIV-2 and HTLV-1 Infections in Spain

Author

Treviño A, Caballero E, de Mendoza C, Aguilera A, Pirón M, Soriano V, Rodríguez M, del Romero J, Marcaida G, Ocete MD, Molina I, Rodríguez-Calviño JJ, Navarro D, Regueiro B, Benito R, Algarate S, Gil J, Ortiz de Lejarazu R, Rojo S, Eirós JM, Manzardo C, Miró JM, García J, Paz I, Poveda E, Calderón E, Mateos M, Dronda F, Escudero D, Trigo M, Diz J, García-Campello M, Rodríguez-Iglesias M, Hernández-Betancor A, Martín AM, Ramos JM, Gimeno A, Gutiérrez F, Rodríguez JC, Sanchez V, Gómez-Hernando C, Cilla G, Pérez-Trallero E, López-Aldeguer J, Fernández-Pereira L, Niubó J, Hernández M, López-Lirola AM, Gómez-Sirvent JL, Force L, Cifuentes C, Pérez S, Morano L, Raya C, González-Praetorius A, Pérez JL, Peñaranda M, Hernáez-Crespo S, Montejo JM, Roc L, Martínez-Sapiña A, Viciana I, Cabezas T, Lozano A, Fernández JM, García-Bermejo I, Gaspar G, García R, Górgolas M, Vegas MC, Vegas C, Blas J, Miralles P, Aldamiz T, Margall N, Guardia C, Do Pico E, Polo I, Aguinaga A, Ezpeleta C, Sauleda S, Torres P, Jiménez A, Blanco L, González R, Suárez A, Requena S, Benítez-Gutiérrez L, Cuervas-Mons V, and Barreiro P

Subjects
virus diseases
Abstract

HIV-2 and HTLV-1 infections are globally less frequent than those produced by HIV-1, the classical AIDS agent. In Spain and up to the end of 2014, a total of 310 cases of HIV-2, 274 of HTLV-1, and 776 of HTLV-2 infections had been reported. No cases of HTLV-3 or HTLV-4 infections have been identified so far in Spain. Most persons infected with HIV-2 or HTLV-1 acknowledge epidemiological risk factors for contagion, such as originating from or living in endemic regions and/or having had sexual partners from those areas. However, risk factors could not be recognized in up to 20-25% of carriers in Spain. Thus, it seems worth keeping a high level of clinical suspicion in order to identify earlier these neglected human retroviral infections, since diagnostic procedures and antiviral treatment are specific for each of these agents. In this article we summarize the major contributions reported at the meeting of the Spanish Group for HIV-2/HTLV held in Madrid in December 2014

Published
2015

6. HIV-2 and HTLV-1 infections in Spain, a non-endemic region

Author

Mendoza, C., Caballero, E., Aguilera, A., Pirón, M., Lejarazu, R. O., Rodríguez, C., Cabezas, T., González, R., Treviño, A., Soriano, V., Vera, M., Del Romero, J., Marcaida, G., Ocete, M. D., Tuset, T., Molina, I., Rodríguez-Calviño, J. J., Navarro, D., Regueiro, B., Benito, R., Gil, J., Borrás, M., Ortiz Lejarazu, R., Eirós, J. M., Manzardo, C., Miró, J. M., García, J., Paz, I., Poveda, E., Calderón, E., Vallejo, A., Abad, M., Dronda, F., Moreno, S., Escudero, D., Trigo, M., Diz, J., Álvarez, P., Cortizo, S., García-Campello, M., Manuel Antonio Rodríguez Iglesias, Hernández-Betancor, A., Martín, A. M., Ramos, J. M., Gutiérrez, F., Rodríguez, J. C., Gómez-Hernando, C., Cilla, G., Pérez-Trallero, E., López-Aldeguer, J., Fernández-Pereira, L., Niubó, J., Hernández, M., López-Lirola, A. M., Gómez-Sirvent, J. L., Force, L., Cifuentes, C., Pérez, S., Morano, L., Raya, C., González-Praetorius, A., Pérez, J. L., Peñaranda, M., Hernáez-Crespo, S., Montejo, J. M., Roc, L., Martínez-Sapiña, A., Viciana, I., Lozano, A., Fernández, J. M., García Bermejo, I., Gaspar, G., García, R., Górgolas, M., Miralles, P., Aldamiz, T., Sauleda, S., Torres, P., Suárez, A., and Benítez-Gutiérrez, L.

7. HIV-2 and HTLV-1 infections in Spain, a non-endemic region

Author

Mendoza, C., Caballero, E., Aguilera, A., Pirón, M., Lejarazu, R. O., Rodríguez, C., Cabezas, T., González, R., Treviño, A., Vicente Soriano, Vera, M., Del Romero, J., Marcaida, G., Ocete, M. D., Tuset, T., Molina, I., Rodríguez-Calviño, J. J., Navarro, D., Regueiro, B., Benito, R., Gil, J., Borrás, M., Eirós, J. M., Manzardo, C., Miró, J. M., García, J., Paz, I., Poveda, E., Calderón, E., Vallejo, A., Abad, M., Dronda, F., Moreno, S., Escudero, D., Trigo, M., Diz, J., Álvarez, P., Cortizo, S., García-Campello, M., Rodríguez-Iglesias, M., Hernández-Betancor, A., Martín, A. M., Ramos, J. M., Gutiérrez, F., Rodríguez, J. C., Gómez-Hernando, C., Cilla, G., Pérez-Trallero, E., López-Aldeguer, J., Fernández-Pereira, L., Niubó, J., Hernández, M., López-Lirola, A. M., Gómez-Sirvent, J. L., Force, L., Cifuentes, C., Pérez, S., Morano, L., Raya, C., González-Praetorius, A., Pérez, J. L., Peñaranda, M., Hernáez-Crespo, S., Montejo, J. M., Roc, L., Martínez-Sapiña, A., Viciana, I., Lozano, A., Fernández, J. M., García Bermejo, I., Gaspar, G., García, R., Górgolas, M., Miralles, P., Aldamiz, T., Sauleda, S., Torres, P., Suárez, A., and Benítez-Gutiérrez, L.

8. Rapid subacute myelopathy following kidney transplantation from HTLV-1 donors: role of immunosuppresors and failure of antiretrovirals

Author

Roc, Lourdes, de Mendoza, Carmen, Fernández-Alonso, Miriam, Reina, Gabriel, Soriano, Vicente, Rodríguez, C., Vera, M., del Romero, J., Marcaida, G., Ocete, M.D., Caballero, E., Molina, I., Aguilera, A., Rodríguez-Calviño, J.J., Navarro, D., Rivero, C., Vilariño, M.D., Benito, R., Algarate, S., Gil, J., Ortiz de Lejarazu, R., Rojo, S., Eirós, J.M., San Miguel, A., Manzardo, C., Miró, J.M., García, J., Paz, I., Poveda, E., Calderón, E., Escudero, D., Trigo, M., Diz, J., García-Campello, M., Rodríguez-Iglesias, M., Hernández-Betancor, A., Martín, A.M., Ramos, J.M., Gimeno, A., Gutiérrez, F., Rodríguez, J.C., Sánchez, V., Gómez-Hernando, C., Cilla, G., Pérez-Trallero, E., López-Aldeguer, J., Fernández-Pereira, L., Niubó, J., Hernández, M., López-Lirola, A.M., Gómez-Sirvent, J.L., Force, L., Cifuentes, C., Pérez, S., Morano, L., Raya, C., González-Praetorius, A., Pérez, J.L., Peñaranda, M., Hernáez-Crespo, S., Montejo, J.M., Roc, L., Martínez-Sapiña, A., Viciana, I., Cabezas, T., Lozano, A., Fernández, J.M., García-Bermejo, I., Gaspar, G., García, R., Górgolas, M., Vegas, C., Blas, J., Miralles, P., Valeiro, M., Aldamiz, T., Margall, N., Guardia, C., do Pico, E., Polo, I., Aguinaga, A., Ezpeleta, C., Sauleda, S., Pirón, M., González, R., Barea, L., Jiménez, A., Blanco, L., Suárez, A., Rodríguez-Avial, I., Pérez-Rivilla, A., Parra, P., Fernández, M., Fernández-Alonso, M., Reina, G., Treviño, A., Requena, S., Benítez-Gutiérrez, L., Cuervas-Mons, V., de Mendoza, C., Barreiro, P., Soriano, V., Corral, O., and Gómez-Gallego, F.

Abstract

Two kidney transplant recipients from a single donor became infected with HTLV-1 (human T-lymphotropic virus type 1) in Spain. One developed myelopathy 8 months following surgery despite early prescription of antiretroviral therapy. The allograft was removed from the second recipient at month 8 due to rejection and immunosuppressors discontinued. To date, 3 years later, this patient remains infected but asymptomatic. HTLV-1 infection was recognized retrospectively in the donor, a native Spaniard who had sex partners from endemic regions. Our findings call for a reappraisal of screening policies on donor–recipient organ transplantation. Based on the high risk of disease development and the large flux of persons from HTLV-1 endemic regions, pre-transplant HTLV-1 testing should be mandatory in Spain.

Published
2019
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9. 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 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, and Comas I

Subjects
COVID-19 virology, Communicable Disease Control methods, Humans, Incidence, Phylogeny, Physical Distancing, Quarantine methods, Quarantine organization & administration, SARS-CoV-2 classification, SARS-CoV-2 pathogenicity, Severity of Illness Index, Spain epidemiology, COVID-19 epidemiology, COVID-19 transmission, Communicable Disease Control organization & administration, Models, Statistical, SARS-CoV-2 genetics
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 (R e  < 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., (© 2021. The Author(s), under exclusive licence to Springer Nature America, Inc.)

Published
2021
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10. Multicenter evaluation of the Panbio™ COVID-19 rapid antigen-detection test for the diagnosis of SARS-CoV-2 infection.

Author

Merino P, Guinea J, Muñoz-Gallego I, González-Donapetry P, Galán JC, Antona N, Cilla G, Hernáez-Crespo S, Díaz-de Tuesta JL, Gual-de Torrella A, González-Romo F, Escribano P, Sánchez-Castellano MÁ, Sota-Busselo M, Delgado-Iribarren A, García J, Cantón R, Muñoz P, Folgueira MD, Cuenca-Estrella M, and Oteo-Iglesias J

Abstract

Objectives: The standard RT-PCR assay for coronavirus disease 2019 (COVID-19) is laborious and time-consuming, limiting testing availability. Rapid antigen-detection tests are faster and less expensive; however, the reliability of these tests must be validated before they can be used widely. The objective of this study was to determine the performance of the Panbio™ COVID-19 Ag Rapid Test Device (PanbioRT) (Abbott) in detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in nasopharyngeal swab specimens., Methods: This prospective multicentre study was carried out in ten Spanish university hospitals and included individuals with clinical symptoms or epidemiological criteria of COVID-19. Only individuals with ≤7 days from the onset of symptoms or from exposure to a confirmed case of COVID-19 were included. Two nasopharyngeal samples were taken to perform the PanbioRT as a point-of-care test and a diagnostic RT-PCR test., Results: Among the 958 patients studied, 325 (90.5%) had true-positive results. The overall sensitivity and specificity for the PanbioRT were 90.5% (95%CI 87.5-93.6) and 98.8% (95%CI 98-99.7), respectively. Sensitivity in participants who had a threshold cycle (C T ) < 25 for the RT-PCR test was 99.5% (95%CI 98.4-100), and in participants with ≤5 days of the clinical course it was 91.8% (95%CI 88.8-94.8). Agreement between techniques was 95.7% (κ score 0.90; 95%CI 0.88-0.93)., Conclusions: The PanbioRT performs well clinically, with even more reliable results for patients with a shorter clinical course of the disease or a higher viral load. The results must be interpreted based on the local epidemiological context., (Copyright © 2021 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.)

Published
2021
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11. Phylogeny and Phylogeography of a Recent HIV-1 Subtype F Outbreak among Men Who Have Sex with Men in Spain Deriving from a Cluster with a Wide Geographic Circulation in Western Europe.

Author

Delgado E, Cuevas MT, Domínguez F, Vega Y, Cabello M, Fernández-García A, Pérez-Losada M, Castro MÁ, Montero V, Sánchez M, Mariño A, Álvarez H, Ordóñez P, Ocampo A, Miralles C, Pérez-Castro S, López-Álvarez MJ, Rodríguez R, Trigo M, Diz-Arén J, Hinojosa C, Bachiller P, Hernáez-Crespo S, Cisterna R, Garduño E, Pérez-Álvarez L, and Thomson MM

Subjects
Antiretroviral Therapy, Highly Active, Bayes Theorem, Disease Outbreaks, Drug Resistance, Viral, Europe epidemiology, Genotype, HIV Infections drug therapy, HIV Infections transmission, HIV-1 drug effects, Humans, Male, Molecular Sequence Data, Prevalence, Spain epidemiology, HIV Infections epidemiology, HIV Infections virology, HIV-1 classification, HIV-1 genetics, Homosexuality, Male, Phylogeny, Phylogeography
Abstract

We recently reported the rapid expansion of an HIV-1 subtype F cluster among men who have sex with men (MSM) in the region of Galicia, Northwest Spain. Here we update this outbreak, analyze near full-length genomes, determine phylogenetic relationships, and estimate its origin. For this study, we used sequences of HIV-1 protease-reverse transcriptase and env V3 region, and for 17 samples, near full-length genome sequences were obtained. Phylogenetic analyses were performed via maximum likelihood. Locations and times of most recent common ancestors were estimated using Bayesian inference. Among samples analyzed by us, 100 HIV-1 F1 subsubtype infections of monophyletic origin were diagnosed in Spain, including 88 in Galicia and 12 in four other regions. Most viruses (n = 90) grouped in a subcluster (Galician subcluster), while 7 from Valladolid (Central Spain) grouped in another subcluster. At least 94 individuals were sexually-infected males and at least 71 were MSM. Seventeen near full-length genomes were uniformly of F1 subsubtype. Through similarity searches and phylogenetic analyses, we identified 18 viruses from four other Western European countries [Switzerland (n = 8), Belgium (n = 5), France (n = 3), and United Kingdom (n = 2)] and one from Brazil, from samples collected in 2005-2011, which branched within the subtype F cluster, outside of both Spanish subclusters, most of them corresponding to recently infected individuals. The most probable geographic origin and age of the Galician subcluster was Ferrol, Northwest Galicia, around 2007, while the Western European cluster probably emerged in Switzerland around 2002. In conclusion, a recently expanded HIV-1 subtype F cluster, the largest non-subtype B cluster reported in Western Europe, continues to spread among MSM in Spain; this cluster is part of a larger cluster with a wide geographic circulation in diverse Western European countries.

Published
2015
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