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  1. Article ; Online: Translating virus evolution into epidemiology.

    Grubaugh, Nathan D

    Cell host & microbe

    2022  Volume 30, Issue 4, Page(s) 444–448

    Abstract: 6 years ago, I published a Cell Host and Microbe paper that described randomization of virus genetic populations during mosquito infection. From within the evolutionary chaos, however, there is an order that can reveal a virus' past. Using these insights, ...

    Abstract 6 years ago, I published a Cell Host and Microbe paper that described randomization of virus genetic populations during mosquito infection. From within the evolutionary chaos, however, there is an order that can reveal a virus' past. Using these insights, I forged a career harnessing virus evolution to understand epidemiological patterns.
    MeSH term(s) Animals ; DNA Viruses ; Evolution, Molecular ; Genetics, Population ; Viruses/genetics
    Language English
    Publishing date 2022-04-07
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2278004-X
    ISSN 1934-6069 ; 1931-3128
    ISSN (online) 1934-6069
    ISSN 1931-3128
    DOI 10.1016/j.chom.2022.03.006
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Resurgence of Dengue in the Era of Genomic Surveillance and Vaccines.

    Huits, Ralph / Grubaugh, Nathan D / Libman, Michael / Hamer, Davidson H

    Annals of internal medicine

    2024  

    Language English
    Publishing date 2024-03-19
    Publishing country United States
    Document type Editorial
    ZDB-ID 336-0
    ISSN 1539-3704 ; 0003-4819
    ISSN (online) 1539-3704
    ISSN 0003-4819
    DOI 10.7326/M24-0496
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  3. Article ; Online: Of variants and vaccines.

    Grubaugh, Nathan D / Cobey, Sarah

    Cell

    2021  Volume 184, Issue 26, Page(s) 6222–6223

    Abstract: In this issue of Cell, Bushman et al. show how more transmissible variants, even if they do not escape immunity, can be strongly selected during the early pandemic. This explains the dynamics of past SARS-CoV-2 variants, but as immunity increases, it is ... ...

    Abstract In this issue of Cell, Bushman et al. show how more transmissible variants, even if they do not escape immunity, can be strongly selected during the early pandemic. This explains the dynamics of past SARS-CoV-2 variants, but as immunity increases, it is difficult to predict what will emerge next.
    MeSH term(s) COVID-19 ; COVID-19 Vaccines ; Humans ; SARS-CoV-2 ; Vaccines
    Chemical Substances COVID-19 Vaccines ; Vaccines
    Language English
    Publishing date 2021-12-22
    Publishing country United States
    Document type Journal Article ; Comment
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/j.cell.2021.11.013
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  4. Article: Of variants and vaccines

    Grubaugh, Nathan D. / Cobey, Sarah

    Cell. 2021 Dec. 22, v. 184, no. 26

    2021  

    Abstract: In this issue of Cell, Bushman et al. show how more transmissible variants, even if they do not escape immunity, can be strongly selected during the early pandemic. This explains the dynamics of past SARS-CoV-2 variants, but as immunity increases, it is ... ...

    Abstract In this issue of Cell, Bushman et al. show how more transmissible variants, even if they do not escape immunity, can be strongly selected during the early pandemic. This explains the dynamics of past SARS-CoV-2 variants, but as immunity increases, it is difficult to predict what will emerge next.
    Keywords Severe acute respiratory syndrome coronavirus 2 ; immunity ; pandemic
    Language English
    Dates of publication 2021-1222
    Size p. 6222-6223.
    Publishing place Elsevier Inc.
    Document type Article
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/j.cell.2021.11.013
    Database NAL-Catalogue (AGRICOLA)

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  5. Article ; Online: Leveraging insect-specific viruses to elucidate mosquito population structure and dynamics.

    Hollingsworth, Brandon D / Grubaugh, Nathan D / Lazzaro, Brian P / Murdock, Courtney C

    PLoS pathogens

    2023  Volume 19, Issue 8, Page(s) e1011588

    Abstract: Several aspects of mosquito ecology that are important for vectored disease transmission and control have been difficult to measure at epidemiologically important scales in the field. In particular, the ability to describe mosquito population structure ... ...

    Abstract Several aspects of mosquito ecology that are important for vectored disease transmission and control have been difficult to measure at epidemiologically important scales in the field. In particular, the ability to describe mosquito population structure and movement rates has been hindered by difficulty in quantifying fine-scale genetic variation among populations. The mosquito virome represents a possible avenue for quantifying population structure and movement rates across multiple spatial scales. Mosquito viromes contain a diversity of viruses, including several insect-specific viruses (ISVs) and "core" viruses that have high prevalence across populations. To date, virome studies have focused on viral discovery and have only recently begun examining viral ecology. While nonpathogenic ISVs may be of little public health relevance themselves, they provide a possible route for quantifying mosquito population structure and dynamics. For example, vertically transmitted viruses could behave as a rapidly evolving extension of the host's genome. It should be possible to apply established analytical methods to appropriate viral phylogenies and incidence data to generate novel approaches for estimating mosquito population structure and dispersal over epidemiologically relevant timescales. By studying the virome through the lens of spatial and genomic epidemiology, it may be possible to investigate otherwise cryptic aspects of mosquito ecology. A better understanding of mosquito population structure and dynamics are key for understanding mosquito-borne disease ecology and methods based on ISVs could provide a powerful tool for informing mosquito control programs.
    MeSH term(s) Animals ; Insect Viruses ; Ecology ; Genetic Vectors ; Genomics ; Insecta
    Language English
    Publishing date 2023-08-31
    Publishing country United States
    Document type Journal Article ; Review ; Research Support, N.I.H., Extramural
    ZDB-ID 2205412-1
    ISSN 1553-7374 ; 1553-7374
    ISSN (online) 1553-7374
    ISSN 1553-7374
    DOI 10.1371/journal.ppat.1011588
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  6. Article ; Online: Powassan Virus Lineage I in Field-Collected Dermacentor variabilis Ticks, New York, USA.

    Hart, Charles / Hassett, Erin / Vogels, Chantal B F / Shapley, Daniel / Grubaugh, Nathan D / Thangamani, Saravanan

    Emerging infectious diseases

    2023  Volume 29, Issue 2, Page(s) 415–417

    Abstract: ... We detected Powassan virus lineage I from a pool of field-collected D. variabilis ticks in New York, USA. ...

    Abstract Powassan virus is a tickborne flavivirus that can cause lethal or debilitating neurologic illness. It is canonically transmitted by Ixodes spp. ticks but might spill over to sympatric Dermacentor species. We detected Powassan virus lineage I from a pool of field-collected D. variabilis ticks in New York, USA.
    MeSH term(s) Animals ; Encephalitis Viruses, Tick-Borne/genetics ; New York ; Ixodes ; Dermacentor
    Language English
    Publishing date 2023-01-24
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1380686-5
    ISSN 1080-6059 ; 1080-6040
    ISSN (online) 1080-6059
    ISSN 1080-6040
    DOI 10.3201/eid2902.220410
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 4778: Show issues Location:
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  7. Article ; Online: Why does Japan have so few cases of COVID-19?

    Iwasaki, Akiko / Grubaugh, Nathan D

    EMBO molecular medicine

    2020  Volume 12, Issue 5, Page(s) e12481

    Abstract: The COVID-19 pandemic has spread to many countries around the world, but the infection and death rates vary widely. One country that appeared to have kept the infection under control despite limited societal restrictions is Japan. This commentary ... ...

    Abstract The COVID-19 pandemic has spread to many countries around the world, but the infection and death rates vary widely. One country that appeared to have kept the infection under control despite limited societal restrictions is Japan. This commentary explores why Japan may have, up to now, been spared an escalation of the SARS-CoV-2 infections.
    MeSH term(s) Angiotensin-Converting Enzyme 2 ; BCG Vaccine/immunology ; Betacoronavirus ; COVID-19 ; Communicable Disease Control ; Coronavirus Infections/epidemiology ; Coronavirus Infections/genetics ; Coronavirus Infections/immunology ; Culture ; Fatty Acids, Monounsaturated ; Genetic Variation ; Histocompatibility Antigens Class I/genetics ; Histocompatibility Antigens Class I/immunology ; Humans ; Japan/epidemiology ; Pandemics ; Peptidyl-Dipeptidase A/genetics ; Pneumonia, Viral/epidemiology ; Pneumonia, Viral/genetics ; Pneumonia, Viral/immunology ; SARS-CoV-2
    Chemical Substances BCG Vaccine ; Fatty Acids, Monounsaturated ; Histocompatibility Antigens Class I ; musk (095I377U8F) ; Peptidyl-Dipeptidase A (EC 3.4.15.1) ; ACE2 protein, human (EC 3.4.17.23) ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23)
    Keywords covid19
    Language English
    Publishing date 2020-04-28
    Publishing country England
    Document type Journal Article
    ZDB-ID 2467145-9
    ISSN 1757-4684 ; 1757-4676
    ISSN (online) 1757-4684
    ISSN 1757-4676
    DOI 10.15252/emmm.202012481
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  8. Article ; Online: Saliva for Detection of SARS-CoV-2. Reply.

    Wyllie, Anne L / Vogels, Chantal B F / Grubaugh, Nathan D

    The New England journal of medicine

    2021  Volume 384, Issue 9, Page(s) e31

    MeSH term(s) COVID-19 ; Humans ; Nasopharynx ; SARS-CoV-2 ; Saliva ; Specimen Handling
    Language English
    Publishing date 2021-02-03
    Publishing country United States
    Document type Letter ; Comment
    ZDB-ID 207154-x
    ISSN 1533-4406 ; 0028-4793
    ISSN (online) 1533-4406
    ISSN 0028-4793
    DOI 10.1056/NEJMc2032165
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  9. Article ; Online: Why does Japan have so few cases of COVID‐19?

    Akiko Iwasaki / Nathan D Grubaugh

    EMBO Molecular Medicine, Vol 12, Iss 5, Pp n/a-n/a (2020)

    2020  

    Keywords Medicine (General) ; R5-920 ; Genetics ; QH426-470 ; covid19
    Language English
    Publishing date 2020-05-01T00:00:00Z
    Publisher Wiley
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: Incorporating variant frequencies data into short-term forecasting for COVID-19 cases and deaths in the USA: a deep learning approach.

    Du, Hongru / Dong, Ensheng / Badr, Hamada S / Petrone, Mary E / Grubaugh, Nathan D / Gardner, Lauren M

    EBioMedicine

    2023  Volume 89, Page(s) 104482

    Abstract: Background: Since the US reported its first COVID-19 case on January 21, 2020, the science community has been applying various techniques to forecast incident cases and deaths. To date, providing an accurate and robust forecast at a high spatial ... ...

    Abstract Background: Since the US reported its first COVID-19 case on January 21, 2020, the science community has been applying various techniques to forecast incident cases and deaths. To date, providing an accurate and robust forecast at a high spatial resolution has proved challenging, even in the short term.
    Method: Here we present a novel multi-stage deep learning model to forecast the number of COVID-19 cases and deaths for each US state at a weekly level for a forecast horizon of 1-4 weeks. The model is heavily data driven, and relies on epidemiological, mobility, survey, climate, demographic, and SARS-CoV-2 variant frequencies data. We implement a rigorous and robust evaluation of our model-specifically we report on weekly performance over a one-year period based on multiple error metrics, and explicitly assess how our model performance varies over space, chronological time, and different outbreak phases.
    Findings: The proposed model is shown to consistently outperform the CDC ensemble model for all evaluation metrics in multiple spatiotemporal settings, especially for the longer-term (3 and 4 weeks ahead) forecast horizon. Our case study also highlights the potential value of variant frequencies data for use in short-term forecasting to identify forthcoming surges driven by new variants.
    Interpretation: Based on our findings, the proposed forecasting framework improves upon the available state-of-the-art forecasting tools currently used to support public health decision making with respect to COVID-19 risk.
    Funding: This work was funded the NSF Rapid Response Research (RAPID) grant Award ID 2108526 and the CDC Contract #75D30120C09570.
    MeSH term(s) Humans ; United States ; COVID-19 ; SARS-CoV-2 ; Deep Learning ; Benchmarking ; Forecasting
    Language English
    Publishing date 2023-02-21
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2851331-9
    ISSN 2352-3964
    ISSN (online) 2352-3964
    DOI 10.1016/j.ebiom.2023.104482
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