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  1. Article: Molecular characterization & recombination analysis of complete enterovirus-88 isolated from acute flaccid paralysis cases in India.

    Munivenkatappa, Ashok / Nyayanit, Dimpal A / Mohandas, Sreelekshmy / Luwang, Asia / Shete, Anita / Hanumaiah, H / Mourya, Devendra T / Yadav, Pragya D

    The Indian journal of medical research

    2023  Volume 157, Issue 1, Page(s) 41–50

    Abstract: Background & objectives: Focus on non-polio enteroviruses (NPEVs) causing acute flaccid paralysis (AFP) due to myelitis has increased with the containment of the poliovirus. Enterovirus-B88 (EV-B88) has been associated with the AFP cases in Bangladesh, ... ...

    Abstract Background & objectives: Focus on non-polio enteroviruses (NPEVs) causing acute flaccid paralysis (AFP) due to myelitis has increased with the containment of the poliovirus. Enterovirus-B88 (EV-B88) has been associated with the AFP cases in Bangladesh, Ghana, South Africa, Thailand and India. In India, EV-B88 infection was linked to AFP a decade ago; however, to date, no complete genome has been made available. In this study, the complete genome sequence of EV-B88 was identified and reported from two different States (Bihar and Uttar Pradesh) in India using the next-generation sequencing technique.
    Methods: Virus isolation was performed on the three AFP suspected cases as per the WHO-recommended protocol. Samples showing cytopathic effects in the human Rhabdocarcinoma were labelled as NPEVs. Next-generation sequencing was performed on these NPEVs to identify the aetiological agent. The contiguous sequences (contigs) generated were identified, and reference-based mapping was performed.
    Results: EV-B88 sequences retrieved in our study were found to be 83 per cent similar to the EV-B88 isolate from Bangladesh in 2001 (strain: BAN01-10398; Accession number: AY843306.1). Recombination analyses of these samples demonstrate recombination events with sequences from echovirus-18 and echovirus-30.
    Interpretation & conclusions: Recombination events in the EV-B serotypes are known, and this work reconfirms the same for EV-B88 isolates also. This study is a step in increasing the awareness about EV-B88 in India and emphasizes future studies to be conducted in the identification of other types of EV present in India.
    MeSH term(s) Humans ; Enterovirus/genetics ; alpha-Fetoproteins/genetics ; Paralysis ; Phylogeny ; Enterovirus Infections/complications ; India ; Myelitis/complications ; Recombination, Genetic
    Chemical Substances alpha-Fetoproteins
    Language English
    Publishing date 2023-04-11
    Publishing country India
    Document type Journal Article
    ZDB-ID 390883-5
    ISSN 0971-5916 ; 0019-5340
    ISSN 0971-5916 ; 0019-5340
    DOI 10.4103/ijmr.IJMR_1767_19
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Quasispecies analysis of the SARS-CoV-2 from representative clinical samples: A preliminary analysis.

    Nyayanit, Dimpal A / Yadav, Pragya D / Kharde, Rutuja / Shete-Aich, Anita

    The Indian journal of medical research

    2020  Volume 152, Issue 1 & 2, Page(s) 105–107

    MeSH term(s) Betacoronavirus/genetics ; Betacoronavirus/pathogenicity ; COVID-19 ; Coronavirus Infections/epidemiology ; Coronavirus Infections/genetics ; Coronavirus Infections/pathology ; Coronavirus Infections/virology ; Humans ; Pandemics ; Pneumonia, Viral/epidemiology ; Pneumonia, Viral/genetics ; Pneumonia, Viral/pathology ; Pneumonia, Viral/virology ; Quasispecies/genetics ; SARS-CoV-2
    Keywords covid19
    Language English
    Publishing date 2020-08-10
    Publishing country India
    Document type Letter ; Research Support, Non-U.S. Gov't
    ZDB-ID 390883-5
    ISSN 0971-5916 ; 0019-5340
    ISSN 0971-5916 ; 0019-5340
    DOI 10.4103/ijmr.IJMR_2251_20
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Book ; Online: Mathematical model for autoregulated miRNA biogenesis

    Nyayanit, Dimpal A / Gadgil, Chetan J

    2020  

    Abstract: MicroRNAs are small non-coding nucleotide sequences that regulate target protein expression at post-transcriptional levels. Biogenesis of microRNA is a highly regulated multi-step pathway. Regulation of miRNA biogenesis can be caused directly by the ... ...

    Abstract MicroRNAs are small non-coding nucleotide sequences that regulate target protein expression at post-transcriptional levels. Biogenesis of microRNA is a highly regulated multi-step pathway. Regulation of miRNA biogenesis can be caused directly by the components of the biogenesis pathway or indirectly by other regulators. In this study, we have built a detailed mathematical model of microRNA biogenesis to investigate the regulatory role of biogenesis pathway components. We extended a previous model to incorporate Microprocessor regulation of DGCR8 synthesis, exportin-mediated transport to the cytoplasm, and positive auto-regulation catalysed by mature miRNA translocation into the nucleus. Our simulation results lead to three hypotheses (i) Biogenesis is robust to Dicer protein levels at higher Exportin protein levels; (ii) Higher miRNA transcript formation may lead to lower RISC levels: an optimal level of both precursor miRNA and Dicer is required for optimal miRNA formation at lower levels of Exportin protein; and (iii) The positive auto-regulation by mature miRNA translocation into the nucleus can decrease the net functional cytoplasmic miRNA. Wherever possible, we compare these results to experimental observations not used in the model construction or calibration.
    Keywords Quantitative Biology - Molecular Networks
    Subject code 570
    Publishing date 2020-01-30
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Natural Selection Plays an Important Role in Shaping the Codon Usage of Structural Genes of the Viruses Belonging to the

    Nyayanit, Dimpal A / Yadav, Pragya D / Kharde, Rutuja / Cherian, Sarah

    Viruses

    2020  Volume 13, Issue 1

    Abstract: Viruses belonging to ... ...

    Abstract Viruses belonging to the
    MeSH term(s) Algorithms ; Base Composition ; Biological Evolution ; Codon ; Codon Usage ; Coronaviridae/genetics ; Evolution, Molecular ; Humans ; Models, Genetic ; Mutation ; Selection, Genetic ; Viral Structural Proteins/genetics
    Chemical Substances Codon ; Viral Structural Proteins
    Language English
    Publishing date 2020-12-22
    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/v13010003
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: SARS-CoV-2 Delta and delta derivatives impact on neutralization of Covishield recipient sera.

    Sahay, Rima R / Patil, Deepak Y / Sapkal, Gajanan N / Deshpande, Gururaj R / Shete, Anita M / Nyayanit, Dimpal A / Kumar, Sanjay / Yadav, Pragya D

    The Journal of infection

    2022  Volume 84, Issue 4, Page(s) e36–e38

    MeSH term(s) Antibodies, Neutralizing ; COVID-19 ; ChAdOx1 nCoV-19 ; Humans ; SARS-CoV-2 ; Spike Glycoprotein, Coronavirus
    Chemical Substances Antibodies, Neutralizing ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; ChAdOx1 nCoV-19 (B5S3K2V0G8)
    Language English
    Publishing date 2022-02-19
    Publishing country England
    Document type Letter ; Research Support, Non-U.S. Gov't
    ZDB-ID 424417-5
    ISSN 1532-2742 ; 0163-4453
    ISSN (online) 1532-2742
    ISSN 0163-4453
    DOI 10.1016/j.jinf.2022.02.018
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: SARS-CoV-2 & influenza A virus co-infection in an elderly patient with pneumonia.

    Munivenkatappa, Ashok / Yadav, Pragya D / Swetha, K / Jayaswamy, Manjunatha / Nyayanit, Dimpal A / Sahay, Rima Rakeshkumar / Basavaraj, T J

    The Indian journal of medical research

    2021  Volume 153, Issue 1 & 2, Page(s) 190–195

    MeSH term(s) Aged ; COVID-19/complications ; COVID-19/diagnosis ; Coinfection ; Humans ; Influenza A virus ; Influenza, Human/complications ; Influenza, Human/diagnosis ; Pneumonia/complications ; Pneumonia/virology ; SARS-CoV-2
    Language English
    Publishing date 2021-01-12
    Publishing country India
    Document type Case Reports ; Letter ; Research Support, Non-U.S. Gov't
    ZDB-ID 390883-5
    ISSN 0971-5916 ; 0019-5340
    ISSN 0971-5916 ; 0019-5340
    DOI 10.4103/ijmr.IJMR_2711_20
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: Quasispecies analysis of the SARS-CoV-2 from representative clinical samples: A preliminary analysis

    Nyayanit, Dimpal A / Yadav, Pragya D / Kharde, Rutuja / Shete-Aich, Anita

    Indian J Med Res

    Keywords covid19
    Publisher WHO
    Document type Article
    Note WHO #Covidence: #710102
    Database COVID19

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  8. Article: Molecular characterization of varicella zoster virus isolated from clinical samples in India.

    Nyayanit, Dimpal Amol / Chaubal, Gouri / Sahay, Rima / Jain, Shilpi / Shete, Anita / Majumdar, Triparna / Shrivastava, Anish / Yadav, Pragya D

    The Indian journal of medical research

    2022  Volume 154, Issue 4, Page(s) 592–597

    Abstract: Background & objectives: Varicella zoster virus (VZV) strains are classified into six different clades based on the sequencing of its genome. Clades 4 and 5 are reported from India based on the single-nucleotide polymorphism (SNP). Till now, multiple ... ...

    Abstract Background & objectives: Varicella zoster virus (VZV) strains are classified into six different clades based on the sequencing of its genome. Clades 4 and 5 are reported from India based on the single-nucleotide polymorphism (SNP). Till now, multiple clade circulations using partial sequences have been reported from India due to the lack of availability of the full VZV genome sequence. This study conducted a genome sequencing of VZV in India to identify circulating clade.
    Methods: Four clinical samples obtained from symptomatic patients tested positive for VZV by real-time PCR were used. These four samples were preferred to retrieve the genomic VZV sequence using the next-generation sequencing method. A reference-based assembly method was used to retrieve the genome of VZV, which was further analyzed.
    Results: At the least, 98 per cent of the whole-genome sequences were recovered from the four samples. The VZV sequences obtained in this study formed a separate monophyletic branch with clade 5, indicating it to be evolved from a distinct ancestor. The nucleotide-based analysis revealed 13 different SNP mutations and one multiple nucleotide variation in the VZV sequences when compared to one of the clade 5 genomes having accession number: DQ457052.1.
    Interpretation & conclusions: The present study described approximately 98 per cent of the genome sequence of VZV from India. The availability of these genomic sequences will lead to enrichment in the clinical genomic data set from India. The available data would help in the development of diagnostic methods along with evolutionary analysis. We hypothesize the existence of a new sub-clade that belongs to clade 5 and propose further experiments to confirm these results.
    MeSH term(s) Humans ; Genome, Viral/genetics ; Genotype ; Herpes Zoster/epidemiology ; Herpes Zoster/genetics ; Herpesvirus 3, Human/genetics ; Phylogeny ; Polymorphism, Single Nucleotide
    Language English
    Publishing date 2022-04-18
    Publishing country India
    Document type Journal Article
    ZDB-ID 390883-5
    ISSN 0971-5916 ; 0019-5340
    ISSN 0971-5916 ; 0019-5340
    DOI 10.4103/ijmr.IJMR_434_19
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Quasispecies analysis of the SARS-CoV-2 from representative clinical samples

    Dimpal A Nyayanit / Pragya D Yadav / Rutuja Kharde / Anita Shete-Aich

    Indian Journal of Medical Research, Vol 152, Iss 1, Pp 105-

    A preliminary analysis

    2020  Volume 107

    Keywords Medicine ; R ; covid19
    Language English
    Publishing date 2020-01-01T00:00:00Z
    Publisher Wolters Kluwer Medknow Publications
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: Protective Immunity of the Primary SARS-CoV-2 Infection Reduces Disease Severity Post Re-Infection with Delta Variants in Syrian Hamsters.

    Mohandas, Sreelekshmy / Yadav, Pragya D / Shete, Anita / Nyayanit, Dimpal / Jain, Rajlaxmi / Sapkal, Gajanan / Mote, Chandrashekhar

    Viruses

    2022  Volume 14, Issue 3

    Abstract: The Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) Delta variant has evolved to become the dominant SARS-CoV-2 lineage with multiple sub-lineages and there are also reports of re-infections caused by this variant. We studied the disease ... ...

    Abstract The Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) Delta variant has evolved to become the dominant SARS-CoV-2 lineage with multiple sub-lineages and there are also reports of re-infections caused by this variant. We studied the disease characteristics induced by the Delta AY.1 variant and compared it with the Delta and B.1 variants in Syrian hamsters. We also assessed the potential of re-infection by these variants in Coronavirus disease 2019 recovered hamsters 3 months after initial infection. The variants produced disease characterized by high viral load in the respiratory tract and interstitial pneumonia. The Delta AY.1 variant produced mild disease in the hamster model and did not show any evidence of neutralization resistance due to the presence of the K417N mutation, as speculated. Re-infection with a high virus dose of the Delta and B.1 variants 3 months after B.1 variant infection resulted in reduced virus shedding, disease severity and increased neutralizing antibody levels in the re-infected hamsters. The reduction in viral load and lung disease after re-infection with the Delta AY.1 variant was not marked. Upper respiratory tract viral RNA loads remained similar after re-infection in all the groups. The present findings show that prior infection could not produce sterilizing immunity but that it can broaden the neutralizing response and reduce disease severity in case of reinfection.
    MeSH term(s) Animals ; COVID-19 ; Cricetinae ; Mesocricetus ; Reinfection ; SARS-CoV-2/genetics ; Severity of Illness Index ; Trachea
    Language English
    Publishing date 2022-03-13
    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/v14030596
    Database MEDical Literature Analysis and Retrieval System OnLINE

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