LIVIVO - The Search Portal for Life Sciences

zur deutschen Oberfläche wechseln
Advanced search

Search results

Result 1 - 8 of total 8

Search options

  1. Article ; Online: Correction: Martínez-Murcia et al. SARS-CoV-2 Variants Identification; A Fast and Affordable Strategy Based on Partial S-Gene Targeted PCR Sequencing.

    Martínez-Murcia, Antonio / Garcia-Sirera, Adrian / Navarro, Aaron / Pérez, Laura

    Viruses

    2023  Volume 15, Issue 3

    Abstract: In the original publication [ ... ]. ...

    Abstract In the original publication [...].
    Language English
    Publishing date 2023-03-17
    Publishing country Switzerland
    Document type Published Erratum
    ZDB-ID 2516098-9
    ISSN 1999-4915 ; 1999-4915
    ISSN (online) 1999-4915
    ISSN 1999-4915
    DOI 10.3390/v15030771
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    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.

  2. Article ; Online: SARS-CoV-2 Variants Identification; A Fast and Affordable Strategy Based on Partial S-Gene Targeted PCR Sequencing.

    Martínez-Murcia, Antonio / Garcia-Sirera, Adrian / Navarro, Aaron / Pérez, Laura

    Viruses

    2022  Volume 14, Issue 11

    Abstract: A considerable number of new SARS-CoV-2 lineages have emerged since the first COVID-19 cases were reported in Wuhan. As a few variants showed higher COVID-19 disease transmissibility and the ability to escape from immune responses, surveillance became ... ...

    Abstract A considerable number of new SARS-CoV-2 lineages have emerged since the first COVID-19 cases were reported in Wuhan. As a few variants showed higher COVID-19 disease transmissibility and the ability to escape from immune responses, surveillance became relevant at that time. Single-nucleotide mutation PCR-based protocols were not always specific, and consequently, determination of a high number of informative sites was needed for accurate lineage identification. A detailed in silico analysis of SARS-CoV-2 sequences retrieved from GISAID database revealed the S gene 921 bp-fragment, positions 22784-23705 of SARS-CoV-2 reference genome, as the most informative fragment (30 variable sites) to determine relevant SARS-CoV-2 variants. Consequently, a method consisting of the PCR-amplification of this fragment, followed by Sanger's sequencing and a "single-click" informatic program based on a reference database, was developed and validated. PCR-fragments obtained from clinical SARS-CoV-2 samples were compared with homologous variant-sequences and the resulting phylogenetic tree allowed the identification of Alpha, Delta, Omicron, Beta, Gamma, and other variants. The data analysis procedure was automatized and simplified to the point that it did not require specific technical skills. The method is faster and cheaper than current whole-genome sequencing methods; it is available worldwide, and it may help to enhance efficient surveillance in the fight against the COVID-19 pandemic.
    MeSH term(s) Humans ; SARS-CoV-2/genetics ; Phylogeny ; Genome, Viral ; COVID-19/diagnosis ; COVID-19/epidemiology ; Pandemics ; Polymerase Chain Reaction
    Language English
    Publishing date 2022-11-21
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2516098-9
    ISSN 1999-4915 ; 1999-4915
    ISSN (online) 1999-4915
    ISSN 1999-4915
    DOI 10.3390/v14112588
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    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.

  3. Article ; Online: Current RT-qPCR to detect SARS-CoV-2 may give positive results for related coronaviruses.

    Martínez-Murcia, Antonio / García-Sirera, Adrián / Navarro, Aaron / Pérez, Laura

    Archives of microbiology

    2022  Volume 204, Issue 7, Page(s) 415

    Abstract: Some weeks after the first CoVID-19 outbreak, the World Health Organization published some real-time PCR (qPCR) protocols developed by different health reference centers. These qPCR designs are being used worldwide to detect SARS-CoV-2 in the population, ...

    Abstract Some weeks after the first CoVID-19 outbreak, the World Health Organization published some real-time PCR (qPCR) protocols developed by different health reference centers. These qPCR designs are being used worldwide to detect SARS-CoV-2 in the population, to monitor the prevalence of the virus during the pandemic. Moreover, some of these protocols to detect SARS-CoV-2 have widely been applied to environmental samples for epidemiological surveillance purposes. In the present work, the specificity of these currently used RT-qPCR designs was validated in vitro using SARS-CoV-2 and highly related coronaviral genomic sequences and compared to performance of the commercially available GPS™ CoVID-19 dtec-RT-qPCR Test. Assays performed with SARS-CoV-2-related genomes showed positive amplification when using some of these qPCR methods, indicating they may give SARS-CoV-2 false positives. This finding may be particularly relevant for SARS-CoV-2 monitoring of environmental samples, where an unknown pool of phylogenetically close-related viruses may exist.
    MeSH term(s) COVID-19/diagnosis ; Humans ; Pandemics ; Real-Time Polymerase Chain Reaction/methods ; SARS-CoV-2/genetics ; Sensitivity and Specificity
    Language English
    Publishing date 2022-06-23
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 124824-8
    ISSN 1432-072X ; 0302-8933
    ISSN (online) 1432-072X
    ISSN 0302-8933
    DOI 10.1007/s00203-022-03029-y
    Database MEDical Literature Analysis and Retrieval System OnLINE

    Full text online

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 805: 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.

  4. Article: Internal Validation of a Real-Time qPCR Kit following the UNE/EN ISO/IEC 17025:2005 for Detection of the Re-Emerging

    Martínez-Murcia, Antonio / Navarro, Aaron / Garcia-Sirera, Adrian / Pérez, Laura / Bru, Gema

    Diagnostics (Basel, Switzerland)

    2023  Volume 13, Issue 9

    Abstract: Human mpox is caused by ... ...

    Abstract Human mpox is caused by the
    Language English
    Publishing date 2023-04-26
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2662336-5
    ISSN 2075-4418
    ISSN 2075-4418
    DOI 10.3390/diagnostics13091560
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    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.

  5. Article: Current RT-qPCR to detect SARS-CoV-2 may give positive results for related coronaviruses

    Martínez-Murcia, Antonio / García-Sirera, Adrián / Navarro, Aaron / Pérez, Laura

    Archives of microbiology. 2022 July, v. 204, no. 7

    2022  

    Abstract: Some weeks after the first CoVID-19 outbreak, the World Health Organization published some real-time PCR (qPCR) protocols developed by different health reference centers. These qPCR designs are being used worldwide to detect SARS-CoV-2 in the population, ...

    Abstract Some weeks after the first CoVID-19 outbreak, the World Health Organization published some real-time PCR (qPCR) protocols developed by different health reference centers. These qPCR designs are being used worldwide to detect SARS-CoV-2 in the population, to monitor the prevalence of the virus during the pandemic. Moreover, some of these protocols to detect SARS-CoV-2 have widely been applied to environmental samples for epidemiological surveillance purposes. In the present work, the specificity of these currently used RT-qPCR designs was validated in vitro using SARS-CoV-2 and highly related coronaviral genomic sequences and compared to performance of the commercially available GPS™ CoVID-19 dtec-RT-qPCR Test. Assays performed with SARS-CoV-2-related genomes showed positive amplification when using some of these qPCR methods, indicating they may give SARS-CoV-2 false positives. This finding may be particularly relevant for SARS-CoV-2 monitoring of environmental samples, where an unknown pool of phylogenetically close-related viruses may exist.
    Keywords COVID-19 infection ; Severe acute respiratory syndrome coronavirus 2 ; World Health Organization ; genome ; genomics ; monitoring ; pandemic ; phylogeny ; quantitative polymerase chain reaction ; viruses
    Language English
    Dates of publication 2022-07
    Size p. 415.
    Publishing place Springer Berlin Heidelberg
    Document type Article
    ZDB-ID 124824-8
    ISSN 1432-072X ; 0302-8933
    ISSN (online) 1432-072X
    ISSN 0302-8933
    DOI 10.1007/s00203-022-03029-y
    Database NAL-Catalogue (AGRICOLA)

    More links

    Kategorien

    In stock of ZB MED Bonn / Germany

    Z 75/91: Show issues

    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.

    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.

  6. Article ; Online: Current quantitative polymerase chain reaction to detect severe acute respiratory syndrome coronavirus 2 may give positive results for other described coronavirus

    Martinez-Murcia, Antonio / Garcia-Sirera, Adrian / Navarro, Aaron / Ros-Tarraga, Patricia / Perez, Laura

    medRxiv

    Abstract: Some weeks after the first CoVID-19 outbreak, the WHO published some qPCR protocol assays developed by different institutions worldwide. These qPCR designs are being used to detect the presence of SARS-CoV-2 in the population, which allow us to monitore ... ...

    Abstract Some weeks after the first CoVID-19 outbreak, the WHO published some qPCR protocol assays developed by different institutions worldwide. These qPCR designs are being used to detect the presence of SARS-CoV-2 in the population, which allow us to monitore the prevalence of the virus during the pandemic. Moreover, the use of these designs is wide spreading and nowadays they are used to detect SARS-CoV-2 in environmental samples to act as epidemiological surveillance tool. However, at the time of designing the published RT-qPCR assays, a lack of SARS-CoV-2 genomes available may explain a low exclusivity in some cases. In this study, we are reporting experimental data which demonstrate that some of the current qPCR used to detect SARS-CoV-2 may give positive results for other described coronavirus different from SARS-CoV-2.
    Keywords covid19
    Language English
    Publishing date 2021-02-09
    Publisher Cold Spring Harbor Laboratory Press
    Document type Article ; Online
    DOI 10.1101/2021.02.08.21251332
    Database COVID19

    Full text online

    Kategorien

    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.

  7. Article ; Online: In silico design and validation of commercial kit GPS™ CoVID-19 dtec-RT-qPCR Test under criteria of UNE/EN ISO 17025:2005 and ISO/IEC 15189:2012

    Martínez-Murcia, Antonio / Bru, Gema / Navarro, Aaron / Ros-Tárraga, Patricia / García-Sirera, Adrián / Pérez, Laura

    bioRxiv

    Abstract: Background The Corona Virus Disease 2019 (COVID-19), caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), has become a serious infectious disease affecting human health worldwide and rapidly declared a pandemic by WHO. Early, several ... ...

    Abstract Background The Corona Virus Disease 2019 (COVID-19), caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), has become a serious infectious disease affecting human health worldwide and rapidly declared a pandemic by WHO. Early, several RT-qPCR were designed by using only the first SARS-CoV-2 genome sequence. Objectives A few days later, when additional SARS-CoV-2 genome were retrieved, the kit GPS™ CoVID-19 dtec-RT-qPCR Test was designed to provide a highly specific detection method and commercially available worldwide. The kit was validated following criteria recommended by the UNE/EN ISO 17025:2005 and ISO/IEC 15189:2012. Methods The present study approached the in silico specificity of the GPS™ CoVID-19 dtec-RT-qPCR Test and RT-qPCR designs currently published. The empirical validation parameters specificity (inclusivity/exclusivity), quantitative phase analysis (10-106 copies), reliability (repeatability/reproducibility) and sensitivity (detection/quantification limits) were evaluated for a minimum of 10-15 assays. Diagnostic validation was achieved by two independent reference laboratories, the Instituto de Salud Carlos III (ISCIII), (Madrid, Spain) and the Public Health England (PHE; Colindale, London, UK). Results The GPS™ RT-qPCR primers and probe showed the highest number of mismatches with the closet related non-SARS-CoV-2 coronavirus, including some indels. The kits passed all parameters of validation with strict acceptance criteria. Results from reference laboratories 100% correlated with these obtained by suing reference methods and received an evaluation with 100% of diagnostic sensitivity and specificity. Conclusions The GPS™ CoVID-19 dtec-RT-qPCR Test, available with full analytical and diagnostic validation, represents a case of efficient transfer of technology being successfully used since the pandemic was declared. The analysis suggested the GPS™ CoVID-19 dtec-RT-qPCR Test is the more exclusive by far.
    Keywords covid19
    Publisher BioRxiv; WHO
    Document type Article ; Online
    DOI 10.1101/2020.04.27.065383
    Database COVID19

    Kategorien

    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.

  8. Article ; Online: In silico analysis of RT-qPCR designs recommended by WHO for detection of SARS-CoV-2 and a commercial kit validated following UNE/EN ISO 17025:2005 and two reference laboratories

    Martinez-Murcia, Antonio J / Bru, Gema / Navarro, Aaron / Ros-Tárraga, Patricia / García-Sirera, Adrián / Pérez, Laura

    bioRxiv

    Abstract: The Corona Virus Disease 2019 (COVID-19), caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), has become a serious infectious disease affecting human health worldwide and rapidly declared a pandemic by WHO. Early, because the urgent ... ...

    Abstract The Corona Virus Disease 2019 (COVID-19), caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), has become a serious infectious disease affecting human health worldwide and rapidly declared a pandemic by WHO. Early, because the urgent need of reliable and rapid SARS-CoV-2 detection strategies and once the first SARS-CoV-2 genome sequence was available, several reference laboratories developed RT-qPCR methods which have been deposited in the WHO website. Only weeks later, after additional SARS-CoV-2 genomes were sequenced by several unrelated laboratories, the kit GPS<sup>TM</sup> CoVID-19 dtec-RT-qPCR Test developed by scientific team from Genetic PCR Solutions<sup>TM</sup> (GPS<sup>TM</sup>, Alicante, Spain) was one of the first commercially available worldwide. The parameters specificity (inclusivity/exclusivity), quantitative phase analysis (10-10<sup>6</sup> copies), reliability (repeatability/reproducibility) and sensitivity (detection/quantification limits) of this qPCR kit were validated with the strict acceptance criteria recommended by the UNE/EN ISO 17025:2005 and ISO/IEC 15189:2012. Diagnostic validation was achieved by two independent reference laboratories, the Instituto de Salud Carlos III (ISCIII), (Madrid, Spain) and the Public Health England (PHE; Colindale, London, UK). The present study approached the in silico specificity of the protocols currently recommended by WHO (16, 18, 23-27), a recently published RT-qPCR method, and the GPS<sup>TM</sup> CoVID-19 dtec-RT-qPCR Test. The analysis suggested the later RT-qPCR design as the more exclusive by far.
    Keywords covid19
    Language English
    Publishing date 2020-04-29
    Publisher Cold Spring Harbor Laboratory
    Document type Article ; Online
    DOI 10.1101/2020.04.27.065383
    Database COVID19

    Full text online

    Kategorien

    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.

To top