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Article: Altering Compositional Properties of Viral Genomes to Design Live-Attenuated Vaccines.

Pereira-Gómez, Marianoel / Carrau, Lucía / Fajardo, Álvaro / Moreno, Pilar / Moratorio, Gonzalo

2021 Volume 12, Page(s) 676582

Abstract: Live-attenuated vaccines have been historically used to successfully prevent numerous diseases caused by a broad variety of RNA viruses due to their ability to elicit strong and perdurable immune-protective responses. In recent years, various strategies ... ...

Abstract	Live-attenuated vaccines have been historically used to successfully prevent numerous diseases caused by a broad variety of RNA viruses due to their ability to elicit strong and perdurable immune-protective responses. In recent years, various strategies have been explored to achieve viral attenuation by rational genetic design rather than using classic and empirical approaches, based on successive passages in cell culture. A deeper understanding of evolutionary implications of distinct viral genomic compositional aspects, as well as substantial advances in synthetic biology technologies, have provided a framework to achieve new viral attenuation strategies. Herein, we will discuss different approaches that are currently applied to modify compositional features of viruses in order to develop novel live-attenuated vaccines.
Language	English
Publishing date	2021-06-30
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2021.676582
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Effect of mismatch repair on the mutation rate of bacteriophage ϕX174.

Pereira-Gómez, Marianoel / Sanjuán, Rafael

Virus evolution

2015 Volume 1, Issue 1, Page(s) vev010

Abstract: Viral mutation rates vary widely in nature, yet the mechanistic and evolutionary determinants of this variability remain unclear. Small DNA viruses mutate orders of magnitude faster than their hosts despite using host-encoded polymerases for replication, ...

Abstract	Viral mutation rates vary widely in nature, yet the mechanistic and evolutionary determinants of this variability remain unclear. Small DNA viruses mutate orders of magnitude faster than their hosts despite using host-encoded polymerases for replication, which suggests these viruses may avoid post-replicative repair. Supporting this, the genome of bacteriophage ϕX174 is completely devoid of GATC sequence motifs, which are required for methyl-directed mismatch repair in
Keywords	covid19
Language	English
Publishing date	2015-09-10
Publishing country	England
Document type	Journal Article
ZDB-ID	2818949-8
ISSN	2057-1577
ISSN	2057-1577
DOI	10.1093/ve/vev010
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Article: One-year monitoring SARS-CoV-2 RNA surface contamination in hospitals reveals no correlation with organic material and negative pressure as a limiting factor for contamination.

Pereira-Gómez, Marianoel / Arce, Rodrigo / Ferla, Diego / Simón, Diego / Salazar, Cecilia / Perbolianachis, Paula / Costábile, Alicia / Fajardo, Alvaro / Aldunate, Fabián / Nin, Nicolás / Hurtado, Javier / Iraola, Gregorio / Moreno, Pilar / Moratorio, Gonzalo

Heliyon

2023 Volume 9, Issue 3, Page(s) e13875

Abstract: Understanding transmission routes of SARS-CoV-2 is crucial to establish effective interventions in healthcare institutions. Although the role of surface contamination in SARS-CoV-2 transmission has been controversial, fomites have been proposed as a ... ...

Abstract	Understanding transmission routes of SARS-CoV-2 is crucial to establish effective interventions in healthcare institutions. Although the role of surface contamination in SARS-CoV-2 transmission has been controversial, fomites have been proposed as a contributing factor. Longitudinal studies about SARS-CoV-2 surface contamination in hospitals with different infrastructure (presence or absence of negative pressure systems) are needed to improve our understanding of their effectiveness on patient healthcare and to advance our knowledge about the viral spread. We performed a one-year longitudinal study to evaluate surface contamination with SARS-CoV-2 RNA in reference hospitals. These hospitals have to admit all COVID-19 patients from public health services that require hospitalization. Surfaces samples were molecular tested for SARS-CoV-2 RNA presence considering three factors: the dirtiness by measuring organic material, the circulation of a high transmissibility variant, and the presence or absence of negative pressure systems in hospitalized patients' rooms. Our results show that: (i) There is no correlation between the amount of organic material dirtiness and SARS-CoV-2 RNA detected on surfaces; (ii) SARS-CoV-2 high transmissible Gamma variant introduction significantly increased surface contamination; (iii) the hospital with negative pressure systems was associated with lower levels of SARS-CoV-2 surface contamination and, iv) most environmental samples recovered from contaminated surfaces were assigned as non-infectious. This study provides data gathered for one year about the surface contamination with SARS-CoV-2 RNA sampling hospital settings. Our results suggest that spatial dynamics of SARS-CoV-2 RNA contamination varies according with the type of SARS-CoV-2 genetic variant and the presence of negative pressure systems. In addition, we showed that there is no correlation between the amount of organic material dirtiness and the quantity of viral RNA detected in hospital settings. Our findings suggest that SARS CoV-2 RNA surface contamination monitoring might be useful for the understanding of SARS-CoV-2 dissemination with impact on hospital management and public health policies. This is of special relevance for the Latin-American region where ICU rooms with negative pressure are insufficient.
Language	English
Publishing date	2023-02-18
Publishing country	England
Document type	Journal Article
ZDB-ID	2835763-2
ISSN	2405-8440
ISSN	2405-8440
DOI	10.1016/j.heliyon.2023.e13875
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Article ; Online: One-year monitoring SARS-CoV-2 RNA surface contamination in hospitals reveals no correlation with organic material and negative pressure as a limiting factor for contamination

Pereira-Gómez, Marianoel / Arce, Rodrigo / Ferla, Diego / Simón, Diego / Salazar de la Torre, Cecilia / Perbolianachis, Paula / Costábile, Alicia / Fajardo, Alvaro / Aldunate, Fabián / Nin, Nicolás / Hurtado, Javier / Iraola, Gregorio / Moreno, Pilar / Moratorio, Gonzalo

Heliyon. 2023 Mar., v. 9, no. 3 p.e13875-

2023

Abstract	Understanding transmission routes of SARS-CoV-2 is crucial to establish effective interventions in healthcare institutions. Although the role of surface contamination in SARS-CoV-2 transmission has been controversial, fomites have been proposed as a contributing factor. Longitudinal studies about SARS-CoV-2 surface contamination in hospitals with different infrastructure (presence or absence of negative pressure systems) are needed to improve our understanding of their effectiveness on patient healthcare and to advance our knowledge about the viral spread. We performed a one-year longitudinal study to evaluate surface contamination with SARS-CoV-2 RNA in reference hospitals. These hospitals have to admit all COVID-19 patients from public health services that require hospitalization. Surfaces samples were molecular tested for SARS-CoV-2 RNA presence considering three factors: the dirtiness by measuring organic material, the circulation of a high transmissibility variant, and the presence or absence of negative pressure systems in hospitalized patients' rooms. Our results show that: (i) There is no correlation between the amount of organic material dirtiness and SARS-CoV-2 RNA detected on surfaces; (ii) SARS-CoV-2 high transmissible Gamma variant introduction significantly increased surface contamination; (iii) the hospital with negative pressure systems was associated with lower levels of SARS-CoV-2 surface contamination and, iv) most environmental samples recovered from contaminated surfaces were assigned as non-infectious. This study provides data gathered for one year about the surface contamination with SARS-CoV-2 RNA sampling hospital settings. Our results suggest that spatial dynamics of SARS-CoV-2 RNA contamination varies according with the type of SARS-CoV-2 genetic variant and the presence of negative pressure systems. In addition, we showed that there is no correlation between the amount of organic material dirtiness and the quantity of viral RNA detected in hospital settings. Our findings suggest that SARS CoV-2 RNA surface contamination monitoring might be useful for the understanding of SARS-CoV-2 dissemination with impact on hospital management and public health policies. This is of special relevance for the Latin-American region where ICU rooms with negative pressure are insufficient.
Keywords	RNA ; Severe acute respiratory syndrome coronavirus 2 ; fomites ; health services ; hospitals ; longitudinal studies ; patients ; public health ; SARS-CoV2 RNA ; Ct value ; Organic material dirtiness ; ATP measurements ; Negative pressure system ; Variant of concern
Language	English
Dates of publication	2023-03
Publishing place	Elsevier Ltd
Document type	Article ; Online
Note	Use and reproduction
ZDB-ID	2835763-2
ISSN	2405-8440
ISSN	2405-8440
DOI	10.1016/j.heliyon.2023.e13875
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Article ; Online: One-year monitoring SARS-CoV-2 RNA surface contamination in hospitals reveals no correlation with organic material and negative pressure as a limiting factor for contamination

Marianoel Pereira-Gómez / Rodrigo Arce / Diego Ferla / Diego Simón / Cecilia Salazar / Paula Perbolianachis / Alicia Costábile / Alvaro Fajardo / Fabián Aldunate / Nicolás Nin / Javier Hurtado / Gregorio Iraola / Pilar Moreno / Gonzalo Moratorio

Heliyon, Vol 9, Iss 3, Pp e13875- (2023)

2023

Abstract	Understanding transmission routes of SARS-CoV-2 is crucial to establish effective interventions in healthcare institutions. Although the role of surface contamination in SARS-CoV-2 transmission has been controversial, fomites have been proposed as a contributing factor. Longitudinal studies about SARS-CoV-2 surface contamination in hospitals with different infrastructure (presence or absence of negative pressure systems) are needed to improve our understanding of their effectiveness on patient healthcare and to advance our knowledge about the viral spread.We performed a one-year longitudinal study to evaluate surface contamination with SARS-CoV-2 RNA in reference hospitals. These hospitals have to admit all COVID-19 patients from public health services that require hospitalization. Surfaces samples were molecular tested for SARS-CoV-2 RNA presence considering three factors: the dirtiness by measuring organic material, the circulation of a high transmissibility variant, and the presence or absence of negative pressure systems in hospitalized patients' rooms.Our results show that: (i) There is no correlation between the amount of organic material dirtiness and SARS-CoV-2 RNA detected on surfaces; (ii) SARS-CoV-2 high transmissible Gamma variant introduction significantly increased surface contamination; (iii) the hospital with negative pressure systems was associated with lower levels of SARS-CoV-2 surface contamination and, iv) most environmental samples recovered from contaminated surfaces were assigned as non-infectious.This study provides data gathered for one year about the surface contamination with SARS-CoV-2 RNA sampling hospital settings. Our results suggest that spatial dynamics of SARS-CoV-2 RNA contamination varies according with the type of SARS-CoV-2 genetic variant and the presence of negative pressure systems. In addition, we showed that there is no correlation between the amount of organic material dirtiness and the quantity of viral RNA detected in hospital settings. Our findings suggest that ...
Keywords	SARS-CoV2 RNA ; Ct value ; Fomites ; Organic material dirtiness ; ATP measurements ; Negative pressure system ; Science (General) ; Q1-390 ; Social sciences (General) ; H1-99
Subject code	360
Language	English
Publishing date	2023-03-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Delayed lysis confers resistance to the nucleoside analogue 5-fluorouracil and alleviates mutation accumulation in the single-stranded DNA bacteriophage ϕX174.

Pereira-Gómez, Marianoel / Sanjuán, Rafael

Journal of virology

2014 Volume 88, Issue 9, Page(s) 5042–5049

Abstract: ... Pereira-Gomez, and R. Sanjuán, J. Virol. 86:: 9640-9646, 2012, doi:10.1128/JVI.00613-12). Here, we found ...

Abstract	Unlabelled: Rates of spontaneous mutation determine viral fitness and adaptability. In RNA viruses, treatment with mutagenic nucleoside analogues selects for polymerase variants with increased fidelity, showing that viral mutation rates can be adjusted in response to imposed selective pressures. However, this type of resistance is not possible in viruses that do not encode their own polymerases, such as single-stranded DNA viruses. We previously showed that serial passaging of bacteriophage ϕX174 in the presence of the nucleoside analogue 5-fluorouracil (5-FU) favored substitutions in the lysis protein E (P. Domingo-Calap, M. Pereira-Gomez, and R. Sanjuán, J. Virol. 86:: 9640-9646, 2012, doi:10.1128/JVI.00613-12). Here, we found that approximately half (6/12) of the amino acid replacements in the N-terminal region of this protein led to delayed lysis, and two of these changes (V2A and D8A) also conferred partial resistance to 5-FU. By delaying lysis, the V2A and D8A substitutions allowed the virus to increase the burst size per cell in the presence of 5-FU. Furthermore, these substitutions tended to alleviate drug-induced mutagenesis by reducing the number of rounds of copying required for population growth, revealing a new mechanism of resistance. This form of mutation rate regulation may also be utilized by other viruses whose replication mode is similar to that of bacteriophage ϕX174. Importance: Many viruses display high rates of spontaneous mutations due to defects in proofreading or postreplicative repair, allowing them to rapidly adapt to changing environments. Viral mutation rates may have been optimized to achieve high adaptability without incurring an excessive genetic load. Supporting this, RNA viruses subjected to chemical mutagenesis treatments have been shown to evolve higher-fidelity polymerases. However, many viruses cannot modulate replication fidelity because they do not encode their own polymerase. Here, we show a new mechanism for regulating viral mutation rates. We found that, under mutagenic conditions, the single-stranded bacteriophage ϕX174 evolved delayed lysis, and that this allowed the virus to increase the amount of progeny produced per cell. As a result, the viral population was amplified in fewer infection cycles, reducing the chances for mutation appearance.
MeSH term(s)	Adaptation, Biological ; Bacteriolysis ; Bacteriophages/genetics ; Bacteriophages/growth & development ; Bacteriophages/physiology ; DNA, Single-Stranded/metabolism ; DNA, Viral/metabolism ; Fluorouracil/metabolism ; Mutant Proteins/genetics ; Mutant Proteins/metabolism ; Mutation Rate ; Mutation, Missense ; Selection, Genetic ; Viral Proteins/genetics ; Viral Proteins/metabolism
Chemical Substances	DNA, Single-Stranded ; DNA, Viral ; E protein, bacteriophage X174 ; Mutant Proteins ; Viral Proteins ; Fluorouracil (U3P01618RT)
Keywords	covid19
Language	English
Publishing date	2014-02-19
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	80174-4
ISSN	1098-5514 ; 0022-538X
ISSN (online)	1098-5514
ISSN	0022-538X
DOI	10.1128/JVI.02147-13
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Article ; Online: An evolutionary insight into emerging Ebolavirus strains isolated in Africa.

Pereira-Gomez, Marianoel / Lopez-Tort, Fernando / Fajardo, Alvaro / Cristina, Juan

Journal of medical virology

2019 Volume 92, Issue 8, Page(s) 988–995

Abstract: On July 19, 2019, the World Health Organization declared the current Ebolavirus (EBOV) outbreak in Congo Democratic Republic (COD) a public health emergency of international concern. To address the potential threat of EBOV evolution outpacing antibody ... ...

Abstract	On July 19, 2019, the World Health Organization declared the current Ebolavirus (EBOV) outbreak in Congo Democratic Republic (COD) a public health emergency of international concern. To address the potential threat of EBOV evolution outpacing antibody treatment and vaccine efforts, a detailed evolutionary analysis of EBOV strains circulating in different African countries was performed. Genome composition of EBOV strains was studied using multivariate statistical analysis. To investigate the patterns of evolution of EBOV strains, a Bayesian Markov Chain Monte Carlo approach was used. Two different genetic lineages, with a distinct genome composition gave rise to the recent EBOV outbreaks in central and western Africa. Strains isolated in COD in 2018 fall into two different genetic clusters, according to their geographical location of isolation. Different amino acid substitutions among strains from these two clusters have been found, particularly in NP, GP, and L proteins. Significant differences in codon and amino acid usage among clusters were found. Strains isolated in COD in 2018 belong to two distinct genetic clusters, with distinct codon and amino acid usage. Geographical diversity plays an important role in shaping the molecular evolution of EBOV populations.
MeSH term(s)	Africa, Central/epidemiology ; Africa, Western/epidemiology ; Amino Acid Substitution ; Bayes Theorem ; Codon Usage ; Disease Outbreaks ; Ebolavirus/genetics ; Ebolavirus/isolation & purification ; Evolution, Molecular ; Genome, Viral ; Hemorrhagic Fever, Ebola/epidemiology ; Hemorrhagic Fever, Ebola/virology ; Humans ; Markov Chains ; Monte Carlo Method ; Nucleocapsid Proteins/chemistry ; Nucleocapsid Proteins/genetics ; RNA-Dependent RNA Polymerase/chemistry ; RNA-Dependent RNA Polymerase/genetics ; Viral Envelope Proteins/chemistry ; Viral Envelope Proteins/genetics
Chemical Substances	Nucleocapsid Proteins ; Viral Envelope Proteins ; envelope glycoprotein, Ebola virus ; nucleocapsid protein, Ebola virus ; RNA-Dependent RNA Polymerase (EC 2.7.7.48)
Language	English
Publishing date	2019-11-18
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	752392-0
ISSN	1096-9071 ; 0146-6615
ISSN (online)	1096-9071
ISSN	0146-6615
DOI	10.1002/jmv.25627
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Article: Evaluation of SYBR Green real time PCR for detecting SARS-CoV-2 from clinical samples

Pereira-Gómez, Marianoel / Fajardo, Álvaro / Echeverría, Natalia / López-Tort, Fernando / Perbolianachis, Paula / Costábile, Alicia / Aldunate, Fabián / Moreno, Pilar / Moratorio, Gonzalo

Journal of virological methods. 2021 Mar., v. 289

2021

Abstract: The pandemic caused by SARS-CoV-2 has triggered an extraordinary collapse of healthcare systems and hundred thousand of deaths worldwide. Following the declaration of the outbreak as a Public Health Emergency of International Concern by the World Health ... ...

Abstract	The pandemic caused by SARS-CoV-2 has triggered an extraordinary collapse of healthcare systems and hundred thousand of deaths worldwide. Following the declaration of the outbreak as a Public Health Emergency of International Concern by the World Health Organization (WHO) on January 30th, 2020, it has become imperative to develop diagnostic tools to reliably detect the virus in infected patients. Several methods based on real time reverse transcription polymerase chain reaction (RT-qPCR) for the detection of SARS-CoV-2 genomic RNA have been developed. In addition, these methods have been recommended by the WHO for laboratory diagnosis. Since most of these protocols are based on the use of fluorogenic probes and one-step reagents (cDNA synthesis followed by PCR amplification in the same tube), these techniques can be difficult to perform given the limited supply of reagents in low- and middle-income countries. In order to develop an inexpensive SARS-CoV-2 detection protocol using available resources we evaluated the SYBR Green based detection of SARS-CoV-2 to establish a suitable assay. To do so, we adapted one of the WHO recommended TaqMan-based one-step real time PCR protocols (from the University of Hong Kong) to SYBR Green. Our results indicate that SYBR-Green detection of ORF1b-nsp14 target represents a reliable cost-effective alternative to increase the testing capacity.
Keywords	RNA ; Severe acute respiratory syndrome coronavirus 2 ; World Health Organization ; cost effectiveness ; genomics ; health services ; laboratory diagnosis ; pandemic ; public health ; quantitative polymerase chain reaction ; reverse transcriptase polymerase chain reaction ; viruses ; China
Language	English
Dates of publication	2021-03
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	8013-5
ISSN	1879-0984 ; 0166-0934
ISSN (online)	1879-0984
ISSN	0166-0934
DOI	10.1016/j.jviromet.2020.114035
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Article ; Online: Evaluation of SYBR Green real time PCR for detecting SARS-CoV-2 from clinical samples.

Pereira-Gómez, Marianoel / Fajardo, Álvaro / Echeverría, Natalia / López-Tort, Fernando / Perbolianachis, Paula / Costábile, Alicia / Aldunate, Fabián / Moreno, Pilar / Moratorio, Gonzalo

Journal of virological methods

2020 Volume 289, Page(s) 114035

Abstract	The pandemic caused by SARS-CoV-2 has triggered an extraordinary collapse of healthcare systems and hundred thousand of deaths worldwide. Following the declaration of the outbreak as a Public Health Emergency of International Concern by the World Health Organization (WHO) on January 30th, 2020, it has become imperative to develop diagnostic tools to reliably detect the virus in infected patients. Several methods based on real time reverse transcription polymerase chain reaction (RT-qPCR) for the detection of SARS-CoV-2 genomic RNA have been developed. In addition, these methods have been recommended by the WHO for laboratory diagnosis. Since most of these protocols are based on the use of fluorogenic probes and one-step reagents (cDNA synthesis followed by PCR amplification in the same tube), these techniques can be difficult to perform given the limited supply of reagents in low- and middle-income countries. In order to develop an inexpensive SARS-CoV-2 detection protocol using available resources we evaluated the SYBR Green based detection of SARS-CoV-2 to establish a suitable assay. To do so, we adapted one of the WHO recommended TaqMan-based one-step real time PCR protocols (from the University of Hong Kong) to SYBR Green. Our results indicate that SYBR-Green detection of ORF1b-nsp14 target represents a reliable cost-effective alternative to increase the testing capacity.
MeSH term(s)	COVID-19/diagnosis ; COVID-19/epidemiology ; COVID-19 Nucleic Acid Testing/methods ; Clinical Laboratory Techniques/methods ; Humans ; Pandemics ; RNA, Viral/analysis ; Real-Time Polymerase Chain Reaction/methods ; SARS-CoV-2/isolation & purification
Chemical Substances	RNA, Viral
Language	English
Publishing date	2020-12-04
Publishing country	Netherlands
Document type	Evaluation Study ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	8013-5
ISSN	1879-0984 ; 0166-0934
ISSN (online)	1879-0984
ISSN	0166-0934
DOI	10.1016/j.jviromet.2020.114035
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Article ; Online: What have we learned from a case of convalescent plasma treatment in a two-time kidney transplant recipient COVID-19 patient? A case report from the perspective of viral load evolution and immune response.

Aldunate, Fabian / Fajardo, Alvaro / Ibañez, Natalia / Rammauro, Florencia / Daghero, Hellen / Arce, Rodrigo / Ferla, Diego / Pereira-Gomez, Marianoel / Salazar, Cecilia / Iraola, Gregorio / Pritsch, Otto / Hurtado, Javier / Tenzi, Jordan / Bollati-Fogolín, Mariela / Bianchi, Sergio / Nin, Nicolas / Moratorio, Gonzalo / Moreno, Pilar

Frontiers in nephrology

2023 Volume 3, Page(s) 1132763

Abstract: Coronavirus disease 2019 (COVID-19), an infectious disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, can have a wide range of clinical manifestations, ranging from asymptomatic disease to potentially life- ... ...

Abstract	Coronavirus disease 2019 (COVID-19), an infectious disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, can have a wide range of clinical manifestations, ranging from asymptomatic disease to potentially life-threatening complications. Convalescent plasma therapy has been proposed as an effective alternative for the treatment of severe cases. The aim of this study was to follow a two-time renal transplant patient with severe COVID-19 treated with convalescent plasma over time from an immunologic and virologic perspective. A 42-year-old female patient, who was a two-time kidney transplant recipient, was hospitalized with COVID-19. Due to worsening respiratory symptoms, she was admitted to the intensive care unit, where she received two doses of convalescent plasma. We analyzed the dynamics of viral load in nasopharyngeal swab, saliva, and tracheal aspirate samples, before and after convalescent plasma transfusion. The levels of pro-inflammatory cytokines and antibody titers were also measured in serum samples. A significant decrease in viral load was observed after treatment in the saliva and nasopharyngeal swab samples, and a slight decrease was observed in tracheal aspirate samples. In addition, we found evidence of an increase in antibody titers after transfusion, accompanied by a decrease in the levels of several cytokines responsible for cytokine storm.
Language	English
Publishing date	2023-06-23
Publishing country	Switzerland
Document type	Case Reports
ISSN	2813-0626
ISSN (online)	2813-0626
DOI	10.3389/fneph.2023.1132763
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