LIVIVO - Search results -

Search results

Result 1 - 10 of total 23

Search options

Article ; Online: A comprehensive analysis of genome composition and codon usage patterns of emerging coronaviruses.

Tort, Fernando L / Castells, Matías / Cristina, Juan

2020 Volume 283, Page(s) 197976

Abstract: An outbreak of atypical pneumonia caused by a novel Betacoronavirus (βCoV), named SARS-CoV-2 has been declared a public health emergency of international concern by the World Health Organization. In order to gain insight into the emergence, evolution and ...

Abstract	An outbreak of atypical pneumonia caused by a novel Betacoronavirus (βCoV), named SARS-CoV-2 has been declared a public health emergency of international concern by the World Health Organization. In order to gain insight into the emergence, evolution and adaptation of SARS-CoV-2 viruses, a comprehensive analysis of genome composition and codon usage of βCoV circulating in China was performed. A biased nucleotide composition was found for SARS-CoV-2 genome. This bias in genomic composition is reflected in its codon and amino acid usage patterns. The overall codon usage in SARS-CoV-2 is similar among themselves and slightly biased. Most of the highly frequent codons are A- and U-ending, which strongly suggests that mutational bias is the main force shaping codon usage in this virus. Significant differences in relative synonymous codon usage frequencies among SARS-CoV-2 and human cells were found. These differences are due to codon usage preferences.
MeSH term(s)	Amino Acids/genetics ; Animals ; Betacoronavirus/classification ; Betacoronavirus/genetics ; Betacoronavirus/isolation & purification ; China/epidemiology ; Chiroptera/virology ; Codon Usage/genetics ; Communicable Diseases, Emerging/virology ; Coronavirus Infections/epidemiology ; Coronavirus Infections/veterinary ; Coronavirus Infections/virology ; Evolution, Molecular ; Ferrets/virology ; Gene Expression Regulation, Viral/genetics ; Genome, Viral/genetics ; Genomics ; Humans ; Mutagenesis/genetics ; Open Reading Frames/genetics ; SARS-CoV-2 ; Viverridae/virology
Chemical Substances	Amino Acids
Keywords	covid19
Language	English
Publishing date	2020-04-12
Publishing country	Netherlands
Document type	Comparative Study ; Journal Article
ZDB-ID	605780-9
ISSN	1872-7492 ; 0168-1702
ISSN (online)	1872-7492
ISSN	0168-1702
DOI	10.1016/j.virusres.2020.197976
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 1965: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

Details ▾
- See ZB MED holdings
- Order with fees

Article: A comprehensive analysis of genome composition and codon usage patterns of emerging coronaviruses

Tort, Fernando L / Castells, Matías / Cristina, Juan

Virus research. 2020 July 02, v. 283

2020

Abstract	An outbreak of atypical pneumonia caused by a novel Betacoronavirus (βCoV), named SARS-CoV-2 has been declared a public health emergency of international concern by the World Health Organization. In order to gain insight into the emergence, evolution and adaptation of SARS-CoV-2 viruses, a comprehensive analysis of genome composition and codon usage of βCoV circulating in China was performed. A biased nucleotide composition was found for SARS-CoV-2 genome. This bias in genomic composition is reflected in its codon and amino acid usage patterns. The overall codon usage in SARS-CoV-2 is similar among themselves and slightly biased. Most of the highly frequent codons are A- and U-ending, which strongly suggests that mutational bias is the main force shaping codon usage in this virus. Significant differences in relative synonymous codon usage frequencies among SARS-CoV-2 and human cells were found. These differences are due to codon usage preferences.
Keywords	Betacoronavirus ; amino acids ; codon usage ; genomics ; humans ; pneumonia ; public health ; viruses ; China ; covid19
Language	English
Dates of publication	2020-0702
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	605780-9
ISSN	1872-7492 ; 0168-1702
ISSN (online)	1872-7492
ISSN	0168-1702
DOI	10.1016/j.virusres.2020.197976
Database	NAL-Catalogue (AGRICOLA)

In stock of ZB MED Cologne/Königswinter

Zs.A 1965: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Husbandry Protocols for Juvenile Loggerhead Sea Turtles (

Usategui-Martín, Alejandro / Liria-Loza, Ana / Valverde, Roldán A / Tort, Lluis / Tuya, Fernando / Montero, Daniel

Journal of applied animal welfare science : JAAWS

2024 , Page(s) 1–13

Abstract: When necessary, sea turtles are held captive for veterinarian care and research purposes. Protocols and basic guidelines have been described for husbandry of sea turtles with veterinarian needs but not considering physiological indicators of animal ... ...

Abstract	When necessary, sea turtles are held captive for veterinarian care and research purposes. Protocols and basic guidelines have been described for husbandry of sea turtles with veterinarian needs but not considering physiological indicators of animal welfare. Because all sea turtle are imperiled species, monitoring their welfare is important. The aim of this study was to standardize husbandry protocols for loggerhead (
Language	English
Publishing date	2024-02-18
Publishing country	England
Document type	Journal Article
ISSN	1532-7604
ISSN (online)	1532-7604
DOI	10.1080/10888705.2024.2315048
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: Reduced ability to neutralize the Omicron variant among adults after infection and complete vaccination with BNT162b2, ChAdOx1, or CoronaVac and heterologous boosting.

Espíndola, Otávio Melo / Fuller, Trevon L / de Araújo, Mia Ferreira / Tort, Luis Fernando Lopez / Guaraldo, Lusiele / Calvet, Guilherme / Resende, Paola / Bonaldo, Myrna / Whitworth, Jimmy / Smith, Chris / Siqueira, Marilda / Brasil, Patrícia

Scientific reports

2023 Volume 13, Issue 1, Page(s) 7437

Abstract: COVID-19 vaccines have dramatically reduced rates of severe infection requiring hospitalization. However, SARS-CoV-2 variants have reduced vaccine effectiveness at preventing any symptomatic infection. This real-world study analyzed binding and ... ...

Abstract	COVID-19 vaccines have dramatically reduced rates of severe infection requiring hospitalization. However, SARS-CoV-2 variants have reduced vaccine effectiveness at preventing any symptomatic infection. This real-world study analyzed binding and neutralizing antibodies generated after complete vaccination and boosting across three vaccine platforms. Binding antibodies decayed most slowly in people under 60 with hybrid immunity. Neutralizing antibodies against Omicron BA.1 were reduced compared to other variants. The anamnestic anti-spike IgG response to the first boost was more pronounced than after the second boost. Monitoring of the effects of SARS-CoV-2 mutations on disease severity and the effectiveness of therapeutics is warranted.
MeSH term(s)	Adult ; Humans ; COVID-19 Vaccines ; BNT162 Vaccine ; COVID-19/prevention & control ; SARS-CoV-2/genetics ; Vaccination ; Antibodies, Neutralizing ; Antibodies, Viral
Chemical Substances	sinovac COVID-19 vaccine ; COVID-19 Vaccines ; BNT162 Vaccine ; Antibodies, Neutralizing ; Antibodies, Viral
Language	English
Publishing date	2023-05-08
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-34035-9
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article: A comprehensive analysis of genome composition and codon usage patterns of emerging coronaviruses

Tort, Fernando L / Castells, Matías / Cristina, Juan

Virus Res

Abstract: An outbreak of atypical pneumonia caused by a novel Betacoronavirus (ßCoV), named SARS-CoV-2 has been declared a public health emergency of international concern by the World Health Organization. In order to gain insight into the emergence, evolution and ...

Abstract	An outbreak of atypical pneumonia caused by a novel Betacoronavirus (ßCoV), named SARS-CoV-2 has been declared a public health emergency of international concern by the World Health Organization. In order to gain insight into the emergence, evolution and adaptation of SARS-CoV-2 viruses, a comprehensive analysis of genome composition and codon usage of ßCoV circulating in China was performed. A biased nucleotide composition was found for SARS-CoV-2 genome. This bias in genomic composition is reflected in its codon and amino acid usage patterns. The overall codon usage in SARS-CoV-2 is similar among themselves and slightly biased. Most of the highly frequent codons are A- and U-ending, which strongly suggests that mutational bias is the main force shaping codon usage in this virus. Significant differences in relative synonymous codon usage frequencies among SARS-CoV-2 and human cells were found. These differences are due to codon usage preferences.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #46070
Database	COVID19

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Details ▾

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: ... GP, and L proteins. Significant differences in codon and amino acid usage among clusters were found ...

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
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Accessible to users with ZB MED library card

In stock of ZB MED Cologne/Königswinter

Zs.A 1320: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾

Article ; Online: SARS-CoV-2 variant N.9 identified in Rio de Janeiro, Brazil.

Tort, Luis Fernando Lopez / Ribeiro, Ieda Pereira / Menezes, Lidiane Souza Raphael / Dos Santos, Alexandre Araújo Cunha / Santos, Marta Pereira / Damasceno, Luana / Silva, Paola Cristina Resende / de Siqueira, Marilda Agudo Mendonça Teixeira / Brasil, Patricia / Bonaldo, Myrna Cristina

Memorias do Instituto Oswaldo Cruz

2021 Volume 116, Page(s) e210166

Abstract: Background: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) B.1.1.33-derived lineage named N.9 was described recently in Brazil and it's considered a potential variant of interest (VOI) due to the presence of E484K substitution at the ... ...

Abstract	Background: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) B.1.1.33-derived lineage named N.9 was described recently in Brazil and it's considered a potential variant of interest (VOI) due to the presence of E484K substitution at the receptor-binding domain (RBD) of the Spike (S) protein. Objective: To describe the first detection of variant N.9 in Rio de Janeiro State. Methods: SARS-CoV-2 N.9 was confirmed by quantitative reverse transcription polymerase chain reaction (qRT-PCR), whole-genome sequencing and phylogenetic analysis. Findings: Here, we report two SARS-CoV-2 N.9 lineage strains in Rio de Janeiro. One of them had only the E484K substitution of the six N.9 lineage-defining mutations. Other three strains pre-defined as N.9 have the same genomic profile. These four strains are grouped within the B.1.1.33 lineage and basal to the N.9 lineage in our phylogenetic analysis, and we call them "N.9-like/B.1.1.33 + E484K". Main conclusions: The phylogenetic analysis shows four independent introductions of N.9 in the state of Rio de Janeiro in October and December 2020, January and March 2021. SARS-CoV-2 N.9 dissemination in the Rio de Janeiro could have been limited by the emergence and dominance of other variants, mainly by the lineage P.2 VOI Zeta that emerged in the same period and co-circulated with N.9, as observed in the neighboring State of São Paulo.
MeSH term(s)	Brazil ; COVID-19 ; Humans ; Mutation ; Phylogeny ; SARS-CoV-2
Language	English
Publishing date	2021-11-08
Publishing country	Brazil
Document type	Journal Article
ZDB-ID	953293-6
ISSN	1678-8060 ; 0074-0276
ISSN (online)	1678-8060
ISSN	0074-0276
DOI	10.1590/0074-02760210166
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Ud II Zs.33: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Evaluation Of SYBR Green Real Time PCR For Detecting SARS-CoV-2 From Clinical Samples

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

bioRxiv

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 all 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 the interest of economy, time and availability of chemicals and consumables, the SYBR Green-based detection was implemented to establish a convenient assay. Therefore, we adapted one of WHO recommended Taqman-based one-step real time PCR protocols (from the University of Hong Kong) to SYBR Green. Our results suggest that SYBR-Green detection represents a reliable cost-effective alternative to increase the testing capacity.
Keywords	covid19
Publisher	BioRxiv; WHO
Document type	Article ; Online
DOI	10.1101/2020.05.13.093609
Database	COVID19

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Details ▾

Article ; Online: Microbial Source Tracking Analysis Using Viral Indicators in Santa Lucía and Uruguay Rivers, Uruguay.

Bortagaray, Viviana / Lizasoain, Andrés / Piccini, Claudia / Gillman, Luciana / Berois, Mabel / Pou, Sonia / Díaz, María Del Pilar / Tort, Fernando López / Colina, Rodney / Victoria, Matías

Food and environmental virology

2019 Volume 11, Issue 3, Page(s) 259–267

Abstract: The aim of this study was to determine the origin (human, bovine or porcine) and the concentration of the fecal sources of contamination in waters from Santa Lucía basin and Uruguay River in Uruguay by using host-specific viral markers (adenoviruses and ... ...

Abstract	The aim of this study was to determine the origin (human, bovine or porcine) and the concentration of the fecal sources of contamination in waters from Santa Lucía basin and Uruguay River in Uruguay by using host-specific viral markers (adenoviruses and polyomaviruses) as microbial source tracking (MST). Between June 2015 and May 2016, monthly collections of surface water samples were performed in six sites in Santa Lucía basin and four sites in Uruguay River (n = 120 samples). Viral concentration was carried out using an absorption-elution method. Detection and quantification of human and porcine adenovirus (HAdV and PAdV, respectively) and human and bovine polyomavirus (HPyV and BoPyV, respectively) were performed by quantitative PCR (qPCR). To evaluate the infectivity of circulating HAdV, an integrated cell culture-qPCR (ICC-qPCR) was used. A logistic regression analysis was carried out to estimate the influence of environmental variables on the virus presence in surface waters. Overall, HAdV was the prevalent (18%; 21/120) followed by BoPyV (11%; 13/120) and HPyV (3%; 3/120), whereas PAdV was not detected in this study. The mean concentration ranged from 1.5 × 10
MeSH term(s)	Animals ; Cattle ; Feces/virology ; Humans ; Real-Time Polymerase Chain Reaction ; Rivers/virology ; Sewage/virology ; Swine ; Uruguay ; Viruses/classification ; Viruses/genetics ; Viruses/isolation & purification ; Water Pollution/analysis
Chemical Substances	Sewage
Language	English
Publishing date	2019-04-03
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2487173-4
ISSN	1867-0342 ; 1867-0334
ISSN (online)	1867-0342
ISSN	1867-0334
DOI	10.1007/s12560-019-09384-2
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Accessible to users with ZB MED library card

Order via subito

Details ▾
- Full text online
- Order with fees

Article ; Online: S100B protein and neuron-specific enolase as predictors of cognitive dysfunction after coronary artery bypass graft surgery: A prospective observational study.

Silva, Fernando P / Schmidt, Andre P / Valentin, Livia S / Pinto, Katia O / Zeferino, Suely P / Oses, Jean P / Wiener, Carolina D / Otsuki, Denise A / Tort, Adriano B L / Portela, Luis V / Souza, Diogo O / Auler, Jose O C / Carmona, Maria J C

European journal of anaesthesiology

2016 Volume 33, Issue 9, Page(s) 681–689

Abstract: Background: Postoperative cognitive dysfunction (POCD) may be related to the systemic inflammatory response and an increase in serum markers of brain injury such as S100B protein and neuron-specific enolase (NSE).: Objective: The study aims to ... ...

Abstract	Background: Postoperative cognitive dysfunction (POCD) may be related to the systemic inflammatory response and an increase in serum markers of brain injury such as S100B protein and neuron-specific enolase (NSE). Objective: The study aims to evaluate the association between POCD and serum levels of S100B and NSE after coronary artery bypass grafting surgery (CABG). Design: Prospective observational study. Setting: Single university teaching hospital. Patients: We investigated 88 patients undergoing CABG. Main outcomes measures: Cognitive function was measured preoperatively, and at the 21st and 180th postoperative days (i.e. 6 months after surgery). S100B protein and NSE serum levels were evaluated preoperatively, after induction of anaesthesia, at the end of surgery and at 6 and 24 h after surgery. Results: The incidence of POCD was 26.1% at 21 days after surgery and 22.7% at 6 months after surgery. Increased serum levels of S100B protein and NSE were observed postoperatively and may indicate brain damage. Conclusion: Although serum levels of S100B protein and NSE are both significantly increased postoperatively, our findings indicate that serum levels of S100B protein may be more accurate than NSE in the detection of POCD after CABG. Trial registration: NCT01550159.
Language	English
Publishing date	2016-09
Publishing country	England
Document type	Journal Article
ZDB-ID	605770-6
ISSN	1365-2346 ; 0265-0215
ISSN (online)	1365-2346
ISSN	0265-0215
DOI	10.1097/EJA.0000000000000450
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 1955: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

To top

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

Order via subito

Kategorien

Inter-library loan at ZB MED

Full text online

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

Kategorien

Inter-library loan at ZB MED

Full text online

More links

Kategorien

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito