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  1. Article ; Online: Changing COVID-19 cases and deaths detection in Florida.

    Toh, Kok Ben / Cummings, Derek A T / Longini, Ira M / Hladish, Thomas J

    PloS one

    2024  Volume 19, Issue 3, Page(s) e0299143

    Abstract: Epidemic data are often difficult to interpret due to inconsistent detection and reporting. As these data are critically relied upon to inform policy and epidemic projections, understanding reporting trends is similarly important. Early reporting of the ... ...

    Abstract Epidemic data are often difficult to interpret due to inconsistent detection and reporting. As these data are critically relied upon to inform policy and epidemic projections, understanding reporting trends is similarly important. Early reporting of the COVID-19 pandemic in particular is complicated, due to changing diagnostic and testing protocols. An internal audit by the State of Florida, USA found numerous specific examples of irregularities in COVID-19 case and death reports. Using case, hospitalization, and death data from the the first year of the COVID-19 pandemic in Florida, we present approaches that can be used to identify the timing, direction, and magnitude of some reporting changes. Specifically, by establishing a baseline of detection probabilities from the first (spring) wave, we show that transmission trends among all age groups were similar, with the exception of the second summer wave, when younger people became infected earlier than seniors, by approximately 2 weeks. We also found a substantial drop in case-fatality risk (CFR) among all age groups over the three waves during the first year of the pandemic, with the most drastic changes seen in the 0 to 39 age group. The CFR trends provide useful insights into infection detection that would not be possible by relying on the number of tests alone. During the third wave, for which we have reliable hospitalization data, the CFR was remarkably stable across all age groups. In contrast, the hospitalization-to-case ratio varied inversely with cases while the death-to-hospitalization ratio varied proportionally. Although specific trends are likely to vary between locales, the approaches we present here offer a generic way to understand the substantial changes that occurred in the relationships among the key epidemic indicators.
    MeSH term(s) Humans ; Infant, Newborn ; COVID-19/diagnosis ; COVID-19/epidemiology ; SARS-CoV-2 ; Florida/epidemiology ; Pandemics ; Hospitalization
    Language English
    Publishing date 2024-03-28
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0299143
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Closing the health inequity gap during the pandemic: COVID-19 mortality among racial and ethnic groups in Connecticut, March 2020 to December 2021.

    Schultes, Olivia / Lind, Margaret L / Brockmeyer, Jessica / Sosensky, Peri / Cummings, Derek A T / Ko, Albert I

    Journal of epidemiology and community health

    2022  Volume 76, Issue 7, Page(s) 695–696

    MeSH term(s) COVID-19 ; Connecticut/epidemiology ; Ethnicity ; Health Inequities ; Health Status Disparities ; Healthcare Disparities ; Humans ; Minority Groups ; Pandemics ; United States
    Language English
    Publishing date 2022-04-15
    Publishing country England
    Document type Letter ; Research Support, Non-U.S. Gov't
    ZDB-ID 391868-3
    ISSN 1470-2738 ; 0142-467X ; 0141-7681 ; 0143-005X
    ISSN (online) 1470-2738
    ISSN 0142-467X ; 0141-7681 ; 0143-005X
    DOI 10.1136/jech-2022-218975
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Reconstructed influenza A/H3N2 infection histories reveal variation in incidence and antibody dynamics over the life course.

    Hay, James A / Zhu, Huachen / Jiang, Chao Qiang / Kwok, Kin On / Shen, Ruiyin / Kucharski, Adam / Yang, Bingyi / Read, Jonathan M / Lessler, Justin / Cummings, Derek A T / Riley, Steven

    medRxiv : the preprint server for health sciences

    2024  

    Abstract: Humans experience many influenza infections over their lives, resulting in complex and varied immunological histories. Although experimental and quantitative analyses have improved our understanding of the immunological processes defining an individual's ...

    Abstract Humans experience many influenza infections over their lives, resulting in complex and varied immunological histories. Although experimental and quantitative analyses have improved our understanding of the immunological processes defining an individual's antibody repertoire, how these within-host processes are linked to population-level influenza epidemiology remains unclear. Here, we used a multi-level mathematical model to jointly infer antibody dynamics and individual-level lifetime influenza A/H3N2 infection histories for 1,130 individuals in Guangzhou, China, using 67,683 haemagglutination inhibition (HI) assay measurements against 20 A/H3N2 strains from repeat serum samples collected between 2009 and 2015. These estimated infection histories allowed us to reconstruct historical seasonal influenza patterns and to investigate how influenza incidence varies over time, space and age in this population. We estimated median annual influenza infection rates to be approximately 18% from 1968 to 2015, but with substantial variation between years. 88% of individuals were estimated to have been infected at least once during the study period (2009-2015), and 20% were estimated to have three or more infections in that time. We inferred decreasing infection rates with increasing age, and found that annual attack rates were highly correlated across all locations, regardless of their distance, suggesting that age has a stronger impact than fine-scale spatial effects in determining an individual's antibody profile. Finally, we reconstructed each individual's expected antibody profile over their lifetime and inferred an age-stratified relationship between probability of infection and HI titre. Our analyses show how multi-strain serological panels provide rich information on long term, epidemiological trends, within-host processes and immunity when analyzed using appropriate inference methods, and adds to our understanding of the life course epidemiology of influenza A/H3N2.
    Language English
    Publishing date 2024-04-05
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2024.03.18.24304371
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Antibodies to Aedes spp. salivary proteins

    Veronique Etienne / Adriana Gallagher / Rebecca C. Christofferson / Michael K. McCracken / Derek A.T. Cummings / Maureen T. Long

    Frontiers in Tropical Diseases, Vol

    a systematic review and pooled analysis

    2023  Volume 4

    Abstract: Aedes spp. mosquitos are responsible for transmitting several viruses that pose significant public health risks, including dengue, Zika, yellow fever, chikungunya, and West Nile viruses. However, quantifying the number of individuals at risk and their ... ...

    Abstract Aedes spp. mosquitos are responsible for transmitting several viruses that pose significant public health risks, including dengue, Zika, yellow fever, chikungunya, and West Nile viruses. However, quantifying the number of individuals at risk and their exposure to Aedes spp. mosquitos over time is challenging due to various factors. Even accurate estimation of mosquito numbers at the population level may not fully capture the fluctuations in human exposure based on factors that affect biting rates of mosquitoes. Measuring the antibody response of humans to mosquito salivary proteins (MSP) has been proposed as a method to assess human exposure to mosquito bites and predict disease risk. The presence of antibodies to MSP can be quantified using the enzyme-linked immunosorbent assay (ELISA). While there is known variability in laboratory methods, the consistency of MSP measurements across different research groups has not been quantitatively examined. Variation in laboratory protocols, antigens used, and the human populations sampled all may contribute to differences observed in measured anti-MSP responses. In this study, we conducted a systematic review of the published literature focusing on antibody responses to MSP in humans and other vertebrate hosts. Whenever possible, we extracted individual-level anti-MSP IgG data from these studies and performed a pooled analysis of quantitative outcomes obtained from ELISAs, specifically optical densities (OD). We analyzed the pooled data to quantify variation between studies and identify sample and study characteristics associated with OD scores. Our candidate list of characteristics included the type of antigen used, age of human subjects, mosquito species, population-level mosquito exposure, collection season, Köppen-Geiger climate classification, and OD reporting method. Our findings revealed that the type of antigen, population-level mosquito exposure, and Köppen-Geiger climate classification were significantly associated with ELISA values. Furthermore, we developed a ...
    Keywords mosquito ; biomarker ; IgG ; IgE ; Aedes ; Köppen-Geiger climate classification ; Arctic medicine. Tropical medicine ; RC955-962
    Subject code 333
    Language English
    Publishing date 2023-11-01T00:00:00Z
    Publisher Frontiers Media S.A.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Integration of population-level data sources into an individual-level clinical prediction model for dengue virus test positivity.

    Williams, Robert J / Brintz, Ben J / Ribeiro Dos Santos, Gabriel / Huang, Angkana T / Buddhari, Darunee / Kaewhiran, Surachai / Iamsirithaworn, Sopon / Rothman, Alan L / Thomas, Stephen / Farmer, Aaron / Fernandez, Stefan / Cummings, Derek A T / Anderson, Kathryn B / Salje, Henrik / Leung, Daniel T

    Science advances

    2024  Volume 10, Issue 7, Page(s) eadj9786

    Abstract: The differentiation of dengue virus (DENV) infection, a major cause of acute febrile illness in tropical regions, from other etiologies, may help prioritize laboratory testing and limit the inappropriate use of antibiotics. While traditional clinical ... ...

    Abstract The differentiation of dengue virus (DENV) infection, a major cause of acute febrile illness in tropical regions, from other etiologies, may help prioritize laboratory testing and limit the inappropriate use of antibiotics. While traditional clinical prediction models focus on individual patient-level parameters, we hypothesize that for infectious diseases, population-level data sources may improve predictive ability. To create a clinical prediction model that integrates patient-extrinsic data for identifying DENV among febrile patients presenting to a hospital in Thailand, we fit random forest classifiers combining clinical data with climate and population-level epidemiologic data. In cross-validation, compared to a parsimonious model with the top clinical predictors, a model with the addition of climate data, reconstructed susceptibility estimates, force of infection estimates, and a recent case clustering metric significantly improved model performance.
    MeSH term(s) Humans ; Dengue Virus ; Dengue/diagnosis ; Dengue/epidemiology ; Models, Statistical ; Prognosis ; Climate ; Fever
    Language English
    Publishing date 2024-02-16
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2810933-8
    ISSN 2375-2548 ; 2375-2548
    ISSN (online) 2375-2548
    ISSN 2375-2548
    DOI 10.1126/sciadv.adj9786
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: A population-based serological survey of

    Clutter, Christy H / Klarman, Molly B / Cajusma, Youseline / Cato, Emilie T / Sayeed, Abu / Brinkley, Lindsey / Jensen, Owen / Baril, Chantale / De Rochars, V Madsen Beau / Azman, Andrew S / Long, Maureen T / Cummings, Derek / Leung, Daniel T / Nelson, Eric J

    medRxiv : the preprint server for health sciences

    2023  

    Abstract: After three years with no confirmed cholera cases in Haiti, an outbreak ... ...

    Abstract After three years with no confirmed cholera cases in Haiti, an outbreak of
    Language English
    Publishing date 2023-02-08
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.02.06.23285537
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Use of Recently Vaccinated Individuals to Detect Bias in Test-Negative Case-Control Studies of COVID-19 Vaccine Effectiveness.

    Hitchings, Matt D T / Lewnard, Joseph A / Dean, Natalie E / Ko, Albert I / Ranzani, Otavio T / Andrews, Jason R / Cummings, Derek A T

    Epidemiology (Cambridge, Mass.)

    2022  Volume 33, Issue 4, Page(s) 450–456

    Abstract: Postauthorization observational studies play a key role in understanding COVID-19 vaccine effectiveness following the demonstration of efficacy in clinical trials. Although bias due to confounding, selection bias, and misclassification can be mitigated ... ...

    Abstract Postauthorization observational studies play a key role in understanding COVID-19 vaccine effectiveness following the demonstration of efficacy in clinical trials. Although bias due to confounding, selection bias, and misclassification can be mitigated through careful study design, unmeasured confounding is likely to remain in these observational studies. Phase III trials of COVID-19 vaccines have shown that protection from vaccination does not occur immediately, meaning that COVID-19 risk should be similar in recently vaccinated and unvaccinated individuals, in the absence of confounding or other bias. Several studies have used the estimated effectiveness among recently vaccinated individuals as a negative control exposure to detect bias in vaccine effectiveness estimates. In this paper, we introduce a theoretical framework to describe the interpretation of such a bias indicator in test-negative studies, and outline strong assumptions that would allow vaccine effectiveness among recently vaccinated individuals to serve as a negative control exposure.
    MeSH term(s) COVID-19/prevention & control ; COVID-19 Vaccines/therapeutic use ; Case-Control Studies ; Humans ; Vaccination ; Vaccine Efficacy
    Chemical Substances COVID-19 Vaccines
    Language English
    Publishing date 2022-04-01
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 1053263-8
    ISSN 1531-5487 ; 1044-3983
    ISSN (online) 1531-5487
    ISSN 1044-3983
    DOI 10.1097/EDE.0000000000001484
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article: Differentiation of Multiple Fluorescent Powders, Powder Transfer, and Effect on Mating in

    Rojas-Araya, Diana / Alto, Barry W / Cummings, Derek A T / Burkett-Cadena, Nathan D

    Insects

    2020  Volume 11, Issue 11

    Abstract: Five different fluorescent powders (orange, yellow, green, blue, and violet) were tested ... ...

    Abstract Five different fluorescent powders (orange, yellow, green, blue, and violet) were tested on
    Language English
    Publishing date 2020-10-24
    Publishing country Switzerland
    Document type Journal Article
    ISSN 2075-4450
    ISSN 2075-4450
    DOI 10.3390/insects11110727
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Accounting for assay performance when estimating the temporal dynamics in SARS-CoV-2 seroprevalence in the U.S.

    García-Carreras, Bernardo / Hitchings, Matt D T / Johansson, Michael A / Biggerstaff, Matthew / Slayton, Rachel B / Healy, Jessica M / Lessler, Justin / Quandelacy, Talia / Salje, Henrik / Huang, Angkana T / Cummings, Derek A T

    Nature communications

    2023  Volume 14, Issue 1, Page(s) 2235

    Abstract: Reconstructing the incidence of SARS-CoV-2 infection is central to understanding the state of the pandemic. Seroprevalence studies are often used to assess cumulative infections as they can identify asymptomatic infection. Since July 2020, commercial ... ...

    Abstract Reconstructing the incidence of SARS-CoV-2 infection is central to understanding the state of the pandemic. Seroprevalence studies are often used to assess cumulative infections as they can identify asymptomatic infection. Since July 2020, commercial laboratories have conducted nationwide serosurveys for the U.S. CDC. They employed three assays, with different sensitivities and specificities, potentially introducing biases in seroprevalence estimates. Using models, we show that accounting for assays explains some of the observed state-to-state variation in seroprevalence, and when integrating case and death surveillance data, we show that when using the Abbott assay, estimates of proportions infected can differ substantially from seroprevalence estimates. We also found that states with higher proportions infected (before or after vaccination) had lower vaccination coverages, a pattern corroborated using a separate dataset. Finally, to understand vaccination rates relative to the increase in cases, we estimated the proportions of the population that received a vaccine prior to infection.
    MeSH term(s) Humans ; SARS-CoV-2 ; COVID-19/epidemiology ; Seroepidemiologic Studies ; Asymptomatic Infections ; Biological Assay ; Antibodies, Viral
    Chemical Substances Antibodies, Viral
    Language English
    Publishing date 2023-04-19
    Publishing country England
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-023-37944-5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Novel coronavirus 2019-nCoV (COVID-19): early estimation of epidemiological parameters and epidemic size estimates.

    Read, Jonathan M / Bridgen, Jessica R E / Cummings, Derek A T / Ho, Antonia / Jewell, Chris P

    Philosophical transactions of the Royal Society of London. Series B, Biological sciences

    2021  Volume 376, Issue 1829, Page(s) 20200265

    Abstract: Since it was first identified, the epidemic scale of the recently emerged novel coronavirus (2019-nCoV) in Wuhan, China, has increased rapidly, with cases arising across China and other countries and regions. Using a transmission model, we estimate a ... ...

    Abstract Since it was first identified, the epidemic scale of the recently emerged novel coronavirus (2019-nCoV) in Wuhan, China, has increased rapidly, with cases arising across China and other countries and regions. Using a transmission model, we estimate a basic reproductive number of 3.11 (95% CI, 2.39-4.13), indicating that 58-76% of transmissions must be prevented to stop increasing. We also estimate a case ascertainment rate in Wuhan of 5.0% (95% CI, 3.6-7.4). The true size of the epidemic may be significantly greater than the published case counts suggest, with our model estimating 21 022 (prediction interval, 11 090-33 490) total infections in Wuhan between 1 and 22 January. We discuss our findings in the light of more recent information. This article is part of the theme issue 'Modelling that shaped the early COVID-19 pandemic response in the UK'.
    MeSH term(s) Basic Reproduction Number ; COVID-19/epidemiology ; COVID-19/transmission ; COVID-19/virology ; China/epidemiology ; Humans ; Pandemics ; SARS-CoV-2/genetics ; SARS-CoV-2/pathogenicity
    Language English
    Publishing date 2021-05-31
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 208382-6
    ISSN 1471-2970 ; 0080-4622 ; 0264-3839 ; 0962-8436
    ISSN (online) 1471-2970
    ISSN 0080-4622 ; 0264-3839 ; 0962-8436
    DOI 10.1098/rstb.2020.0265
    Database MEDical Literature Analysis and Retrieval System OnLINE

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