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  1. Article ; Online: Modelling disease mitigation at mass gatherings: A case study of COVID-19 at the 2022 FIFA World Cup.

    Grunnill, Martin / Arino, Julien / McCarthy, Zachary / Bragazzi, Nicola Luigi / Coudeville, Laurent / Thommes, Edward W / Amiche, Amine / Ghasemi, Abbas / Bourouiba, Lydia / Tofighi, Mohammadali / Asgary, Ali / Baky-Haskuee, Mortaza / Wu, Jianhong

    PLoS computational biology

    2024  Volume 20, Issue 1, Page(s) e1011018

    Abstract: The 2022 FIFA World Cup was the first major multi-continental sporting Mass Gathering Event (MGE) of the post COVID-19 era to allow foreign spectators. Such large-scale MGEs can potentially lead to outbreaks of infectious disease and contribute to the ... ...

    Abstract The 2022 FIFA World Cup was the first major multi-continental sporting Mass Gathering Event (MGE) of the post COVID-19 era to allow foreign spectators. Such large-scale MGEs can potentially lead to outbreaks of infectious disease and contribute to the global dissemination of such pathogens. Here we adapt previous work and create a generalisable model framework for assessing the use of disease control strategies at such events, in terms of reducing infections and hospitalisations. This framework utilises a combination of meta-populations based on clusters of people and their vaccination status, Ordinary Differential Equation integration between fixed time events, and Latin Hypercube sampling. We use the FIFA 2022 World Cup as a case study for this framework (modelling each match as independent 7 day MGEs). Pre-travel screenings of visitors were found to have little effect in reducing COVID-19 infections and hospitalisations. With pre-match screenings of spectators and match staff being more effective. Rapid Antigen (RA) screenings 0.5 days before match day performed similarly to RT-PCR screenings 1.5 days before match day. Combinations of pre-travel and pre-match testing led to improvements. However, a policy of ensuring that all visitors had a COVID-19 vaccination (second or booster dose) within a few months before departure proved to be much more efficacious. The State of Qatar abandoned all COVID-19 related travel testing and vaccination requirements over the period of the World Cup. Our work suggests that the State of Qatar may have been correct in abandoning the pre-travel testing of visitors. However, there was a spike in COVID-19 cases and hospitalisations within Qatar over the World Cup. Given our findings and the spike in cases, we suggest a policy requiring visitors to have had a recent COVID-19 vaccination should have been in place to reduce cases and hospitalisations.
    MeSH term(s) Humans ; Mass Gatherings ; COVID-19 Vaccines ; COVID-19/epidemiology ; COVID-19/prevention & control ; Soccer ; Sports
    Chemical Substances COVID-19 Vaccines
    Language English
    Publishing date 2024-01-18
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2193340-6
    ISSN 1553-7358 ; 1553-734X
    ISSN (online) 1553-7358
    ISSN 1553-734X
    DOI 10.1371/journal.pcbi.1011018
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  2. Article ; Online: "Hot-spotting" to improve vaccine allocation by harnessing digital contact tracing technology: An application of percolation theory.

    Penney, Mark D / Yargic, Yigit / Smolin, Lee / Thommes, Edward W / Anand, Madhur / Bauch, Chris T

    PloS one

    2021  Volume 16, Issue 9, Page(s) e0256889

    Abstract: Vaccinating individuals with more exposure to others can be disproportionately effective, in theory, but identifying these individuals is difficult and has long prevented implementation of such strategies. Here, we propose how the technology underlying ... ...

    Abstract Vaccinating individuals with more exposure to others can be disproportionately effective, in theory, but identifying these individuals is difficult and has long prevented implementation of such strategies. Here, we propose how the technology underlying digital contact tracing could be harnessed to boost vaccine coverage among these individuals. In order to assess the impact of this "hot-spotting" proposal we model the spread of disease using percolation theory, a collection of analytical techniques from statistical physics. Furthermore, we introduce a novel measure which we call the efficiency, defined as the percentage decrease in the reproduction number per percentage of the population vaccinated. We find that optimal implementations of the proposal can achieve herd immunity with as little as half as many vaccine doses as a non-targeted strategy, and is attractive even for relatively low rates of app usage.
    MeSH term(s) COVID-19/immunology ; COVID-19/prevention & control ; COVID-19/transmission ; COVID-19 Vaccines/administration & dosage ; Contact Tracing/instrumentation ; Contact Tracing/statistics & numerical data ; Humans ; Immunity, Herd ; Mass Vaccination/statistics & numerical data ; Mobile Applications ; Models, Statistical ; SARS-CoV-2/pathogenicity
    Chemical Substances COVID-19 Vaccines
    Language English
    Publishing date 2021-09-22
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0256889
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  3. Book ; Online: Population mobility, well-mixed clustering and disease spread

    Lyver, David / Nica, Mihai / Cot, Corentin / Cacciapaglia, Giacomo / Mohammadi, Zahra / Thommes, Edward W. / Cojocaru, Monica-Gabriela

    a look at COVID-19 Spread in the United States and preventive policy insights

    2023  

    Abstract: The epidemiology of pandemics is classically viewed using geographical and political borders; however, these artificial divisions can result in a misunderstanding of the current epidemiological state within a given region. To improve upon current methods, ...

    Abstract The epidemiology of pandemics is classically viewed using geographical and political borders; however, these artificial divisions can result in a misunderstanding of the current epidemiological state within a given region. To improve upon current methods, we propose a clustering algorithm which is capable of recasting regions into well-mixed clusters such that they have a high level of interconnection while minimizing the external flow of the population towards other clusters. Moreover, we analyze and identify so called core clusters, clusters that retain their features over time (temporally stable) and independent of the presence or absence of policy measures. In order to demonstrate the capabilities of this algorithm, we use US county-level cellular mobility data to divide the country into such clusters. Herein, we show a more granular spread of SARS-CoV-2 throughout the first weeks of the pandemic. Moreover, we are able to identify areas (groups of counties) that were experiencing above average levels of transmission within a state, as well as pan-state areas (clusters overlapping more than one state) with very similar disease spread. Therefore, our method enables policymakers to make more informed decisions on the use of public health interventions within their jurisdiction, as well as guide collaboration with surrounding regions to benefit the general population in controlling the spread of communicable diseases.

    Comment: 18 pages, 16 figures
    Keywords Quantitative Biology - Populations and Evolution ; Physics - Physics and Society
    Publishing date 2023-11-25
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Large-scale frequent testing and tracing to supplement control of Covid-19 and vaccination rollout constrained by supply.

    Humphrey, Lia / Thommes, Edward W / Fields, Roie / Coudeville, Laurent / Hakim, Naseem / Chit, Ayman / Wu, Jianhong / Cojocaru, Monica G

    Infectious Disease Modelling

    2021  Volume 6, Page(s) 955–974

    Abstract: Non-pharmaceutical interventions (NPI) were implemented all around the world in the fight against COVID-19: Social distancing, shelter-in-place, mask wearing, etc. to mitigate transmission, together with testing and contact-tracing to identify, isolate ... ...

    Abstract Non-pharmaceutical interventions (NPI) were implemented all around the world in the fight against COVID-19: Social distancing, shelter-in-place, mask wearing, etc. to mitigate transmission, together with testing and contact-tracing to identify, isolate and treat the infected. The majority of countries have relied on the former measures, followed by a ramping up of their testing and tracing capabilities. We present here the cases of South Korea, Italy, Canada and the United States, as a look back to lessons that can be drawn for controlling the pandemic, specifically through the means of testing and tracing. By fitting a disease transmission model to daily case report data in each of the four countries, we first show that their combination of social-distancing and testing/tracing have had a significant impact on the evolution of their first wave of pandemic curves. We then consider the hypothetical scenario where the only NPI measures implemented past the first pandemic wave consisted of isolating individuals due to repeated, country-scale testing and contact tracing, as a mean of lifting social distancing measures without a resurgence of COVID-19. We give estimates on the average isolation rates needed to occur in each country. We find that testing and tracing each individual of a country, on average, every 4.5 days (South Korea), 5.7 days (Canada), 6 days (Italy) and 3.5 days (US), would have been sufficient to mitigate their second pandemic waves. We also considered the situation in Canada to see how a frequent large-scale asymptomatic testing and contact tracing could have been used in combination with vaccination rollout to reduce the infection in the population. This could offer an alternative approach towards preventing and controlling an outbreak when vaccine supply is limited, while testing capacity has been increasingly enhanced.
    Language English
    Publishing date 2021-07-24
    Publishing country China
    Document type Journal Article
    ZDB-ID 3015225-2
    ISSN 2468-0427 ; 2468-2152
    ISSN (online) 2468-0427
    ISSN 2468-2152
    DOI 10.1016/j.idm.2021.06.008
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  5. Article ; Online: Influenza vaccine in chronic obstructive pulmonary disease among elderly male veterans.

    Young-Xu, Yinong / Smith, Jeremy / Nealon, Joshua / Mahmud, Salaheddin M / Van Aalst, Robertus / Thommes, Edward W / Neupane, Nabin / Lee, Jason K H / Chit, Ayman

    PloS one

    2022  Volume 17, Issue 1, Page(s) e0262072

    Abstract: Background: Prior studies have established those elderly patients with chronic obstructive pulmonary disease (COPD) are at elevated risk for developing influenza-associated complications such as hospitalization, intensive-care admission, and death. This ...

    Abstract Background: Prior studies have established those elderly patients with chronic obstructive pulmonary disease (COPD) are at elevated risk for developing influenza-associated complications such as hospitalization, intensive-care admission, and death. This study sought to determine whether influenza vaccination could improve survival among elderly patients with COPD.
    Materials/methods: This study included Veterans (age ≥ 65 years) diagnosed with COPD that received care at the United States Veterans Health Administration (VHA) during four influenza seasons, from 2012-2013 to 2015-2016. We linked VHA electronic medical records and Medicare administrative files to Centers for Disease Control and Prevention National Death Index cause of death records as well as influenza surveillance data. A multivariable time-dependent Cox proportional hazards model was used to compare rates of mortality of recipients of influenza vaccination to those who did not have records of influenza vaccination. We estimated hazard ratios (HRs) adjusted for age, gender, race, socioeconomic status, comorbidities, and healthcare utilization.
    Results: Over a span of four influenza seasons, we included 1,856,970 person-seasons of observation where 1,199,275 (65%) had a record of influenza vaccination and 657,695 (35%) did not have a record of influenza vaccination. After adjusting for comorbidities, demographic and socioeconomic characteristics, influenza vaccination was associated with reduced risk of death during the most severe periods of influenza seasons: 75% all-cause (HR = 0.25; 95% CI: 0.24-0.26), 76% respiratory causes (HR = 0.24; 95% CI: 0.21-0.26), and 82% pneumonia/influenza cause (HR = 0.18; 95% CI: 0.13-0.26). A significant part of the effect could be attributed to "healthy vaccinee" bias as reduced risk of mortality was also found during the periods when there was no influenza activity and before patients received vaccination: 30% all-cause (HR = 0.70; 95% CI: 0.65-0.75), 32% respiratory causes (HR = 0.68; 95% CI: 0.60-0.78), and 51% pneumonia/influenza cause (HR = 0.49; 95% CI: 0.31-0.78). However, as a falsification study, we found that influenza vaccination had no impact on hospitalization due to urinary tract infection (HR = 0.97; 95% CI: 0.80-1.18).
    Conclusions: Among elderly patients with COPD, influenza vaccination was associated with reduced risk for all-cause and cause-specific mortality.
    MeSH term(s) Influenza Vaccines
    Chemical Substances Influenza Vaccines
    Language English
    Publishing date 2022-01-04
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0262072
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  6. Article ; Online: Laboratory-confirmed influenza infection and acute myocardial infarction among United States senior Veterans.

    Young-Xu, Yinong / Smith, Jeremy / Mahmud, Salaheddin M / Van Aalst, Robertus / Thommes, Edward W / Neupane, Nabin / Lee, Jason K H / Chit, Ayman

    PloS one

    2020  Volume 15, Issue 12, Page(s) e0243248

    Abstract: Background: Previous studies established an association between laboratory-confirmed influenza infection (LCI) and hospitalization for acute myocardial infarction (AMI) but not causality. We aimed to explore the underlying mechanisms by adding ... ...

    Abstract Background: Previous studies established an association between laboratory-confirmed influenza infection (LCI) and hospitalization for acute myocardial infarction (AMI) but not causality. We aimed to explore the underlying mechanisms by adding biological mediators to an established study design used by earlier studies.
    Methods: With data on biomarkers, we used a self-controlled case-series design to evaluate the effect of LCI on hospitalization for AMI among Veterans Health Administration (VHA) patients. We included senior Veterans (age 65 years and older) with LCI between 2010 through 2015. Patient-level data from VHA electronic medical records were used to capture laboratory results, hospitalizations, and baseline patient characteristics. We defined the "risk interval" as the first 7 days after specimen collection and the "control interval" as 1 year before and 1 year after the risk interval. More importantly, using mediation analysis, we examined the role of abnormal white blood cell (WBC) and platelet count in the relationship between LCI and AMI to explore the thrombogenic nature of this association, thus potential causality.
    Results: We identified 391 hospitalizations for AMI that occurred within +/-1 year of a positive influenza test, of which 31 (31.1 admissions/week) occurred during the risk interval and 360 (3.5/per week) during the control interval, resulting in an incidence ratio (IR) for AMI admission of 8.89 (95% confidence interval [CI]: 6.16-12.84). In stratified analyses, AMI risk was significantly elevated among patients with high WBC count (IR, 12.43; 95% CI: 6.99-22.10) and high platelet count (IR, 15.89; 95% CI: 3.59-70.41).
    Conclusion: We confirmed a significant association between LCI and AMI. The risk was elevated among those with high WBC or platelet count, suggesting a potential role for inflammation and platelet activation in the underlying mechanism.
    MeSH term(s) Aged ; Aged, 80 and over ; Female ; Hospitalization ; Humans ; Incidence ; Influenza, Human/complications ; Influenza, Human/diagnosis ; Male ; Myocardial Infarction/diagnosis ; Myocardial Infarction/etiology ; Risk Factors ; United States/epidemiology ; Veterans
    Language English
    Publishing date 2020-12-11
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1932-6203
    ISSN (online) 1932-6203
    DOI 10.1371/journal.pone.0243248
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  7. Article ; Online: Vaccine Prioritisation Using Bluetooth Exposure Notification Apps

    Penney, Mark D / Yargic, Yigit / Smolin, Lee / Thommes, Edward W / Anand, Madhur / Bauch, Chris T

    medRxiv

    Abstract: The results of COVID-19 vaccine clinical trials suggest that an end to the pandemic is within reach. However, public health authorities worldwide are faced with the difficult task of prioritizing their allocation. Theory indicates that prioritizing ... ...

    Abstract The results of COVID-19 vaccine clinical trials suggest that an end to the pandemic is within reach. However, public health authorities worldwide are faced with the difficult task of prioritizing their allocation. Theory indicates that prioritizing vaccination of individuals with more contacts can be disproportionately effective. However, implementation of such strategies has been hampered by inability to determine population contact structure. One of the novel tools introduced during the pandemic has been the use of Bluetooth technology to assist in contact tracing and exposure notification. Here we show that the technology underlying these Bluetooth exposure notification applications can be leveraged to efficiently prioritise vaccine allocation. Our approach is based on the insight that these apps also act as local sensing devices measuring each user9s total exposure time to other app users, thereby enabling the implementation of a previously impossible vaccine strategy that prioritises potential super-spreaders based on total exposure time. To compare vaccination strategies we introduce a novel and widely generalizable measure of vaccination efficiency. By extending percolation theory we furthermore demonstrate that our proposed 99hot-spotting" strategy can achieve herd immunity with less than half as many vaccines as distributing the vaccines uniformly in the population.
    Keywords covid19
    Language English
    Publishing date 2020-12-16
    Publisher Cold Spring Harbor Laboratory Press
    Document type Article ; Online
    DOI 10.1101/2020.12.14.20248186
    Database COVID19

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  8. Article ; Online: A path out of COVID-19 quarantine: an analysis of policy scenarios

    Humphrey, Lia / Thommes, Edward W / Fields, Roie / Hakim, Naseem / Chit, Ayman / Cojocaru, Monica Gabriela

    medRxiv

    Abstract: In this work we present an analysis of the two major strategies currently implemented around the world in the fight against COVID-19: Social distancing & shelter-in-place measures to protect the susceptible, and testing & contact-tracing to identify, ... ...

    Abstract In this work we present an analysis of the two major strategies currently implemented around the world in the fight against COVID-19: Social distancing & shelter-in-place measures to protect the susceptible, and testing & contact-tracing to identify, isolate and treat the infected. The majority of countries have principally relied on the former; we consider the examples of Italy, Canada and the United States. By fitting a disease transmission model to daily case report data, we infer that in each of the three countries, the current level of national shutdown is equivalent to about half the population being under quarantine. We demonstrate that in the absence of other measures, scaling back social distancing in such a way as to prevent a second wave will take prohibitively long. In contrast, South Korea, a country that has managed to control and suppress its outbreak principally through mass testing and contact tracing, and has only instated a partial shutdown. For all four countries, we estimate the level of testing which would be required to allow a complete exit from shutdown and a full lifting of social distancing measures, without a resurgence of COVID-19. We find that a "brute-force" approach of untargeted universal testing requires an average testing rate of once every 36 to 48 hours for every individual, depending on the country. If testing is combined with contact tracing, and/or if tests are able to identify latent infection, then an average rate of once every 4 to 5 days is sufficient.
    Keywords covid19
    Language English
    Publishing date 2020-04-29
    Publisher Cold Spring Harbor Laboratory Press
    Document type Article ; Online
    DOI 10.1101/2020.04.23.20077503
    Database COVID19

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  9. Article: Analysis of relative effectiveness of high-dose versus standard-dose influenza vaccines using an instrumental variable method

    Young-Xu, Yinong / Snider, Julia Thornton / van Aalst, Robertus / Mahmud, Salaheddin M / Thommes, Edward W / Lee, Jason K.H / Greenberg, David P / Chit, Ayman

    Vaccine. 2019 Mar. 07, v. 37, no. 11

    2019  

    Abstract: Observational studies of the relative effectiveness of influenza vaccines are essential for public health decision making. Their estimates, however, are subject to bias due to unmeasured confounders. Instrumental variable (IV) methods can control for ... ...

    Abstract Observational studies of the relative effectiveness of influenza vaccines are essential for public health decision making. Their estimates, however, are subject to bias due to unmeasured confounders. Instrumental variable (IV) methods can control for observed and unobserved confounders.We used linked electronic medical record databases in the Veterans Health Administration (VHA) as well as Medicare administrative files to examine the relative vaccine effectiveness (rVE) of high-dose influenza vaccine (HD) versus standard-dose influenza vaccines (SD) in preventing hospitalizations among VHA-enrolled Veterans ≥65 years of age during 5 influenza seasons (2010–2011 through 2014–2015). Using multivariable IV Poisson regression modeling to address unmeasured confounding and bias, we analyzed the data by each season and through longitudinal analysis of all five seasons.We included 3,638,924 person–influenza seasons of observation where 158,636 (4%) were among HD vaccine recipients and 3,480,288 (96%) were among SD vaccine recipients. Of the 1,728,562 Veterans, 1,702,824 (98.5%) were male and 1,299,412 (75%) were non-Hispanic white. Based on the longitudinal analysis of all five seasons, the IV-adjusted rVE estimate of HD vs. SD was 10% (95% CI, 8–12%) against all-cause hospitalization; 18% (95% CI, 15–21%) against cardiorespiratory-associated hospitalization; and 14% (95% CI, 6–22%) against influenza/pneumonia-associated hospitalization. The findings by season were similar.Our analysis of VHA clinical data collected from approximately 1.7 million Veterans 65 years and older during five seasons demonstrates that high-dose influenza vaccine is more effective than standard-dose influenza vaccines in preventing influenza- or pneumonia-associated hospitalizations, cardiorespiratory hospitalizations, and all-cause hospitalizations.
    Keywords data collection ; databases ; decision making ; influenza ; influenza vaccines ; longitudinal studies ; males ; medical records ; observational studies ; public health ; veterans
    Language English
    Dates of publication 2019-0307
    Size p. 1484-1490.
    Publishing place Elsevier Ltd
    Document type Article
    ZDB-ID 605674-x
    ISSN 1873-2518 ; 0264-410X
    ISSN (online) 1873-2518
    ISSN 0264-410X
    DOI 10.1016/j.vaccine.2019.01.063
    Database NAL-Catalogue (AGRICOLA)

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  10. Article ; Online: Cost-effectiveness of seasonal quadrivalent versus trivalent influenza vaccination in the United States: A dynamic transmission modeling approach.

    Brogan, Anita J / Talbird, Sandra E / Davis, Ashley E / Thommes, Edward W / Meier, Genevieve

    Human vaccines & immunotherapeutics

    2016  Volume 13, Issue 3, Page(s) 533–542

    Abstract: Trivalent inactivated influenza vaccines (IIV3s) protect against 2 A strains and one B lineage; quadrivalent versions (IIV4s) protect against an additional B lineage. The objective was to assess projected health and economic outcomes associated with IIV4  ...

    Abstract Trivalent inactivated influenza vaccines (IIV3s) protect against 2 A strains and one B lineage; quadrivalent versions (IIV4s) protect against an additional B lineage. The objective was to assess projected health and economic outcomes associated with IIV4 versus IIV3 for preventing seasonal influenza in the US. A cost-effectiveness model was developed to interact with a dynamic transmission model. The transmission model tracked vaccination, influenza cases, infection-spreading interactions, and recovery over 10 y (2012-2022). The cost-effectiveness model estimated influenza-related complications, direct and indirect costs (2013-2014 US$), health outcomes, and cost-effectiveness. Inputs were taken from published/public sources or estimated using regression or calibration. Outcomes were discounted at 3% per year. Scenario analyses tested the reliability of the results. Seasonal vaccination with IIV4 versus IIV3 is predicted to reduce annual influenza cases by 1,973,849 (discounted; 2,325,644 undiscounted), resulting in 12-13% fewer cases and influenza-related complications and deaths. These reductions are predicted to translate into 18,485 more quality-adjusted life years (QALYs) accrued annually for IIV4 versus IIV3. Increased vaccine-related costs ($599 million; 5.7%) are predicted to be more than offset by reduced influenza treatment costs ($699 million; 12.2%), resulting in direct medical cost saving annually ($100 million; 0.6%). Including indirect costs, savings with IIV4 are predicted to be $7.1 billion (5.6%). Scenario analyses predict IIV4 to be cost-saving in all scenarios tested apart from low infectivity, where IIV4 is predicted to be cost-effective. In summary, seasonal influenza vaccination in the US with IIV4 versus IIV3 is predicted to improve health outcomes and reduce costs.
    MeSH term(s) Adolescent ; Adult ; Aged ; Aged, 80 and over ; Child ; Child, Preschool ; Cost-Benefit Analysis ; Female ; Humans ; Infant ; Infant, Newborn ; Influenza Vaccines/administration & dosage ; Influenza Vaccines/economics ; Influenza Vaccines/immunology ; Influenza, Human/prevention & control ; Male ; Middle Aged ; United States ; Vaccination/economics ; Vaccination/statistics & numerical data ; Young Adult
    Chemical Substances Influenza Vaccines
    Language English
    Publishing date 2016-10-26
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2664176-8
    ISSN 2164-554X ; 2164-5515
    ISSN (online) 2164-554X
    ISSN 2164-5515
    DOI 10.1080/21645515.2016.1242541
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