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  1. Article ; Online: Rational Selection of PCR Primer/Probe Design Sites for SARS-CoV-2

    Rana, Divya RSJB

    bioRxiv

    Abstract: Various reports of decreased analytical sensitivities of real-time PCR-based detection of Coronavirus Disease 2019 (COVID-19) have been associated with occurrence of mutations in the target area of primer/probe binding. Knowledge about propensities of ... ...

    Abstract Various reports of decreased analytical sensitivities of real-time PCR-based detection of Coronavirus Disease 2019 (COVID-19) have been associated with occurrence of mutations in the target area of primer/probe binding. Knowledge about propensities of different genes to undergo mutation can inform researchers to select optimal genes to target for the qPCR design. We analyzed supplementary data from over 45 thousand SARS-CoV-2 genomes provided by Mercatelli et al to calculate the unique and prevalent mutations in different genes of SARS-CoV-2. We found that non-structural proteins in the ORF1ab region were more conserved compared to structural genes. Further factors which need to be relied upon for proper selection of genes for qPCR design are discussed.
    Keywords covid19
    Language English
    Publishing date 2021-04-05
    Publisher Cold Spring Harbor Laboratory
    Document type Article ; Online
    DOI 10.1101/2021.04.04.438420
    Database COVID19

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  2. Article ; Online: Serological rapid diagnostics test kit "Wondfo" for COVID-19 in Nepal

    Rana, Divya RSJB

    Journal of Patan Academy of Health Sciences; Vol 7 No; 4-6 ; 2091-2757 ; 2091-2749

    2020  Volume 1

    Keywords covid19
    Language English
    Publishing date 2020-04-30
    Publisher Patan Academy of Health Sciences
    Publishing country np
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Charting the challenges behind the testing of COVID-19 in developing countries: Nepal as a case study.

    Giri, Anil K / Rana, Divya Rsjb

    Biosafety and health

    2020  Volume 2, Issue 2, Page(s) 53–56

    Abstract: The infrastructure needed to detect Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection (COVID-19) that complies completely with WHO guidelines is lacking across many parts of the globe, especially in developing countries, including ... ...

    Abstract The infrastructure needed to detect Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection (COVID-19) that complies completely with WHO guidelines is lacking across many parts of the globe, especially in developing countries, including Nepal. We outline the problems faced by such countries and suggest that the national and international community should collaborate in the development and adoption of novel protocols for the rapid detection of COVID-19 according to locally available infrastructure, in order to fight against the outbreak.
    Language English
    Publishing date 2020-05-13
    Publishing country Netherlands
    Document type Editorial
    ISSN 2590-0536
    ISSN (online) 2590-0536
    DOI 10.1016/j.bsheal.2020.05.002
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Rational Primer and Probe Construction in PCR-Based Assays for the Efficient Diagnosis of Drifting Variants of SARS-CoV-2.

    Rana, Divya Rsjb / Pokhrel, Nischal / Dulal, Santosh

    Advances in virology

    2022  Volume 2022, Page(s) 2965666

    Abstract: The genome sequence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been evolving via genomic drifts resulting in "emerging/drifting variants" circulating worldwide. The construction of polymerase chain reaction (PCR) assays for the ... ...

    Abstract The genome sequence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been evolving via genomic drifts resulting in "emerging/drifting variants" circulating worldwide. The construction of polymerase chain reaction (PCR) assays for the reliable, efficient, and specific diagnosis of the drifting variants of SARS-CoV-2 is specifically governed by the selection and construction of primers and probes. The efficiency of molecular diagnosis is impacted by the identity/homology of the genome sequence of SARS-CoV-2 with other coronaviruses, drifting variants or variants of concern (VOCs) circulating in communities, inherent capacity of mutation(s) of various target genes of SARS-CoV-2, and concentration of genes of interest in host cells. The precise amplicon selection and construction of primers and probes for PCR-based assays can efficiently discriminate specific SARS-CoV-2 drifting variants. The construction of single nucleotide polymorphism (SNP)-specific primers and probes for PCR assays is pivotal to specifically distinguish SARS-CoV-2 variants present in the communities and contributes to better diagnosis and prevention of the ongoing COVID-19 pandemic. In this study, we have utilized
    Language English
    Publishing date 2022-05-13
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2625776-2
    ISSN 1687-8647 ; 1687-8639
    ISSN (online) 1687-8647
    ISSN 1687-8639
    DOI 10.1155/2022/2965666
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Sequence mismatch in PCR probes may mask the COVID-19 detection in Nepal.

    Rana, Divya Rsjb / Pokhrel, Nischal

    Molecular and cellular probes

    2020  Volume 53, Page(s) 101599

    Abstract: Most of the COVID-19 cases in Nepal are in the Southern districts of Nepal bordering India with travel histories to India.•Very few positive cases of COVID-19 are detected in Nepal which could either be due to early national lockdown.•Low PCR positivity ...

    Abstract •Most of the COVID-19 cases in Nepal are in the Southern districts of Nepal bordering India with travel histories to India.•Very few positive cases of COVID-19 are detected in Nepal which could either be due to early national lockdown.•Low PCR positivity rates could also be due to inefficiency of the PCR methods.•Whole genomes of 93 clinical samples from COVID-19 patients were analyzed to find the primer and probe binding sites.•Mutations in probe binding sites were found which could impact PCR efficiency resulting in false negative results.
    MeSH term(s) Betacoronavirus/classification ; Betacoronavirus/genetics ; Betacoronavirus/pathogenicity ; COVID-19 ; COVID-19 Testing ; Clinical Laboratory Techniques/methods ; Coronavirus Infections/diagnosis ; Coronavirus Infections/epidemiology ; Coronavirus Infections/transmission ; Coronavirus Infections/virology ; DNA Probes/standards ; False Negative Reactions ; Genome, Viral ; Humans ; India/epidemiology ; Mutation ; Nepal/epidemiology ; Pandemics ; Pneumonia, Viral/diagnosis ; Pneumonia, Viral/epidemiology ; Pneumonia, Viral/transmission ; Pneumonia, Viral/virology ; RNA, Viral/genetics ; Reagent Kits, Diagnostic/standards ; Reverse Transcriptase Polymerase Chain Reaction/standards ; SARS-CoV-2 ; Severity of Illness Index ; Transients and Migrants
    Chemical Substances DNA Probes ; RNA, Viral ; Reagent Kits, Diagnostic
    Keywords covid19
    Language English
    Publishing date 2020-05-18
    Publishing country England
    Document type Journal Article
    ZDB-ID 639082-1
    ISSN 1096-1194 ; 0890-8508
    ISSN (online) 1096-1194
    ISSN 0890-8508
    DOI 10.1016/j.mcp.2020.101599
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Charting the challenges behind the testing of COVID-19 in developing countries

    Giri, Anil K. / Rana, Divya RSJB

    Biosafety and Health

    Nepal as a case study

    2020  Volume 2, Issue 2, Page(s) 53–56

    Keywords covid19
    Language English
    Publisher Elsevier BV
    Publishing country us
    Document type Article ; Online
    ISSN 2590-0536
    DOI 10.1016/j.bsheal.2020.05.002
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Sequence mismatch in PCR probes may mask the COVID-19 detection in Nepal

    Rana, Divya RSJB / Pokhrel, Nischal

    Molecular and Cellular Probes

    2020  Volume 53, Page(s) 101599

    Keywords Cell Biology ; Molecular Biology ; covid19
    Language English
    Publisher Elsevier BV
    Publishing country us
    Document type Article ; Online
    ZDB-ID 639082-1
    ISSN 1096-1194 ; 0890-8508
    ISSN (online) 1096-1194
    ISSN 0890-8508
    DOI 10.1016/j.mcp.2020.101599
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: Charting the challenges behind the testing of COVID-19 in developing countries

    Anil K. Giri / Divya RSJB Rana

    Biosafety and Health, Vol 2, Iss 2, Pp 53-

    Nepal as a case study

    2020  Volume 56

    Abstract: The infrastructure needed to detect Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection (COVID-19) that complies completely with WHO guidelines is lacking across many parts of the globe, especially in developing countries, including ... ...

    Abstract The infrastructure needed to detect Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection (COVID-19) that complies completely with WHO guidelines is lacking across many parts of the globe, especially in developing countries, including Nepal. We outline the problems faced by such countries and suggest that the national and international community should collaborate in the development and adoption of novel protocols for the rapid detection of COVID-19 according to locally available infrastructure, in order to fight against the outbreak.
    Keywords COVID-19 ; SARS-CoV-2 ; Loop-mediated isothermal amplification (LAMP) assay ; Biosafety Level-2 (BSL-2) ; Infectious and parasitic diseases ; RC109-216 ; Public aspects of medicine ; RA1-1270 ; covid19
    Language English
    Publishing date 2020-06-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: Therapeutic Application of Chloroquine in Clinical Trials for COVID-19

    Rana, Divya RSJB / Dulal, Santosh

    medRxiv

    Abstract: The novel corona virus disease -2019 (COVID-19) pandemic has caused a massive global public health havoc. Recent clinical trials carried out in China has found a promising therapeutic application of chloroquine and hydroxychloroquine for COVID-19. This ... ...

    Abstract The novel corona virus disease -2019 (COVID-19) pandemic has caused a massive global public health havoc. Recent clinical trials carried out in China has found a promising therapeutic application of chloroquine and hydroxychloroquine for COVID-19. This study meticulously evaluated the various dosages of chloroquine and hydroxychloroquine utilized in clinical trials registered in Chinese and US clinical trial registries for the treatment of pneumonia caused by SARS-CoV-2.
    Keywords covid19
    Language English
    Publishing date 2020-03-27
    Publisher Cold Spring Harbor Laboratory Press
    Document type Article ; Online
    DOI 10.1101/2020.03.22.20040964
    Database COVID19

    Kategorien

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