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Huo Y, Yang Y, Halloran ME, Longini IM, Dean NE. Hypothesis testing and sample size considerations for the test-negative design. Res Sq 2023:rs.3.rs-3783493. [PMID: 38234799 PMCID: PMC10793497 DOI: 10.21203/rs.3.rs-3783493/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
The test-negative design (TND) is an observational study design to evaluate vaccine effectiveness (VE) that enrolls individuals receiving diagnostic testing for a target disease as part of routine care. VE is estimated as one minus the adjusted odds ratio of testing positive versus negative comparing vaccinated and unvaccinated patients. Although the TND is related to case-control studies, it is distinct in that the ratio of test-positive cases to test-negative controls is not typically pre-specified. For both types of studies, sparse cells are common when vaccines are highly effective. We consider the implications of these features on power for the TND. We use simulation studies to explore three hypothesis-testing procedures and associated sample size calculations for case-control and TND studies. These tests, all based on a simple logistic regression model, are a standard Wald test, a continuity-corrected Wald test, and a score test. The Wald test performs poorly in both case-control and TND when VE is high because the number of vaccinated test-positive cases can be low or zero. Continuity corrections help to stabilize the variance but induce bias. We observe superior performance with the score test as the variance is pooled under the null hypothesis of no group differences. We recommend using a score-based approach to design and analyze both case-control and TND. We propose a modification to the TND score sample size to account for additional variability in the ratio of controls over cases. This work expands our understanding of the data mechanisms of the TND.
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Affiliation(s)
- Yanan Huo
- Gilead Sciences, Foster City, CA, USA
| | - Yang Yang
- Department of Statistics, Franklin College of Arts and Sciences, University of Georgia, Athens, GA, USA
| | | | - Ira M Longini
- Department of Biostatistics, University of Florida, Gainesville, FL, USA
| | - Natalie E Dean
- Department of Biostatistics & Bioinformatics, Emory University, Atlanta, GA, USA
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2
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Lee Y, Buchanan AL, Ogburn EL, Friedman SR, Halloran ME, Katenka NV, Wu J, Nikolopoulos G. Finding influential subjects in a network using a causal framework. Biometrics 2023; 79:3715-3727. [PMID: 36788358 PMCID: PMC10423748 DOI: 10.1111/biom.13841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 02/06/2023] [Indexed: 02/16/2023]
Abstract
Researchers across a wide array of disciplines are interested in finding the most influential subjects in a network. In a network setting, intervention effects and health outcomes can spill over from one node to another through network ties, and influential subjects are expected to have a greater impact than others. For this reason, network research in public health has attempted to maximize health and behavioral changes by intervening on a subset of influential subjects. Although influence is often defined only implicitly in most of the literature, the operative notion of influence is inherently causal in many cases: influential subjects are those we should intervene on to achieve the greatest overall effect across the entire network. In this work, we define a causal notion of influence using potential outcomes. We review existing influence measures, such as node centrality, that largely rely on the particular features of the network structure and/or on certain diffusion models that predict the pattern of information or diseases spreads through network ties. We provide simulation studies to demonstrate when popular centrality measures can agree with our causal measure of influence. As an illustrative example, we apply several popular centrality measures to the HIV risk network in the Transmission Reduction Intervention Project and demonstrate the assumptions under which each centrality can represent the causal influence of each participant in the study.
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Affiliation(s)
- Youjin Lee
- Department of Biostatistics, Brown University, USA
| | | | | | | | - M. Elizabeth Halloran
- Biostatistics, Bioinformatics, and Epidemiology Program, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center
- Department of Biostatistics, University of Washington, USA
| | - Natallia V. Katenka
- Department of Computer Science and Statistics, University of Rhode Island, USA
| | - Jing Wu
- Department of Computer Science and Statistics, University of Rhode Island, USA
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3
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Lee T, Buchanan AL, Katenka NV, Forastiere L, Halloran ME, Friedman SR, Nikolopoulos G. Estimating Causal Effects of HIV Prevention Interventions with Interference in Network-based Studies among People Who Inject Drugs. Ann Appl Stat 2023; 17:2165-2191. [PMID: 38250709 PMCID: PMC10798667 DOI: 10.1214/22-aoas1713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
Evaluating causal effects in the presence of interference is challenging in network-based studies of hard-to-reach populations. Like many such populations, people who inject drugs (PWID) are embedded in social networks and often exert influence on others in their network. In our setting, the study design is observational with a non-randomized network-based HIV prevention intervention. Information is available on each participant and their connections that confer possible HIV risk through injection and sexual behaviors. We considered two inverse probability weighted (IPW) estimators to quantify the population-level spillover effects of non-randomized interventions on subsequent health outcomes. We demonstrated that these two IPW estimators are consistent, asymptotically normal, and derived a closed-form estimator for the asymptotic variance, while allowing for overlapping interference sets (groups of individuals in which the interference is assumed possible). A simulation study was conducted to evaluate the finite-sample performance of the estimators. We analyzed data from the Transmission Reduction Intervention Project, which ascertained a network of PWID and their contacts in Athens, Greece, from 2013 to 2015. We evaluated the effects of community alerts on subsequent HIV risk behavior in this observed network, where the connections or links between participants were defined by using substances or having unprotected sex together. In the study, community alerts were distributed to inform people of recent HIV infections among individuals in close proximity in the observed network. The estimates of the risk differences for spillover using either IPW estimator demonstrated a protective effect. The results suggest that HIV risk behavior could be mitigated by exposure to a community alert when an increased risk of HIV is detected in the network.
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Affiliation(s)
- TingFang Lee
- Department of Pharmacy Practice, University of Rhode Island
| | | | - Natallia V Katenka
- Department of Computer Science and Statistics, University of Rhode Island
| | | | - M Elizabeth Halloran
- Biostatistics, Bioinformatics, and Epidemiology Program, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, and Department of Biostatistics, University of Washington
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4
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Rane MS, Wakefield J, Rohani P, Halloran ME. Association between pertussis vaccination coverage and other sociodemographic factors and pertussis incidence using surveillance data. Epidemics 2023; 44:100689. [PMID: 37295130 PMCID: PMC10584035 DOI: 10.1016/j.epidem.2023.100689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 04/11/2023] [Accepted: 05/12/2023] [Indexed: 06/12/2023] Open
Abstract
Routine vaccination with pertussis vaccines has been successful in driving down pertussis mortality and morbidity globally. Despite high vaccination coverage, countries such as Australia, USA, and UK have experienced increase in pertussis activity over the last few decades. This may be due to local pockets of low vaccination coverage that result in persistence of pertussis in the population and occasionally lead to large outbreaks. The objective of this study was to characterize the association between pertussis vaccination coverage and sociodemographic factors and pertussis incidence at the school district level in King County, Washington, USA. We used monthly pertussis incidence data for all ages reported to the Public Health Seattle and King County between January 1, 2010 and December 31, 2017 to obtain school district level pertussis incidence. We obtained immunization data from the Washington State Immunization Information System to estimate school-district level vaccination coverage as proportion of 19-35 month old children fully vaccinated with ≥4 doses of the Diphtheria-Tetanus-acellular-Pertussis (DTaP) vaccine in a school district. We used two methods to quantify the effects of vaccination coverage on pertussis incidence: an ecological vaccine model and an endemic-epidemic model. Even though the effect of vaccination is modeled differently in the two approaches, both models can be used to estimate the association between vaccination coverage and pertussis incidence. Using the ecological vaccine model, we estimated the vaccine effectiveness of 4 doses of Diphtheria-Tetanus-acellular-Pertussis vaccine to be 83% (95% credible interval: 63%, 95%). In the endemic-epidemic model, under-vaccination was statistically significantly associated with epidemic risk of pertussis (adjusted Relative Risk, aRR: 2.76; 95% confidence interval: 1.44, 16.6). Household size and median income were statistically significantly associated with endemic pertussis risk. The endemic-epidemic model suffers from ecological bias, whereas the ecological vaccine model provides less biased and more interpretable estimates of epidemiological parameters, such as DTaP vaccine effectiveness, for each school district.
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Affiliation(s)
- Madhura S Rane
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA.
| | - Jonathan Wakefield
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA; Department of Statistics, University of Washington, Seattle, WA 98195, USA
| | - Pejman Rohani
- Odum School of Ecology, University of Georgia, Athens, GA, 30602, USA; Department of Infectious Diseases, University of Georgia, Athens, GA, 30602, USA
| | - M Elizabeth Halloran
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA; Department of Biostatistics, University of Washington, Seattle, WA 98195, USA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
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5
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Prasad PV, Steele MK, Reed C, Meyers LA, Du Z, Pasco R, Alfaro-Murillo JA, Lewis B, Venkatramanan S, Schlitt J, Chen J, Orr M, Wilson ML, Eubank S, Wang L, Chinazzi M, Pastore y Piontti A, Davis JT, Halloran ME, Longini I, Vespignani A, Pei S, Galanti M, Kandula S, Shaman J, Haw DJ, Arinaminpathy N, Biggerstaff M. Multimodeling approach to evaluating the efficacy of layering pharmaceutical and nonpharmaceutical interventions for influenza pandemics. Proc Natl Acad Sci U S A 2023; 120:e2300590120. [PMID: 37399393 PMCID: PMC10334766 DOI: 10.1073/pnas.2300590120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 05/21/2023] [Indexed: 07/05/2023] Open
Abstract
When an influenza pandemic emerges, temporary school closures and antiviral treatment may slow virus spread, reduce the overall disease burden, and provide time for vaccine development, distribution, and administration while keeping a larger portion of the general population infection free. The impact of such measures will depend on the transmissibility and severity of the virus and the timing and extent of their implementation. To provide robust assessments of layered pandemic intervention strategies, the Centers for Disease Control and Prevention (CDC) funded a network of academic groups to build a framework for the development and comparison of multiple pandemic influenza models. Research teams from Columbia University, Imperial College London/Princeton University, Northeastern University, the University of Texas at Austin/Yale University, and the University of Virginia independently modeled three prescribed sets of pandemic influenza scenarios developed collaboratively by the CDC and network members. Results provided by the groups were aggregated into a mean-based ensemble. The ensemble and most component models agreed on the ranking of the most and least effective intervention strategies by impact but not on the magnitude of those impacts. In the scenarios evaluated, vaccination alone, due to the time needed for development, approval, and deployment, would not be expected to substantially reduce the numbers of illnesses, hospitalizations, and deaths that would occur. Only strategies that included early implementation of school closure were found to substantially mitigate early spread and allow time for vaccines to be developed and administered, especially under a highly transmissible pandemic scenario.
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Affiliation(s)
- Pragati V. Prasad
- Applied Research and Modeling Team, Influenza Division, United States Centers for Disease Control and Prevention, Atlanta, GA30333
| | - Molly K. Steele
- Applied Research and Modeling Team, Influenza Division, United States Centers for Disease Control and Prevention, Atlanta, GA30333
| | - Carrie Reed
- Applied Research and Modeling Team, Influenza Division, United States Centers for Disease Control and Prevention, Atlanta, GA30333
| | - Lauren Ancel Meyers
- Section of Integrative Biology and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX78712
| | - Zhanwei Du
- Section of Integrative Biology and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX78712
| | - Remy Pasco
- Section of Integrative Biology and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX78712
| | - Jorge A. Alfaro-Murillo
- Department of Biostatistics & Center for Infectious Disease Modeling and Analysis, Yale School of Public Health, New Haven, CT06510
| | - Bryan Lewis
- Biocomplexity Institute & Initiative, University of Virginia, Charlottesville, VA22911
| | | | - James Schlitt
- Biocomplexity Institute & Initiative, University of Virginia, Charlottesville, VA22911
| | - Jiangzhuo Chen
- Biocomplexity Institute & Initiative, University of Virginia, Charlottesville, VA22911
| | - Mark Orr
- Biocomplexity Institute & Initiative, University of Virginia, Charlottesville, VA22911
| | - Mandy L. Wilson
- Biocomplexity Institute & Initiative, University of Virginia, Charlottesville, VA22911
| | - Stephen Eubank
- Biocomplexity Institute & Initiative, University of Virginia, Charlottesville, VA22911
- Public Health Sciences, University of Virginia, Charlottesville, VA22903
| | - Lijing Wang
- Biocomplexity Institute & Initiative, University of Virginia, Charlottesville, VA22911
| | - Matteo Chinazzi
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA02115
| | - Ana Pastore y Piontti
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA02115
| | - Jessica T. Davis
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA02115
| | - M. Elizabeth Halloran
- Fred Hutchinson Cancer Research Center, Seattle, WA98109
- Department of Biostatistics, University of Washington, Seattle, WA98195
| | - Ira Longini
- Department of Biostatistics, College of Public Health and Health Professions, University of Florida, Gainesville, FL32603
| | - Alessandro Vespignani
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA02115
| | - Sen Pei
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY10032
| | - Marta Galanti
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY10032
| | - Sasikiran Kandula
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY10032
| | - Jeffrey Shaman
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY10032
| | - David J. Haw
- Medical Research Council Centre for Global Infectious Disease Analysis, Imperial College London, LondonSW7 2AZ, United Kingdom
| | - Nimalan Arinaminpathy
- Medical Research Council Centre for Global Infectious Disease Analysis, Imperial College London, LondonSW7 2AZ, United Kingdom
| | - Matthew Biggerstaff
- Applied Research and Modeling Team, Influenza Division, United States Centers for Disease Control and Prevention, Atlanta, GA30333
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6
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Rogers JH, Cox SN, Link AC, Nwanne G, Han PD, Pfau B, Chow EJ, Wolf CR, Boeckh M, Hughes JP, Halloran ME, Uyeki TM, Shim MM, Duchin J, Englund JA, Mosites E, Rolfes MA, Starita LA, Chu HY. Incidence of SARS-CoV-2 infection and associated risk factors among staff and residents at homeless shelters in King County, Washington: an active surveillance study. Epidemiol Infect 2023; 151:e129. [PMID: 37424310 PMCID: PMC10540173 DOI: 10.1017/s0950268823001036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 03/16/2023] [Accepted: 06/12/2023] [Indexed: 07/11/2023] Open
Abstract
Homeless shelter residents and staff may be at higher risk of SARS-CoV-2 infection. However, SARS-CoV-2 infection estimates in this population have been reliant on cross-sectional or outbreak investigation data. We conducted routine surveillance and outbreak testing in 23 homeless shelters in King County, Washington, to estimate the occurrence of laboratory-confirmed SARS-CoV-2 infection and risk factors during 1 January 2020-31 May 2021. Symptom surveys and nasal swabs were collected for SARS-CoV-2 testing by RT-PCR for residents aged ≥3 months and staff. We collected 12,915 specimens from 2,930 unique participants. We identified 4.74 (95% CI 4.00-5.58) SARS-CoV-2 infections per 100 individuals (residents: 4.96, 95% CI 4.12-5.91; staff: 3.86, 95% CI 2.43-5.79). Most infections were asymptomatic at the time of detection (74%) and detected during routine surveillance (73%). Outbreak testing yielded higher test positivity than routine surveillance (2.7% versus 0.9%). Among those infected, residents were less likely to report symptoms than staff. Participants who were vaccinated against seasonal influenza and were current smokers had lower odds of having an infection detected. Active surveillance that includes SARS-CoV-2 testing of all persons is essential in ascertaining the true burden of SARS-CoV-2 infections among residents and staff of congregate settings.
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Affiliation(s)
- Julia H. Rogers
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Sarah N. Cox
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Amy C. Link
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Gift Nwanne
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Peter D. Han
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Brian Pfau
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Eric J. Chow
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Caitlin R. Wolf
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Michael Boeckh
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - James P. Hughes
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - M. Elizabeth Halloran
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Timothy M. Uyeki
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - M. Mia Shim
- Public Health – Seattle & King County, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Jeffrey Duchin
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA, USA
- Public Health – Seattle & King County, Seattle, WA, USA
| | - Janet A. Englund
- Division of Pediatric Infectious Diseases, Department of Pediatrics, University of Washington, Seattle Children’s Research Institute, Seattle, WA, USA
| | - Emily Mosites
- Office of the Deputy Director for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Melissa A. Rolfes
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Lea A. Starita
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Helen Y. Chu
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA, USA
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7
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Madewell ZJ, Yang Y, Longini IM, Halloran ME, Vespignani A, Dean NE. Rapid review and meta-analysis of serial intervals for SARS-CoV-2 Delta and Omicron variants. BMC Infect Dis 2023; 23:429. [PMID: 37365505 DOI: 10.1186/s12879-023-08407-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 06/20/2023] [Indexed: 06/28/2023] Open
Abstract
BACKGROUND The serial interval is the period of time between symptom onset in the primary case and symptom onset in the secondary case. Understanding the serial interval is important for determining transmission dynamics of infectious diseases like COVID-19, including the reproduction number and secondary attack rates, which could influence control measures. Early meta-analyses of COVID-19 reported serial intervals of 5.2 days (95% CI: 4.9-5.5) for the original wild-type variant and 5.2 days (95% CI: 4.87-5.47) for Alpha variant. The serial interval has been shown to decrease over the course of an epidemic for other respiratory diseases, which may be due to accumulating viral mutations and implementation of more effective nonpharmaceutical interventions. We therefore aggregated the literature to estimate serial intervals for Delta and Omicron variants. METHODS This study followed Preferred Reporting Items for Systematic Reviews and Meta-analyses guidelines. A systematic literature search was conducted of PubMed, Scopus, Cochrane Library, ScienceDirect, and preprint server medRxiv for articles published from April 4, 2021, through May 23, 2023. Search terms were: ("serial interval" or "generation time"), ("Omicron" or "Delta"), and ("SARS-CoV-2" or "COVID-19"). Meta-analyses were done for Delta and Omicron variants using a restricted maximum-likelihood estimator model with a random effect for each study. Pooled average estimates and 95% confidence intervals (95% CI) are reported. RESULTS There were 46,648 primary/secondary case pairs included for the meta-analysis of Delta and 18,324 for Omicron. Mean serial interval for included studies ranged from 2.3-5.8 days for Delta and 2.1-4.8 days for Omicron. The pooled mean serial interval for Delta was 3.9 days (95% CI: 3.4-4.3) (20 studies) and Omicron was 3.2 days (95% CI: 2.9-3.5) (20 studies). Mean estimated serial interval for BA.1 was 3.3 days (95% CI: 2.8-3.7) (11 studies), BA.2 was 2.9 days (95% CI: 2.7-3.1) (six studies), and BA.5 was 2.3 days (95% CI: 1.6-3.1) (three studies). CONCLUSIONS Serial interval estimates for Delta and Omicron were shorter than ancestral SARS-CoV-2 variants. More recent Omicron subvariants had even shorter serial intervals suggesting serial intervals may be shortening over time. This suggests more rapid transmission from one generation of cases to the next, consistent with the observed faster growth dynamic of these variants compared to their ancestors. Additional changes to the serial interval may occur as SARS-CoV-2 continues to circulate and evolve. Changes to population immunity (due to infection and/or vaccination) may further modify it.
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Affiliation(s)
- Zachary J Madewell
- Department of Biostatistics, University of Florida, Gainesville, FL, USA.
| | - Yang Yang
- Department of Statistics, University of Georgia, Athens, GA, USA
| | - Ira M Longini
- Department of Biostatistics, University of Florida, Gainesville, FL, USA
| | - M Elizabeth Halloran
- Department of Biostatistics, University of Washington, Seattle, WA, USA
- Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Alessandro Vespignani
- Laboratory for the Modeling of Biological and Socio-Technical Systems, Northeastern University, Boston, MA, USA
| | - Natalie E Dean
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA, USA
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8
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Gozzi N, Chinazzi M, Dean NE, Longini IM, Halloran ME, Perra N, Vespignani A. Estimating the impact of COVID-19 vaccine inequities: a modeling study. Nat Commun 2023; 14:3272. [PMID: 37277329 DOI: 10.1038/s41467-023-39098-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 05/25/2023] [Indexed: 06/07/2023] Open
Abstract
Access to COVID-19 vaccines on the global scale has been drastically hindered by structural socio-economic disparities. Here, we develop a data-driven, age-stratified epidemic model to evaluate the effects of COVID-19 vaccine inequities in twenty lower middle and low income countries (LMIC) selected from all WHO regions. We investigate and quantify the potential effects of higher or earlier doses availability. In doing so, we focus on the crucial initial months of vaccine distribution and administration, exploring counterfactual scenarios where we assume the same per capita daily vaccination rate reported in selected high income countries. We estimate that more than 50% of deaths (min-max range: [54-94%]) that occurred in the analyzed countries could have been averted. We further consider scenarios where LMIC had similarly early access to vaccine doses as high income countries. Even without increasing the number of doses, we estimate an important fraction of deaths (min-max range: [6-50%]) could have been averted. In the absence of the availability of high-income countries, the model suggests that additional non-pharmaceutical interventions inducing a considerable relative decrease of transmissibility (min-max range: [15-70%]) would have been required to offset the lack of vaccines. Overall, our results quantify the negative impacts of vaccine inequities and underscore the need for intensified global efforts devoted to provide faster access to vaccine programs in low and lower-middle-income countries.
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Affiliation(s)
- Nicolò Gozzi
- Networks and Urban Systems Centre, University of Greenwich, London, UK
- ISI Foundation, Turin, Italy
| | - Matteo Chinazzi
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA, USA
| | - Natalie E Dean
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA, USA
| | - Ira M Longini
- Department of Biostatistics, College of Public Health and Health Professions, University of Florida, Gainesville, FL, USA
| | - M Elizabeth Halloran
- Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Nicola Perra
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA, USA.
- School of Mathematical Sciences, Queen Mary University, London, UK.
| | - Alessandro Vespignani
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA, USA
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9
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Crisp AM, Halloran ME, Longini IM, Vazquez-Prokopec G, Dean NE. Covariate-constrained randomization with cluster selection and substitution. Clin Trials 2023; 20:284-292. [PMID: 36932663 PMCID: PMC10257748 DOI: 10.1177/17407745231160556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
Abstract
BACKGROUND An ongoing cluster-randomized trial for the prevention of arboviral diseases utilizes covariate-constrained randomization to balance two treatment arms across four specified covariates and geographic sector. Each cluster is within a census tract of the city of Mérida, Mexico, and there were 133 eligible tracts from which to select 50. As some selected clusters may have been subsequently found unsuitable in the field, we desired a strategy to substitute new clusters while maintaining covariate balance. METHODS We developed an algorithm that successfully identified a subset of clusters that maximized the average minimum pairwise distance between clusters in order to reduce contamination and balanced the specified covariates both before and after substitutions were made. SIMULATIONS Simulations were performed to explore some limitations of this algorithm. The number of selected clusters and eligible clusters were varied along with the method of selecting the final allocation pattern. CONCLUSION The algorithm is presented here as a series of optional steps that can be added to the standard covariate-constrained randomization process in order to achieve spatial dispersion, cluster subsampling, and cluster substitution. Simulation results indicate that these extensions can be used without loss of statistical validity, given a sufficient number of clusters included in the trial.
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Affiliation(s)
- Amy M Crisp
- Department of Biostatistics, Colleges of Public Health and Health Professions, and Medicine, University of Florida, Gainesville, FL, USA
| | - M Elizabeth Halloran
- Department of Biostatistics, University of Washington, Seattle, WA, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Ira M Longini
- Department of Biostatistics, Colleges of Public Health and Health Professions, and Medicine, University of Florida, Gainesville, FL, USA
| | | | - Natalie E Dean
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA, USA
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10
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Schwartz LM, Oshinsky J, Reymann M, Esona MD, Bowen MD, Jahangir Hossain M, Zaman SMA, Jones JCM, Antonio M, Badji H, Sarwar G, Sow SO, Sanogo D, Keita AM, Tamboura B, Traoré A, Onwuchekwa U, Omore R, Verani JR, Awuor AO, Ochieng JB, Juma J, Ogwel B, Parashar UD, Tate JE, Kasumba IN, Tennant SM, Neuzil KM, Rowhani-Rahbar A, Elizabeth Halloran M, Atmar RL, Pasetti MF, Kotloff KL. Histo-Blood Group Antigen Null Phenotypes Associated With a Decreased Risk of Clinical Rotavirus Vaccine Failure Among Children <2 Years of Age Participating in the Vaccine Impact on Diarrhea in Africa (VIDA) Study in Kenya, Mali, and the Gambia. Clin Infect Dis 2023; 76:S153-S161. [PMID: 37074435 PMCID: PMC10116560 DOI: 10.1093/cid/ciac910] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023] Open
Abstract
BACKGROUND Previously studied risk factors for rotavirus vaccine failure have not fully explained reduced rotavirus vaccine effectiveness in low-income settings. We assessed the relationship between histo-blood group antigen (HBGA) phenotypes and clinical rotavirus vaccine failure among children <2 years of age participating in the Vaccine Impact on Diarrhea in Africa Study in 3 sub-Saharan African countries. METHODS Saliva was collected and tested for HBGA phenotype in children who received rotavirus vaccine. The association between secretor and Lewis phenotypes and rotavirus vaccine failure was examined overall and by infecting rotavirus genotype using conditional logistic regression in 218 rotavirus-positive cases with moderate-to-severe diarrhea and 297 matched healthy controls. RESULTS Both nonsecretor and Lewis-negative phenotypes (null phenotypes) were associated with decreased rotavirus vaccine failure across all sites (matched odds ratio, 0.30 [95% confidence interval: 0.16-0.56] or 0.39 [0.25-0.62], respectively]. A similar decrease in risk against rotavirus vaccine failure among null HBGA phenotypes was observed for cases with P[8] and P[4] infection and their matched controls. While we found no statistically significant association between null HBGA phenotypes and vaccine failure among P[6] infections, the matched odds ratio point estimate for Lewis-negative individuals was >4. CONCLUSIONS Our study demonstrated a significant relationship between null HBGA phenotypes and decreased rotavirus vaccine failure in a population with P[8] as the most common infecting genotype. Further studies are needed in populations with a large burden of P[6] rotavirus diarrhea to understand the role of host genetics in reduced rotavirus vaccine effectiveness.
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Affiliation(s)
- Lauren M Schwartz
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Jennifer Oshinsky
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Mardi Reymann
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Mathew D Esona
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Michael D Bowen
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - M Jahangir Hossain
- Medical Research Council Unit, The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Syed M A Zaman
- Medical Research Council Unit, The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Joquina Chiquita M Jones
- Medical Research Council Unit, The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Martin Antonio
- Medical Research Council Unit, The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Henry Badji
- Medical Research Council Unit, The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Golam Sarwar
- Medical Research Council Unit, The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Samba O Sow
- Centre pour le Développement des Vaccins du Mali, Bamako, Mali
| | - Doh Sanogo
- Centre pour le Développement des Vaccins du Mali, Bamako, Mali
| | | | - Boubou Tamboura
- Centre pour le Développement des Vaccins du Mali, Bamako, Mali
| | - Awa Traoré
- Centre pour le Développement des Vaccins du Mali, Bamako, Mali
| | - Uma Onwuchekwa
- Centre pour le Développement des Vaccins du Mali, Bamako, Mali
| | - Richard Omore
- Kenya Medical Research Institute, Center for Global Health Research, Kisumu, Kenya
| | - Jennifer R Verani
- Division of Global Health Protection, US Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Alex O Awuor
- Kenya Medical Research Institute, Center for Global Health Research, Kisumu, Kenya
| | - John B Ochieng
- Kenya Medical Research Institute, Center for Global Health Research, Kisumu, Kenya
| | - Jane Juma
- Kenya Medical Research Institute, Center for Global Health Research, Kisumu, Kenya
| | - Billy Ogwel
- Kenya Medical Research Institute, Center for Global Health Research, Kisumu, Kenya
| | - Umesh D Parashar
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jacqueline E Tate
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Irene N Kasumba
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Sharon M Tennant
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Kathleen M Neuzil
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Ali Rowhani-Rahbar
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, Washington, USA
| | - M Elizabeth Halloran
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, Washington, USA
- Center for Inference and Dynamics of Infectious Diseases, Seattle, Washington, USA
| | - Robert L Atmar
- Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Marcela F Pasetti
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Karen L Kotloff
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, Maryland, USA
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11
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Aroke H, Buchanan A, Katenka N, Crawford FW, Lee T, Halloran ME, Latkin C. Evaluating the Mediating Role of Recall of Intervention Knowledge in the Relationship Between a Peer-Driven Intervention and HIV Risk Behaviors Among People Who Inject Drugs. AIDS Behav 2023; 27:578-590. [PMID: 35932359 PMCID: PMC10408304 DOI: 10.1007/s10461-022-03792-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/07/2022] [Indexed: 11/01/2022]
Abstract
Peer-driven interventions can be effective in reducing HIV injection risk behaviors among people who inject drugs (PWID). We employed a causal mediation framework to examine the mediating role of recall of intervention knowledge in the relationship between a peer-driven intervention and subsequent self-reported HIV injection-related risk behavior among PWID in the HIV Prevention Trials Network (HPTN) 037 study. For each intervention network, the index participant received training at baseline to become a peer educator, while non-index participants and all participants in the control networks received only HIV testing and counseling; recall of intervention knowledge was measured at the 6-month visit for each participant, and each participant was followed to ascertain HIV injection-related risk behaviors at the 12-month visit. We used inverse probability weighting to fit marginal structural models to estimate the total effect (TE) and controlled direct effect (CDE) of the intervention on the outcome. The proportion eliminated (PE) by intervening to remove mediation by the recall of intervention knowledge was computed. There were 385 participants (47% in intervention networks) included in the analysis. The TE and CDE risk ratios for the intervention were 0.47 [95% confidence interval (CI): 0.28, 0.78] and 0.73 (95% CI: 0.26, 2.06) and the PE was 49%. Compared to participants in the control networks, the peer-driven intervention reduced the risk of HIV injection-related risk behavior by 53%. The mediating role of recall of intervention knowledge accounted for less than 50% of the total effect of the intervention, suggesting that other potential causal pathways between the intervention and the outcome, such as motivation and skill, self-efficacy, social norms and behavior modeling, should be considered in future studies.
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Affiliation(s)
- Hilary Aroke
- Department of Pharmacy Practice, College of Pharmacy, University of Rhode Island, 7 Greenhouse Road, Kingston, RI, 02881, USA.
| | - Ashley Buchanan
- Department of Pharmacy Practice, College of Pharmacy, University of Rhode Island, 7 Greenhouse Road, Kingston, RI, 02881, USA
- Department of Computer Science and Statistics, College of Arts & Science, University of Rhode Island, Kingston, RI, 02281, USA
| | - Natallia Katenka
- Department of Computer Science and Statistics, College of Arts & Science, University of Rhode Island, Kingston, RI, 02281, USA
| | - Forrest W Crawford
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, 06510, USA
- Department of Statistics & Data Science, Yale University, New Haven, CT, 06510, USA
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, 06510, USA
- Yale School of Management, Yale University, New Haven, CT, 06510, USA
| | - TingFang Lee
- Department of Pharmacy Practice, College of Pharmacy, University of Rhode Island, 7 Greenhouse Road, Kingston, RI, 02881, USA
| | - M Elizabeth Halloran
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seatle, WA, 98109, USA
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA, 98195, USA
| | - Carl Latkin
- Department of Health, Behavior, and Society, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
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12
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Abstract
Rosenbaum and Rubin's (1983) propensity score revolutionized the field of causal inference and has emerged as a standard tool when researchers reason about cause-and-effect relationship across many disciplines. This discussion centers around the key "no interference" assumption in Rosenbaum and Rubin's original development of the propensity score and reviews some recent advances in extending the propensity score to studies involving dependent happenings.
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Affiliation(s)
- Bo Zhang
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Michael G Hudgens
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - M Elizabeth Halloran
- Department of Biostatistics, University of Washington, and Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington
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13
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Longini IM, Yang Y, Fleming TR, Muñoz-Fontela C, Wang R, Ellenberg SS, Qian G, Halloran ME, Nason M, Gruttola VD, Mulangu S, Huang Y, Donnelly CA, Henao Restrepo AM. A platform trial design for preventive vaccines against Marburg virus and other emerging infectious disease threats. Clin Trials 2022; 19:647-654. [PMID: 35866633 PMCID: PMC9679315 DOI: 10.1177/17407745221110880] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
BACKGROUND The threat of a possible Marburg virus disease outbreak in Central and Western Africa is growing. While no Marburg virus vaccines are currently available for use, several candidates are in the pipeline. Building on knowledge and experiences in the designs of vaccine efficacy trials against other pathogens, including SARS-CoV-2, we develop designs of randomized Phase 3 vaccine efficacy trials for Marburg virus vaccines. METHODS A core protocol approach will be used, allowing multiple vaccine candidates to be tested against controls. The primary objective of the trial will be to evaluate the effect of each vaccine on the rate of virologically confirmed Marburg virus disease, although Marburg infection assessed via seroconversion could be the primary objective in some cases. The overall trial design will be a mixture of individually and cluster-randomized designs, with individual randomization done whenever possible. Clusters will consist of either contacts and contacts of contacts of index cases, that is, ring vaccination, or other transmission units. RESULTS The primary efficacy endpoint will be analysed as a time-to-event outcome. A vaccine will be considered successful if its estimated efficacy is greater than 50% and has sufficient precision to rule out that true efficacy is less than 30%. This will require approximately 150 total endpoints, that is, cases of confirmed Marburg virus disease, per vaccine/comparator combination. Interim analyses will be conducted after 50 and after 100 events. Statistical analysis of the trial will be blended across the different types of designs. Under the assumption of a 6-month attack rate of 1% of the participants in the placebo arm for both the individually and cluster-randomized populations, the most likely sample size is about 20,000 participants per arm. CONCLUSION This event-driven design takes into the account the potentially sporadic spread of Marburg virus. The proposed trial design may be applicable for other pathogens against which effective vaccines are not yet available.
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Affiliation(s)
- Ira M Longini
- Department of Biostatistics, University of Florida, Gainesville, FL, USA,Ira M Longini, Department of Biostatistics, University of Florida, Gainesville, FL 32611, USA.
| | - Yang Yang
- Department of Biostatistics, University of Florida, Gainesville, FL, USA
| | - Thomas R Fleming
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - César Muñoz-Fontela
- Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Germany,German Center for Infection Research, DZIF, Partner site Hamburg, Hamburg, Germany
| | - Rui Wang
- Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, Boston, MA, USA,Department of Biostatistics, Harvard University, Boston, MA, USA
| | - Susan S Ellenberg
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, PA, USA
| | - George Qian
- London School of Hygiene & Tropical Medicine, London, UK
| | - M Elizabeth Halloran
- Department of Biostatistics, University of Washington, Seattle, WA, USA,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Martha Nason
- Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases (NIAID/NIH), Bethesda, MD, USA
| | | | - Sabue Mulangu
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | - Yunda Huang
- London School of Hygiene & Tropical Medicine, London, UK
| | - Christl A Donnelly
- Department of Statistics, University of Oxford, Oxford, UK,Department of Infectious Disease Epidemiology, Imperial College London, London, UK
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14
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Gozzi N, Chinazzi M, Dean NE, Longini IM, Halloran ME, Perra N, Vespignani A. Estimating the impact of COVID-19 vaccine allocation inequities: a modeling study. medRxiv 2022:2022.11.18.22282514. [PMID: 36415459 PMCID: PMC9681050 DOI: 10.1101/2022.11.18.22282514] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Access to COVID-19 vaccines on the global scale has been drastically impacted by structural socio-economic inequities. Here, we develop a data-driven, age-stratified epidemic model to evaluate the effects of COVID-19 vaccine inequities in twenty lower middle and low income countries (LMIC) sampled from all WHO regions. We focus on the first critical months of vaccine distribution and administration, exploring counterfactual scenarios where we assume the same per capita daily vaccination rate reported in selected high income countries. We estimate that, in this high vaccine availability scenario, more than 50% of deaths (min-max range: [56% - 99%]) that occurred in the analyzed countries could have been averted. We further consider a scenario where LMIC had similarly early access to vaccine doses as high income countries; even without increasing the number of doses, we estimate an important fraction of deaths (min-max range: [7% - 73%]) could have been averted. In the absence of equitable allocation, the model suggests that considerable additional non-pharmaceutical interventions would have been required to offset the lack of vaccines (min-max range: [15% - 75%]). Overall, our results quantify the negative impacts of vaccines inequities and call for amplified global efforts to provide better access to vaccine programs in low and lower middle income countries.
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15
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Johnson PLF, Bergstrom CT, Regoes RR, Longini IM, Halloran ME, Antia R. Evolutionary consequences of delaying intervention for monkeypox. Lancet 2022; 400:1191-1193. [PMID: 36152668 PMCID: PMC9534010 DOI: 10.1016/s0140-6736(22)01789-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 09/05/2022] [Indexed: 01/06/2023]
Affiliation(s)
- Philip L F Johnson
- Department of Biology, University of Maryland, College Park, MA, 20742, USA.
| | - Carl T Bergstrom
- Department of Biology, University of Washington, Seattle, WA, USA
| | - Roland R Regoes
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Ira M Longini
- Department of Biostatistics, University of Florida, Gainesville, FL, USA
| | - M Elizabeth Halloran
- Department of Biostatistics, University of Washington, Seattle, WA, USA; Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Rustom Antia
- Department of Biology, Emory University, Atlanta, GA, USA
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16
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Aleta A, Martín-Corral D, Bakker MA, Pastore Y Piontti A, Ajelli M, Litvinova M, Chinazzi M, Dean NE, Halloran ME, Longini IM, Pentland A, Vespignani A, Moreno Y, Moro E. Quantifying the importance and location of SARS-CoV-2 transmission events in large metropolitan areas. Proc Natl Acad Sci U S A 2022; 119:e2112182119. [PMID: 35696558 DOI: 10.1101/2020.12.15.20248273] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023] Open
Abstract
Detailed characterization of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission across different settings can help design less disruptive interventions. We used real-time, privacy-enhanced mobility data in the New York City, NY and Seattle, WA metropolitan areas to build a detailed agent-based model of SARS-CoV-2 infection to estimate the where, when, and magnitude of transmission events during the pandemic's first wave. We estimate that only 18% of individuals produce most infections (80%), with about 10% of events that can be considered superspreading events (SSEs). Although mass gatherings present an important risk for SSEs, we estimate that the bulk of transmission occurred in smaller events in settings like workplaces, grocery stores, or food venues. The places most important for transmission change during the pandemic and are different across cities, signaling the large underlying behavioral component underneath them. Our modeling complements case studies and epidemiological data and indicates that real-time tracking of transmission events could help evaluate and define targeted mitigation policies.
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Affiliation(s)
| | - David Martín-Corral
- Departamento de Matemáticas, Universidad Carlos III de Madrid, 28911 Leganés, Spain
- Grupo Interdisciplinar de Sistemas Complejos, Universidad Carlos III de Madrid, 28911 Leganés, Spain
- Zensei Technologies S.L., 28010 Madrid, Spain
| | - Michiel A Bakker
- Connection Science, Institute for Data Science and Society, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Ana Pastore Y Piontti
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA 02115
| | - Marco Ajelli
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA 02115
- Laboratory for Computational Epidemiology and Public Health, Department of Epidemiology and Biostatistics, Indiana University School of Public Health, Bloomington, IN 47405
| | - Maria Litvinova
- Laboratory for Computational Epidemiology and Public Health, Department of Epidemiology and Biostatistics, Indiana University School of Public Health, Bloomington, IN 47405
| | - Matteo Chinazzi
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA 02115
| | - Natalie E Dean
- Department of Biostatistics, College of Public Health and Health Professions, University of Florida, Gainesville, FL 32611
| | - M Elizabeth Halloran
- Biostatistics, Bioinformatics, and Epidemiology Program, Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
- Department of Biostatistics, University of Washington, Seattle, WA 98195
| | - Ira M Longini
- Department of Biostatistics, College of Public Health and Health Professions, University of Florida, Gainesville, FL 32611
| | - Alex Pentland
- Connection Science, Institute for Data Science and Society, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Alessandro Vespignani
- ISI Foundation, 10126 Turin, Italy
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA 02115
| | - Yamir Moreno
- ISI Foundation, 10126 Turin, Italy
- Institute for Biocomputation and Physics of Complex Systems, University of Zaragoza, 50018 Zaragoza, Spain
- Department of Theoretical Physics, Faculty of Sciences, University of Zaragoza, 50009 Zaragoza, Spain
| | - Esteban Moro
- Departamento de Matemáticas, Universidad Carlos III de Madrid, 28911 Leganés, Spain
- Grupo Interdisciplinar de Sistemas Complejos, Universidad Carlos III de Madrid, 28911 Leganés, Spain
- Connection Science, Institute for Data Science and Society, Massachusetts Institute of Technology, Cambridge, MA 02139
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17
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Madewell ZJ, Yang Y, Longini IM, Halloran ME, Dean NE. Household Secondary Attack Rates of SARS-CoV-2 by Variant and Vaccination Status: An Updated Systematic Review and Meta-analysis. JAMA Netw Open 2022; 5:e229317. [PMID: 35482308 PMCID: PMC9051991 DOI: 10.1001/jamanetworkopen.2022.9317] [Citation(s) in RCA: 100] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
IMPORTANCE An overall household secondary attack rate (SAR) of 18.9% (95% CI, 16.2%-22.0%) through June 17, 2021 was previously reported for SARS-CoV-2. Emerging variants of concern and increased vaccination have affected transmission rates. OBJECTIVE To evaluate how reported household SARs changed over time and whether SARs varied by viral variant and index case and contact vaccination status. DATA SOURCES PubMed and medRxiv from June 18, 2021, through March 8, 2022, and reference lists of eligible articles. Preprints were included. STUDY SELECTION Articles with original data reporting the number of infected and total number of household contacts. Search terms included SARS-CoV-2, COVID-19, variant, vaccination, secondary attack rate, secondary infection rate, household, index case, family contacts, close contacts, and family transmission. DATA EXTRACTION AND SYNTHESIS The Preferred Reporting Items for Systematic Reviews and Meta-Analyses reporting guideline was followed. Meta-analyses used generalized linear mixed models to obtain SAR estimates and 95% CIs. MAIN OUTCOMES AND MEASURES SAR stratified by covariates according to variant, index case and contact vaccination status, and index case identification period. SARs were used to estimate vaccine effectiveness on the basis of the transmission probability for susceptibility to infection (VES,p), infectiousness given infection (VEI,p), and total vaccine effectiveness (VET,p). RESULTS Household SARs were higher for 33 studies with midpoints in 2021 to 2022 (37.3%; 95% CI, 32.7% to 42.1%) compared with 63 studies with midpoints through April 2020 (15.5%; 95% CI, 13.2% to 18.2%). Household SARs were 42.7% (95% CI, 35.4% to 50.4%) for Omicron (7 studies), 36.4% (95% CI, 33.4% to 39.5%) for Alpha (11 studies), 29.7% (95% CI, 23.0% to 37.3%) for Delta (16 studies), and 22.5% (95% CI, 18.6% to 26.8%) for Beta (3 studies). For full vaccination, VES,p was 78.6% (95% CI, 76.0% to 80.9%) for Alpha, 56.4% (95% CI, 54.6% to 58.1%) for Delta, and 18.1% (95% CI, -18.3% to 43.3%) for Omicron; VEI,p was 75.3% (95% CI, 69.9% to 79.8%) for Alpha, 21.9% (95% CI, 11.0% to 31.5%) for Delta, and 18.2% (95% CI, 0.6% to 32.6%) for Omicron; and VET,p was 94.7% (95% CI, 93.3% to 95.8%) for Alpha, 64.4% (95% CI, 58.0% to 69.8%) for Delta, and 35.8% (95% CI, 13.0% to 52.6%) for Omicron. CONCLUSIONS AND RELEVANCE These results suggest that emerging SARS-CoV-2 variants of concern have increased transmissibility. Full vaccination was associated with reductions in susceptibility and infectiousness, but more so for Alpha than Delta and Omicron. The changes in estimated vaccine effectiveness underscore the challenges of developing effective vaccines concomitant with viral evolution.
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Affiliation(s)
| | - Yang Yang
- Department of Biostatistics, University of Florida, Gainesville
| | - Ira M. Longini
- Department of Biostatistics, University of Florida, Gainesville
| | - M. Elizabeth Halloran
- Fred Hutchinson Cancer Research Center, Seattle, Washington
- Department of Biostatistics, University of Washington, Seattle
| | - Natalie E. Dean
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, Georgia
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18
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Ulrich AK, McKearnan SB, Lammert S, Wolfson J, Pletcher J, Halloran ME, Basta NE. Validity of university students' self-reported vaccination status after a meningococcal B outbreak. J Am Coll Health 2022; 70:824-829. [PMID: 32672510 PMCID: PMC7881838 DOI: 10.1080/07448481.2020.1772270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 01/29/2020] [Accepted: 03/29/2020] [Indexed: 06/11/2023]
Abstract
After an outbreak of meningococcal B (MenB) disease at a university, we surveyed students regarding their vaccination status 2 months and 20 months after campus-led vaccination campaigns and compared students' self-report to vaccination records. Nearly all participants accurately reported the number of vaccine doses at both visits. Among those who received two doses of the vaccine, accurate recall of the timing of MenB vaccination was 85.7% (95% CI: 82.7-88.6) in the short term and 62.9% (95% CI: 56.0-69.8) in the long term. After the outbreak, only one-third reported feeling 'very confident' in their MenB disease and vaccine knowledge. Our findings suggest that the validity of self-reported vaccination status among university students in an outbreak setting is high, but that if the duration of protection is unknown and additional doses of vaccine may be needed, documented vaccination records may be preferred over self-report to assess timing of vaccine receipt.
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Affiliation(s)
- Angela K Ulrich
- University of Minnesota, School of Public Health, Division of Epidemiology and Community Health, Minneapolis, MN, USA
| | - Shannon B McKearnan
- University of Minnesota, School of Public Health, Division of Biostatistics, Minneapolis, MN, USA
| | - Sara Lammert
- University of Minnesota, School of Public Health, Division of Epidemiology and Community Health, Minneapolis, MN, USA
| | - Julian Wolfson
- University of Minnesota, School of Public Health, Division of Biostatistics, Minneapolis, MN, USA
| | - Jonathan Pletcher
- Princeton University, University Health Services, Princeton, NJ, USA
| | - M Elizabeth Halloran
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
- University of Washington, School of Public Health, Department of Biostatistics, Seattle, WA, USA
| | - Nicole E Basta
- McGill University, Faculty of Medicine, Department of Epidemiology, Biostatistics, and Occupational Health, Montreal, Quebec, Canada
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19
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Abstract
How much do COVID-19 vaccines reduce transmission? The answer is a moving target.
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Affiliation(s)
- Natalie E Dean
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA, USA
| | - M Elizabeth Halloran
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Biostatistics, University of Washington, Seattle, WA, USA
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20
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Madewell ZJ, Yang Y, Longini IM, Halloran ME, Dean NE. Household secondary attack rates of SARS-CoV-2 by variant and vaccination status: an updated systematic review and meta-analysis. medRxiv 2022:2022.01.09.22268984. [PMID: 35043125 PMCID: PMC8764734 DOI: 10.1101/2022.01.09.22268984] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We previously reported a household secondary attack rate (SAR) for SARS-CoV-2 of 18.9% through June 17, 2021. To examine how emerging variants and increased vaccination have affected transmission rates, we searched PubMed from June 18, 2021, through January 7, 2022. Meta-analyses used generalized linear mixed models to obtain SAR estimates and 95%CI, disaggregated by several covariates. SARs were used to estimate vaccine effectiveness based on the transmission probability for susceptibility ( VE S,p ), infectiousness ( VE I,p ), and total vaccine effectiveness ( VE T,p ). Household SAR for 27 studies with midpoints in 2021 was 35.8% (95%CI, 30.6%-41.3%), compared to 15.7% (95%CI, 13.3%-18.4%) for 62 studies with midpoints through April 2020. Household SARs were 38.0% (95%CI, 36.0%-40.0%), 30.8% (95%CI, 23.5%-39.3%), and 22.5% (95%CI, 18.6%-26.8%) for Alpha, Delta, and Beta, respectively. VE I,p , VE S,p , and VE T,p were 56.6% (95%CI, 28.7%-73.6%), 70.3% (95%CI, 59.3%-78.4%), and 86.8% (95%CI, 76.7%-92.5%) for full vaccination, and 27.5% (95%CI, -6.4%-50.7%), 43.9% (95%CI, 21.8%-59.7%), and 59.9% (95%CI, 34.4%-75.5%) for partial vaccination, respectively. Household contacts exposed to Alpha or Delta are at increased risk of infection compared to the original wild-type strain. Vaccination reduced susceptibility to infection and transmission to others. SUMMARY Household secondary attack rates (SARs) were higher for Alpha and Delta variants than previous estimates. SARs were higher to unvaccinated contacts than to partially or fully vaccinated contacts and were higher from unvaccinated index cases than from fully vaccinated index cases.
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Affiliation(s)
| | - Yang Yang
- Department of Biostatistics, University of Florida, Gainesville, FL
| | - Ira M. Longini
- Department of Biostatistics, University of Florida, Gainesville, FL
| | - M. Elizabeth Halloran
- Fred Hutchinson Cancer Research Center, Seattle, WA
- Department of Biostatistics, University of Washington, Seattle, WA
| | - Natalie E. Dean
- Department of Biostatistics, University of Florida, Gainesville, FL
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21
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Potter GE, Carnegie NB, Sugimoto JD, Diallo A, Victor JC, Neuzil KM, Halloran ME. Using social contact data to improve the overall effect estimate of a cluster-randomized influenza vaccination program in Senegal. J R Stat Soc Ser C Appl Stat 2022; 71:70-90. [PMID: 35721226 PMCID: PMC9202735 DOI: 10.1111/rssc.12522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
This study estimates the overall effect of two influenza vaccination programs consecutively administered in a cluster-randomized trial in western Senegal over the course of two influenza seasons from 2009-2011. We apply cutting-edge methodology combining social contact data with infection data to reduce bias in estimation arising from contamination between clusters. Our time-varying estimates reveal a reduction in seasonal influenza from the intervention and a nonsignificant increase in H1N1 pandemic influenza. We estimate an additive change in overall cumulative incidence (which was 6.13% in the control arm) of -0.68 percentage points during Year 1 of the study (95% CI: -2.53, 1.18). When H1N1 pandemic infections were excluded from analysis, the estimated change was -1.45 percentage points and was significant (95% CI, -2.81, -0.08). Because cross-cluster contamination was low (0-3% of contacts for most villages), an estimator assuming no contamination was only slightly attenuated (-0.65 percentage points). These findings are encouraging for studies carefully designed to minimize spillover. Further work is needed to estimate contamination - and its effect on estimation - in a variety of settings.
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Affiliation(s)
- Gail E. Potter
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, and the Emmes Company, Rockville Maryland, USA
| | | | - Jonathan D. Sugimoto
- University of Washington and Epidemiologic Research and Information Center, Veterans Affairs Puget Sound Health Care System and Fred Hutchinson Cancer Research Center, Seattle Washington, USA
| | - Aldiouma Diallo
- Institut de Recherche pour le Développement, Niakhar Senegal
| | | | | | - M. Elizabeth Halloran
- University of Washington Department of Biostatistics and Fred Hutchinson Cancer Research Center, Seattle Washington, USA
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22
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Davis JT, Chinazzi M, Perra N, Mu K, Pastore Y Piontti A, Ajelli M, Dean NE, Gioannini C, Litvinova M, Merler S, Rossi L, Sun K, Xiong X, Longini IM, Halloran ME, Viboud C, Vespignani A. Cryptic transmission of SARS-CoV-2 and the first COVID-19 wave. Nature 2021; 600:127-132. [PMID: 34695837 PMCID: PMC8636257 DOI: 10.1038/s41586-021-04130-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 10/13/2021] [Indexed: 11/24/2022]
Abstract
Considerable uncertainty surrounds the timeline of introductions and onsets of local transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) globally1-7. Although a limited number of SARS-CoV-2 introductions were reported in January and February 2020 (refs.8,9), the narrowness of the initial testing criteria, combined with a slow growth in testing capacity and porous travel screening10, left many countries vulnerable to unmitigated, cryptic transmission. Here we use a global metapopulation epidemic model to provide a mechanistic understanding of the early dispersal of infections and the temporal windows of the introduction of SARS-CoV-2 and onset of local transmission in Europe and the USA. We find that community transmission of SARS-CoV-2 was likely to have been present in several areas of Europe and the USA by January 2020, and estimate that by early March, only 1 to 4 in 100 SARS-CoV-2 infections were detected by surveillance systems. The modelling results highlight international travel as the key driver of the introduction of SARS-CoV-2, with possible introductions and transmission events as early as December 2019 to January 2020. We find a heterogeneous geographic distribution of cumulative infection attack rates by 4 July 2020, ranging from 0.78% to 15.2% across US states and 0.19% to 13.2% in European countries. Our approach complements phylogenetic analyses and other surveillance approaches and provides insights that can be used to design innovative, model-driven surveillance systems that guide enhanced testing and response strategies.
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Affiliation(s)
- Jessica T Davis
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA, USA
| | - Matteo Chinazzi
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA, USA
| | - Nicola Perra
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA, USA
- Networks and Urban Systems Centre, University of Greenwich, London, UK
| | - Kunpeng Mu
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA, USA
| | - Ana Pastore Y Piontti
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA, USA
| | - Marco Ajelli
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health, Bloomington, IN, USA
| | - Natalie E Dean
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA, USA
| | | | - Maria Litvinova
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health, Bloomington, IN, USA
| | | | | | - Kaiyuan Sun
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Xinyue Xiong
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA, USA
| | - Ira M Longini
- Department of Biostatistics, College of Public Health and Health Professions, University of Florida, Gainesville, FL, USA
| | - M Elizabeth Halloran
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Cécile Viboud
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Alessandro Vespignani
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA, USA.
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23
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Madewell ZJ, Dean NE, Berlin JA, Coplan PM, Davis KJ, Struchiner CJ, Halloran ME. Challenges of evaluating and modelling vaccination in emerging infectious diseases. Epidemics 2021; 37:100506. [PMID: 34628108 PMCID: PMC8491997 DOI: 10.1016/j.epidem.2021.100506] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 08/25/2021] [Accepted: 10/04/2021] [Indexed: 12/17/2022] Open
Abstract
Outbreaks of emerging pathogens pose unique methodological and practical challenges for the design, implementation, and evaluation of vaccine efficacy trials. Lessons learned from COVID-19 highlight the need for innovative and flexible study design and application to quickly identify promising candidate vaccines. Trial design strategies should be tailored to the dynamics of the specific pathogen, location of the outbreak, and vaccine prototypes, within the regional socioeconomic constraints. Mathematical and statistical models can assist investigators in designing infectious disease clinical trials. We introduce key challenges for planning, evaluating, and modelling vaccine efficacy trials for emerging pathogens.
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Affiliation(s)
- Zachary J Madewell
- Department of Biostatistics, University of Florida, Gainesville, FL, USA.
| | - Natalie E Dean
- Department of Biostatistics, University of Florida, Gainesville, FL, USA
| | - Jesse A Berlin
- Global Epidemiology, Johnson & Johnson, Titusville, NJ, USA
| | - Paul M Coplan
- Medical Device Epidemiology and Real World Data Sciences, Johnson & Johnson, New Brunswick, NJ, USA; Department of Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, PA, USA
| | | | | | - M Elizabeth Halloran
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Department of Biostatistics, University of Washington, Seattle, WA, USA
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24
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Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its associated disease, coronavirus disease 2019 (COVID-19), has caused a devastating pandemic worldwide. Here, we explain basic concepts underlying the transition from an epidemic to an endemic state, where a pathogen is stably maintained in a population. We discuss how the number of infections and the severity of disease change in the transition from the epidemic to the endemic phase and consider the implications of this transition in the context of COVID-19.
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Affiliation(s)
| | - M Elizabeth Halloran
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA; University of Washington, Seattle, WA, USA
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25
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Katzelnick LC, Zambrana JV, Elizondo D, Collado D, Garcia N, Arguello S, Mercado JC, Miranda T, Ampie O, Mercado BL, Narvaez C, Gresh L, Binder RA, Ojeda S, Sanchez N, Plazaola M, Latta K, Schiller A, Coloma J, Carrillo FB, Narvaez F, Halloran ME, Gordon A, Kuan G, Balmaseda A, Harris E. Dengue and Zika virus infections in children elicit cross-reactive protective and enhancing antibodies that persist long term. Sci Transl Med 2021; 13:eabg9478. [PMID: 34613812 DOI: 10.1126/scitranslmed.abg9478] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Leah C Katzelnick
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA 94720-3370, USA.,Viral Epidemiology and Immunity Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-3203, USA
| | | | | | | | - Nadezna Garcia
- Sustainable Sciences Institute, Managua 14007, Nicaragua
| | - Sonia Arguello
- Sustainable Sciences Institute, Managua 14007, Nicaragua
| | - Juan Carlos Mercado
- Sustainable Sciences Institute, Managua 14007, Nicaragua.,Laboratorio Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministry of Health, Managua 16064, Nicaragua
| | | | | | | | - César Narvaez
- Sustainable Sciences Institute, Managua 14007, Nicaragua
| | - Lionel Gresh
- Sustainable Sciences Institute, Managua 14007, Nicaragua
| | - Raquel A Binder
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA 94720-3370, USA.,Sustainable Sciences Institute, Managua 14007, Nicaragua
| | - Sergio Ojeda
- Sustainable Sciences Institute, Managua 14007, Nicaragua
| | - Nery Sanchez
- Sustainable Sciences Institute, Managua 14007, Nicaragua
| | | | - Krista Latta
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109-2029, USA
| | - Amy Schiller
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109-2029, USA
| | - Josefina Coloma
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA 94720-3370, USA
| | - Fausto Bustos Carrillo
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA 94720-3370, USA
| | | | - M Elizabeth Halloran
- Department of Biostatistics, University of Washington, Seattle, WA 98195-1617, USA.,Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA
| | - Aubree Gordon
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109-2029, USA
| | - Guillermina Kuan
- Sustainable Sciences Institute, Managua 14007, Nicaragua.,Centro de Salud Sócrates Flores Vivas, Ministry of Health, Managua 12014, Nicaragua
| | - Angel Balmaseda
- Sustainable Sciences Institute, Managua 14007, Nicaragua.,Laboratorio Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministry of Health, Managua 16064, Nicaragua
| | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA 94720-3370, USA
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26
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Rane MS, Rohani P, Halloran ME. Durability of protection after 5 doses of acellular pertussis vaccine among 5-9 year old children in King County, Washington. Vaccine 2021; 39:6144-6150. [PMID: 34493409 DOI: 10.1016/j.vaccine.2021.08.070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 08/17/2021] [Accepted: 08/18/2021] [Indexed: 11/26/2022]
Abstract
PURPOSE Waning of immunity after vaccination with the acellular Pertussis (aP) vaccine has been proposed as one of the main reasons for pertussis resurgence in the US. In this study, we estimated time-varying vaccine effectiveness after 5 doses of aP vaccine. METHODS We conducted a retrospective cohort study among children 5-9 years old (born between 2008 and 2012) living in King County, Washington, USA, who participated in the Washington State Immunization Information System. We estimated time-varying vaccine effectiveness after 5 doses of aP using smoothed scaled Schoenfeld residuals obtained from fitting Cox proportional hazards models to the data as well as piecewise constant Poisson regression. RESULTS There were 55 pertussis cases in this cohort, of whom 22 (40%) were fully-vaccinated and 33 (60%) were under-vaccinated. Vaccine effectiveness (VE) remained high for up to 42 months after the fifth dose (VE(t) = 89%; 95% CI: 64%, 97%) as estimated using survival analysis methods and up to 4 years (VE(t) = 93%; 95% CI: 67%, 98%) as estimated using Poisson regression. CONCLUSION We did not find evidence for waning of vaccine effectiveness for up to four years after 5 doses of aP among 5 -9 years old children in King County, WA.
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Affiliation(s)
- Madhura S Rane
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA.
| | - Pejman Rohani
- Odum School of Ecology, University of Georgia, Athens, GA 30602, USA; Department of Infectious Diseases, University of Georgia, Athens, GA 30602, USA
| | - M Elizabeth Halloran
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
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27
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Halloran ME. Discussion on "Estimating vaccine efficacy over time after a randomized study is unblinded" by Anastasios A. Tsiatis and Marie Davidian. Biometrics 2021; 78:839-840. [PMID: 34420223 PMCID: PMC8653263 DOI: 10.1111/biom.13540] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/16/2021] [Accepted: 06/24/2021] [Indexed: 11/27/2022]
Affiliation(s)
- M Elizabeth Halloran
- Biostatistics, Bioinformatics, and Epidemiology Program, Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Department of Biostatistics, University of Washington, Seattle, Washington, USA
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28
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Madewell ZJ, Yang Y, Longini IM, Halloran ME, Dean NE. Factors Associated With Household Transmission of SARS-CoV-2: An Updated Systematic Review and Meta-analysis. JAMA Netw Open 2021; 4:e2122240. [PMID: 34448865 PMCID: PMC8397928 DOI: 10.1001/jamanetworkopen.2021.22240] [Citation(s) in RCA: 97] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 06/19/2021] [Indexed: 12/14/2022] Open
Abstract
Importance A previous systematic review and meta-analysis of household transmission of SARS-CoV-2 that summarized 54 published studies through October 19, 2020, found an overall secondary attack rate (SAR) of 16.6% (95% CI, 14.0%-19.3%). However, the understanding of household secondary attack rates for SARS-CoV-2 is still evolving, and updated analysis is needed. Objective To use newly published data to further the understanding of SARS-CoV-2 transmission in the household. Data Sources PubMed and reference lists of eligible articles were used to search for records published between October 20, 2020, and June 17, 2021. No restrictions on language, study design, time, or place of publication were applied. Studies published as preprints were included. Study Selection Articles with original data that reported at least 2 of the following factors were included: number of household contacts with infection, total number of household contacts, and secondary attack rates among household contacts. Studies that reported household infection prevalence (which includes index cases), that tested contacts using antibody tests only, and that included populations overlapping with another included study were excluded. Search terms were SARS-CoV-2 or COVID-19 with secondary attack rate, household, close contacts, contact transmission, contact attack rate, or family transmission. Data Extraction and Synthesis Meta-analyses were performed using generalized linear mixed models to obtain SAR estimates and 95% CIs. The Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) reporting guideline was followed. Main Outcomes and Measures Overall household SAR for SARS-CoV-2, SAR by covariates (contact age, sex, ethnicity, comorbidities, and relationship; index case age, sex, symptom status, presence of fever, and presence of cough; number of contacts; study location; and variant), and SAR by index case identification period. Results A total of 2722 records (2710 records from database searches and 12 records from the reference lists of eligible articles) published between October 20, 2020, and June 17, 2021, were identified. Of those, 93 full-text articles reporting household transmission of SARS-CoV-2 were assessed for eligibility, and 37 studies were included. These 37 new studies were combined with 50 of the 54 studies (published through October 19, 2020) from our previous review (4 studies from Wuhan, China, were excluded because their study populations overlapped with another recent study), resulting in a total of 87 studies representing 1 249 163 household contacts from 30 countries. The estimated household SAR for all 87 studies was 18.9% (95% CI, 16.2%-22.0%). Compared with studies from January to February 2020, the SAR for studies from July 2020 to March 2021 was higher (13.4% [95% CI, 10.7%-16.7%] vs 31.1% [95% CI, 22.6%-41.1%], respectively). Results from subgroup analyses were similar to those reported in a previous systematic review and meta-analysis; however, the SAR was higher to contacts with comorbidities (3 studies; 50.0% [95% CI, 41.4%-58.6%]) compared with previous findings, and the estimated household SAR for the B.1.1.7 (α) variant was 24.5% (3 studies; 95% CI, 10.9%-46.2%). Conclusions and Relevance The findings of this study suggest that the household remains an important site of SARS-CoV-2 transmission, and recent studies have higher household SAR estimates compared with the earliest reports. More transmissible variants and vaccines may be associated with further changes.
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Affiliation(s)
| | - Yang Yang
- Department of Biostatistics, University of Florida, Gainesville
| | - Ira M. Longini
- Department of Biostatistics, University of Florida, Gainesville
| | - M. Elizabeth Halloran
- Fred Hutchinson Cancer Research Center, Seattle, Washington
- Department of Biostatistics, University of Washington, Seattle
| | - Natalie E. Dean
- Department of Biostatistics, University of Florida, Gainesville
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29
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Rane MS, Rohani P, Halloran ME. Association of Diphtheria-Tetanus-Acellular Pertussis Vaccine Timeliness and Number of Doses With Age-Specific Pertussis Risk in Infants and Young Children. JAMA Netw Open 2021; 4:e2119118. [PMID: 34374773 PMCID: PMC8356064 DOI: 10.1001/jamanetworkopen.2021.19118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
IMPORTANCE In most countries, the diphtheria-tetanus-acellular pertussis (DTaP) vaccine is administered as a 3-dose infant series followed by additional booster doses in the first 5 years of life. Short-term immunity from the DTaP vaccine can depend on the number, timing, and interval between doses. Not receiving doses in a timely manner might be associated with a higher pertussis risk. OBJECTIVE To examine the association between number and timeliness of vaccine doses and age-specific pertussis risk. DESIGN, SETTING, AND PARTICIPANTS This population-based, retrospective cohort study used Washington State Immunization Information System data and pertussis surveillance data from Public Health Seattle and King County, Washington. Included participants were children aged 3 months to 9 years born or living in King County, Washington, between January 1, 2008, and December 31, 2017. Data were analyzed from June 30 to December 1, 2019. EXPOSURES Being undervaccinated (receiving fewer than recommended doses at a given age) or delayed vaccination (not receiving doses within time frames recommended by Centers for Disease Control and Prevention). MAIN OUTCOMES AND MEASURES Suspected, probable, and confirmed pertussis diagnosis. RESULTS A total of 316 404 children (median age, 65.2 months [interquartile range, 35.3-94.1 months]; 162 025 boys [51.2%]) as of December 31, 2017, with 17.4 million person-months of follow-up were included in the analysis. A total of 19 943 children (6.3%) had no vaccines recorded in the Immunization Information System, 116 193 (36.7%) received a vaccine with a delay, and 180 268 (56.9%) were fully vaccinated with no delay. Delayed vaccination and undervaccination rates were higher for older children (17.6% delayed or undervaccinated at age 2 months for dose 1 at 3 months vs 41.6% at age 5 years for dose 5) but improved for successive birth cohorts (52.2% for 2008 birth cohort vs 32.3% for 2017 birth cohort). Undervaccination was significantly associated with higher risk of pertussis for the 3-dose primary series (adjusted relative risk [aRR], 4.8; 95% CI, 3.1-7.6), the first booster (aRR, 3.2; 95% CI, 2.3-4.5), and the second booster (aRR, 4.6; 95% CI, 2.6-8.2). However, delay in vaccination among children who received the recommended number of vaccine doses was not associated with pertussis risk. CONCLUSIONS AND RELEVANCE The results of this cohort study suggest that undervaccination is associated with higher pertussis risk. Short delays in vaccine receipt may be less important if the age-appropriate number of doses is administered, but delaying doses is not recommended. Ensuring that children receive all doses of pertussis vaccine, even if there is some delay, is important.
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Affiliation(s)
- Madhura S. Rane
- Department of Epidemiology, University of Washington, Seattle
- Institute for Implementation Science in Population Health, City University of New York, New York
| | - Pejman Rohani
- Odum School of Ecology, University of Georgia, Athens
- Department of Infectious Diseases, University of Georgia, Athens
| | - M. Elizabeth Halloran
- Fred Hutchinson Cancer Research Center, Seattle, Washington
- Department of Biostatistics, University of Washington, Seattle
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30
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Madewell ZJ, Pastore Y Piontti A, Zhang Q, Burton N, Yang Y, Longini IM, Halloran ME, Vespignani A, Dean NE. Using simulated infectious disease outbreaks to inform site selection and sample size for individually randomized vaccine trials during an ongoing epidemic. Clin Trials 2021; 18:630-638. [PMID: 34218667 PMCID: PMC8478719 DOI: 10.1177/17407745211028898] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Background: Novel strategies are needed to make vaccine efficacy trials more robust given uncertain epidemiology of infectious disease outbreaks, such as arboviruses like Zika. Spatially resolved mathematical and statistical models can help investigators identify sites at highest risk of future transmission and prioritize these for inclusion in trials. Models can also characterize uncertainty in whether transmission will occur at a site, and how nearby or connected sites may have correlated outcomes. A structure is needed for how trials can use models to address key design questions, including how to prioritize sites, the optimal number of sites, and how to allocate participants across sites. Methods: We illustrate the added value of models using the motivating example of Zika vaccine trial planning during the 2015–2017 Zika epidemic. We used a stochastic, spatially resolved, transmission model (the Global Epidemic and Mobility model) to simulate epidemics and site-level incidence at 100 high-risk sites in the Americas. We considered several strategies for prioritizing sites (average site-level incidence of infection across epidemics, median incidence, probability of exceeding 1% incidence), selecting the number of sites, and allocating sample size across sites (equal enrollment, proportional to average incidence, proportional to rank). To evaluate each design, we stochastically simulated trials in each hypothetical epidemic by drawing observed cases from site-level incidence data. Results: When constraining overall trial size, the optimal number of sites represents a balance between prioritizing highest-risk sites and having enough sites to reduce the chance of observing too few endpoints. The optimal number of sites remained roughly constant regardless of the targeted number of events, although it is necessary to increase the sample size to achieve the desired power. Though different ranking strategies returned different site orders, they performed similarly with respect to trial power. Instead of enrolling participants equally from each site, investigators can allocate participants proportional to projected incidence, though this did not provide an advantage in our example because the top sites had similar risk profiles. Sites from the same geographic region may have similar outcomes, so optimal combinations of sites may be geographically dispersed, even when these are not the highest ranked sites. Conclusion: Mathematical and statistical models may assist in designing successful vaccination trials by capturing uncertainty and correlation in future transmission. Although many factors affect site selection, such as logistical feasibility, models can help investigators optimize site selection and the number and size of participating sites. Although our study focused on trial design for an emerging arbovirus, a similar approach can be made for any infectious disease with the appropriate model for the particular disease.
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Affiliation(s)
- Zachary J Madewell
- Department of Biostatistics, University of Florida, Gainesville, FL, USA
| | - Ana Pastore Y Piontti
- Laboratory for the Modeling of Biological and Socio-Technical Systems, Northeastern University, Boston, MA, USA
| | - Qian Zhang
- Laboratory for the Modeling of Biological and Socio-Technical Systems, Northeastern University, Boston, MA, USA
| | - Nathan Burton
- Institute for Child Health Policy, University of Florida College of Medicine, Gainesville, FL, USA
| | - Yang Yang
- Department of Biostatistics, University of Florida, Gainesville, FL, USA
| | - Ira M Longini
- Department of Biostatistics, University of Florida, Gainesville, FL, USA
| | - M Elizabeth Halloran
- Biostatistics, Bioinformatics, and Epidemiology Program, Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Alessandro Vespignani
- Laboratory for the Modeling of Biological and Socio-Technical Systems, Northeastern University, Boston, MA, USA
| | - Natalie E Dean
- Department of Biostatistics, University of Florida, Gainesville, FL, USA
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31
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Niang MN, Sugimoto JD, Diallo A, Diarra B, Ortiz JR, Lewis KDC, Lafond KE, Halloran ME, Widdowson MA, Neuzil KM, Victor JC. Estimates of Inactivated Influenza Vaccine Effectiveness Among Children in Senegal: Results From 2 Consecutive Cluster-Randomized Controlled Trials in 2010 and 2011. Clin Infect Dis 2021; 72:e959-e969. [PMID: 33165566 DOI: 10.1093/cid/ciaa1689] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 10/30/2020] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND We report results of years 2 and 3 of consecutive cluster-randomized controlled trials of trivalent inactivated influenza vaccine (IIV3) in Senegal. METHODS We cluster-randomized (1:1) 20 villages to annual vaccination with IIV3 or inactivated poliovirus vaccine (IPV) of age-eligible residents (6 months-10 years). The primary outcome was total vaccine effectiveness against laboratory-confirmed influenza illness (LCI) among age-eligible children (modified intention-to-treat population [mITT]). Secondary outcomes were indirect (herd protection) and population (overall community) vaccine effectiveness. RESULTS We vaccinated 74% of 12 408 age-eligible children in year 2 (June 2010-April 11) and 74% of 11 988 age-eligible children in year 3 (April 2011-December 2011) with study vaccines. Annual cumulative incidence of LCI was 4.7 (year 2) and 4.2 (year 3) per 100 mITT child vaccinees of IPV villages. In year 2, IIV3 matched circulating influenza strains. The total effectiveness was 52.8% (95% confidence interval [CI], 32.3-67.0), and the population effectiveness was 36.0% (95% CI, 10.2-54.4) against LCI caused by any influenza strain. The indirect effectiveness against LCI by A/H3N2 was 56.4% (95% CI, 39.0-68.9). In year 3, 74% of influenza detections were vaccine-mismatched to circulating B/Yamagata and 24% were vaccine-matched to circulating A/H3N2. The year 3 total effectiveness against LCI was -14.5% (95% CI, -81.2-27.6). Vaccine effectiveness varied by type/subtype of influenza in both years. CONCLUSIONS IIV3 was variably effective against influenza illness in Senegalese children, with total and indirect vaccine effectiveness present during the year when all circulating strains matched the IIV3 formulation. CLINICAL TRIALS REGISTRATION NCT00893906.
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Affiliation(s)
| | - Jonathan D Sugimoto
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Seattle Epidemiologic Research and Information Center, Department of Veterans Affairs Office of Research and Development, Seattle, Washington, USA.,Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | - Aldiouma Diallo
- VITROME, Institut de Recherche Pour le Développement, Dakar, Senegal
| | - Bou Diarra
- VITROME, Institut de Recherche Pour le Développement, Dakar, Senegal
| | - Justin R Ortiz
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | | | - Kathryn E Lafond
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - M Elizabeth Halloran
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - Marc-Alain Widdowson
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA.,Institute of Tropical Medicine, Antwerp, Belgium
| | - Kathleen M Neuzil
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
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32
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Feldstein LR, Self WH, Ferdinands JM, Randolph AG, Aboodi M, Baughman AH, Brown SM, Exline MC, Files DC, Gibbs K, Ginde AA, Gong MN, Grijalva CG, Halasa N, Khan A, Lindsell CJ, Newhams M, Peltan ID, Prekker ME, Rice TW, Shapiro NI, Steingrub J, Talbot HK, Halloran ME, Patel M. Incorporating Real-time Influenza Detection Into the Test-negative Design for Estimating Influenza Vaccine Effectiveness: The Real-time Test-negative Design (rtTND). Clin Infect Dis 2021; 72:1669-1675. [PMID: 32974644 DOI: 10.1093/cid/ciaa1453] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 09/21/2020] [Indexed: 01/17/2023] Open
Abstract
With rapid and accurate molecular influenza testing now widely available in clinical settings, influenza vaccine effectiveness (VE) studies can prospectively select participants for enrollment based on real-time results rather than enrolling all eligible patients regardless of influenza status, as in the traditional test-negative design (TND). Thus, we explore advantages and disadvantages of modifying the TND for estimating VE by using real-time, clinically available viral testing results paired with acute respiratory infection eligibility criteria for identifying influenza cases and test-negative controls prior to enrollment. This modification, which we have called the real-time test-negative design (rtTND), has the potential to improve influenza VE studies by optimizing the case-to-test-negative control ratio, more accurately classifying influenza status, improving study efficiency, reducing study cost, and increasing study power to adequately estimate VE. Important considerations for limiting biases in the rtTND include the need for comprehensive clinical influenza testing at study sites and accurate influenza tests.
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Affiliation(s)
- Leora R Feldstein
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Wesley H Self
- Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jill M Ferdinands
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Adrienne G Randolph
- Department of Anesthesiology, Critical Care, and Pain Medicine, Boston Children's Hospital, Boston, Massachusetts, USA.,Departments of Anesthesia and Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Michael Aboodi
- Division of Critical Care Medicine, Albert Einstein College of Medicine, Bronx, New York, USA
| | | | - Samuel M Brown
- Division of Pulmonary/Critical Care, Department of Medicine, Intermountain Medical Center and University of Utah, Murray, Utah, USA
| | - Matthew C Exline
- The Ohio State University, College of Nursing, Columbus, Ohio, USA
| | - D Clark Files
- Pulmonary Critical Care Allergy and Immunological Diseases, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Kevin Gibbs
- Pulmonary Critical Care Allergy and Immunological Diseases, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Adit A Ginde
- Department of Emergency Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Michelle N Gong
- Division of Critical Care Medicine, Division of Pulmonary Medicine, Department of Medicine, Department of Epidemiology and Population Health, Montefiore Healthcare System, Albert Einstein College of Medicine, Bronx, New York, USA
| | | | - Natasha Halasa
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Akram Khan
- Department of Pulmonary and Critical Care, Oregon Health and Science University, Portland, Oregon, USA
| | | | - Margaret Newhams
- Department of Anesthesiology, Critical Care, and Pain Medicine, Boston Children's Hospital, Boston, Massachusetts, USA.,Departments of Anesthesia and Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Ithan D Peltan
- Division of Pulmonary/Critical Care, Department of Medicine, Intermountain Medical Center and University of Utah, Murray, Utah, USA
| | - Matthew E Prekker
- Department of Medicine, Division of Pulmonary and Critical Care and Department of Emergency Medicine, Hennepin County Medical Center and the University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Todd W Rice
- Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Nathan I Shapiro
- Department of Emergency Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Jay Steingrub
- Division of Critical Care Pulmonary Medicine, Baystate Medical Center, Springfield, Massachusetts, USA
| | - H Keipp Talbot
- Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - M Elizabeth Halloran
- Department of Biostatistics, University of Washington, Seattle, Washington, USA.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Manish Patel
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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33
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Feldstein LR, Ferdinands JM, Self WH, Randolph AG, Aboodi M, Baughman AH, Brown SM, Exline MC, Files DC, Gibbs K, Ginde AA, Gong MN, Grijalva CG, Halasa N, Khan A, Lindsell CJ, Newhams M, Peltan ID, Prekker ME, Rice TW, Shapiro NI, Steingrub J, Talbot HK, Halloran ME, Patel M. Modeling the impacts of clinical influenza testing on influenza vaccine effectiveness estimates. J Infect Dis 2021; 224:2035-2042. [PMID: 34013330 DOI: 10.1093/infdis/jiab273] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 05/14/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Test-negative design studies for evaluating influenza vaccine effectiveness (VE) enroll patients with acute respiratory infection. Enrollment typically occurs before influenza status is determined, resulting in over-enrollment of influenza-negative patients. With availability of rapid and accurate molecular clinical testing, influenza status could be ascertained prior to enrollment, thus improving study efficiency. We estimate potential biases in VE when using clinical testing. METHODS We simulate data assuming 60% vaccinated, 25% of those vaccinated are influenza positive, and VE of 50%. We show the effect on VE in five scenarios. RESULTS VE is affected only when clinical testing preferentially targets patients based on both vaccination and influenza status. VE is overestimated by 10% if non-testing occurs in 39% of vaccinated influenza-positive patients and 24% of others; and if non-testing occurs in 8% of unvaccinated influenza-positive patients and 27% of others. VE is underestimated by 10% if non-testing occurs in 32% of unvaccinated influenza-negative patients and 18% of others. CONCLUSIONS Although differential clinical testing by vaccine receipt and influenza positivity may produce errors in estimated VE, bias in testing would have to be substantial and overall proportion of patients tested would have to be small to result in a meaningful difference in VE.
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Affiliation(s)
- Leora R Feldstein
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jill M Ferdinands
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Wesley H Self
- Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Adrienne G Randolph
- Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children's Hospital, Boston, Massachusetts, USA.,Departments of Anesthesia and Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Michael Aboodi
- Division of Critical Care Medicine, Albert Einstein College of Medicine, Bronx, New York, USA
| | | | - Samuel M Brown
- Division of Pulmonary/Critical Care, Department of Medicine, Intermountain Medical Center and University of Utah, Murray, Utah, USA
| | - Matthew C Exline
- The Ohio State University, College of Nursing, Columbus, Ohio, USA
| | - D Clark Files
- Pulmonary Critical Care Allergy and Immunological Diseases, Wake Forest School of Medicine, Winston Salem North Carolina, USA
| | - Kevin Gibbs
- Pulmonary Critical Care Allergy and Immunological Diseases, Wake Forest School of Medicine, Winston Salem North Carolina, USA
| | - Adit A Ginde
- Department of Emergency Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Michelle N Gong
- Division of Critical Care Medicine, Division of Pulmonary Medicine, Department of Medicine, Department of Epidemiology and Population Health, Montefiore Healthcare System, Albert Einstein College of Medicine, Bronx, New York, USA
| | | | - Natasha Halasa
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Akram Khan
- Department of Pulmonary & Critical Care, Oregon Health & Science University, Portland, Oregon, USA
| | | | - Margaret Newhams
- Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children's Hospital, Boston, Massachusetts, USA.,Departments of Anesthesia and Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Ithan D Peltan
- Division of Pulmonary/Critical Care, Department of Medicine, Intermountain Medical Center and University of Utah, Murray, Utah, USA
| | - Matthew E Prekker
- Department of Medicine, Division of Pulmonary & Critical Care and Department of Emergency Medicine, Hennepin County Medical Center and the University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Todd W Rice
- Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Nathan I Shapiro
- Department of Emergency Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Jay Steingrub
- Division of Critical Care Pulmonary Medicine, Baystate Medical Center, Springfield, Massachusetts, USA
| | - H Keipp Talbot
- Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - M Elizabeth Halloran
- Department of Biostatistics, University of Washington, Seattle, Washington, USA.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Manish Patel
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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34
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Halloran ME. Comment on AIDS and COVID-19: A tale of two pandemics and the role of statisticians. Stat Med 2021; 40:2524-2525. [PMID: 33963578 PMCID: PMC8207094 DOI: 10.1002/sim.8937] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 02/13/2021] [Indexed: 11/25/2022]
Affiliation(s)
- M Elizabeth Halloran
- Biostatistics, Bioinformatics, and Epidemiology Program, Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Department of Biostatistics, University of Washington, Seattle, Washington
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35
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Buchanan AL, Bessey S, Goedel WC, King M, Murray EJ, Friedman SR, Halloran ME, Marshall BDL. Disseminated Effects in Agent-Based Models: A Potential Outcomes Framework and Application to Inform Preexposure Prophylaxis Coverage Levels for HIV Prevention. Am J Epidemiol 2021; 190:939-948. [PMID: 33128066 DOI: 10.1093/aje/kwaa239] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 09/14/2020] [Accepted: 10/20/2020] [Indexed: 12/25/2022] Open
Abstract
Preexposure prophylaxis (PrEP) for prevention of human immunodeficiency virus (HIV) infection may benefit not only the person who uses it but also their uninfected sexual risk contacts. We developed an agent-based model using a novel trial emulation approach to quantify disseminated effects of PrEP use among men who have sex with men in Atlanta, Georgia, from 2015 to 2017. Model components (subsets of agents connected through partnerships in a sexual network but not sharing partnerships with any other agents) were first randomized to an intervention coverage level or the control group; then, within intervention components, eligible agents were randomized to receive or not receive PrEP. We calculated direct and disseminated (indirect) effects using randomization-based estimators and report corresponding 95% simulation intervals across scenarios ranging from 10% coverage in the intervention components to 90% coverage. A population of 11,245 agents was simulated, with an average of 1,551 components identified. When comparing agents randomized to no PrEP in 70% coverage components with control agents, there was a 15% disseminated risk reduction in HIV incidence (risk ratio = 0.85, 95% simulation interval: 0.65, 1.05). Persons not on PrEP may receive a protective benefit by being in a sexual network with higher PrEP coverage. Agent-based models are useful for evaluating possible direct and disseminated effects of HIV prevention modalities in sexual networks.
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36
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Li F, Li YY, Liu MJ, Fang LQ, Dean NE, Wong GWK, Yang XB, Longini I, Halloran ME, Wang HJ, Liu PL, Pang YH, Yan YQ, Liu S, Xia W, Lu XX, Liu Q, Yang Y, Xu SQ. Household transmission of SARS-CoV-2 and risk factors for susceptibility and infectivity in Wuhan: a retrospective observational study. Lancet Infect Dis 2021; 21:617-628. [PMID: 33476567 PMCID: PMC7833912 DOI: 10.1016/s1473-3099(20)30981-6] [Citation(s) in RCA: 141] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/08/2020] [Accepted: 12/07/2020] [Indexed: 01/25/2023]
Abstract
BACKGROUND Wuhan was the first epicentre of COVID-19 in the world, accounting for 80% of cases in China during the first wave. We aimed to assess household transmissibility of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and risk factors associated with infectivity and susceptibility to infection in Wuhan. METHODS This retrospective cohort study included the households of all laboratory-confirmed or clinically confirmed COVID-19 cases and laboratory-confirmed asymptomatic SARS-CoV-2 infections identified by the Wuhan Center for Disease Control and Prevention between Dec 2, 2019, and April 18, 2020. We defined households as groups of family members and close relatives who did not necessarily live at the same address and considered households that shared common contacts as epidemiologically linked. We used a statistical transmission model to estimate household secondary attack rates and to quantify risk factors associated with infectivity and susceptibility to infection, accounting for individual-level exposure history. We assessed how intervention policies affected the household reproductive number, defined as the mean number of household contacts a case can infect. FINDINGS 27 101 households with 29 578 primary cases and 57 581 household contacts were identified. The secondary attack rate estimated with the transmission model was 15·6% (95% CI 15·2-16·0), assuming a mean incubation period of 5 days and a maximum infectious period of 22 days. Individuals aged 60 years or older were at a higher risk of infection with SARS-CoV-2 than all other age groups. Infants aged 0-1 years were significantly more likely to be infected than children aged 2-5 years (odds ratio [OR] 2·20, 95% CI 1·40-3·44) and children aged 6-12 years (1·53, 1·01-2·34). Given the same exposure time, children and adolescents younger than 20 years of age were more likely to infect others than were adults aged 60 years or older (1·58, 1·28-1·95). Asymptomatic individuals were much less likely to infect others than were symptomatic cases (0·21, 0·14-0·31). Symptomatic cases were more likely to infect others before symptom onset than after (1·42, 1·30-1·55). After mass isolation of cases, quarantine of household contacts, and restriction of movement policies were implemented, household reproductive numbers declined by 52% among primary cases (from 0·25 [95% CI 0·24-0·26] to 0·12 [0·10-0·13]) and by 63% among secondary cases (from 0·17 [0·16-0·18] to 0·063 [0·057-0·070]). INTERPRETATION Within households, children and adolescents were less susceptible to SARS-CoV-2 infection but were more infectious than older individuals. Presymptomatic cases were more infectious and individuals with asymptomatic infection less infectious than symptomatic cases. These findings have implications for devising interventions for blocking household transmission of SARS-CoV-2, such as timely vaccination of eligible children once resources become available. FUNDING National Natural Science Foundation of China, Fundamental Research Funds for the Central Universities, US National Institutes of Health, and US National Science Foundation.
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Affiliation(s)
- Fang Li
- Wuhan Center for Disease Control and Prevention, Wuhan, Hubei, China
| | - Yuan-Yuan Li
- School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Ming-Jin Liu
- Department of Biostatistics, College of Public Health and Health Professions & Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Li-Qun Fang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Natalie E Dean
- Department of Biostatistics, College of Public Health and Health Professions & Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Gary W K Wong
- Department of Pediatrics, Faculty of Medicine, Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Xiao-Bing Yang
- Wuhan Center for Disease Control and Prevention, Wuhan, Hubei, China
| | - Ira Longini
- Department of Biostatistics, College of Public Health and Health Professions & Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - M Elizabeth Halloran
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA,Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Huai-Ji Wang
- Wuhan Center for Disease Control and Prevention, Wuhan, Hubei, China
| | - Pu-Lin Liu
- Wuhan Center for Disease Control and Prevention, Wuhan, Hubei, China
| | - Yan-Hui Pang
- Wuhan Center for Disease Control and Prevention, Wuhan, Hubei, China
| | - Ya-Qiong Yan
- Wuhan Center for Disease Control and Prevention, Wuhan, Hubei, China
| | - Su Liu
- Wuhan Center for Disease Control and Prevention, Wuhan, Hubei, China
| | - Wei Xia
- School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xiao-Xia Lu
- Department of Respiratory Medicine, Wuhan Children's Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Qi Liu
- School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yang Yang
- Department of Biostatistics, College of Public Health and Health Professions & Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA,Dr Yang Yang, Department of Biostatistics, College of Public Health and Health Professions & Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA
| | - Shun-Qing Xu
- School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China,Correspondence to: Dr Shun-Qing Xu, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
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37
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Rane MS, Halloran ME. Estimating population-level effects of the acellular pertussis vaccine using routinely collected immunization data. Clin Infect Dis 2021; 73:2101-2107. [PMID: 33881527 DOI: 10.1093/cid/ciab333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 04/16/2021] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Measuring and reporting the different population-level effects of the acellular pertussis vaccine on pertussis disease in addition to direct effects can increase the cost-effectiveness of a vaccine. METHODS We conducted a retrospective cohort study of children born between January 1, 2008, and December 31, 2017, in King County, Washington, who were enrolled in the Washington State Immunization Information System. Diphtheria-Tetanus-acellular-Pertussis (DTaP) vaccination data from WA-IIS was linked with pertussis case data from Public Health Seattle and King County. Census-level vaccination coverage was estimated as proportion of age-appropriately vaccinated children residing in it. Direct vaccine effectiveness was estimated by comparing pertussis risk in fully-vaccinated and under-vaccinated children. Population-level vaccine effects were estimated by comparing pertussis risk in census tracts in the highest vaccination coverage quartile to that in the lowest vaccination coverage quartile. RESULTS For direct protection, estimated vaccine effectiveness was 76% (95% CI: 63% - 84%) in low vaccination coverage clusters and it decreased to 47% (95% CI: 13% - 68%) in high vaccination coverage clusters, after adjusting for potential confounders. The estimated indirect effect was 45.0% (95% CI: 1%, 70%), total effect was 93.9% (95% CI: 91%, 96%), and overall effect was 42.2% (95% CI: 19%, 60%). CONCLUSION Our findings suggest that DTaP vaccination provided direct as well as indirect protection in the highly immunized King County, WA. Routine DTaP vaccination programs may have the potential to provide not only protection for vaccinated individuals but also for the under-vaccinated individuals living in the same area.
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Affiliation(s)
- Madhura S Rane
- Department of Epidemiology, University of Washington, Seattle USA
| | - M Elizabeth Halloran
- Department of Epidemiology, University of Washington, Seattle USA.,Department of Biostatistics University of Washington, Seattle USA.,Biostatistics, Bioinformatics, and Epidemiology Program, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, USA
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38
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Davis JT, Chinazzi M, Perra N, Mu K, Piontti APY, Ajelli M, Dean NE, Gioannini C, Litvinova M, Merler S, Rossi L, Sun K, Xiong X, Halloran ME, Longini IM, Viboud C, Vespignani A. Cryptic transmission of SARS-CoV-2 and the first COVID-19 wave in Europe and the United States. medRxiv 2021:2021.03.24.21254199. [PMID: 33791745 PMCID: PMC8010777 DOI: 10.1101/2021.03.24.21254199] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Given the narrowness of the initial testing criteria, the SARS-CoV-2 virus spread through cryptic transmission in January and February, setting the stage for the epidemic wave experienced in March and April, 2020. We use a global metapopulation epidemic model to provide a mechanistic understanding of the global dynamic underlying the establishment of the COVID-19 pandemic in Europe and the United States (US). The model is calibrated on international case introductions at the early stage of the pandemic. We find that widespread community transmission of SARS-CoV-2 was likely in several areas of Europe and the US by January 2020, and estimate that by early March, only 1 - 3 in 100 SARS-CoV-2 infections were detected by surveillance systems. Modeling results indicate international travel as the key driver of the introduction of SARS-CoV-2 with possible importation and transmission events as early as December, 2019. We characterize the resulting heterogeneous spatio-temporal spread of SARS-CoV-2 and the burden of the first COVID-19 wave (February-July 2020). We estimate infection attack rates ranging from 0.78%-15.2% in the US and 0.19%-13.2% in Europe. The spatial modeling of SARS-CoV-2 introductions and spreading provides insights into the design of innovative, model-driven surveillance systems and preparedness plans that have a broader initial capacity and indication for testing.
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Affiliation(s)
- Jessica T. Davis
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA USA
| | - Matteo Chinazzi
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA USA
| | - Nicola Perra
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA USA
- Networks and Urban Systems Centre, University of Greenwich, London, UK
| | - Kunpeng Mu
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA USA
| | - Ana Pastore y Piontti
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA USA
| | - Marco Ajelli
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA USA
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health,, Bloomington, IN, USA
| | - Natalie E. Dean
- Department of Biostatistics, College of Public Health and Health Professions, University of Florida, Gainesville, USA
| | | | - Maria Litvinova
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health,, Bloomington, IN, USA
| | | | | | - Kaiyuan Sun
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Xinyue Xiong
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA USA
| | - M. Elizabeth Halloran
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Biostatistics, University of Washington, Seattle, WA. USA
| | - Ira M. Longini
- Department of Biostatistics, College of Public Health and Health Professions, University of Florida, Gainesville, USA
| | - Cécile Viboud
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Alessandro Vespignani
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA USA
- ISI Foundation, Turin, Italy
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Chakladar S, Rosin S, Hudgens MG, Halloran ME, Clemens JD, Ali M, Emch ME. Inverse probability weighted estimators of vaccine effects accommodating partial interference and censoring. Biometrics 2021; 78:777-788. [PMID: 33768557 DOI: 10.1111/biom.13459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 11/10/2020] [Accepted: 03/12/2021] [Indexed: 12/01/2022]
Abstract
Estimating population-level effects of a vaccine is challenging because there may be interference, that is, the outcome of one individual may depend on the vaccination status of another individual. Partial interference occurs when individuals can be partitioned into groups such that interference occurs only within groups. In the absence of interference, inverse probability weighted (IPW) estimators are commonly used to draw inference about causal effects of an exposure or treatment. Tchetgen Tchetgen and VanderWeele proposed a modified IPW estimator for causal effects in the presence of partial interference. Motivated by a cholera vaccine study in Bangladesh, this paper considers an extension of the Tchetgen Tchetgen and VanderWeele IPW estimator to the setting where the outcome is subject to right censoring using inverse probability of censoring weights (IPCW). Censoring weights are estimated using proportional hazards frailty models. The large sample properties of the IPCW estimators are derived, and simulation studies are presented demonstrating the estimators' performance in finite samples. The methods are then used to analyze data from the cholera vaccine study.
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Affiliation(s)
- Sujatro Chakladar
- Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina
| | - Samuel Rosin
- Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina
| | - Michael G Hudgens
- Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina
| | - M Elizabeth Halloran
- Department of Biostatistics, University of Washington, Seattle, Washington.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - John D Clemens
- Department of Epidemiology, University of California, Los Angeles, California.,International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Mohammad Ali
- Department of International Health, Johns Hopkins University, Baltimore, Maryland
| | - Michael E Emch
- Department of Geography, University of North Carolina, Chapel Hill, North Carolina
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Rane MS, Page LC, McVeigh E, Miller K, Baure D, Elizabeth Halloran M, Duchin JS. Improving adolescent human papillomavirus (HPV) immunization uptake in school-based health centers through awareness campaigns. Vaccine 2021; 39:1765-1772. [PMID: 33640146 DOI: 10.1016/j.vaccine.2021.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 12/17/2020] [Accepted: 02/04/2021] [Indexed: 10/22/2022]
Abstract
PURPOSE The aim of this study was to measure the effect of a multicomponent human papillomavirus (HPV) vaccine promotion campaign on adolescent HPV vaccine uptake at school-based health centers (SBHCs) in Seattle, WA. METHODS Youth-led HPV vaccine promotion campaigns were introduced in 2016 in 13 schools with SBHCs in Seattle. Five other schools with SBHCs served as controls. Vaccination records for students were obtained from the Washington Immunization Information System from September 2012 to August 2018. We compared increase in HPV vaccine uptake in SBHCs between 1) intervention and control schools, and 2) pre- and post-intervention periods in intervention schools using generalized estimating equations. RESULTS HPV vaccine uptake was high at baseline among students that use SBHCs for vaccines and has steadily increased between 2012 and 2018. Implementing the promotion campaign resulted in 14% higher (95% Confidence Interval (CI): 1%, 30%) HPV vaccine uptake in intervention SBHCs compared to control SBHCs, adjusting for time and confounders. Comparing pre-and post-intervention periods in intervention SBHCs, HPV vaccine uptake was 14% higher (95% CI: -4%, 35%) in the post-intervention period. SBHCs that received more active intervention activities saw 9% higher (95% CI: 1%, 21%) vaccine uptake compared to those that received passive intervention. CONCLUSION The vaccination promotion program implemented in a school-based setting resulted in higher HPV vaccine uptake in the post-intervention period compared to pre-intervention period, but this increase was not statistically significant. Even so, schools that received more intervention activities for longer periods of time had higher HPV vaccine uptake.
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Affiliation(s)
- Madhura S Rane
- Department of Epidemiology, University of Washington, Seattle, WA, USA; Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
| | - Libby C Page
- Public Health, Seattle & King County, Seattle, WA, USA
| | - Emma McVeigh
- Public Health, Seattle & King County, Seattle, WA, USA
| | | | - David Baure
- Public Health, Seattle & King County, Seattle, WA, USA
| | - M Elizabeth Halloran
- Department of Epidemiology, University of Washington, Seattle, WA, USA; Department of Biostatistics, University of Washington, Seattle, WA, USA; Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jeffrey S Duchin
- Public Health, Seattle & King County, Seattle, WA, USA; Division of Allergy and Infectious Diseases and School of Public Health and Community Medicine, University of Washington, Seattle, WA, USA
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Mistry D, Litvinova M, Pastore Y Piontti A, Chinazzi M, Fumanelli L, Gomes MFC, Haque SA, Liu QH, Mu K, Xiong X, Halloran ME, Longini IM, Merler S, Ajelli M, Vespignani A. Inferring high-resolution human mixing patterns for disease modeling. Nat Commun 2021; 12:323. [PMID: 33436609 PMCID: PMC7803761 DOI: 10.1038/s41467-020-20544-y] [Citation(s) in RCA: 101] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 12/08/2020] [Indexed: 01/29/2023] Open
Abstract
Mathematical and computational modeling approaches are increasingly used as quantitative tools in the analysis and forecasting of infectious disease epidemics. The growing need for realism in addressing complex public health questions is, however, calling for accurate models of the human contact patterns that govern the disease transmission processes. Here we present a data-driven approach to generate effective population-level contact matrices by using highly detailed macro (census) and micro (survey) data on key socio-demographic features. We produce age-stratified contact matrices for 35 countries, including 277 sub-national administratvie regions of 8 of those countries, covering approximately 3.5 billion people and reflecting the high degree of cultural and societal diversity of the focus countries. We use the derived contact matrices to model the spread of airborne infectious diseases and show that sub-national heterogeneities in human mixing patterns have a marked impact on epidemic indicators such as the reproduction number and overall attack rate of epidemics of the same etiology. The contact patterns derived here are made publicly available as a modeling tool to study the impact of socio-economic differences and demographic heterogeneities across populations on the epidemiology of infectious diseases.
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Affiliation(s)
- Dina Mistry
- Institute for Disease Modeling, Global Health Division, Bill and Melinda Gates Foundation, Seattle, WA, USA
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA, USA
| | - Maria Litvinova
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA, USA
- ISI Foundation, Turin, Italy
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health, Bloomington, IN, USA
| | - Ana Pastore Y Piontti
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA, USA
| | - Matteo Chinazzi
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA, USA
| | | | - Marcelo F C Gomes
- Fiocruz, Scientific Computing Program, Grupo de Métodos Analíticos em Vigilância Epidemiológica, Rio de Janeiro, Brazil
| | - Syed A Haque
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA, USA
| | - Quan-Hui Liu
- College of Computer Science, Sichuan University, Chengdu, Sichuan, China
| | - Kunpeng Mu
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA, USA
| | - Xinyue Xiong
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA, USA
| | - M Elizabeth Halloran
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Ira M Longini
- Department of Biostatistics, College of Public Health and Health Professions, University of Florida, Gainesville, FL, USA
| | | | - Marco Ajelli
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA, USA.
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health, Bloomington, IN, USA.
| | - Alessandro Vespignani
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA, USA.
- ISI Foundation, Turin, Italy.
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Matrajt L, Halloran ME, Antia R. Successes and Failures of the Live-attenuated Influenza Vaccine: Can We Do Better? Clin Infect Dis 2021; 70:1029-1037. [PMID: 31056675 PMCID: PMC7319054 DOI: 10.1093/cid/ciz358] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 04/30/2019] [Indexed: 11/17/2022] Open
Abstract
Background The effectiveness of the live-attenuated influenza vaccine (LAIV) can vary widely, ranging from 0% to 50%. The reasons for these discrepancies remain largely unclear. Methods We use mathematical models to explore how the efficacy of LAIV is affected by the degree of mismatch with the currently circulating influenza strain and interference with pre-existing immunity. The models incorporate 3 key antigenic distances: the distances between the vaccine strain, pre-existing immunity, and the challenge strain. Results Our models show that an LAIV that is matched with the currently circulating strain is likely to have only modest efficacy. Our results suggest that the efficacy of the vaccine would be increased (optimized) if, rather than being matched to the circulating strain, it is antigenically slightly further from pre-existing immunity than the circulating strain. The models also suggest 2 regimes in which LAIV that is matched to circulating strains may be protective: in children before they have built immunity to circulating strains and in response to novel strains (such as antigenic shifts) which are at substantial antigenic distance from previously circulating strains. We provide an explanation for the variation in vaccine effectiveness between studies and countries of vaccine effectiveness observed during the 2014–2015 influenza season. Conclusions LAIV is offered to children across the world; however, its effectiveness significantly varies between studies. Here, we propose a mechanistic explanation to understand these differences. We further propose a way to select the LAIV strain that would have a higher chance of being protective.
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Affiliation(s)
- Laura Matrajt
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center
| | - M Elizabeth Halloran
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center.,Department of Biostatistics, University of Washington, Seattle
| | - Rustom Antia
- Department of Biology, Emory University, Atlanta, Georgia
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Wenzel NS, Atkins KE, van Leeuwen E, Halloran ME, Baguelin M. Cost-effectiveness of live-attenuated influenza vaccination among school-age children. Vaccine 2020; 39:447-456. [PMID: 33280855 DOI: 10.1016/j.vaccine.2020.10.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 09/20/2020] [Accepted: 10/01/2020] [Indexed: 10/22/2022]
Abstract
The current pediatric vaccination program in England and Wales administers Live-Attenuated Influenza Vaccine (LAIV) to children ages 2-16 years old. Annual administration of LAIV to this age group is costly and poses substantial logistical issues. This study aims to evaluate the cost-effectiveness of prioritizing vaccination to age groups within the 2-16 year old age range to mitigate the operational and resource challenges of the current strategy. We performed economic evaluations comparing the influenza vaccination program from 1995-2013 to seven alternative strategies targeted at low risk individuals along the school age divisions Preschool (2-4 years old), Primary school (5-11 years old), and Secondary school (12-16 years old). These extensions are evaluated incrementally on the status quo scenario (vaccinating subgroups at high risk of influenza-related complications and individuals 65+ years old). Impact of vaccination was assessed using a transmission model from a previously published study and updated with new data. At all levels of coverage, all strategies had a 100% probability of being cost-effective at the current National Health Service threshold, £20,000/QALY gained. The incremental analysis demonstrated vaccinating Primary School children was the most cost-efficient strategy compared incrementally against others with an Incremental Cost-Effectiveness Ratio of £639 spent per QALY gained (Net Benefit: 404 M£ [155, 795]). When coverage was varied between 30%, 55%, and 70% strategies which included Primary school children had a higher probability of being cost-effective at lower willingness-to-pay levels. Although children were the vaccine target the majority of QALY gains occurred in the 25-44 years old and 65+ age groups. Influenza strain A/H3N2 incurred the greatest costs and QALYs lost regardless of which strategy was used. Improvement could be made to the current LAIV pediatric vaccination strategy by eliminating vaccination of 2-4 year olds and focusing on school-based delivery to Primary and Secondary school children in tandem.
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Affiliation(s)
- Natasha S Wenzel
- Department of Epidemiology, University of Washington, Seattle 98195, USA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle 98109, USA.
| | - Katherine E Atkins
- Centre for Global Health, Usher Institute of Population Health Sciences and Informatics, Edinburgh Medical School, The University of Edinburgh, Edinburgh EH8 9AG, UK; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK; Department for Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Edwin van Leeuwen
- National Infections Service, Public Health England, London NW9 5EQ, UK
| | - M Elizabeth Halloran
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle 98109, USA; Department of Biostatistics, University of Washington, Seattle 98195, USA
| | - Marc Baguelin
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK; Respiratory Diseases Department, Public Health England, London NW9 5EQ, UK; School of Public Health, Infectious Disease Epidemiology, Imperial College London, London SW7 2AZ, UK
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Abstract
Importance Crowded indoor environments, such as households, are high-risk settings for the transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Objectives To examine evidence for household transmission of SARS-CoV-2, disaggregated by several covariates, and to compare it with other coronaviruses. Data Source PubMed, searched through October 19, 2020. Search terms included SARS-CoV-2 or COVID-19 with secondary attack rate, household, close contacts, contact transmission, contact attack rate, or family transmission. Study Selection All articles with original data for estimating household secondary attack rate were included. Case reports focusing on individual households and studies of close contacts that did not report secondary attack rates for household members were excluded. Data Extraction and Synthesis Meta-analyses were done using a restricted maximum-likelihood estimator model to yield a point estimate and 95% CI for secondary attack rate for each subgroup analyzed, with a random effect for each study. To make comparisons across exposure types, study was treated as a random effect, and exposure type was a fixed moderator. The Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) reporting guideline was followed. Main Outcomes and Measures Secondary attack rate for SARS-CoV-2, disaggregated by covariates (ie, household or family contact, index case symptom status, adult or child contacts, contact sex, relationship to index case, adult or child index cases, index case sex, number of contacts in household) and for other coronaviruses. Results A total of 54 relevant studies with 77 758 participants reporting household secondary transmission were identified. Estimated household secondary attack rate was 16.6% (95% CI, 14.0%-19.3%), higher than secondary attack rates for SARS-CoV (7.5%; 95% CI, 4.8%-10.7%) and MERS-CoV (4.7%; 95% CI, 0.9%-10.7%). Household secondary attack rates were increased from symptomatic index cases (18.0%; 95% CI, 14.2%-22.1%) than from asymptomatic index cases (0.7%; 95% CI, 0%-4.9%), to adult contacts (28.3%; 95% CI, 20.2%-37.1%) than to child contacts (16.8%; 95% CI, 12.3%-21.7%), to spouses (37.8%; 95% CI, 25.8%-50.5%) than to other family contacts (17.8%; 95% CI, 11.7%-24.8%), and in households with 1 contact (41.5%; 95% CI, 31.7%-51.7%) than in households with 3 or more contacts (22.8%; 95% CI, 13.6%-33.5%). Conclusions and Relevance The findings of this study suggest that given that individuals with suspected or confirmed infections are being referred to isolate at home, households will continue to be a significant venue for transmission of SARS-CoV-2.
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Affiliation(s)
| | - Yang Yang
- Department of Biostatistics, University of Florida, Gainesville
| | - Ira M. Longini
- Department of Biostatistics, University of Florida, Gainesville
| | - M. Elizabeth Halloran
- Fred Hutchinson Cancer Research Center, Seattle, Washington
- Department of Biostatistics, University of Washington, Seattle
| | - Natalie E. Dean
- Department of Biostatistics, University of Florida, Gainesville
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Dean NE, Halloran ME, Longini IM. Temporal Confounding in the Test-Negative Design. Am J Epidemiol 2020; 189:1402-1407. [PMID: 32415834 DOI: 10.1093/aje/kwaa084] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 05/04/2020] [Accepted: 05/05/2020] [Indexed: 11/15/2022] Open
Abstract
In the test-negative design, routine testing at health-care facilities is leveraged to estimate the effectiveness of an intervention such as a vaccine. The odds of vaccination for individuals who test positive for a target pathogen is compared with the odds of vaccination for individuals who test negative for that pathogen, adjusting for key confounders. The design is rapidly growing in popularity, but many open questions remain about its properties. In this paper, we examine temporal confounding by generalizing derivations to allow for time-varying vaccine status, including out-of-season controls, and open populations. We confirm that calendar time is an important confounder when vaccine status varies during the study. We demonstrate that, where time is not a confounder, including out-of-season controls can improve precision. We generalize these results to open populations. We use our theoretical findings to interpret 3 recent papers utilizing the test-negative design. Through careful examination of the theoretical properties of this study design, we provide key insights that can directly inform the implementation and analysis of future test-negative studies.
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Manrique-Saide P, Dean NE, Halloran ME, Longini IM, Collins MH, Waller LA, Gomez-Dantes H, Lenhart A, Hladish TJ, Che-Mendoza A, Kirstein OD, Romer Y, Correa-Morales F, Palacio-Vargas J, Mendez-Vales R, Pérez PG, Pavia-Ruz N, Ayora-Talavera G, Vazquez-Prokopec GM. The TIRS trial: protocol for a cluster randomized controlled trial assessing the efficacy of preventive targeted indoor residual spraying to reduce Aedes-borne viral illnesses in Merida, Mexico. Trials 2020; 21:839. [PMID: 33032661 PMCID: PMC7542575 DOI: 10.1186/s13063-020-04780-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 09/29/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Current urban vector control strategies have failed to contain dengue epidemics and to prevent the global expansion of Aedes-borne viruses (ABVs: dengue, chikungunya, Zika). Part of the challenge in sustaining effective ABV control emerges from the paucity of evidence regarding the epidemiological impact of any Aedes control method. A strategy for which there is limited epidemiological evidence is targeted indoor residual spraying (TIRS). TIRS is a modification of classic malaria indoor residual spraying that accounts for Aedes aegypti resting behavior by applying residual insecticides on exposed lower sections of walls (< 1.5 m), under furniture, and on dark surfaces. METHODS/DESIGN We are pursuing a two-arm, parallel, unblinded, cluster randomized controlled trial to quantify the overall efficacy of TIRS in reducing the burden of laboratory-confirmed ABV clinical disease (primary endpoint). The trial will be conducted in the city of Merida, Yucatan State, Mexico (population ~ 1million), where we will prospectively follow 4600 children aged 2-15 years at enrollment, distributed in 50 clusters of 5 × 5 city blocks each. Clusters will be randomly allocated (n = 25 per arm) using covariate-constrained randomization. A "fried egg" design will be followed, in which all blocks of the 5 × 5 cluster receive the intervention, but all sampling to evaluate the epidemiological and entomological endpoints will occur in the "yolk," the center 3 × 3 city blocks of each cluster. TIRS will be implemented as a preventive application (~ 1-2 months prior to the beginning of the ABV season). Active monitoring for symptomatic ABV illness will occur through weekly household visits and enhanced surveillance. Annual sero-surveys will be performed after each transmission season and entomological evaluations of Ae. aegypti indoor abundance and ABV infection rates monthly during the period of active surveillance. Epidemiological and entomological evaluation will continue for up to three transmission seasons. DISCUSSION The findings from this study will provide robust epidemiological evidence of the efficacy of TIRS in reducing ABV illness and infection. If efficacious, TIRS could drive a paradigm shift in Aedes control by considering Ae. aegypti behavior to guide residual insecticide applications and changing deployment to preemptive control (rather than in response to symptomatic cases), two major enhancements to existing practice. TRIAL REGISTRATION ClinicalTrials.gov NCT04343521 . Registered on 13 April 2020. The protocol also complies with the WHO International Clinical Trials Registry Platform (ICTRP) (Additional file 1). PRIMARY SPONSOR National Institutes of Health, National Institute of Allergy and Infectious Diseases (NIH/NIAID).
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Affiliation(s)
- Pablo Manrique-Saide
- Unidad Colaborativa de Bioensayos Entomológicos, Campus de Ciencias Biológicas y Agropecuarias, Universidad Autónoma de Yucatán, Merida, Mexico
| | - Natalie E Dean
- Department of Biostatistics, University of Florida, Gainesville, FL, 32611, USA
| | - M Elizabeth Halloran
- Center for Inference and Dynamics of Infectious Diseases, Seattle, WA, 98109, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Biostatistics, University of Washington, Seattle, WA, 98109, USA
| | - Ira M Longini
- Department of Biostatistics, University of Florida, Gainesville, FL, 32611, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Matthew H Collins
- Hope Clinic of the Emory Vaccine Center, Division of Infectious Diseases, Department of Medicine, School of Medicine, Emory University, Decatur, GA, 30030, USA
| | - Lance A Waller
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA, 30322, USA
| | - Hector Gomez-Dantes
- Health Systems Research Center, National Institute of Public Health, Cuernavaca, Mexico
| | - Audrey Lenhart
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Thomas J Hladish
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, 32611, USA
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Azael Che-Mendoza
- Unidad Colaborativa de Bioensayos Entomológicos, Campus de Ciencias Biológicas y Agropecuarias, Universidad Autónoma de Yucatán, Merida, Mexico
| | - Oscar D Kirstein
- Department of Environmental Sciences, Math and Science Center, Emory University, 400 Dowman Drive, 5th floor, Suite E530, Atlanta, GA, 30322, USA
| | - Yamila Romer
- Department of Environmental Sciences, Math and Science Center, Emory University, 400 Dowman Drive, 5th floor, Suite E530, Atlanta, GA, 30322, USA
| | - Fabian Correa-Morales
- Centro Nacional de Programas Preventivos y Control de Enfermedades (CENAPRECE) Secretaría de Salud Mexico, Mexico City, Mexico
| | | | | | | | - Norma Pavia-Ruz
- Centro de Investigaciones Regionales Hideyo Noguchi, Universidad Autonoma de Yucatan, Merida, Mexico
| | - Guadalupe Ayora-Talavera
- Centro de Investigaciones Regionales Hideyo Noguchi, Universidad Autonoma de Yucatan, Merida, Mexico
| | - Gonzalo M Vazquez-Prokopec
- Department of Environmental Sciences, Math and Science Center, Emory University, 400 Dowman Drive, 5th floor, Suite E530, Atlanta, GA, 30322, USA.
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Magaret AS, Jacob ST, Halloran ME, Guthrie KA, Magaret CA, Johnston C, Simon NR, Wald A. Multigroup, Adaptively Randomized Trials Are Advantageous for Comparing Coronavirus Disease 2019 (COVID-19) Interventions. Ann Intern Med 2020; 173:576-577. [PMID: 32525715 PMCID: PMC7322770 DOI: 10.7326/m20-2933] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
In this commentary, the authors explain and call for a broader use of outcome-adaptive randomization when designing clinical trials to test multiple COVID-19 interventions. This design potentially reduces the number of deaths or other adverse outcomes incurred during a trial.
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Affiliation(s)
- Amalia S Magaret
- University of Washington and Fred Hutchinson Cancer Research Center, Seattle, Washington (A.S.M., M.E.H., C.J., A.W.)
| | - Shevin T Jacob
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom, and University of Washington, Seattle, Washington (S.T.J.)
| | - M Elizabeth Halloran
- University of Washington and Fred Hutchinson Cancer Research Center, Seattle, Washington (A.S.M., M.E.H., C.J., A.W.)
| | - Katherine A Guthrie
- Fred Hutchinson Cancer Research Center, Seattle, Washington (K.A.G., C.A.M.)
| | - Craig A Magaret
- Fred Hutchinson Cancer Research Center, Seattle, Washington (K.A.G., C.A.M.)
| | - Christine Johnston
- University of Washington and Fred Hutchinson Cancer Research Center, Seattle, Washington (A.S.M., M.E.H., C.J., A.W.)
| | - Noah R Simon
- University of Washington, Seattle, Washington (N.R.S.)
| | - Anna Wald
- University of Washington and Fred Hutchinson Cancer Research Center, Seattle, Washington (A.S.M., M.E.H., C.J., A.W.)
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Diallo A, Diop OM, Diop D, Niang MN, Sugimoto JD, Ortiz JR, Faye EHA, Diarra B, Goudiaby D, Lewis KDC, Emery SL, Zangeneh SZ, Lafond KE, Sokhna C, Halloran ME, Widdowson MA, Neuzil KM, Victor JC. Effectiveness of Seasonal Influenza Vaccination in Children in Senegal During a Year of Vaccine Mismatch: A Cluster-randomized Trial. Clin Infect Dis 2020; 69:1780-1788. [PMID: 30689757 DOI: 10.1093/cid/ciz066] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 01/18/2019] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND The population effects of influenza vaccination in children have not been extensively studied, especially in tropical, developing countries. In rural Senegal, we assessed the total (primary objective) and indirect effectiveness of a trivalent inactivated influenza vaccine (IIV3). METHODS In this double-blind, cluster-randomized trial, villages were randomly allocated (1:1) for the high-coverage vaccination of children aged 6 months through 10 years with either the 2008-09 northern hemisphere IIV3 or an inactivated polio vaccine (IPV). Vaccinees were monitored for serious adverse events. All village residents, vaccinated and unvaccinated, were monitored for signs and symptoms of influenza illness using weekly home visits and surveillance in designated clinics. The primary outcome was all laboratory-confirmed symptomatic influenza. RESULTS Between 23 May and 11 July 2009, 20 villages were randomized, and 66.5% of age-eligible children were enrolled (3918 in IIV3 villages and 3848 in IPV villages). Follow-up continued until 28 May 2010. There were 4 unrelated serious adverse events identified. Among vaccinees, the total effectiveness against illness caused by the seasonal influenza virus (presumed to all be drifted A/H3N2, based on antigenic characterization data) circulating at high rates among children was 43.6% (95% confidence interval [CI] 18.6-60.9%). The indirect effectiveness against seasonal A/H3N2 was 15.4% (95% CI -22.0 to 41.3%). The total effectiveness against illness caused by the pandemic influenza virus (A/H1N1pdm09) was -52.1% (95% CI -177.2 to 16.6%). CONCLUSIONS IIV3 provided statistically significant, moderate protection to children in Senegal against circulating, pre-2010 seasonal influenza strains, but not against A/H1N1pdm09, which was not included in the vaccine. No indirect effects were measured. Further study in low-resource populations is warranted. CLINICAL TRIALS REGISTRATION NCT00893906.
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Affiliation(s)
- Aldiouma Diallo
- UMR VITROME, Institut de Recherche Pour le Développement, Dakar, Senegal
| | | | - Doudou Diop
- UMR VITROME, Institut de Recherche Pour le Développement, Dakar, Senegal
| | | | - Jonathan D Sugimoto
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Justin R Ortiz
- Center for Vaccine Development, University of Maryland, Baltimore
| | | | - Bou Diarra
- UMR VITROME, Institut de Recherche Pour le Développement, Dakar, Senegal
| | | | | | - Shannon L Emery
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Sahar Z Zangeneh
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Kathryn E Lafond
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Cheikh Sokhna
- UMR VITROME, Institut de Recherche Pour le Développement, Dakar, Senegal
| | - M Elizabeth Halloran
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Department of Biostatistics, University of Washington, Seattle
| | - Marc-Alain Widdowson
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
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49
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Schwartz LM, Zaman K, Yunus M, Basunia AUH, Faruque ASG, Ahmed T, Rahman M, Sugimoto JD, Halloran ME, Rowhani-Rahbar A, Neuzil KM, Victor JC. Impact of Rotavirus Vaccine Introduction in Children Less Than 2 Years of Age Presenting for Medical Care With Diarrhea in Rural Matlab, Bangladesh. Clin Infect Dis 2020; 69:2059-2070. [PMID: 30753368 PMCID: PMC6880338 DOI: 10.1093/cid/ciz133] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Accepted: 02/07/2019] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Following the conclusion of a human rotavirus vaccine (HRV) cluster-randomized, controlled trial (CRT) in Matlab, Bangladesh, HRV was included in Matlab's routine immunization program. We describe the population-level impact of programmatic rotavirus vaccination in Bangladesh in children <2 years of age. METHODS Interrupted time series were used to estimate the impact of HRV introduction. We used diarrheal surveillance collected between 2000 and 2014 within the 2 service delivery areas (International Centre for Diarrhoeal Disease Research, Bangladesh [icddr,b] service area [ISA] and government service area [GSA]) of the Matlab Health and Demographic Surveillance System, administered by icddr,b. Age group-specific incidence rates were calculated for both rotavirus-positive (RV+) and rotavirus-negative (RV-) diarrhea diagnoses of any severity presenting to the hospital. We used 2 models to assess the impact within each service area: Model 1 used the pre-vaccine time period in all villages (HRV- and control-only) and Model 2 combined the pre-vaccine time period and the CRT time period, using outcomes from control-only villages. RESULTS Both models demonstrated a downward trend in RV+ diarrheal incidences in the ISA villages during 3.5 years of routine HRV use, though only Model 2 was statistically significant. Significant impacts of HRV on RV+ diarrhea incidences in GSA villages were not observed in either model. Differences in population-level impacts between the 2 delivery areas may be due to the varied rotavirus vaccine coverage and presentation rates to the hospital. CONCLUSIONS This study provides initial evidence of the population-level impact of rotavirus vaccines in children <2 years of age in Matlab, Bangladesh. Further studies are needed of the rotavirus vaccine impact after the nationwide introduction in Bangladesh.
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Affiliation(s)
- Lauren M Schwartz
- Department of Epidemiology, School of Public Health, University of Washington, Seattle.,Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle
| | - K Zaman
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka
| | - Md Yunus
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka
| | | | | | - Tahmeed Ahmed
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka
| | - Mustafizur Rahman
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka
| | - Jonathan D Sugimoto
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle
| | - M Elizabeth Halloran
- Department of Epidemiology, School of Public Health, University of Washington, Seattle.,Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle.,Department of Biostatistics, School of Public Health, University of Washington, Seattle.,Center for Inference and Dynamics of Infectious Diseases, Seattle
| | - Ali Rowhani-Rahbar
- Department of Epidemiology, School of Public Health, University of Washington, Seattle
| | - Kathleen M Neuzil
- Center for Vaccine Development, University of Maryland School of Medicine, Baltimore
| | - John C Victor
- Center for Vaccine Innovation and Access, PATH, Seattle, Washington
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50
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Dean NE, Pastore Y Piontti A, Madewell ZJ, Cummings DAT, Hitchings MDT, Joshi K, Kahn R, Vespignani A, Halloran ME, Longini IM. Ensemble forecast modeling for the design of COVID-19 vaccine efficacy trials. Vaccine 2020; 38:7213-7216. [PMID: 33012602 PMCID: PMC7492005 DOI: 10.1016/j.vaccine.2020.09.031] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 08/25/2020] [Accepted: 09/10/2020] [Indexed: 11/26/2022]
Abstract
To rapidly evaluate the safety and efficacy of COVID-19 vaccine candidates, prioritizing vaccine trial sites in areas with high expected disease incidence can speed endpoint accrual and shorten trial duration. Mathematical and statistical forecast models can inform the process of site selection, integrating available data sources and facilitating comparisons across locations. We recommend the use of ensemble forecast modeling – combining projections from independent modeling groups – to guide investigators identifying suitable sites for COVID-19 vaccine efficacy trials. We describe an appropriate structure for this process, including minimum requirements, suggested output, and a user-friendly tool for displaying results. Importantly, we advise that this process be repeated regularly throughout the trial, to inform decisions about enrolling new participants at existing sites with waning incidence versus adding entirely new sites. These types of data-driven models can support the implementation of flexible efficacy trials tailored to the outbreak setting.
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Affiliation(s)
- Natalie E Dean
- Department of Biostatistics, University of Florida, Gainesville, FL, United States.
| | - Ana Pastore Y Piontti
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA, United States
| | - Zachary J Madewell
- Department of Biostatistics, University of Florida, Gainesville, FL, United States
| | - Derek A T Cummings
- Department of Biology, University of Florida, Gainesville, FL, United States
| | | | - Keya Joshi
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Rebecca Kahn
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Alessandro Vespignani
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA, United States
| | - M Elizabeth Halloran
- Fred Hutchinson Cancer Research Center, Seattle, WA, United States; Department of Biostatistics, University of Washington, Seattle, WA, United States
| | - Ira M Longini
- Department of Biostatistics, University of Florida, Gainesville, FL, United States
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