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  1. Article ; Online: Primary Infection May Be an Underlying Factor Contributing to Lethal Hemorrhagic Disease Caused by Elephant Endotheliotropic Herpesvirus 3 in African Elephants (

    Pursell, Taylor / Spencer Clinton, Jennifer L / Tan, Jie / Peng, Rongsheng / Qin, Xiang / Doddapaneni, Harshavardhan / Menon, Vipin / Momin, Zeineen / Kottapalli, Kavya / Howard, Lauren / Latimer, Erin / Heaggans, Sarah / Hayward, Gary S / Ling, Paul D

    Microbiology spectrum

    2021  Volume 9, Issue 2, Page(s) e0098321

    Abstract: Distinct but related species of elephant endotheliotropic herpesviruses (EEHVs) circulate within Asian and African elephant populations. Primary infection with EEHVs endemic among Asian elephants can cause clinical illness and lethal EEHV hemorrhagic ... ...

    Abstract Distinct but related species of elephant endotheliotropic herpesviruses (EEHVs) circulate within Asian and African elephant populations. Primary infection with EEHVs endemic among Asian elephants can cause clinical illness and lethal EEHV hemorrhagic disease (EEHV-HD). The degree to which this occurs among African elephants has not been fully established. Recent cases of EEHV-HD caused by the EEHV3 species in African elephants housed in North American zoos has heightened concern about the susceptibility of this elephant species to EEHV-HD. In this study, we utilize the luciferase immunoprecipitation system (LIPS) to generate a serological assay specific for EEHV3 in African elephants by detecting antibodies against the EEHV3 E34 protein. The results showed that the majority of tested elephants from four separate and genetically unrelated herds, including five elephants that survived clinical illness associated with EEHV3, were positive for prior infection with EEHV3. However, African elephants who succumbed to EEHV3-HD were seronegative for EEHV3 prior to lethal infection. This supports the hypothesis that fatal EEHV-HD caused by EEHV3 is associated with primary infection rather than reactivation of latent virus. Lastly, we observed that African elephants, like Asian elephants, acquire abundant anti-EEHV antibodies prenatally and that anti-EEHV3 specific antibodies were either never detected or declined to undetectable levels in those animals that died from lethal disease following EEHV3 infection.
    MeSH term(s) Animals ; Animals, Zoo/virology ; Antibodies, Viral/blood ; Elephants/virology ; Female ; Hemorrhagic Disorders/diagnosis ; Hemorrhagic Disorders/veterinary ; Hemorrhagic Disorders/virology ; Herpesvirus 3, Equid/immunology ; Herpesvirus 3, Equid/pathogenicity ; Male ; Serologic Tests ; Viral Zoonoses/diagnosis ; Viral Zoonoses/mortality ; Viral Zoonoses/pathology
    Chemical Substances Antibodies, Viral
    Language English
    Publishing date 2021-10-20
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2807133-5
    ISSN 2165-0497 ; 2165-0497
    ISSN (online) 2165-0497
    ISSN 2165-0497
    DOI 10.1128/Spectrum.00983-21
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Fully resolved assembly of Cryptosporidium parvum.

    Menon, Vipin K / Okhuysen, Pablo C / Chappell, Cynthia L / Mahmoud, Medhat / Meng, Qingchang / Doddapaneni, Harsha / Vee, Vanesa / Han, Yi / Salvi, Sejal / Bhamidipati, Sravya / Kottapalli, Kavya / Weissenberger, George / Shen, Hua / Ross, Matthew C / Hoffman, Kristi L / Cregeen, Sara Javornik / Muzny, Donna M / Metcalf, Ginger A / Gibbs, Richard A /
    Petrosino, Joseph F / Sedlazeck, Fritz J

    GigaScience

    2022  Volume 11

    Abstract: Background: Cryptosporidium parvum is an apicomplexan parasite commonly found across many host species with a global infection prevalence in human populations of 7.6%. Understanding its diversity and genomic makeup can help in fighting established ... ...

    Abstract Background: Cryptosporidium parvum is an apicomplexan parasite commonly found across many host species with a global infection prevalence in human populations of 7.6%. Understanding its diversity and genomic makeup can help in fighting established infections and prohibiting further transmission. The basis of every genomic study is a high-quality reference genome that has continuity and completeness, thus enabling comprehensive comparative studies.
    Findings: Here, we provide a highly accurate and complete reference genome of Cryptosporidium parvum. The assembly is based on Oxford Nanopore reads and was improved using Illumina reads for error correction. We also outline how to evaluate and choose from different assembly methods based on 2 main approaches that can be applied to other Cryptosporidium species. The assembly encompasses 8 chromosomes and includes 13 telomeres that were resolved. Overall, the assembly shows a high completion rate with 98.4% single-copy BUSCO genes.
    Conclusions: This high-quality reference genome of a zoonotic IIaA17G2R1 C. parvum subtype isolate provides the basis for subsequent comparative genomic studies across the Cryptosporidium clade. This will enable improved understanding of diversity, functional, and association studies.
    MeSH term(s) Cryptosporidiosis/epidemiology ; Cryptosporidiosis/genetics ; Cryptosporidiosis/parasitology ; Cryptosporidium/genetics ; Cryptosporidium parvum/genetics ; Genome ; Genomics/methods ; Humans
    Language English
    Publishing date 2022-02-15
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2708999-X
    ISSN 2047-217X ; 2047-217X
    ISSN (online) 2047-217X
    ISSN 2047-217X
    DOI 10.1093/gigascience/giac010
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Oligonucleotide capture sequencing of the SARS-CoV-2 genome and subgenomic fragments from COVID-19 individuals.

    Doddapaneni, Harsha / Cregeen, Sara Javornik / Sucgang, Richard / Meng, Qingchang / Qin, Xiang / Avadhanula, Vasanthi / Chao, Hsu / Menon, Vipin / Nicholson, Erin / Henke, David / Piedra, Felipe-Andres / Rajan, Anubama / Momin, Zeineen / Kottapalli, Kavya / Hoffman, Kristi L / Sedlazeck, Fritz J / Metcalf, Ginger / Piedra, Pedro A / Muzny, Donna M /
    Petrosino, Joseph F / Gibbs, Richard A

    PloS one

    2021  Volume 16, Issue 8, Page(s) e0244468

    Abstract: The newly emerged and rapidly spreading SARS-CoV-2 causes coronavirus disease 2019 (COVID-19). To facilitate a deeper understanding of the viral biology we developed a capture sequencing methodology to generate SARS-CoV-2 genomic and transcriptome ... ...

    Abstract The newly emerged and rapidly spreading SARS-CoV-2 causes coronavirus disease 2019 (COVID-19). To facilitate a deeper understanding of the viral biology we developed a capture sequencing methodology to generate SARS-CoV-2 genomic and transcriptome sequences from infected patients. We utilized an oligonucleotide probe-set representing the full-length genome to obtain both genomic and transcriptome (subgenomic open reading frames [ORFs]) sequences from 45 SARS-CoV-2 clinical samples with varying viral titers. For samples with higher viral loads (cycle threshold value under 33, based on the CDC qPCR assay) complete genomes were generated. Analysis of junction reads revealed regions of differential transcriptional activity among samples. Mixed allelic frequencies along the 20kb ORF1ab gene in one sample, suggested the presence of a defective viral RNA species subpopulation maintained in mixture with functional RNA in one sample. The associated workflow is straightforward, and hybridization-based capture offers an effective and scalable approach for sequencing SARS-CoV-2 from patient samples.
    MeSH term(s) COVID-19/pathology ; COVID-19/virology ; DNA, Complementary/chemistry ; DNA, Complementary/metabolism ; Gene Frequency ; Genetic Variation ; Genome, Viral ; Humans ; Open Reading Frames/genetics ; RNA, Viral/genetics ; RNA, Viral/metabolism ; Real-Time Polymerase Chain Reaction ; SARS-CoV-2/genetics ; SARS-CoV-2/isolation & purification ; Sequence Analysis, DNA/methods ; Viral Load
    Chemical Substances DNA, Complementary ; RNA, Viral
    Language English
    Publishing date 2021-08-25
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0244468
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Oligonucleotide Capture Sequencing of the SARS-CoV-2 Genome and Subgenomic Fragments from COVID-19 Individuals.

    Doddapaneni, Harsha / Cregeen, Sara Javornik / Sucgang, Richard / Meng, Qingchang / Qin, Xiang / Avadhanula, Vasanthi / Chao, Hsu / Menon, Vipin / Nicholson, Erin / Henke, David / Piedra, Felipe-Andres / Rajan, Anubama / Momin, Zeineen / Kottapalli, Kavya / Hoffman, Kristi L / Sedlazeck, Fritz J / Metcalf, Ginger / Piedra, Pedro A / Muzny, Donna M /
    Petrosino, Joseph F / Gibbs, Richard A

    bioRxiv : the preprint server for biology

    2020  

    Abstract: The newly emerged and rapidly spreading SARS-CoV-2 causes coronavirus disease 2019 (COVID-19). To facilitate a deeper understanding of the viral biology we developed a capture sequencing methodology to generate SARS-CoV-2 genomic and transcriptome ... ...

    Abstract The newly emerged and rapidly spreading SARS-CoV-2 causes coronavirus disease 2019 (COVID-19). To facilitate a deeper understanding of the viral biology we developed a capture sequencing methodology to generate SARS-CoV-2 genomic and transcriptome sequences from infected patients. We utilized an oligonucleotide probe-set representing the full-length genome to obtain both genomic and transcriptome (subgenomic open reading frames [ORFs]) sequences from 45 SARS-CoV-2 clinical samples with varying viral titers. For samples with higher viral loads (cycle threshold value under 33, based on the CDC qPCR assay) complete genomes were generated. Analysis of junction reads revealed regions of differential transcriptional activity and provided evidence of expression of ORF10. Heterogeneous allelic frequencies along the 20kb ORF1ab gene suggested the presence of a defective interfering viral RNA species subpopulation in one sample. The associated workflow is straightforward, and hybridization-based capture offers an effective and scalable approach for sequencing SARS-CoV-2 from patient samples.
    Language English
    Publishing date 2020-12-11
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2020.12.11.421057
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Oligonucleotide capture sequencing of the SARS-CoV-2 genome and subgenomic fragments from COVID-19 individuals.

    Doddapaneni, Harsha / Cregeen, Sara Javornik / Sucgang, Richard / Meng, Qingchang / Qin, Xiang / Avadhanula, Vasanthi / Chao, Hsu / Menon, Vipin / Nicholson, Erin / Henke, David / Piedra, Felipe-Andres / Rajan, Anubama / Momin, Zeineen / Kottapalli, Kavya / Hoffman, Kristi L / Sedlazeck, Fritz J / Metcalf, Ginger / Piedra, Pedro A / Muzny, Donna M /
    Petrosino, Joseph F / Gibbs, Richard A

    bioRxiv : the preprint server for biology

    2020  

    Abstract: The newly emerged and rapidly spreading SARS-CoV-2 causes coronavirus disease 2019 (COVID-19). To facilitate a deeper understanding of the viral biology we developed a capture sequencing methodology to generate SARS-CoV-2 genomic and transcriptome ... ...

    Abstract The newly emerged and rapidly spreading SARS-CoV-2 causes coronavirus disease 2019 (COVID-19). To facilitate a deeper understanding of the viral biology we developed a capture sequencing methodology to generate SARS-CoV-2 genomic and transcriptome sequences from infected patients. We utilized an oligonucleotide probe-set representing the full-length genome to obtain both genomic and transcriptome (subgenomic open reading frames [ORFs]) sequences from 45 SARS-CoV-2 clinical samples with varying viral titers. For samples with higher viral loads (cycle threshold value under 33, based on the CDC qPCR assay) complete genomes were generated. Analysis of junction reads revealed regions of differential transcriptional activity and provided evidence of expression of ORF10. Heterogeneous allelic frequencies along the 20kb ORF1ab gene suggested the presence of a defective interfering viral RNA species subpopulation in one sample. The associated workflow is straightforward, and hybridization-based capture offers an effective and scalable approach for sequencing SARS-CoV-2 from patient samples.
    Keywords covid19
    Language English
    Publishing date 2020-07-27
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2020.07.27.223495
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Structural variation across 138,134 samples in the TOPMed consortium.

    Jun, Goo / English, Adam C / Metcalf, Ginger A / Yang, Jianzhi / Chaisson, Mark Jp / Pankratz, Nathan / Menon, Vipin K / Salerno, William J / Krasheninina, Olga / Smith, Albert V / Lane, John A / Blackwell, Tom / Kang, Hyun Min / Salvi, Sejal / Meng, Qingchang / Shen, Hua / Pasham, Divya / Bhamidipati, Sravya / Kottapalli, Kavya /
    Arnett, Donna K / Ashley-Koch, Allison / Auer, Paul L / Beutel, Kathleen M / Bis, Joshua C / Blangero, John / Bowden, Donald W / Brody, Jennifer A / Cade, Brian E / Chen, Yii-Der Ida / Cho, Michael H / Curran, Joanne E / Fornage, Myriam / Freedman, Barry I / Fingerlin, Tasha / Gelb, Bruce D / Hou, Lifang / Hung, Yi-Jen / Kane, John P / Kaplan, Robert / Kim, Wonji / Loos, Ruth J F / Marcus, Gregory M / Mathias, Rasika A / McGarvey, Stephen T / Montgomery, Courtney / Naseri, Take / Nouraie, S Mehdi / Preuss, Michael H / Palmer, Nicholette D / Peyser, Patricia A / Raffield, Laura M / Ratan, Aakrosh / Redline, Susan / Reupena, Sefuiva / Rotter, Jerome I / Rich, Stephen S / Rienstra, Michiel / Ruczinski, Ingo / Sankaran, Vijay G / Schwartz, David A / Seidman, Christine E / Seidman, Jonathan G / Silverman, Edwin K / Smith, Jennifer A / Stilp, Adrienne / Taylor, Kent D / Telen, Marilyn J / Weiss, Scott T / Williams, L Keoki / Wu, Baojun / Yanek, Lisa R / Zhang, Yingze / Lasky-Su, Jessica / Gingras, Marie Claude / Dutcher, Susan K / Eichler, Evan E / Gabriel, Stacey / Germer, Soren / Kim, Ryan / Viaud-Martinez, Karine A / Nickerson, Deborah A / Luo, James / Reiner, Alex / Gibbs, Richard A / Boerwinkle, Eric / Abecasis, Goncalo / Sedlazeck, Fritz J

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Ever larger Structural Variant (SV) catalogs highlighting the diversity within and between populations help researchers better understand the links between SVs and disease. The identification of SVs from DNA sequence data is non-trivial and requires a ... ...

    Abstract Ever larger Structural Variant (SV) catalogs highlighting the diversity within and between populations help researchers better understand the links between SVs and disease. The identification of SVs from DNA sequence data is non-trivial and requires a balance between comprehensiveness and precision. Here we present a catalog of 355,667 SVs (59.34% novel) across autosomes and the X chromosome (50bp+) from 138,134 individuals in the diverse TOPMed consortium. We describe our methodologies for SV inference resulting in high variant quality and >90% allele concordance compared to long-read de-novo assemblies of well-characterized control samples. We demonstrate utility through significant associations between SVs and important various cardio-metabolic and hemotologic traits. We have identified 690 SV hotspots and deserts and those that potentially impact the regulation of medically relevant genes. This catalog characterizes SVs across multiple populations and will serve as a valuable tool to understand the impact of SV on disease development and progression.
    Language English
    Publishing date 2023-01-25
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.01.25.525428
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: Structural variation across 138,134 samples in the TOPMed consortium.

    Jun, Goo / English, Adam C / Metcalf, Ginger A / Yang, Jianzhi / Chaisson, Mark Jp / Pankratz, Nathan / Menon, Vipin K / Salerno, William J / Krasheninina, Olga / Smith, Albert V / Lane, John A / Blackwell, Tom / Kang, Hyun Min / Salvi, Sejal / Meng, Qingchang / Shen, Hua / Pasham, Divya / Bhamidipati, Sravya / Kottapalli, Kavya /
    Arnett, Donna K / Ashley-Koch, Allison / Auer, Paul L / Beutel, Kathleen M / Bis, Joshua C / Blangero, John / Bowden, Donald W / Brody, Jennifer A / Cade, Brian E / Chen, Yii-Der Ida / Cho, Michael H / Curran, Joanne E / Fornage, Myriam / Freedman, Barry I / Fingerlin, Tasha / Gelb, Bruce D / Hou, Lifang / Hung, Yi-Jen / Kane, John P / Kaplan, Robert / Kim, Wonji / Loos, Ruth J F / Marcus, Gregory M / Mathias, Rasika A / McGarvey, Stephen T / Montgomery, Courtney / Naseri, Take / Nouraie, S Mehdi / Preuss, Michael H / Palmer, Nicholette D / Peyser, Patricia A / Raffield, Laura M / Ratan, Aakrosh / Redline, Susan / Reupena, Sefuiva / Rotter, Jerome I / Rich, Stephen S / Rienstra, Michiel / Ruczinski, Ingo / Sankaran, Vijay G / Schwartz, David A / Seidman, Christine E / Seidman, Jonathan G / Silverman, Edwin K / Smith, Jennifer A / Stilp, Adrienne / Taylor, Kent D / Telen, Marilyn J / Weiss, Scott T / Williams, L Keoki / Wu, Baojun / Yanek, Lisa R / Zhang, Yingze / Lasky-Su, Jessica / Gingras, Marie Claude / Dutcher, Susan K / Eichler, Evan E / Gabriel, Stacey / Germer, Soren / Kim, Ryan / Viaud-Martinez, Karine A / Nickerson, Deborah A / Luo, James / Reiner, Alex / Gibbs, Richard A / Boerwinkle, Eric / Abecasis, Goncalo / Sedlazeck, Fritz J

    Research square

    2023  

    Abstract: Ever larger Structural Variant (SV) catalogs highlighting the diversity within and between populations help researchers better understand the links between SVs and disease. The identification of SVs from DNA sequence data is non-trivial and requires a ... ...

    Abstract Ever larger Structural Variant (SV) catalogs highlighting the diversity within and between populations help researchers better understand the links between SVs and disease. The identification of SVs from DNA sequence data is non-trivial and requires a balance between comprehensiveness and precision. Here we present a catalog of 355,667 SVs (59.34% novel) across autosomes and the X chromosome (50bp+) from 138,134 individuals in the diverse TOPMed consortium. We describe our methodologies for SV inference resulting in high variant quality and >90% allele concordance compared to long-read de-novo assemblies of well-characterized control samples. We demonstrate utility through significant associations between SVs and important various cardio-metabolic and hematologic traits. We have identified 690 SV hotspots and deserts and those that potentially impact the regulation of medically relevant genes. This catalog characterizes SVs across multiple populations and will serve as a valuable tool to understand the impact of SV on disease development and progression.
    Language English
    Publishing date 2023-02-03
    Publishing country United States
    Document type Preprint
    DOI 10.21203/rs.3.rs-2515453/v1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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