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  1. Article ; Online: Reply to: Population genetic considerations regarding the interpretation of within-patient SARS-CoV-2 polymorphism data.

    Nelson, Chase W / Poon, Leo L M / Gu, Haogao

    Nature communications

    2024  Volume 15, Issue 1, Page(s) 3239

    MeSH term(s) Humans ; SARS-CoV-2/genetics ; COVID-19 ; Polymorphism, Genetic ; Genetics, Population
    Language English
    Publishing date 2024-04-16
    Publishing country England
    Document type Letter
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-024-46262-3
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Human papillomavirus genomics: Understanding carcinogenicity.

    Nelson, Chase W / Mirabello, Lisa

    Tumour virus research

    2023  Volume 15, Page(s) 200258

    Abstract: Human papillomavirus (HPV) causes virtually all cervical cancers and many cancers at other anatomical sites in both men and women. However, only 12 of 448 known HPV types are currently classified as carcinogens, and even the most carcinogenic type - ... ...

    Abstract Human papillomavirus (HPV) causes virtually all cervical cancers and many cancers at other anatomical sites in both men and women. However, only 12 of 448 known HPV types are currently classified as carcinogens, and even the most carcinogenic type - HPV16 - only rarely leads to cancer. HPV is therefore necessary but insufficient for cervical cancer, with other contributing factors including host and viral genetics. Over the last decade, HPV whole genome sequencing has established that even fine-scale within-type HPV variation influences precancer/cancer risks, and that these risks vary by histology and host race/ethnicity. In this review, we place these findings in the context of the HPV life cycle and evolution at various levels of viral diversity: between-type, within-type, and within-host. We also discuss key concepts necessary for interpreting HPV genomic data, including features of the viral genome; events leading to carcinogenesis; the role of APOBEC3 in HPV infection and evolution; and methodologies that use deep (high-coverage) sequencing to characterize within-host variation, as opposed to relying on a single representative (consensus) sequence. Given the continued high burden of HPV-associated cancers, understanding HPV carcinogenicity remains important for better understanding, preventing, and treating cancers attributable to infection.
    MeSH term(s) Female ; Humans ; Human Papillomavirus Viruses ; Papillomavirus Infections/complications ; Uterine Cervical Neoplasms/pathology ; Genomics ; Human papillomavirus 16/genetics ; Carcinogenesis/genetics
    Language English
    Publishing date 2023-02-20
    Publishing country Netherlands
    Document type Journal Article ; Review ; Research Support, U.S. Gov't, Non-P.H.S.
    ISSN 2666-6790
    ISSN (online) 2666-6790
    DOI 10.1016/j.tvr.2023.200258
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: COVID-19: time for WHO to reconsider its stance towards Taiwan.

    Nelson, Chase W

    Nature

    2020  Volume 579, Issue 7798, Page(s) 193

    MeSH term(s) COVID-19 ; Coronavirus Infections/epidemiology ; Coronavirus Infections/prevention & control ; Delivery of Health Care/standards ; Humans ; Pneumonia, Viral/epidemiology ; Pneumonia, Viral/prevention & control ; Politics ; Taiwan ; World Health Organization
    Keywords covid19
    Language English
    Publishing date 2020-03-11
    Publishing country England
    Document type Letter
    ZDB-ID 120714-3
    ISSN 1476-4687 ; 0028-0836
    ISSN (online) 1476-4687
    ISSN 0028-0836
    DOI 10.1038/d41586-020-00693-2
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 26: 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)
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  4. Article ; Online: Human papillomavirus genomics: Understanding carcinogenicity

    Nelson, Chase W. / Mirabello, Lisa

    Tumour Virus Research. 2023 June, v. 15 p.200258-

    2023  

    Abstract: Human papillomavirus (HPV) causes virtually all cervical cancers and many cancers at other anatomical sites in both men and women. However, only 12 of 448 known HPV types are currently classified as carcinogens, and even the most carcinogenic type - ... ...

    Abstract Human papillomavirus (HPV) causes virtually all cervical cancers and many cancers at other anatomical sites in both men and women. However, only 12 of 448 known HPV types are currently classified as carcinogens, and even the most carcinogenic type - HPV16 - only rarely leads to cancer. HPV is therefore necessary but insufficient for cervical cancer, with other contributing factors including host and viral genetics. Over the last decade, HPV whole genome sequencing has established that even fine-scale within-type HPV variation influences precancer/cancer risks, and that these risks vary by histology and host race/ethnicity. In this review, we place these findings in the context of the HPV life cycle and evolution at various levels of viral diversity: between-type, within-type, and within-host. We also discuss key concepts necessary for interpreting HPV genomic data, including features of the viral genome; events leading to carcinogenesis; the role of APOBEC3 in HPV infection and evolution; and methodologies that use deep (high-coverage) sequencing to characterize within-host variation, as opposed to relying on a single representative (consensus) sequence. Given the continued high burden of HPV-associated cancers, understanding HPV carcinogenicity remains important for better understanding, preventing, and treating cancers attributable to infection.
    Keywords Papillomaviridae ; carcinogenesis ; carcinogenicity ; evolution ; genomics ; histology ; humans ; microbial genetics ; nationalities and ethnic groups ; research ; uterine cervical neoplasms ; viral genome ; viruses ; Cervical cancer ; HPV16 ; HPV evolution ; HPV genomics ; Next-generation sequencing (NGS) ; Within-host (intrahost) diversity
    Language English
    Dates of publication 2023-06
    Publishing place Elsevier B.V.
    Document type Article ; Online
    Note Use and reproduction
    ISSN 2666-6790
    DOI 10.1016/j.tvr.2023.200258
    Database NAL-Catalogue (AGRICOLA)

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  7. Article ; Online: COVID-19

    Nelson, Chase W.

    Nature

    time for WHO to reconsider its stance towards Taiwan

    2020  Volume 579, Issue 7798, Page(s) 193–193

    Keywords Multidisciplinary ; covid19
    Language English
    Publisher Springer Science and Business Media LLC
    Publishing country us
    Document type Article ; Online
    ZDB-ID 120714-3
    ISSN 1476-4687 ; 0028-0836
    ISSN (online) 1476-4687
    ISSN 0028-0836
    DOI 10.1038/d41586-020-00693-2
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 26: 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)
    Zs.MG 9: Show issues
    Zs.MO 244: Show issues

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  8. Article ; Online: SARS-CoV-2 ORF3d Supplementary Material

    Nelson, Chase W.

    2020  

    Abstract: Supplementary data for study on SARS-CoV-2 ORF3d, available on bioRxiv. Software and example data are freely available at https://github.com/chasewnelson/SARS-CoV-2-ORF3d. ... https://github.com/chasewnelson/SARS-CoV-2- ... ...

    Abstract Supplementary data for study on SARS-CoV-2 ORF3d, available on bioRxiv. Software and example data are freely available at https://github.com/chasewnelson/SARS-CoV-2-ORF3d.

    https://github.com/chasewnelson/SARS-CoV-2-ORF3d
    Keywords Genome annotation ; Natural selection ; ORF3d ; Overlapping genes ; Pandemic ; SARS-CoV-2 ; covid19
    Language English
    Publishing date 2020-09-27
    Publishing country eu
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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  9. Article ; Online: Remembering Austin L. Hughes.

    Nelson, Chase W

    Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases

    2016  Volume 40, Page(s) 262–265

    Language English
    Publishing date 2016
    Publishing country Netherlands
    Document type Letter ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2037068-4
    ISSN 1567-7257 ; 1567-1348
    ISSN (online) 1567-7257
    ISSN 1567-1348
    DOI 10.1016/j.meegid.2016.02.030
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 5645: Show issues Location:
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    ab Jg. 2022: Lesesaal (EG)

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  10. Article: Improved detection of low-frequency within-host variants from deep sequencing: A case study with human papillomavirus.

    Mishra, Sambit K / Nelson, Chase W / Zhu, Bin / Pinheiro, Maisa / Lee, Hyo Jung / Dean, Michael / Burdett, Laurie / Yeager, Meredith / Mirabello, Lisa

    Virus evolution

    2024  Volume 10, Issue 1, Page(s) veae013

    Abstract: High-coverage sequencing allows the study of variants occurring at low frequencies within samples, but is susceptible to false-positives caused by sequencing error. Ion Torrent has a very low single nucleotide variant (SNV) error rate and has been ... ...

    Abstract High-coverage sequencing allows the study of variants occurring at low frequencies within samples, but is susceptible to false-positives caused by sequencing error. Ion Torrent has a very low single nucleotide variant (SNV) error rate and has been employed for the majority of human papillomavirus (HPV) whole genome sequences. However, benchmarking of intrahost SNVs (iSNVs) has been challenging, partly due to limitations imposed by the HPV life cycle. We address this problem by deep sequencing three replicates for each of 31 samples of HPV type 18 (HPV18). Errors, defined as iSNVs observed in only one of three replicates, are dominated by C→T (G→A) changes, independently of trinucleotide context. True iSNVs, defined as those observed in all three replicates, instead show a more diverse SNV type distribution, with particularly elevated C→T rates in CCG context (CCG→CTG; CGG→CAG) and C→A rates in ACG context (ACG→AAG; CGT→CTT). Characterization of true iSNVs allowed us to develop two methods for detecting true variants: (1) VCFgenie, a dynamic binomial filtering tool which uses each variant's allele count and coverage instead of fixed frequency cut-offs; and (2) a machine learning binary classifier which trains eXtreme Gradient Boosting models on variant features such as quality and trinucleotide context. Each approach outperforms fixed-cut-off filtering of iSNVs, and performance is enhanced when both are used together. Our results provide improved methods for identifying true iSNVs in within-host applications across sequencing platforms, specifically using HPV18 as a case study.
    Language English
    Publishing date 2024-02-07
    Publishing country England
    Document type Journal Article
    ZDB-ID 2818949-8
    ISSN 2057-1577
    ISSN 2057-1577
    DOI 10.1093/ve/veae013
    Database MEDical Literature Analysis and Retrieval System OnLINE

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