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  1. AU="Regueiro, Benito"
  2. AU="Bar-Nur, Ori"
  3. AU="Hollander, Jonathan A"
  4. AU="Polidoro, Silvia"
  5. AU="Dausset, J"
  6. AU=Eijkholt Marleen
  7. AU=Sousa Braian L A AU=Sousa Braian L A
  8. AU="Fresel, Marielle"
  9. AU="Ilana Babaev"
  10. AU="Tang, Hang"
  11. AU="McBride, Erin"

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  1. Artikel ; Online: The Modification of the Illumina

    Davina-Nunez, Carlos / Perez-Castro, Sonia / Cabrera-Alvargonzalez, Jorge Julio / Montano-Barrientos, Jhon / Godoy-Diz, Montse / Regueiro, Benito

    International journal of molecular sciences

    2023  Band 24, Heft 22

    Abstract: There is growing interest in the molecular surveillance of the Respiratory Syncytial Virus and the monitorization of emerging mutations that could impair the efficacy of antiviral prophylaxis and treatments. A simple, scalable protocol for viral nucleic ... ...

    Abstract There is growing interest in the molecular surveillance of the Respiratory Syncytial Virus and the monitorization of emerging mutations that could impair the efficacy of antiviral prophylaxis and treatments. A simple, scalable protocol for viral nucleic acid enrichment could improve the surveillance of RSV. We developed a protocol for RSV-A and B amplification based on the Illumina CovidSeq workflow using an RSV primer panel. A total of 135 viral genomes were sequenced from nasopharyngeal samples through the optimization steps of this panel, while an additional 15 samples were used to test the final version. Full coverage of the G gene and over 95% of the coverage of the F gene, the target of the available RSV antivirals or monoclonal antibodies, were obtained. The F:K68N mutation, associated with decreased nirsevimab activity, was detected in our facility. Additionally, phylogenetic analysis showed several sublineages in the 2022-2023 influenza season in Europe. Our protocol allows for a simple and scalable simultaneous amplification of the RSV-A and B whole genome, increasing the yield of RSV sequencing and reducing costs. Its application would allow the world to be ready for the detection of arising mutations in relation to the widespread use of nirsevimab for RSV prevention.
    Mesh-Begriff(e) Humans ; Infant ; Respiratory Syncytial Virus Infections/prevention & control ; Spain/epidemiology ; Seasons ; Phylogeny ; Workflow ; Respiratory Syncytial Virus, Human/genetics ; Genomics
    Sprache Englisch
    Erscheinungsdatum 2023-11-07
    Erscheinungsland Switzerland
    Dokumenttyp Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms242216055
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  2. Artikel: Influence of perinatal and childhood exposure to tobacco and mercury in children's gut microbiota.

    Pérez-Castro, Sonia / D'Auria, Giuseppe / Llambrich, Maria / Fernández-Barrés, Sílvia / Lopez-Espinosa, Maria-Jose / Llop, Sabrina / Regueiro, Benito / Bustamante, Mariona / Francino, M Pilar / Vrijheid, Martine / Maitre, Léa

    Frontiers in microbiology

    2024  Band 14, Seite(n) 1258988

    Abstract: Background: Early life determinants of the development of gut microbiome composition in infants have been widely investigated; however, if early life pollutant exposures, such as tobacco or mercury, have a persistent influence on the gut microbial ... ...

    Abstract Background: Early life determinants of the development of gut microbiome composition in infants have been widely investigated; however, if early life pollutant exposures, such as tobacco or mercury, have a persistent influence on the gut microbial community, its stabilization at later childhood remains largely unknown.
    Objective: In this exposome-wide study, we aimed at identifying the contribution of exposure to tobacco and mercury from the prenatal period to childhood, to individual differences in the fecal microbiome composition of 7-year-old children, considering co-exposure to a width of established lifestyle and clinical determinants.
    Methods: Gut microbiome was studied by 16S rRNA amplicon sequencing in 151 children at the genus level. Exposure to tobacco was quantified during pregnancy through questionnaire (active tobacco consumption, second-hand smoking -SHS) and biomonitoring (urinary cotinine) at 4 years (urinary cotinine, SHS) and 7 years (SHS). Exposure to mercury was quantified during pregnancy (cord blood) and at 4 years (hair). Forty nine other potential environmental determinants (12 at pregnancy/birth/infancy, 15 at 4 years and 22 at 7 years, such as diet, demographics, quality of living/social environment, and clinical records) were registered. We used multiple models to determine microbiome associations with pollutants including multi-determinant multivariate analysis of variance and linear correlations (wUnifrac, Bray-Curtis and Aitchison ß-diversity distances), single-pollutant permutational multivariate analysis of variance adjusting for co-variates (Aitchison), and multivariable association model with single taxa (MaAsLin2; genus). Sensitivity analysis was performed including genetic data in a subset of 107 children.
    Results: Active smoking in pregnancy was systematically associated with microbiome composition and ß-diversity (
    Discussion: Our findings suggest a long-term sustainable effect of prenatal tobacco exposure on the children's gut microbiota. This effect was not found for mercury exposure or tobacco exposure during childhood. Assessing the role of these exposures on the children's microbiota, considering multiple environmental factors, should be further investigated.
    Sprache Englisch
    Erscheinungsdatum 2024-01-05
    Erscheinungsland Switzerland
    Dokumenttyp Journal Article
    ZDB-ID 2587354-4
    ISSN 1664-302X
    ISSN 1664-302X
    DOI 10.3389/fmicb.2023.1258988
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  3. Artikel: The fate of SARS-COV-2 in WWTPS points out the sludge line as a suitable spot for detection of COVID-19

    Balboa, Sabela / Mauricio-Iglesias, Miguel / Rodriguez, Santiago / Martínez-Lamas, Lucía / Vasallo, Francisco J / Regueiro, Benito / Lema, Juan M

    Science of the total environment. 2021 June 10, v. 772

    2021  

    Abstract: SARS-CoV-2 genetic material is detectable in the faeces of a considerable part of COVID-19 cases and hence, in municipal wastewater. This fact was confirmed early during the spread of the COVID-19 pandemic and prompted several studies that proposed ... ...

    Abstract SARS-CoV-2 genetic material is detectable in the faeces of a considerable part of COVID-19 cases and hence, in municipal wastewater. This fact was confirmed early during the spread of the COVID-19 pandemic and prompted several studies that proposed monitoring its incidence by wastewater. This paper studies the fate of SARS-CoV-2 genetic material in wastewater treatment plants using RT-qPCR with a two-fold goal: i) to check its presence in the water effluent and in the produced sludge and ii) based on the understanding of the virus particles fate, to identify the most suitable spots for detecting the incidence of COVID-19 and monitor its evolution. On the grounds of the affinity of enveloped virus towards biosolids, we hypothesized that the sludge line acts as a concentrator of SARS-CoV-2 genetic material. Sampling several spots in primary, secondary and sludge treatment at the Ourense (Spain) WWTP in 5 different days showed that, in effect, most of SARS-CoV-2 particles cannot be detected in the water effluent as they are retained by the sludge line. We identified the sludge thickener as a suitable spot for detecting SARS-CoV-2 particles thanks to its higher solids concentration (more virus particles) and longer residence time (less sensitive to dilution caused by precipitation). These findings could be useful to develop a suitable strategy for early warning of COVID-19 incidence based on WWTP monitoring.
    Schlagwörter COVID-19 infection ; Severe acute respiratory syndrome coronavirus 2 ; biosolids ; environment ; evolution ; feces ; municipal wastewater ; sludge ; thickeners ; viruses ; wastewater treatment ; Spain
    Sprache Englisch
    Erscheinungsverlauf 2021-0610
    Erscheinungsort Elsevier B.V.
    Dokumenttyp Artikel
    Anmerkung NAL-AP-2-clean
    ZDB-ID 121506-1
    ISSN 1879-1026 ; 0048-9697
    ISSN (online) 1879-1026
    ISSN 0048-9697
    DOI 10.1016/j.scitotenv.2021.145268
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  4. Artikel ; Online: In vivo monitoring of Lactiplantibacillus plantarum in the nasal and vaginal mucosa using infrared fluorescence.

    Silva-Bea, Sergio / Francisco-Tomé, Mónica / Cabrera-Alvargonzález, Jorge J / Potel, Carmen / Álvarez, Maximiliano / Pérez, Sonia / Regueiro, Benito / Cabral, Maria P

    Applied microbiology and biotechnology

    2022  Band 106, Heft 18, Seite(n) 6239–6251

    Abstract: Lactic acid bacteria (LAB) of the genus Lactiplantibacillus have been explored as potential mucosal vaccine vectors due to their ability to elicit an immune response against expressed foreign antigens and to their safety. However, tools for monitoring ... ...

    Abstract Lactic acid bacteria (LAB) of the genus Lactiplantibacillus have been explored as potential mucosal vaccine vectors due to their ability to elicit an immune response against expressed foreign antigens and to their safety. However, tools for monitoring LAB distribution and persistence at the mucosal surfaces are needed. Here, we characterize Lactiplantibacillus plantarum bacteria expressing the infrared fluorescent protein IRFP713 for exploring their in vivo distribution in the mucosa and potential use as a mucosal vaccine vector. This bacterial species is commonly used as a vaginal probiotic and was recently found to have a niche in the human nose. Three different fluorescent L. plantarum strains were obtained using the nisin-inducible pNZRK-IRFP713 plasmid which contains the nisRK genes, showing stable and constitutive expression of IRFP713 in vitro. One of these strains was further monitored in BALB/c mice using near-infrared fluorescence, indicating successful colonization of the nasal and vaginal mucosae for up to 72 h. This study thus provides a tool for the in vivo spatiotemporal monitoring of lactiplantibacilli, allowing non-invasive bacterial detection in these mucosal sites. KEY POINTS: • Stable and constitutive expression of the IRFP713 protein was obtained in different L. plantarum strains. • IRFP713
    Mesh-Begriff(e) Animals ; Female ; Humans ; Lactobacillus plantarum/metabolism ; Mice ; Mice, Inbred BALB C ; Mucous Membrane ; Probiotics ; Vaccination
    Sprache Englisch
    Erscheinungsdatum 2022-08-24
    Erscheinungsland Germany
    Dokumenttyp Journal Article
    ZDB-ID 392453-1
    ISSN 1432-0614 ; 0171-1741 ; 0175-7598
    ISSN (online) 1432-0614
    ISSN 0171-1741 ; 0175-7598
    DOI 10.1007/s00253-022-12121-8
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  5. Artikel: In vitro neutralizing activity of BNT162b2 mRNA‐induced antibodies against full B.1.351 SARS‐CoV‐2 variant

    Serrano‐Conde, Esther / Leyva, Alba / Fuentes, Ana / de Salazar, Adolfo / Chueca, Natalia / Pérez‐Castro, Sonia / Regueiro, Benito / Rojas, Almudena / Mendoza, Joaquín / Rojas, Jose / García, Federico

    Transboundary and emerging diseases. 2022 Sept., v. 69, no. 5

    2022  

    Abstract: SARS‐CoV‐2 variation represents a serious challenge to current COVID‐19 vaccines. Recent reports suggest that B.1.351 and other variants may escape the neutralization activity of the antibodies generated by current vaccines. Ninety‐nine healthcare ... ...

    Abstract SARS‐CoV‐2 variation represents a serious challenge to current COVID‐19 vaccines. Recent reports suggest that B.1.351 and other variants may escape the neutralization activity of the antibodies generated by current vaccines. Ninety‐nine healthcare workers undertaking BNT162b2 mRNA vaccination were sampled at baseline, on the day of the second dose, and 14 days after the latter. Neutralization activity against SARS‐CoV‐2 B.1, B.1.1.7 and B.1.351 was investigated using a Vero‐E6 model. Eleven of the study participants had prior infection with SARS‐CoV‐2. Neutralization titers against the B.1 and the B.1.1.7 variants were not statistically different and were significantly higher than titers against the B.1.351 variant across pre‐exposed and non‐pre‐exposed vaccinated individuals (p < .01). While all vaccinated individuals presented neutralizing antibodies against B.1 and B 1.1.7 after the second dose, 14% were negative against B.1.351 and 76% had low titers (1/201/80). Pre‐exposed vaccinated individuals showed higher titers than non‐pre‐exposed after the first (median titers of 1/387 versus 1/28, respectively) and the second doses (1/995 versus 1/703, respectively). As high as 72% of the pre‐exposed vaccines presented titers >1/80 after a single dose, while only 11% of non‐exposed vaccinated individuals had titers >1/80. BNT162b2 mRNA‐induced antibodies show a lower in vitro neutralizing activity against B.1.351 variant compared to neutralization against B.1.1.7 or B.1 variants. Interestingly, for individuals pre‐exposed to SARS‐CoV‐2, one dose of BNT162b2 mRNA may be adequate to produce neutralizing antibodies against B.1.1.7 and B.1, while two doses of BNT162b2 mRNA provide optimal neutralizing antibody response against B.1.351 too.
    Schlagwörter COVID-19 infection ; Severe acute respiratory syndrome coronavirus 2 ; antibody formation ; health services ; models ; neutralization ; vaccination
    Sprache Englisch
    Erscheinungsverlauf 2022-09
    Umfang p. 2649-2655.
    Erscheinungsort John Wiley & Sons, Ltd
    Dokumenttyp Artikel
    Anmerkung JOURNAL ARTICLE
    ZDB-ID 2414822-2
    ISSN 1865-1682 ; 1865-1674
    ISSN (online) 1865-1682
    ISSN 1865-1674
    DOI 10.1111/tbed.14417
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  6. Artikel: In vivo monitoring of Lactiplantibacillus plantarum in the nasal and vaginal mucosa using infrared fluorescence

    Silva-Bea, Sergio / Francisco-Tomé, Mónica / Cabrera-Alvargonzález, Jorge J. / Potel, Carmen / Álvarez, Maximiliano / Pérez, Sonia / Regueiro, Benito / Cabral, Maria P.

    Applied microbiology and biotechnology. 2022 Sept., v. 106, no. 18

    2022  

    Abstract: Lactic acid bacteria (LAB) of the genus Lactiplantibacillus have been explored as potential mucosal vaccine vectors due to their ability to elicit an immune response against expressed foreign antigens and to their safety. However, tools for monitoring ... ...

    Abstract Lactic acid bacteria (LAB) of the genus Lactiplantibacillus have been explored as potential mucosal vaccine vectors due to their ability to elicit an immune response against expressed foreign antigens and to their safety. However, tools for monitoring LAB distribution and persistence at the mucosal surfaces are needed. Here, we characterize Lactiplantibacillus plantarum bacteria expressing the infrared fluorescent protein IRFP713 for exploring their in vivo distribution in the mucosa and potential use as a mucosal vaccine vector. This bacterial species is commonly used as a vaginal probiotic and was recently found to have a niche in the human nose. Three different fluorescent L. plantarum strains were obtained using the nisin-inducible pNZRK-IRFP713 plasmid which contains the nisRK genes, showing stable and constitutive expression of IRFP713 in vitro. One of these strains was further monitored in BALB/c mice using near-infrared fluorescence, indicating successful colonization of the nasal and vaginal mucosae for up to 72 h. This study thus provides a tool for the in vivo spatiotemporal monitoring of lactiplantibacilli, allowing non-invasive bacterial detection in these mucosal sites. KEY POINTS: • Stable and constitutive expression of the IRFP713 protein was obtained in different L. plantarum strains. • IRFP713⁺ L. plantarum 3.12.1 was monitored in vivo using near-infrared fluorescence. • Residence times observed after intranasal and vaginal inoculation were 24–72 h.
    Schlagwörter biotechnology ; fluorescence ; fluorescent proteins ; gene expression ; humans ; immune response ; lactic acid ; microbial detection ; nose ; plasmids ; probiotics ; vaccines ; vaginal mucosa
    Sprache Englisch
    Erscheinungsverlauf 2022-09
    Umfang p. 6239-6251.
    Erscheinungsort Springer Berlin Heidelberg
    Dokumenttyp Artikel
    ZDB-ID 392453-1
    ISSN 1432-0614 ; 0171-1741 ; 0175-7598
    ISSN (online) 1432-0614
    ISSN 0171-1741 ; 0175-7598
    DOI 10.1007/s00253-022-12121-8
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    Z 79/727: Hefte anzeigen

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  7. Artikel ; Online: The fate of SARS-COV-2 in WWTPS points out the sludge line as a suitable spot for detection of COVID-19.

    Balboa, Sabela / Mauricio-Iglesias, Miguel / Rodriguez, Santiago / Martínez-Lamas, Lucía / Vasallo, Francisco J / Regueiro, Benito / Lema, Juan M

    The Science of the total environment

    2021  Band 772, Seite(n) 145268

    Abstract: SARS-CoV-2 genetic material is detectable in the faeces of a considerable part of COVID-19 cases and hence, in municipal wastewater. This fact was confirmed early during the spread of the COVID-19 pandemic and prompted several studies that proposed ... ...

    Abstract SARS-CoV-2 genetic material is detectable in the faeces of a considerable part of COVID-19 cases and hence, in municipal wastewater. This fact was confirmed early during the spread of the COVID-19 pandemic and prompted several studies that proposed monitoring its incidence by wastewater. This paper studies the fate of SARS-CoV-2 genetic material in wastewater treatment plants using RT-qPCR with a two-fold goal: i) to check its presence in the water effluent and in the produced sludge and ii) based on the understanding of the virus particles fate, to identify the most suitable spots for detecting the incidence of COVID-19 and monitor its evolution. On the grounds of the affinity of enveloped virus towards biosolids, we hypothesized that the sludge line acts as a concentrator of SARS-CoV-2 genetic material. Sampling several spots in primary, secondary and sludge treatment at the Ourense (Spain) WWTP in 5 different days showed that, in effect, most of SARS-CoV-2 particles cannot be detected in the water effluent as they are retained by the sludge line. We identified the sludge thickener as a suitable spot for detecting SARS-CoV-2 particles thanks to its higher solids concentration (more virus particles) and longer residence time (less sensitive to dilution caused by precipitation). These findings could be useful to develop a suitable strategy for early warning of COVID-19 incidence based on WWTP monitoring.
    Mesh-Begriff(e) COVID-19 ; Humans ; Pandemics ; SARS-CoV-2 ; Sewage ; Spain ; Wastewater
    Chemische Substanzen Sewage ; Waste Water
    Sprache Englisch
    Erscheinungsdatum 2021-02-02
    Erscheinungsland Netherlands
    Dokumenttyp Journal Article
    ZDB-ID 121506-1
    ISSN 1879-1026 ; 0048-9697
    ISSN (online) 1879-1026
    ISSN 0048-9697
    DOI 10.1016/j.scitotenv.2021.145268
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  8. Artikel ; Online: Perspectiva histórica de la espectrometría de masas en microbiología.

    Mingorance, Jesús / Regueiro, Benito / Muñoz-Bellido, Juan Luis

    Enfermedades infecciosas y microbiologia clinica

    2016  Band 34 Suppl 2, Seite(n) 3–7

    Abstract: La espectrometría de masas (EM) es una técnica de análisis que permite caracterizar muestras midiendo las masas (estrictamente las razones masa-carga) de las moléculas componentes. Cuenta con más de un siglo de historia y evolución tecnológica y a lo ... ...

    Titelübersetzung Historical perspective of mass spectrometry in microbiology.
    Abstract La espectrometría de masas (EM) es una técnica de análisis que permite caracterizar muestras midiendo las masas (estrictamente las razones masa-carga) de las moléculas componentes. Cuenta con más de un siglo de historia y evolución tecnológica y a lo largo de los años ha ampliado su alcance desde los isótopos a moléculas pequeñas, moléculas orgánicas más complejas y, en las últimas décadas, macromoléculas (ácidos nucleicos y proteínas). La EM MALDI-TOF (matrix-assisted laser desorption ionization time-of-flight) es una variante que permite el análisis de mezclas complejas de proteínas y que se ha aplicado recientemente a la identificación de microorganismos en cultivo, convirtiéndose en una herramienta rápida y eficaz para el diagnóstico microbiológico que ha conseguido entrar en poco tiempo en la rutina de muchos servicios de microbiología clínica. El gran impacto que ha tenido está impulsando el desarrollo de nuevas aplicaciones en el campo de la microbiología clínica.
    Sprache Spanisch
    Erscheinungsdatum 2016-06
    Erscheinungsland Spain
    Dokumenttyp English Abstract ; Journal Article
    ZDB-ID 1070941-1
    ISSN 1578-1852 ; 0213-005X
    ISSN (online) 1578-1852
    ISSN 0213-005X
    DOI 10.1016/S0213-005X(16)30184-7
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  9. Artikel ; Online: In vitro neutralizing activity of BNT162b2 mRNA-induced antibodies against full B.1.351 SARS-CoV-2 variant.

    Serrano-Conde, Esther / Leyva, Alba / Fuentes, Ana / de Salazar, Adolfo / Chueca, Natalia / Pérez-Castro, Sonia / Regueiro, Benito / Rojas, Almudena / Mendoza, Joaquín / Rojas, Jose / García, Federico

    Transboundary and emerging diseases

    2022  Band 69, Heft 5, Seite(n) 2649–2655

    Abstract: SARS-CoV-2 variation represents a serious challenge to current COVID-19 vaccines. Recent reports suggest that B.1.351 and other variants may escape the neutralization activity of the antibodies generated by current vaccines. Ninety-nine healthcare ... ...

    Abstract SARS-CoV-2 variation represents a serious challenge to current COVID-19 vaccines. Recent reports suggest that B.1.351 and other variants may escape the neutralization activity of the antibodies generated by current vaccines. Ninety-nine healthcare workers undertaking BNT162b2 mRNA vaccination were sampled at baseline, on the day of the second dose, and 14 days after the latter. Neutralization activity against SARS-CoV-2 B.1, B.1.1.7 and B.1.351 was investigated using a Vero-E6 model. Eleven of the study participants had prior infection with SARS-CoV-2. Neutralization titers against the B.1 and the B.1.1.7 variants were not statistically different and were significantly higher than titers against the B.1.351 variant across pre-exposed and non-pre-exposed vaccinated individuals (p < .01). While all vaccinated individuals presented neutralizing antibodies against B.1 and B 1.1.7 after the second dose, 14% were negative against B.1.351 and 76% had low titers (1/201/80). Pre-exposed vaccinated individuals showed higher titers than non-pre-exposed after the first (median titers of 1/387 versus 1/28, respectively) and the second doses (1/995 versus 1/703, respectively). As high as 72% of the pre-exposed vaccines presented titers >1/80 after a single dose, while only 11% of non-exposed vaccinated individuals had titers >1/80. BNT162b2 mRNA-induced antibodies show a lower in vitro neutralizing activity against B.1.351 variant compared to neutralization against B.1.1.7 or B.1 variants. Interestingly, for individuals pre-exposed to SARS-CoV-2, one dose of BNT162b2 mRNA may be adequate to produce neutralizing antibodies against B.1.1.7 and B.1, while two doses of BNT162b2 mRNA provide optimal neutralizing antibody response against B.1.351 too.
    Mesh-Begriff(e) Animals ; Antibodies, Neutralizing ; Antibodies, Viral ; BNT162 Vaccine ; COVID-19/prevention & control ; COVID-19/veterinary ; COVID-19 Vaccines ; Humans ; Membrane Glycoproteins ; Neutralization Tests/veterinary ; RNA, Messenger/genetics ; SARS-CoV-2/genetics ; Spike Glycoprotein, Coronavirus ; Viral Envelope Proteins/genetics
    Chemische Substanzen Antibodies, Neutralizing ; Antibodies, Viral ; COVID-19 Vaccines ; Membrane Glycoproteins ; RNA, Messenger ; Spike Glycoprotein, Coronavirus ; Viral Envelope Proteins ; spike protein, SARS-CoV-2 ; BNT162 Vaccine (N38TVC63NU)
    Sprache Englisch
    Erscheinungsdatum 2022-01-03
    Erscheinungsland Germany
    Dokumenttyp Journal Article
    ZDB-ID 2414822-2
    ISSN 1865-1682 ; 1865-1674
    ISSN (online) 1865-1682
    ISSN 1865-1674
    DOI 10.1111/tbed.14417
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  10. Artikel: Limited genomic reconstruction of SARS-CoV-2 transmission history within local epidemiological clusters.

    Gallego-García, Pilar / Varela, Nair / Estévez-Gómez, Nuria / De Chiara, Loretta / Fernández-Silva, Iria / Valverde, Diana / Sapoval, Nicolae / Treangen, Todd J / Regueiro, Benito / Cabrera-Alvargonzález, Jorge Julio / Del Campo, Víctor / Pérez, Sonia / Posada, David

    Virus evolution

    2022  Band 8, Heft 1, Seite(n) veac008

    Abstract: A detailed understanding of how and when severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission occurs is crucial for designing effective prevention measures. Other than contact tracing, genome sequencing provides information to help ... ...

    Abstract A detailed understanding of how and when severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission occurs is crucial for designing effective prevention measures. Other than contact tracing, genome sequencing provides information to help infer who infected whom. However, the effectiveness of the genomic approach in this context depends on both (high enough) mutation and (low enough) transmission rates. Today, the level of resolution that we can obtain when describing SARS-CoV-2 outbreaks using just genomic information alone remains unclear. In order to answer this question, we sequenced forty-nine SARS-CoV-2 patient samples from ten local clusters in NW Spain for which partial epidemiological information was available and inferred transmission history using genomic variants. Importantly, we obtained high-quality genomic data, sequencing each sample twice and using unique barcodes to exclude cross-sample contamination. Phylogenetic and cluster analyses showed that consensus genomes were generally sufficient to discriminate among independent transmission clusters. However, levels of intrahost variation were low, which prevented in most cases the unambiguous identification of direct transmission events. After filtering out recurrent variants across clusters, the genomic data were generally compatible with the epidemiological information but did not support specific transmission events over possible alternatives. We estimated the effective transmission bottleneck size to be one to two viral particles for sample pairs whose donor-recipient relationship was likely. Our analyses suggest that intrahost genomic variation in SARS-CoV-2 might be generally limited and that homoplasy and recurrent errors complicate identifying shared intrahost variants. Reliable reconstruction of direct SARS-CoV-2 transmission based solely on genomic data seems hindered by a slow mutation rate, potential convergent events, and technical artifacts. Detailed contact tracing seems essential in most cases to study SARS-CoV-2 transmission at high resolution.
    Sprache Englisch
    Erscheinungsdatum 2022-02-04
    Erscheinungsland England
    Dokumenttyp Journal Article
    ZDB-ID 2818949-8
    ISSN 2057-1577
    ISSN 2057-1577
    DOI 10.1093/ve/veac008
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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