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  1. Article: Cross-reactivity and inclusivity analysis of CRISPR-based diagnostic assays of coronavirus SARS-CoV-2.

    Khan, Kashif Aziz / Duceppe, Marc-Olivier

    PeerJ

    2021  Volume 9, Page(s) e12050

    Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; initially named as 2019-nCoV) is the cause of the novel coronavirus disease 2019 (COVID-19) pandemic. Its diagnosis relies on the molecular detection of the viral RNA by polymerase chain ... ...

    Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; initially named as 2019-nCoV) is the cause of the novel coronavirus disease 2019 (COVID-19) pandemic. Its diagnosis relies on the molecular detection of the viral RNA by polymerase chain reaction (PCR) while newer rapid CRISPR-based diagnostic tools are being developed. As molecular diagnostic assays rely on the detection of unique sequences of viral nucleic acid, the target regions must be common to all coronavirus SARS-CoV-2 circulating strains, yet unique to SARS-CoV-2 with no cross-reactivity with the genome of the host and other normal or pathogenic organisms potentially present in the patient samples. This stage 1 protocol proposes
    Language English
    Publishing date 2021-10-01
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2703241-3
    ISSN 2167-8359
    ISSN 2167-8359
    DOI 10.7717/peerj.12050
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Book ; Online: Acknowledgement table from Presence of mismatches between diagnostic PCR assays and coronavirus SARS-CoV-2 genome

    Kashif Aziz Khan / Peter Cheung

    2020  

    Abstract: List of accession numbers and authors of the ... ...

    Abstract List of accession numbers and authors of the sequences
    Keywords Microbiology ; Health Care ; Diseases ; Epidemiology ; Genomics ; COVID-19 ; coronavirus SARS-CoV-2 ; diagnosis ; sequence variation ; polymerase chain reaction (PCR) ; primer–template mismatch ; covid19
    Publishing date 2020-06-09T01:45:37Z
    Publishing country uk
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Book ; Online: Geographical distribution of removed data from Presence of mismatches between diagnostic PCR assays and coronavirus SARS-CoV-2 genome

    Kashif Aziz Khan / Peter Cheung

    2020  

    Abstract: Geographical analysis of removed data for 3 primers/probe with the highest ... ...

    Abstract Geographical analysis of removed data for 3 primers/probe with the highest frequency
    Keywords Microbiology ; Health Care ; Diseases ; Epidemiology ; Genomics ; COVID-19 ; coronavirus SARS-CoV-2 ; diagnosis ; sequence variation ; polymerase chain reaction (PCR) ; primer–template mismatch ; covid19
    Publishing date 2020-06-09T01:45:39Z
    Publishing country uk
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Book ; Online: Geographical distribution of included sequence dataset and mismatches from Presence of mismatches between diagnostic PCR assays and coronavirus SARS-CoV-2 genome

    Kashif Aziz Khan / Peter Cheung

    2020  

    Abstract: Geographical data used to draw graphs in figure ... ...

    Abstract Geographical data used to draw graphs in figure 4
    Keywords Microbiology ; Health Care ; Diseases ; Epidemiology ; Genomics ; COVID-19 ; coronavirus SARS-CoV-2 ; diagnosis ; sequence variation ; polymerase chain reaction (PCR) ; primer–template mismatch ; covid19
    Publishing date 2020-06-09T01:45:37Z
    Publishing country uk
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Sequence tracing figures from Presence of mismatches between diagnostic PCR assays and coronavirus SARS-CoV-2 genome

    Kashif Aziz Khan / Peter Cheung

    2020  

    Abstract: Sequence tracing figures not shown in the main ... ...

    Abstract Sequence tracing figures not shown in the main article
    Keywords Microbiology ; Health Care ; Diseases ; Epidemiology ; Genomics ; COVID-19 ; coronavirus SARS-CoV-2 ; diagnosis ; sequence variation ; polymerase chain reaction (PCR) ; primer–template mismatch ; covid19
    Publishing date 2020-06-09T01:45:39Z
    Publishing country uk
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article: Presence of mismatches between diagnostic PCR assays and coronavirus SARS-CoV-2 genome.

    Khan, Kashif Aziz / Cheung, Peter

    Royal Society open science

    2020  Volume 7, Issue 6, Page(s) 200636

    Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; initially named as 2019-nCoV) is responsible for the recent COVID-19 pandemic and polymerase chain reaction (PCR) is the current standard method for its diagnosis from patient samples. This ... ...

    Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; initially named as 2019-nCoV) is responsible for the recent COVID-19 pandemic and polymerase chain reaction (PCR) is the current standard method for its diagnosis from patient samples. This study conducted a reassessment of published diagnostic PCR assays, including those recommended by the World Health Organization (WHO), through the evaluation of mismatches with publicly available viral sequences. An exhaustive evaluation of the sequence variability within the primer/probe target regions of the viral genome was performed using more than 17 000 viral sequences from around the world. The analysis showed the presence of mutations/mismatches in primer/probe binding regions of 7 assays out of 27 assays studied. A comprehensive bioinformatics approach for
    Keywords covid19
    Language English
    Publishing date 2020-06-10
    Publishing country England
    Document type Journal Article
    ZDB-ID 2787755-3
    ISSN 2054-5703
    ISSN 2054-5703
    DOI 10.1098/rsos.200636
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Presence of mismatches between diagnostic PCR assays and coronavirus SARS-CoV-2 genome

    Kashif Aziz Khan / Peter Cheung

    Royal Society Open Science, Vol 7, Iss

    2020  Volume 6

    Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; initially named as 2019-nCoV) is responsible for the recent COVID-19 pandemic and polymerase chain reaction (PCR) is the current standard method for its diagnosis from patient samples. This ... ...

    Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; initially named as 2019-nCoV) is responsible for the recent COVID-19 pandemic and polymerase chain reaction (PCR) is the current standard method for its diagnosis from patient samples. This study conducted a reassessment of published diagnostic PCR assays, including those recommended by the World Health Organization (WHO), through the evaluation of mismatches with publicly available viral sequences. An exhaustive evaluation of the sequence variability within the primer/probe target regions of the viral genome was performed using more than 17 000 viral sequences from around the world. The analysis showed the presence of mutations/mismatches in primer/probe binding regions of 7 assays out of 27 assays studied. A comprehensive bioinformatics approach for in silico inclusivity evaluation of PCR diagnostic assays of SARS-CoV-2 was validated using freely available software programs that can be applied to any diagnostic assay of choice. These findings provide potentially important information for clinicians, laboratory professionals and policy-makers.
    Keywords covid-19 ; coronavirus sars-cov-2 ; diagnosis ; sequence variation ; polymerase chain reaction (pcr) ; primer–template mismatch ; Science ; Q
    Language English
    Publishing date 2020-06-01T00:00:00Z
    Publisher The Royal Society
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: Evaluation of the Sequence Variability within the PCR Primer/Probe Target Regions of the SARS-CoV-2 Genome.

    Khan, Kashif Aziz / Cheung, Peter

    Bio-protocol

    2020  Volume 10, Issue 24, Page(s) e3871

    Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; initially named 2019-nCoV) is responsible for the recent coronavirus disease (COVID-19) pandemic, and polymerase chain reaction (PCR) is the current standard method for diagnosis from patient ... ...

    Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; initially named 2019-nCoV) is responsible for the recent coronavirus disease (COVID-19) pandemic, and polymerase chain reaction (PCR) is the current standard method for diagnosis from patient samples. As PCR assays are prone to sequence mismatches due to mutations in the viral genome, it is important to verify the genomic variability at primer/probe binding regions periodically. This step-by-step protocol describes a bioinformatics approach for an extensive evaluation of the sequence variability within the primer/probe target regions of the SARS-CoV-2 genome. The protocol can be applied to any molecular diagnostic assay of choice using freely available software programs and the ready-to-use multiple sequence alignment (MSA) file provided. Graphic abstract
    Language English
    Publishing date 2020-12-20
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2833269-6
    ISSN 2331-8325 ; 2331-8325
    ISSN (online) 2331-8325
    ISSN 2331-8325
    DOI 10.21769/BioProtoc.3871
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Energy Conversion Efficiency Enhancement of Polyethylene Glycol and a SiO

    Zahir, Md Hasan / Rahman, Mohammad Mizanur / Irshad, Kashif / Shaikh, M Nasiruzzaman / Helal, Aasif / Aziz, Md Abdul / Ali, Amjad / Khan, Firoz

    ACS omega

    2022  Volume 7, Issue 26, Page(s) 22657–22670

    Abstract: Doping the ... ...

    Abstract Doping the SiO
    Language English
    Publishing date 2022-06-17
    Publishing country United States
    Document type Journal Article
    ISSN 2470-1343
    ISSN (online) 2470-1343
    DOI 10.1021/acsomega.2c02107
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Exploring the Interplay of the CRISPR-CAS System with Antibiotic Resistance in

    Shabbir, Muhammad Abu Bakr / Ul-Rahman, Aziz / Iftikhar, Muhammad Rizwan / Rasheed, Majeeda / Maan, Muhammad Kashif / Sattar, Adeel / Ahmad, Mehmood / Khan, Farid Ahmed / Ahmad, Waqas / Riaz, Muhammad Ilyas / Aslam, Hassaan Bin

    Medicina (Kaunas, Lithuania)

    2024  Volume 60, Issue 1

    Abstract: Staphylococcus ... ...

    Abstract Staphylococcus aureus
    MeSH term(s) Humans ; Animals ; Pakistan ; Staphylococcus aureus/genetics ; CRISPR-Cas Systems/genetics ; Phylogeny ; Poultry ; Staphylococcal Infections ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics
    Chemical Substances Anti-Bacterial Agents
    Language English
    Publishing date 2024-01-10
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2188113-3
    ISSN 1648-9144 ; 1010-660X
    ISSN (online) 1648-9144
    ISSN 1010-660X
    DOI 10.3390/medicina60010130
    Database MEDical Literature Analysis and Retrieval System OnLINE

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