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Kahn R, Feikin DR, Wiegand RE, Lipsitch M. EXAMINING BIAS FROM DIFFERENTIAL DEPLETION OF SUSCEPTIBLES IN VACCINE EFFECTIVENESS ESTIMATES IN SETTINGS OF WANING. Am J Epidemiol 2024; 193:232-234. [PMID: 37771045 PMCID: PMC10773472 DOI: 10.1093/aje/kwad191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 07/13/2023] [Accepted: 09/26/2023] [Indexed: 09/30/2023] Open
Affiliation(s)
- Rebecca Kahn
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, United States
- Center for Forecasting and Outbreak Analytics, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Daniel R Feikin
- Department of Immunizations, Vaccines and Biologicals, World Health Organization, Geneva, Switzerland
| | - Ryan E Wiegand
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Marc Lipsitch
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, United States
- Center for Forecasting and Outbreak Analytics, Centers for Disease Control and Prevention, Atlanta, GA, United States
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, United States
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Grossmann NV, Milne C, Martinez MR, Relucio K, Sadeghi B, Wiley EN, Holland SN, Rutschmann S, Vugia DJ, Kimura A, Crain C, Akter F, Mukhopadhyay R, Crandall J, Shorrock M, Smith JC, Prasad N, Kahn R, Barskey AE, Lee S, Willby MJ, Kozak-Muiznieks NA, Lucas CE, Henderson KC, Hamlin JAP, Yang E, Clemmons NS, Ritter T, Henn J. Large Community Outbreak of Legionnaires Disease Potentially Associated with a Cooling Tower - Napa County, California, 2022. MMWR Morb Mortal Wkly Rep 2023; 72:1315-1320. [PMID: 38060434 PMCID: PMC10715825 DOI: 10.15585/mmwr.mm7249a1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
Legionnaires disease is a serious infection acquired by inhalation of water droplets from human-made building water systems that contain Legionella bacteria. On July 11 and 12, 2022, Napa County Public Health (NCPH) in California received reports of three positive urinary antigen tests for Legionella pneumophila serogroup 1 in the town of Napa. By July 21, six Legionnaires disease cases had been confirmed among Napa County residents, compared with a baseline of one or two cases per year. NCPH requested assistance from the California Department of Public Health (CDPH) and CDC to aid in the investigations. Close temporal and geospatial clustering permitted a focused environmental sampling strategy of high-risk facilities which, coupled with whole genome sequencing results from samples and investigation of water system maintenance, facilitated potential linking of the outbreak with an environmental source. NCPH, with technical support from CDC and CDPH, instructed and monitored remediation practices for all environmental locations that tested positive for Legionella. The investigation response to this community outbreak illustrates the importance of interdisciplinary collaboration by public health agencies, laboratory support, timely communication with the public, and cooperation of managers of potentially implicated water systems. Timely identification of possible sources, sampling, and remediation of any facility testing positive for Legionella is crucial to interrupting further transmission.
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Joshi K, Kahn R, Boyer C, Lipsitch M. Some principles for using epidemiologic study results to parameterize transmission models. medRxiv 2023:2023.10.03.23296455. [PMID: 37873220 PMCID: PMC10593029 DOI: 10.1101/2023.10.03.23296455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Background Infectious disease models, including individual based models (IBMs), can be used to inform public health response. For these models to be effective, accurate estimates of key parameters describing the natural history of infection and disease are needed. However, obtaining these parameter estimates from epidemiological studies is not always straightforward. We aim to 1) outline challenges to parameter estimation that arise due to common biases found in epidemiologic studies and 2) describe the conditions under which careful consideration in the design and analysis of the study could allow us to obtain a causal estimate of the parameter of interest. In this discussion we do not focus on issues of generalizability and transportability. Methods Using examples from the COVID-19 pandemic, we first identify different ways of parameterizing IBMs and describe ideal study designs to estimate these parameters. Given real-world limitations, we describe challenges in parameter estimation due to confounding and conditioning on a post-exposure observation. We then describe ideal study designs that can lead to unbiased parameter estimates. We finally discuss additional challenges in estimating progression probabilities and the consequences of these challenges. Results Causal estimation can only occur if we are able to accurately measure and control for all confounding variables that create non-causal associations between the exposure and outcome of interest, which is sometimes challenging given the nature of the variables we need to measure. In the absence of perfect control, non-causal parameter estimates should still be used, as sometimes they are the best available information we have. Conclusions Identifying which estimates from epidemiologic studies correspond to the quantities needed to parameterize disease models, and determining whether these parameters have causal interpretations, can inform future study designs and improve inferences from infectious disease models. Understanding the way in which biases can arise in parameter estimation can inform sensitivity analyses or help with interpretation of results if the magnitude and direction of the bias is understood.
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Affiliation(s)
- Keya Joshi
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, 02115 Boston, Massachusetts
| | - Rebecca Kahn
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, 02115 Boston, Massachusetts
| | - Christopher Boyer
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, 02115 Boston, Massachusetts
| | - Marc Lipsitch
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, 02115 Boston, Massachusetts
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, 02115 Boston, Massachusetts
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Kahn R, Zielinski L, Gedlinske A, Askelson NM, Petersen C, Parker AM, Gidengil CA, Albert AP, Jiles AJ, Lindley MC, Kobayashi M, Scherer AM. Health Care Provider Knowledge and Attitudes Regarding Adult Pneumococcal Conjugate Vaccine Recommendations - United States, September 28-October 10, 2022. MMWR Morb Mortal Wkly Rep 2023; 72:979-984. [PMID: 37676840 PMCID: PMC10495187 DOI: 10.15585/mmwr.mm7236a2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
Despite the availability of effective vaccines against pneumococcal disease, pneumococcus is a common bacterial cause of pneumonia, causing approximately 100,000 hospitalizations among U.S. adults per year. In addition, approximately 30,000 invasive pneumococcal disease (IPD) cases and 3,000 IPD deaths occur among U.S. adults each year. Previous health care provider surveys identified gaps in provider knowledge about and understanding of the adult pneumococcal vaccine recommendations, and pneumococcal vaccine coverage remains suboptimal. To assess the feasibility and acceptability domains of the Advisory Committee on Immunization Practices (ACIP) Evidence to Recommendations (EtR) framework, a health care provider knowledge and attitudes survey was conducted during September 28-October 10, 2022, by the Healthcare and Public Perceptions of Immunizations Survey Collaborative before the October 2022 ACIP meeting. Among 751 provider respondents, two thirds agreed or strongly agreed with the policy option under consideration to expand the recommendations for the new 20-valent pneumococcal conjugate vaccine (PCV20) to adults who had only received the previously recommended 13-valent pneumococcal conjugate vaccine (PCV13). Gaps in providers' knowledge and perceived challenges to implementing recommendations were identified and were included in ACIP's EtR framework discussions in late October 2022 when ACIP updated the recommendations for PCV20 use in adults. Currently, use of PCV20 is recommended for certain adults who have previously received PCV13, in addition to those who have never received a pneumococcal conjugate vaccine. The survey findings indicate a need to increase provider awareness and implementation of pneumococcal vaccination recommendations and to provide tools to assist with patient-specific vaccination guidance. Resources available to address the challenges to implementing pneumococcal vaccination recommendations include the PneumoRecs VaxAdvisor mobile app and other CDC-developed tools, including summary documents and overviews of vaccination schedules and CDC's strategic framework to increase confidence in vaccines and reduce vaccine-preventable diseases, Vaccinate with Confidence.
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Monteiro HS, Lima Neto AS, Kahn R, Sousa GS, Carmona HA, Andrade JS, Castro MC. Impact of CoronaVac on Covid-19 outcomes of elderly adults in a large and socially unequal Brazilian city: A target trial emulation study. Vaccine 2023; 41:5742-5751. [PMID: 37573202 DOI: 10.1016/j.vaccine.2023.07.065] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/14/2023]
Abstract
BACKGROUND Although CoronaVac was the only Covid-19 vaccine adopted in the first months of the Brazilian vaccination campaign, randomized clinical trials to evaluate its efficacy in elderly adults were limited. In this study, we use routinely collected surveillance and SARS-CoV-2 vaccination and testing data comprising the population of the fifth largest city of Brazil to evaluate the effectiveness of CoronaVac in adults 60+ years old against severe outcomes. METHODS Using large observational databases on vaccination and surveillance data from the city of Fortaleza, Brazil, we defined a retrospective cohort including 324,302 eligible adults aged ≥60 years to evaluate the effectiveness of the CoronaVac vaccine. The cohort included individuals vaccinated between January 21, 2021, and August 31, 2021, who were matched with unvaccinated persons at the time of rollout following a 1:1 ratio according to baseline covariates of age, sex, and Human Development Index of the neighborhood of residence. Only Covid-19-related severe outcomes were included in the analysis: hospitalization, ICU admission, and death. Vaccine effectiveness for each outcome was calculated by using the risk ratio between the two groups, with the risk obtained by the Kaplan-Meier estimator. RESULTS We obtained 62,643 matched pairs for assessing the effectiveness of the two-dose regimen of CoronaVac. The demographic profile of the matched population was statistically representative of the population of Fortaleza. Using the cumulative incidence as the risk associated with each group, starting at day 14 since the receipt of the second dose, we found an 82.3 % (95 % CI 66.3-93.9) effectiveness against Covid-19-related death, 68.4 % (95 % CI 42.3-86.4) against ICU admission, and 55.8 % (95 % CI 42.7-68.3) against hospital admission. CONCLUSIONS Our results show that, despite critical delays in vaccine delivery and limited evidence in efficacy trial estimates, CoronaVac contributed to preventing deaths and severe morbidity due to Covid-19 in elderly adults.
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Affiliation(s)
- Higor S Monteiro
- Departamento de Física, Universidade Federal do Ceará, Fortaleza, Ceará, Brazil; Secretaria Municipal de Saúde de Fortaleza (SMS-Fortaleza), Fortaleza, Ceará, Brazil.
| | - Antonio S Lima Neto
- Secretaria Municipal de Saúde de Fortaleza (SMS-Fortaleza), Fortaleza, Ceará, Brazil; Centro de Ciências da Saúde, Universidade de Fortaleza (UNIFOR), Fortaleza, Ceará, Brazil
| | - Rebecca Kahn
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
| | - Geziel S Sousa
- Secretaria Municipal de Saúde de Fortaleza (SMS-Fortaleza), Fortaleza, Ceará, Brazil; Centro de Ciências da Saúde, Universidade Estadual do Ceará, Fortaleza, Ceará, Brazil
| | - Humberto A Carmona
- Departamento de Física, Universidade Federal do Ceará, Fortaleza, Ceará, Brazil.
| | - José S Andrade
- Departamento de Física, Universidade Federal do Ceará, Fortaleza, Ceará, Brazil.
| | - Marcia C Castro
- Department of Global Health and Population, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
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Jia KM, Kahn R, Fisher R, Balter S, Lipsitch M. Geographic Targeting of COVID-19 Testing to Maximize Detection in Los Angeles County. Open Forum Infect Dis 2023; 10:ofad331. [PMID: 37469616 PMCID: PMC10352645 DOI: 10.1093/ofid/ofad331] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 06/23/2023] [Indexed: 07/21/2023] Open
Abstract
Background Many severe acute respiratory syndrome coronavirus 2 infections have not been detected, reported, or isolated. For community testing programs to locate the most cases under limited testing resources, we developed and evaluated quantitative approaches for geographic targeting of increased coronavirus disease 2019 testing efforts. Methods For every week from December 5, 2021, to July 23, 2022, testing and vaccination data were obtained in ∼340 cities/communities in Los Angeles County, and models were developed to predict which cities/communities would have the highest test positivity 2 weeks ahead. A series of counterfactual scenarios were constructed to explore the additional number of cases that could be detected under targeted testing. Results The simplest model based on most recent test positivity performed nearly as well as the best model based on most recent test positivity and weekly tests per 100 persons in identifying communities that would maximize the average yield of cases per test in the following 2 weeks and almost as well as the perfect knowledge of the actual positivity 2 weeks ahead. In the counterfactual scenario, increasing testing by 1% 2 weeks ahead and allocating all tests to communities with the top 10% of predicted positivity would yield a 2% increase in detected cases. Conclusions Simple models based on current test positivity can predict which communities may have the highest positivity 2 weeks ahead and hence could be allocated with more testing resources.
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Affiliation(s)
- Katherine M Jia
- Correspondence: Katherine M. Jia, MSc, Department of Epidemiology, Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02115 ()
| | - Rebecca Kahn
- Department of Epidemiology, Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Rebecca Fisher
- Los Angeles County Department of Public Health, Acute Communicable Disease Program, Los Angeles, California, USA
| | - Sharon Balter
- Los Angeles County Department of Public Health, Acute Communicable Disease Program, Los Angeles, California, USA
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Kahn R, Eyal N, Sow SO, Lipsitch M. Mass drug administration of azithromycin: an analysis. Clin Microbiol Infect 2023; 29:326-331. [PMID: 36309328 DOI: 10.1016/j.cmi.2022.10.022] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 10/13/2022] [Accepted: 10/16/2022] [Indexed: 11/19/2022]
Abstract
BACKGROUND WHO recommends mass drug administration (MDA) of the antibiotic azithromycin for children aged 1-11 months in areas with high rates of infant and child mortality. Notwithstanding the substantial potential benefits of lowering childhood mortality, MDA raises understandable concerns about exacerbating antibiotic resistance. OBJECTIVES In this study, we aimed to evaluate the use of MDA using both quantitative and ethical considerations. SOURCES We performed a series of literature searches between July 2019 and June 2022. CONTENT We first compared MDA with other uses of antibiotics using the standard metric of 'number needed to treat', and five additional criteria: (1) other widely accepted uses of anti-infectives (2) absolute use (i.e. total number), of antibiotics, (3) risk-benefit trade-off, (4) availability of short-term alternatives, and (5) the precedent for implementing similar interventions. We found that MDA falls well within a justifiable range when compared with widely accepted uses of antibiotics in terms of the number needed to treat. The other five criteria we considered provided further support for the use of MDA to prevent childhood mortality. IMPLICATIONS Although better data on antibiotic use and resistance are needed, efforts to reduce antibiotic use and resistance should not start with halting MDA of azithromycin in the areas with the highest rates of childhood mortality. Improving data to inform this decision is critical. However, on the basis of the best evidence available, we believe that concerns regarding resistance should not thwart MDA; instead, MDA should be accompanied by robust plans to monitor its efficacy and changes in resistance levels. Similar considerations could be included in a framework for evaluating the benefits of antibiotics against the risk of resistance in other contexts.
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Affiliation(s)
- Rebecca Kahn
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
| | - Nir Eyal
- Center for Population-Level Bioethics, Rutgers University, New Brunswick, NJ, USA; Department of Health Behavior, Society and Policy, Rutgers School of Public Health, Piscataway, NJ, USA; Department of Philosophy, Rutgers University, New Brunswick, NJ, USA
| | - Samba O Sow
- Centre pour le Développement des Vaccins (CVD-Mali), Ministère de La Santé, BP251, Bamako, Mali; Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Marc Lipsitch
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA; Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
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Sturm U, Heyne E, Herrmann E, Arends B, Dieter AL, Dorfman E, Drauschke F, Heller N, Kahn R, Kaiser K, Koch G, Kramar N, Mansilla Sánchez A, Mauelshagen F, Nadim T, Pell R, Petersen M, Schmidt-Loske K, Scholz H, Sterling C, Trischler H, Wagner S. Anthropocenic Objects. Collecting Practices for the Age of Humans. RIO 2022. [DOI: 10.3897/rio.8.e89446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The knowledge needed to tackle future environmental and societal challenges can only be generated through exchange between science and society. The conventional distinction made between natural and cultural heritage in museums and other institutions is no longer appropriate in the Anthropocene. Museums must rethink the social and cultural dimensions of existing museum collections and reinvent the organization of knowledge production for our present. In three workshops at the Museum für Naturkunde Berlin, practitioners and interdisciplinary theorists discussed the concept of “Anthropocenic objects” and considered how they create opportunities for the emergence of new collecting practices involving participatory research and open exchange between research, society, and conservation institutions.
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Linge P, Jern A, Tydén H, Gullstrand B, Yan H, Welinder C, Kahn R, Jonsen A, Semple J, Bengtsson A. POS0458 ENRICHMENT OF COMPLEMENT, IMMUNOGLOBULINS, AND AUTOANTIBODY TARGETS IN THE PROTEOME OF PLATELETS FROM PATIENTS WITH SYSTEMIC LUPUS ERYTHEMATOSUS (SLE). Ann Rheum Dis 2022. [DOI: 10.1136/annrheumdis-2022-eular.2572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BackgroundSystemic Lupus Erythematosus (SLE) is characterized by autoimmunity towards apoptotic/necrotic cells, complement activation and excessive amounts of circulating immune complexes. Platelets are recognized as immune cells that interacts with innate and adaptive immune functions. They are activated in SLE patients and contribute to an increased susceptibility to thrombosis [1]. Decreased platelet size has been observed in patients with SLE [2], but the mechanism(s) remains unclear. In this study, we have analyzed the complete proteome of platelets with normal and decreased size from SLE patients and from healthy controls (HC).ObjectivesOur aim was to find clues that could explain the morphological differences observed in platelets from SLE patients and to better characterize the role of platelets in SLE.MethodsWe included 23 consecutive patients with SLE, median SLEDAI-2K score was 2, and 10 HC. Blood count, serum complement levels and the presence of antiphospholipid or dsDNA antibodies were analyzed in all patients. Platelet size (forward scatter) and activation status (CD154, PAC1, CD32, PAR1, CD62P and Annexin V) was determined using flow cytometry. The proteome of 10 platelet isolates from SLE (five with smallest and the five with largest average size) and five HC were analyzed using liquid chromatography with tandem mass spectrometry (LC-MS/MS). Data were analyzed using ANOVA, t-test, hierarchical cluster analysis, protein interactions using the STRING software and correlation analysis using spearman correlation.ResultsWe identified a total of 2572 proteins from the platelet isolates. Out of the identified proteins, 396 had significantly different levels, meeting an ANOVA q-value ≤ 0.01. Pairwise t-test analysis, using a fold difference (FD) of ≥ 1.5 and a p-value of ≤ 0.05 as cut off reveled significant differences in the distribution of proteins between groups. Platelets of both SLE groups (small and normal sized) shared higher levels of forty proteins and twenty proteins were reduced, compared to HC. Cytoskeletal functions were overrepresentation in the group of reduced proteins, while proteins with higher levels in platelets from SLE patients included proteins associated with complement and autoantibody targets such as Beta-2-glycoprotein 1, Annexin A5, and Prothrombin. Platelets from SLE patients also shared an abundance in immunoglobulin proteins, with even greater accumulation in the normal sized platelets. SLE platelet heavy constant alpha 1 (r -0.85, p=0.003), heavy constant mu (r -0.64, p=0.05) and heavy constant gamma 3 (r -0.80, p=0.008) was inversely correlated with complement C4 in serum and heavy constant gamma 2 (r -0.648, p=0.049) with complement C3.ConclusionThis study revealed an accumulation of complement proteins, immunoglobulins and known autoantigens in platelets from SLE patients compared to HC. The signature was largely independent of platelet size, but the enrichment of proteins involved in SLE pathogenesis indicates that the composition is influenced by SLE disease mechanisms. This was supported by the inverse correlation between platelet immunoglobulin and serum levels of complement protein C3 and C4. Platelets are known to interact with complement and express the low-affinity immunoglobulin gamma Fc region receptor IIA (CD32), suggesting a role in the clearance of immune complexes [3]. Future studies will have to determine if platelets play a role in the turnover of complement and immune complexes and the potential role of platelets as a source of autoantigens.References[1]Linge, P., et al., The non-haemostatic role of platelets in systemic lupus erythematosus. Nat Rev Rheumatol, 2018. 14(4): p. 195-213.[2]Lood, C., et al., Decreased platelet size is associated with platelet activation and anti-phospholipid syndrome in systemic lupus erythematosus. Rheumatology (Oxford), 2017. 56(3): p. 408-416.[3]Huang, Z.Y., et al., Human platelet FcgammaRIIA and phagocytes in immune-complex clearance. Mol Immunol, 2011. 48(4): p. 691-6.Disclosure of InterestsPetrus Linge: None declared, Andreas Jern: None declared, Helena Tydén: None declared, Birgitta Gullstrand: None declared, Hong Yan: None declared, Charlotte Welinder: None declared, Robin Kahn: None declared, Andreas Jonsen Consultant of: Astra Zeneca and glaxosmithkline, John Semple: None declared, Anders Bengtsson: None declared.
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Hambridge HL, Kahn R, Onnela JP. Effect of a two-dose vs three-dose vaccine strategy in residential colleges using an empirical proximity network. Int J Infect Dis 2022; 119:210-213. [PMID: 35405350 PMCID: PMC8989661 DOI: 10.1016/j.ijid.2022.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/03/2022] [Accepted: 04/04/2022] [Indexed: 02/04/2023] Open
Affiliation(s)
- Hali L Hambridge
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, United States.
| | - Rebecca Kahn
- Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, Boston, MA, United States.
| | - Jukka-Pekka Onnela
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, United States.
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Winter I, Davidson M, Fleischhacker W, Kahn R. Effectiveness of oral versus long-acting antipsychotic treatment early-phase schizophrenia patients: an open-label randomized trial. Eur Psychiatry 2022. [PMCID: PMC9564751 DOI: 10.1192/j.eurpsy.2022.356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Introduction Schizophrenia is a chronic psychiatric illness with periods of remission and relapse. Patients vary in the frequency and severity of relapse, time until relapse and time in remission. Discontinuation of antipsychotic medication is by far the most important reason for relapse. A possible method to optimize medication adherence is to treat patients with long-term, depot medication rather than oral medication. Objectives Primary objective is to compare all cause discontinuation rates in patients with schizophrenia randomized to either one of the two depot medications (aripiprazole depot or paliperidone palmitate) with patients randomized to either one of the two oral formulations of the same medication (aripiprazole or paliperidone) over an 19 month follow-up period. Methods Pragmatic, randomized, open label, multicenter, multinational comparative trial consisting of a 19 month treatment period. Patients aged 18 years or older, having experienced the first psychosis 1-7 years ago, currently meeting DSM-IV-R criteria for schizophrenia. Patients are randomized 1:1:1:1 to paliperidone palmitate, aripiprazole depot, oral aripiprazole or oral paliperidone. The primary outcome is all cause discontinuation. Results In the Intent to Treat sample (n=511), no difference was found in time to ACD between the combined oral and combined depot treatment arms, nor between the four individual treatment arms. Conclusions Even though the scientific evidence comparing oral and depot medication has been inconsistent, most studies were conducted in rigorous clinical settings, which may have biased those results. In contract, given the pragmatic, open label design of the current trial, the results may be more representative of common daily practice. Disclosure No significant relationships.
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Kahn R, Schrag SJ, Verani JR, Lipsitch M. Identifying and Alleviating Bias Due to Differential Depletion of Susceptible People in Postmarketing Evaluations of COVID-19 Vaccines. Am J Epidemiol 2022; 191:800-811. [PMID: 35081612 PMCID: PMC8807238 DOI: 10.1093/aje/kwac015] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 01/09/2022] [Accepted: 01/24/2022] [Indexed: 01/06/2023] Open
Abstract
Recent studies have provided key information about SARS-CoV-2 vaccines’ efficacy and effectiveness (VE). One important question that remains is whether the protection conferred by vaccines wanes over time. However, estimates over time are subject to bias from differential depletion of susceptibles between vaccinated and unvaccinated groups. Here we examine the extent to which biases occur under different scenarios and assess whether serologic testing has the potential to correct this bias. By identifying non-vaccine antibodies, these tests could identify individuals with prior infection. We find in scenarios with high baseline VE, differential depletion of susceptibles creates minimal bias in VE estimates, suggesting that any observed declines are likely not due to spurious waning alone. However, if baseline VE is lower, the bias for leaky vaccines (that reduce individual probability of infection given contact) is larger and should be corrected by excluding individuals with past infection if the mechanism is known to be leaky. Conducting analyses both unadjusted and adjusted for past infection could give lower and upper bounds for the true VE. Studies of VE should therefore enroll individuals regardless of prior infection history but also collect information, ideally through serologic testing, on this critical variable.
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Affiliation(s)
- Rebecca Kahn
- Correspondence to Dr. Rebecca Kahn, Center for Communicable Disease Dynamics, 677 Huntington Ave, Suite 506, Boston, MA 02115 ()
| | - Stephanie J Schrag
- COVID-19 Response, US Centers for Disease Control and Prevention, Atlanta, Georgia, United States
| | - Jennifer R Verani
- COVID-19 Response, US Centers for Disease Control and Prevention, Atlanta, Georgia, United States
| | - Marc Lipsitch
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States
- COVID-19 Response, US Centers for Disease Control and Prevention, Atlanta, Georgia, United States
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States
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Kahn R, Holmdahl I, Reddy S, Jernigan J, Mina MJ, Slayton RB. Mathematical Modeling to Inform Vaccination Strategies and Testing Approaches for Coronavirus Disease 2019 (COVID-19) in Nursing Homes. Clin Infect Dis 2022; 74:597-603. [PMID: 34086877 PMCID: PMC8244782 DOI: 10.1093/cid/ciab517] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [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: 02/26/2021] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Nursing home residents and staff were included in the first phase of coronavirus disease 2019 vaccination in the United States. Because the primary trial endpoint was vaccine efficacy (VE) against symptomatic disease, there are limited data on the extent to which vaccines protect against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and the ability to infect others (infectiousness). Assumptions about VE against infection and infectiousness have implications for changes to infection prevention guidance for vaccinated populations, including testing strategies. METHODS We use a stochastic agent-based Susceptible-Exposed-Infectious (Asymptomatic/Symptomatic)-Recovered model of a nursing home to simulate SARS-CoV-2 transmission. We model 3 scenarios, varying VE against infection, infectiousness, and symptoms, to understand the expected impact of vaccination in nursing homes, increasing staff vaccination coverage, and different screening testing strategies under each scenario. RESULTS Increasing vaccination coverage in staff decreases total symptomatic cases in the nursing home (among staff and residents combined) in each VE scenario. In scenarios with 50% and 90% VE against infection and infectiousness, increasing staff coverage reduces symptomatic cases among residents. If vaccination only protects against symptoms, and asymptomatic cases remain infectious, increased staff coverage increases symptomatic cases among residents. However, this is outweighed by the reduction in symptomatic cases among staff. Higher frequency testing-more than once weekly-is needed to reduce total symptomatic cases if the vaccine has lower efficacy against infection and infectiousness, or only protects against symptoms. CONCLUSIONS Encouraging staff vaccination is not only important for protecting staff, but might also reduce symptomatic cases in residents if a vaccine confers at least some protection against infection or infectiousness.
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Affiliation(s)
- Rebecca Kahn
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- COVID-19 Response, US Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Inga Holmdahl
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Sujan Reddy
- COVID-19 Response, US Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - John Jernigan
- COVID-19 Response, US Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Michael J Mina
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Rachel B Slayton
- COVID-19 Response, US Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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14
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Holmdahl I, Kahn R, Slifka KJ, Dooling K, Slayton RB. Modeling the Impact of Vaccination Strategies for Nursing Homes in the Context of Increased Severe Acute Respiratory Syndrome Coronavirus 2 Community Transmission and Variants. Clin Infect Dis 2022; 75:e880-e883. [PMID: 35092678 PMCID: PMC8807308 DOI: 10.1093/cid/ciac062] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Indexed: 01/19/2023] Open
Abstract
Using an agent-based model, we examined the impact of community prevalence, the Delta variant, staff vaccination coverage, and booster vaccines for residents on outbreak dynamics in nursing homes. Increased staff coverage and high booster vaccine effectiveness leads to fewer infections, but cumulative incidence is highly dependent on community transmission.
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Affiliation(s)
| | | | - Kara Jacobs Slifka
- COVID-19 Response, US Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Kathleen Dooling
- COVID-19 Response, US Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Rachel B Slayton
- Correspondence: R. B. Slayton, US Centers for Disease Control and Prevention, Division of Healthcare Quality Promotion, Epidemiology, Research, and Innovations Branch, 1600 Clifton Road NE, MS H16-3, Atlanta, GA, 30329 ()
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15
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Bushman M, Kahn R, Taylor BP, Lipsitch M, Hanage WP. Population impact of SARS-CoV-2 variants with enhanced transmissibility and/or partial immune escape. Cell 2021; 184:6229-6242.e18. [PMID: 34910927 PMCID: PMC8603072 DOI: 10.1016/j.cell.2021.11.026] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [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: 08/30/2021] [Revised: 11/10/2021] [Accepted: 11/15/2021] [Indexed: 12/20/2022]
Abstract
SARS-CoV-2 variants of concern exhibit varying degrees of transmissibility and, in some cases, escape from acquired immunity. Much effort has been devoted to measuring these phenotypes, but understanding their impact on the course of the pandemic-especially that of immune escape-has remained a challenge. Here, we use a mathematical model to simulate the dynamics of wild-type and variant strains of SARS-CoV-2 in the context of vaccine rollout and nonpharmaceutical interventions. We show that variants with enhanced transmissibility frequently increase epidemic severity, whereas those with partial immune escape either fail to spread widely or primarily cause reinfections and breakthrough infections. However, when these phenotypes are combined, a variant can continue spreading even as immunity builds up in the population, limiting the impact of vaccination and exacerbating the epidemic. These findings help explain the trajectories of past and present SARS-CoV-2 variants and may inform variant assessment and response in the future.
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Affiliation(s)
- Mary Bushman
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| | - Rebecca Kahn
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Bradford P Taylor
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Marc Lipsitch
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - William P Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
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16
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Gostic KM, McGough L, Baskerville EB, Abbott S, Joshi K, Tedijanto C, Kahn R, Niehus R, Hay JA, De Salazar PM, Hellewell J, Meakin S, Munday JD, Bosse NI, Sherrat K, Thompson RN, White LF, Huisman JS, Scire J, Bonhoeffer S, Stadler T, Wallinga J, Funk S, Lipsitch M, Cobey S. Correction: Practical considerations for measuring the effective reproductive number, Rt. PLoS Comput Biol 2021; 17:e1009679. [PMID: 34879070 PMCID: PMC8654153 DOI: 10.1371/journal.pcbi.1009679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
[This corrects the article DOI: 10.1371/journal.pcbi.1008409.].
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17
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Hambridge HL, Kahn R, Onnela JP. Examining SARS-CoV-2 Interventions in Residential Colleges Using an Empirical Network. Int J Infect Dis 2021; 113:325-330. [PMID: 34624516 PMCID: PMC8492892 DOI: 10.1016/j.ijid.2021.10.008] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/17/2021] [Accepted: 10/02/2021] [Indexed: 01/11/2023] Open
Abstract
Objectives Universities have turned to SARS-CoV-2 models to examine campus reopening strategies. While these studies have explored a variety of modeling techniques, none have used empirical data. Methods In this study, we use an empirical proximity network of college freshmen obtained using smartphone Bluetooth to simulate the spread of the virus. We investigate the role of immunization, testing, isolation, mask wearing, and social distancing in the presence of implementation challenges and imperfect compliance. Results We show that frequent testing could drastically reduce the spread of the virus if levels of immunity are low, but its effects are limited if immunity is more ubiquitous. Furthermore, moderate levels of mask wearing and social distancing could lead to additional reductions in cumulative incidence, but their benefit decreases rapidly as immunity and testing frequency increase. However, if immunity from vaccination is imperfect or declines over time, scenarios not studied here, frequent testing and other interventions may play more central roles. Conclusions Our findings suggest that although regular testing and isolation are powerful tools, they have limited benefit if immunity is high or other interventions are widely adopted. If universities can attain even moderate levels of vaccination, masking, and social distancing, they may be able to relax the frequency of testing to once every four weeks.
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Affiliation(s)
- Hali L Hambridge
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, United States.
| | - Rebecca Kahn
- Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, Boston, MA, United States.
| | - Jukka-Pekka Onnela
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, United States.
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18
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Abstract
Determining policies to end the SARS-CoV-2 pandemic will require an understanding of the efficacy and effectiveness (hereafter, efficacy) of vaccines. Beyond the efficacy against severe disease and symptomatic and asymptomatic infection, understanding vaccine efficacy against virus transmission, including efficacy against transmission of different viral variants, will help model epidemic trajectory and determine appropriate control measures. Recent studies have proposed using random virologic testing in individual randomized controlled trials to improve estimation of vaccine efficacy against infection. We propose to further use the viral load measures from these tests to estimate efficacy against transmission. This estimation requires a model of the relationship between viral load and transmissibility and assumptions about the vaccine effect on transmission and the progress of the epidemic. We describe these key assumptions, potential violations of them, and solutions that can be implemented to mitigate these violations. Assessing these assumptions and implementing this random sampling, with viral load measures, will enable better estimation of the crucial measure of vaccine efficacy against transmission.
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Affiliation(s)
- Lee Kennedy-Shaffer
- From the Department of Mathematics and Statistics, Vassar College, Poughkeepsie, NY
| | - Rebecca Kahn
- Center for Communicable Disease Dynamics, Harvard T H Chan School of Public Health, Boston, MA
- Department of Epidemiology, Harvard T H Chan School of Public Health, Boston, MA
| | - Marc Lipsitch
- Center for Communicable Disease Dynamics, Harvard T H Chan School of Public Health, Boston, MA
- Department of Epidemiology, Harvard T H Chan School of Public Health, Boston, MA
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19
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Holmdahl I, Kahn R, Slifka KJ, Dooling K, Slayton RB. Modeling the impact of vaccination strategies for nursing homes in the context of increased SARS-CoV-2 community transmission and variants.. [PMID: 34729570 PMCID: PMC8562554 DOI: 10.1101/2021.10.25.21265493] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
AbstractNursing homes (NH) were among the first settings to receive COVID-19 vaccines in the United States, but staff vaccination coverage remains low at an average of 64%. Using an agent-based model, we examined the impact of community prevalence, the Delta variant, staff vaccination coverage, and boosters for residents on outbreak dynamics in nursing homes. We found that increased staff primary series coverage and high booster vaccine effectiveness (VE) in residents leads to fewer infections and that the cumulative incidence is highly dependent on community transmission. Despite high VE, high community transmission resulted in continued symptomatic infections in NHs.
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20
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Abstract
INTRODUCTION Advance planning of vaccine trials conducted during outbreaks increases our ability to rapidly define the efficacy and potential impact of a vaccine. Vaccine efficacy against infectiousness (VEI) is an important measure for understanding a vaccine's full impact, yet it is currently not identifiable in many trial designs because it requires knowledge of infectors' vaccination status. Recent advances in genomics have improved our ability to reconstruct transmission networks. We aim to assess if augmenting trials with pathogen sequence and contact tracing data can permit them to estimate VEI. METHODS We develop a transmission model with a vaccine trial in an outbreak setting, incorporate pathogen sequence data and contact tracing data, and assign probabilities to likely infectors. We then propose and evaluate the performance of an estimator of VEI. RESULTS We find that under perfect knowledge of infector-infectee pairs, we are able to accurately estimate VEI. Use of sequence data results in imperfect reconstruction of transmission networks, biasing estimates of VEI towards the null, with approaches using deep sequence data performing better than approaches using consensus sequence data. Inclusion of contact tracing data reduces the bias. CONCLUSION Pathogen genomics enhance identifiability of VEI, but imperfect transmission network reconstruction biases estimate toward the null and limits our ability to detect VEI. Given the consistent direction of the bias, estimates obtained from trials using these methods will provide lower bounds on the true VEI. A combination of sequence and epidemiologic data results in the most accurate estimates, underscoring the importance of contact tracing.
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Affiliation(s)
- Rebecca Kahn
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, Massachusetts, USA
| | - Rui Wang
- Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, Boston, Massachusetts, USA
- Department of Biostatistics, Harvard TH Chan School of Public Health, Boston, Massachusetts, USA
| | - Sarah V. Leavitt
- Department of Biostatistics, School of Public Health, Boston University, Boston, Massachusetts, USA
| | - William P. Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, Massachusetts, USA
| | - Marc Lipsitch
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, Massachusetts, USA
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, Massachusetts, USA
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21
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Lau YC, Tsang TK, Kennedy-Shaffer L, Kahn R, Lau EHY, Chen D, Wong JY, Ali ST, Wu P, Cowling BJ. Joint Estimation Of Generation Time And Incubation Period For Coronavirus Disease (Covid-19). J Infect Dis 2021; 224:1664-1671. [PMID: 34423821 PMCID: PMC8499762 DOI: 10.1093/infdis/jiab424] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 06/25/2021] [Accepted: 08/21/2021] [Indexed: 01/02/2023] Open
Abstract
Background Coronavirus disease 2019 (COVID-19) has caused a heavy disease burden globally. The impact of process and timing of data collection on the accuracy of estimation of key epidemiological distributions are unclear. Because infection times are typically unobserved, there are relatively few estimates of generation time distribution. Methods We developed a statistical framework to jointly estimate generation time and incubation period from human-to-human transmission pairs, accounting for sampling biases. We applied the framework on 80 laboratory-confirmed human-to-human transmission pairs in China. We further inferred the infectiousness profile, serial interval distribution, proportions of presymptomatic transmission, and basic reproduction number (R0) for COVID-19. Results The estimated mean incubation period was 4.8 days (95% confidence interval [CI], 4.1–5.6), and mean generation time was 5.7 days (95% CI, 4.8–6.5). The estimated R0 based on the estimated generation time was 2.2 (95% CI, 1.9–2.4). A simulation study suggested that our approach could provide unbiased estimates, insensitive to the width of exposure windows. Conclusions Properly accounting for the timing and process of data collection is critical to have correct estimates of generation time and incubation period. R0 can be biased when it is derived based on serial interval as the proxy of generation time.
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Affiliation(s)
- Yiu Chung Lau
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China.,Laboratory of Data Discovery for Health, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Tim K Tsang
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China.,Laboratory of Data Discovery for Health, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Lee Kennedy-Shaffer
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States.,Department of Mathematics and Statistics, Vassar College, Poughkeepsie, New York, United States
| | - Rebecca Kahn
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States
| | - Eric H Y Lau
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China.,Laboratory of Data Discovery for Health, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Dongxuan Chen
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China.,Laboratory of Data Discovery for Health, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Jessica Y Wong
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Sheikh Taslim Ali
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China.,Laboratory of Data Discovery for Health, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Peng Wu
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China.,Laboratory of Data Discovery for Health, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Benjamin J Cowling
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China.,Laboratory of Data Discovery for Health, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
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22
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Regev-Yochay G, Amit S, Bergwerk M, Lipsitch M, Leshem E, Kahn R, Lustig Y, Cohen C, Doolman R, Ziv A, Novikov I, Rubin C, Gimpelevich I, Huppert A, Rahav G, Afek A, Kreiss Y. Decreased infectivity following BNT162b2 vaccination: A prospective cohort study in Israel. Lancet Reg Health Eur 2021; 7:100150. [PMID: 34250518 PMCID: PMC8261633 DOI: 10.1016/j.lanepe.2021.100150] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [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: 12/17/2022]
Abstract
BACKGROUND BNT162b2 was shown to be 92% effective in preventing COVID-19. Prioritizing vaccine rollout, and achievement of herd immunity depend on SARS-CoV-2 transmission reduction. The vaccine's effect on infectivity is thus a critical priority. METHODS Among all 9650 HCW of a large tertiary medical center in Israel, we calculated the prevalence of positive SARS-CoV-2 qRT-PCR cases with asymptomatic presentation, tested following known or presumed exposure and the infectious subset (N-gene-Ct-value<30) of these. Additionally, infection incidence rates were calculated for symptomatic cases and infectious (Ct<30) cases. Vaccine effectiveness within three months of vaccine rollout was measured as one minus the relative risk or rate ratio, respectively. To further assess infectiousness, we compared the mean Ct-value and the proportion of infections with a positive SARS-CoV-2 antigen test of vaccinated vs. unvaccinated. The correlation between IgG levels within the week before detection and Ct level was assessed. FINDINGS Reduced prevalence among fully vaccinated HCW was observed for (i) infections detected due to exposure, with asymptomatic presentation (VE(i)=65.1%, 95%CI 45-79%), (ii) the presumed infectious (Ct<30) subset of these (VE(ii)=69.6%, 95%CI 43-84%) (iii) never-symptomatic infections (VE(iii)=72.3%, 95%CI 48-86%), and (iv) the presumed infectious (Ct<30) subset (VE(iv)=83.0%, 95%CI 51-94%).Incidence of (v) symptomatic and (vi) symptomatic-infectious cases was significantly lower among fully vaccinated vs. unvaccinated individuals (VE(v)= 89.7%, 95%CI 84-94%, VE(vi)=88.1%, 95%CI 80-95%).The mean Ct-value was significantly higher in vaccinated vs. unvaccinated (27.3±1.2 vs. 22.2±1.0, p<0.001) and the proportion of positive SARS-CoV-2 antigen tests was also significantly lower among vaccinated vs. unvaccinated PCR-positive HCW (80% vs. 31%, p<0.001). Lower infectivity was correlated with higher IgG concentrations (R=0.36, p=0.01). INTERPRETATION These results suggest that BNT162b2 is moderately to highly effective in reducing infectivity, via preventing infection and through reducing viral shedding. FUNDING Sheba Medical Center, Israel.
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Affiliation(s)
- Gili Regev-Yochay
- Infection Prevention & Control Unit, Sheba Medical Center, Ramat-Gan, Israel
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Sharon Amit
- Clinical Microbiology, Sheba Medical Center, Ramat Gan, Israel
| | - Moriah Bergwerk
- Infection Prevention & Control Unit, Sheba Medical Center, Ramat-Gan, Israel
| | - Marc Lipsitch
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard Chan School of Public Health, Boston, MA. USA
| | - Eyal Leshem
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
- Infecious Disease Unit, Sheba Medical Center, Ramat Gan, Israel
| | - Rebecca Kahn
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard Chan School of Public Health, Boston, MA. USA
| | - Yaniv Lustig
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
- Central Virology Laboratory, Ministry of Health and Sheba Medical Center, Ramat Gan, Israel
| | - Carmit Cohen
- Infection Prevention & Control Unit, Sheba Medical Center, Ramat-Gan, Israel
| | - Ram Doolman
- Central laboratory, Sheba Medical Center, Ramat Gan, Israel
| | - Arnona Ziv
- Gertner Institute for Epidemiology & Health Policy, Sheba Medical Center, Ramat Gan, Israel
| | - Ilya Novikov
- Gertner Institute for Epidemiology & Health Policy, Sheba Medical Center, Ramat Gan, Israel
| | - Carmit Rubin
- Infection Prevention & Control Unit, Sheba Medical Center, Ramat-Gan, Israel
| | - Irena Gimpelevich
- Gertner Institute for Epidemiology & Health Policy, Sheba Medical Center, Ramat Gan, Israel
| | - Amit Huppert
- Gertner Institute for Epidemiology & Health Policy, Sheba Medical Center, Ramat Gan, Israel
| | - Galia Rahav
- Infecious Disease Unit, Sheba Medical Center, Ramat Gan, Israel
| | - Arnon Afek
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
- General Management, Sheba Medical Center, Ramat Gan, Israel
| | - Yitshak Kreiss
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
- General Management, Sheba Medical Center, Ramat Gan, Israel
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23
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Abstract
Randomized controlled trials (RCTs) have shown high efficacy of multiple vaccines against SARS-CoV-2 disease (COVID-19), and recent studies have shown the vaccines are also effective against infection. Evidence for the effect of each of these vaccines on ability to transmit the virus is also beginning to emerge. We describe an approach to estimate these vaccines' effects on viral positivity, a prevalence measure which under the reasonable assumption that vaccinated individuals who become infected are no more infectious than unvaccinated individuals forms a lower bound on efficacy against transmission. Specifically, we recommend separate analysis of positive tests triggered by symptoms (usually the primary RCT outcome) and cross-sectional prevalence of positive tests obtained regardless of symptoms. The odds ratio of carriage for vaccine vs. placebo provides an unbiased estimate of vaccine effectiveness against viral positivity, under certain assumptions, and we show through simulations that likely departures from these assumptions will only modestly bias this estimate. Applying this approach to published data from the RCT of the Moderna vaccine, we estimate that one dose of vaccine reduces the potential for transmission by at least 61%, possibly considerably more. We describe how these approaches can be translated into observational studies of vaccine effectiveness.
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Affiliation(s)
- Marc Lipsitch
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, United States; Department of Immunology and Infectious Diseases, 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
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24
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Abstract
Randomized controlled trials (RCTs) have shown high efficacy of multiple vaccines against SARS-CoV-2 disease (COVID-19), and recent studies have shown the vaccines are also effective against infection. Evidence for the effect of each of these vaccines on ability to transmit the virus is also beginning to emerge. We describe an approach to estimate these vaccines' effects on viral positivity, a prevalence measure which under the reasonable assumption that vaccinated individuals who become infected are no more infectious than unvaccinated individuals forms a lower bound on efficacy against transmission. Specifically, we recommend separate analysis of positive tests triggered by symptoms (usually the primary outcome) and cross-sectional prevalence of positive tests obtained regardless of symptoms. The odds ratio of carriage for vaccine vs. placebo provides an unbiased estimate of vaccine effectiveness against viral positivity, under certain assumptions, and we show through simulations that likely departures from these assumptions will only modestly bias this estimate. Applying this approach to published data from the RCT of the Moderna vaccine, we estimate that one dose of vaccine reduces the potential for transmission by at least 61%, possibly considerably more. We describe how these approaches can be translated into observational studies of vaccine effectiveness.
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Affiliation(s)
- Marc Lipsitch
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Rebecca Kahn
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
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25
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Holmdahl I, Kahn R, Hay JA, Buckee CO, Mina MJ. Estimation of Transmission of COVID-19 in Simulated Nursing Homes With Frequent Testing and Immunity-Based Staffing. JAMA Netw Open 2021; 4:e2110071. [PMID: 33988707 PMCID: PMC8122229 DOI: 10.1001/jamanetworkopen.2021.10071] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 03/21/2021] [Indexed: 12/29/2022] Open
Abstract
Importance Nursing homes and other long-term care facilities have been disproportionately impacted by the COVID-19 pandemic. Strategies are urgently needed to reduce transmission in these high-risk populations. Objective To evaluate COVID-19 transmission in nursing homes associated with contact-targeted interventions and testing. Design, Setting, and Participants This decision analytical modeling study developed an agent-based susceptible-exposed-infectious (asymptomatic/symptomatic)-recovered model between July and September 2020 to examine SARS-CoV-2 transmission in nursing homes. Residents and staff of a simulated nursing home with 100 residents and 100 staff split among 3 shifts were modeled individually; residents were split into 2 cohorts based on COVID-19 diagnosis. Data were analyzed from September to October 2020. Exposures In the resident cohorting intervention, residents who had recovered from COVID-19 were moved back from the COVID-19 (ie, infected with SARS-CoV-2) cohort to the non-COVID-19 (ie, susceptible and uninfected with SARS-CoV-2) cohort. In the immunity-based staffing intervention, staff who had recovered from COVID-19 were assumed to have protective immunity and were assigned to work in the non-COVID-19 cohort, while susceptible staff worked in the COVID-19 cohort and were assumed to have high levels of protection from personal protective equipment. These interventions aimed to reduce the fraction of people's contacts that were presumed susceptible (and therefore potentially infected) and replaced them with recovered (immune) contacts. A secondary aim of was to evaluate cumulative incidence of SARS-CoV-2 infections associated with 2 types of screening tests (ie, rapid antigen testing and polymerase chain reaction [PCR] testing) conducted with varying frequency. Main Outcomes and Measures Estimated cumulative incidence proportion of SARS-CoV-2 infection after 3 months. Results Among the simulated cohort of 100 residents and 100 staff members, frequency and type of testing were associated with smaller outbreaks than the cohorting and staffing interventions. The testing strategy associated with the greatest estimated reduction in infections was daily antigen testing, which reduced the mean cumulative incidence proportion by 49% in absence of contact-targeted interventions. Under all screening testing strategies, the resident cohorting intervention and the immunity-based staffing intervention were associated with reducing the final estimated size of the outbreak among residents, with the immunity-based staffing intervention reducing it more (eg, by 19% in the absence of testing) than the resident cohorting intervention (eg, by 8% in the absence of testing). The estimated reduction in transmission associated with these interventions among staff varied by testing strategy and community prevalence. Conclusions and Relevance These findings suggest that increasing the frequency of screening testing of all residents and staff, or even staff alone, in nursing homes may reduce outbreaks in this high-risk setting. Immunity-based staffing may further reduce spread at little or no additional cost and becomes particularly important when daily testing is not feasible.
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Affiliation(s)
- Inga Holmdahl
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Rebecca Kahn
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - James A. Hay
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Caroline O. Buckee
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Michael J. Mina
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
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Abstract
Universities have turned to SARS-CoV-2 models to examine campus reopening strategies1-9. While these studies have explored a variety of modeling techniques, all have relied on simulated data. Here, we use an empirical proximity network of college freshmen10, ascertained using smartphone Bluetooth, to simulate the spread of the virus. We investigate the role of testing, isolation, mask wearing, and social distancing in the presence of implementation challenges and imperfect compliance. Here we show that while frequent testing can drastically reduce spread if mask wearing and social distancing are not widely adopted, testing has limited impact if they are ubiquitous. Furthermore, even moderate levels of immunity can significantly reduce new infections, especially when combined with other interventions. Our findings suggest that while testing and isolation are powerful tools, they have limited benefit if other interventions are widely adopted. If universities can attain high levels of masking and social distancing, they may be able to relax testing frequency to once every two to four weeks.
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Affiliation(s)
- Hali L Hambridge
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Rebecca Kahn
- Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Jukka-Pekka Onnela
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA
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Mucci A, Bucci P, Winter Van Rossum I, Arango C, Baandrup L, Glenthøj B, Dazzan P, Demjaha A, Mcguire P, Díaz-Caneja CM, Leucht S, Rodriguez-Jimenez R, Kahn R, Galderisi S. Prediction of drop-out and functional impairment in recent-onset schizophrenia spectrum disorders. Eur Psychiatry 2021. [PMCID: PMC9471881 DOI: 10.1192/j.eurpsy.2021.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Persistent negative symptoms are associated with worse outcome in both first-episode and chronic subjects with schizophrenia. The identification of these symptoms in recent-onset subjects is still controversial as retrospective data are often unavailable. The prospective assessment of persistence of negative symptoms might represent a valid alternative but the length of the persistence is still to be established. The present study investigated the prevalence of negative symptoms of moderate severity, unconfounded by depression and extrapyramidal symptoms at baseline in a large cohort of patients in the early stage of a schizophrenia-spectrum disorder, recruited to the OPTiMiSE trial. Persistent unconfounded negative symptoms were assessed at 4, 10 and 22 weeks of treatment. Symptomatic remission, attrition rate and psychosocial functioning was evaluated in subjects with short-term (4 weeks) persistent negative symptoms (PNS) and in those with negative symptoms that did not persist at follow-up and/or were confounded at baseline (N-PNS). Negative symptoms of moderate severity were observed in 59% of subjects at baseline and were associated to worse global functioning. PNS were observed in 7.9% of the cohort, unconfounded at both baseline and end of 4-week treatment. PNS subjects showed lower remission and higher attrition rates at the end of all treatment phases. Fifty-six percent of subjects completing phase 3 (clozapine treatment) had PNS, and 60% of them were non-remitters at the end of this phase. The presence of short-term PNS during the first phases of psychosis was associated with poor clinical outcome and resistance to antipsychotic treatment, including clozapine.
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Kahn R, Holmdahl I, Reddy S, Jernigan J, Mina MJ, Slayton RB. Mathematical modeling to inform vaccination strategies and testing approaches for COVID-19 in nursing homes. medRxiv 2021:2021.02.26.21252483. [PMID: 33688668 PMCID: PMC7941643 DOI: 10.1101/2021.02.26.21252483] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 11/24/2022]
Abstract
BACKGROUND Nursing home residents and staff were included in the first phase of COVID-19 vaccination in the United States. Because the primary trial endpoint was vaccine efficacy (VE) against symptomatic disease, there are limited data on the extent to which vaccines protect against SARS-CoV-2 infection and the ability to infect others (infectiousness). Assumptions about VE against infection and infectiousness have implications for possible changes to infection prevention guidance for vaccinated populations, including testing strategies. METHODS We use a stochastic agent-based SEIR model of a nursing home to simulate SARS-CoV-2 transmission. We model three scenarios, varying VE against infection, infectiousness, and symptoms, to understand the expected impact of vaccination in nursing homes, increasing staff vaccination coverage, and different screening testing strategies under each scenario. RESULTS Increasing vaccination coverage in staff decreases total symptomatic cases in each scenario. When there is low VE against infection and infectiousness, increasing staff coverage reduces symptomatic cases among residents. If vaccination only protects against symptoms, but asymptomatic cases remain infectious, increased staff coverage increases symptomatic cases among residents through exposure to asymptomatic but infected staff. High frequency testing is needed to reduce total symptomatic cases if the vaccine has low efficacy against infection and infectiousness, or only protects against symptoms. CONCLUSIONS Encouraging staff vaccination is not only important for protecting staff, but might also reduce symptomatic cases in residents if a vaccine confers at least some protection against infection or infectiousness. SUMMARY The extent of efficacy of SARS-CoV-2 vaccines against infection, infectiousness, or disease, impacts strategies for vaccination and testing in nursing homes. If vaccines confer some protection against infection or infectiousness, encouraging vaccination in staff may reduce symptomatic cases in residents.
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Affiliation(s)
- Rebecca Kahn
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- COVID-19 Response, US Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Inga Holmdahl
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Sujan Reddy
- COVID-19 Response, US Centers for Disease Control and Prevention, Atlanta, Georgia
| | - John Jernigan
- COVID-19 Response, US Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Michael J. Mina
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Rachel B. Slayton
- COVID-19 Response, US Centers for Disease Control and Prevention, Atlanta, Georgia
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Kahn R, Kennedy-Shaffer L, Grad YH, Robins JM, Lipsitch M. Potential Biases Arising From Epidemic Dynamics in Observational Seroprotection Studies. Am J Epidemiol 2021; 190:328-335. [PMID: 32870977 PMCID: PMC7499481 DOI: 10.1093/aje/kwaa188] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 08/20/2020] [Accepted: 08/26/2020] [Indexed: 11/23/2022] Open
Abstract
The extent and duration of immunity following infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are critical outstanding questions about the epidemiology of this novel virus, and studies are needed to evaluate the effects of serostatus on reinfection. Understanding the potential sources of bias and methods for alleviating biases in these studies is important for informing their design and analysis. Confounding by individual-level risk factors in observational studies like these is relatively well appreciated. Here, we show how geographic structure and the underlying, natural dynamics of epidemics can also induce noncausal associations. We take the approach of simulating serological studies in the context of an uncontrolled or controlled epidemic, under different assumptions about whether prior infection does or does not protect an individual against subsequent infection, and using various designs and analytical approaches to analyze the simulated data. We find that in studies assessing whether seropositivity confers protection against future infection, comparing seropositive persons with seronegative persons with similar time-dependent patterns of exposure to infection by stratifying or matching on geographic location and time of enrollment is essential in order to prevent bias.
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Affiliation(s)
| | | | | | | | - Marc Lipsitch
- Correspondence to Dr. Marc Lipsitch, Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02115 (e-mail: )
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Accorsi EK, Qiu X, Rumpler E, Kennedy-Shaffer L, Kahn R, Joshi K, Goldstein E, Stensrud MJ, Niehus R, Cevik M, Lipsitch M. How to detect and reduce potential sources of biases in studies of SARS-CoV-2 and COVID-19. Eur J Epidemiol 2021; 36:179-196. [PMID: 33634345 PMCID: PMC7906244 DOI: 10.1007/s10654-021-00727-7] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [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: 11/12/2020] [Accepted: 02/04/2021] [Indexed: 02/07/2023]
Abstract
In response to the coronavirus disease (COVID-19) pandemic, public health scientists have produced a large and rapidly expanding body of literature that aims to answer critical questions, such as the proportion of the population in a geographic area that has been infected; the transmissibility of the virus and factors associated with high infectiousness or susceptibility to infection; which groups are the most at risk of infection, morbidity and mortality; and the degree to which antibodies confer protection to re-infection. Observational studies are subject to a number of different biases, including confounding, selection bias, and measurement error, that may threaten their validity or influence the interpretation of their results. To assist in the critical evaluation of a vast body of literature and contribute to future study design, we outline and propose solutions to biases that can occur across different categories of observational studies of COVID-19. We consider potential biases that could occur in five categories of studies: (1) cross-sectional seroprevalence, (2) longitudinal seroprotection, (3) risk factor studies to inform interventions, (4) studies to estimate the secondary attack rate, and (5) studies that use secondary attack rates to make inferences about infectiousness and susceptibility.
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Affiliation(s)
- Emma K. Accorsi
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115 USA
| | - Xueting Qiu
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115 USA
| | - Eva Rumpler
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115 USA
| | - Lee Kennedy-Shaffer
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115 USA
- Department of Mathematics and Statistics, Vassar College, Poughkeepsie, NY 12604 USA
| | - Rebecca Kahn
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115 USA
| | - Keya Joshi
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115 USA
| | - Edward Goldstein
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115 USA
| | - Mats J. Stensrud
- Department of Mathematics, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Rene Niehus
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115 USA
| | - Muge Cevik
- Division of Infection and Global Health Research, School of Medicine, University of St Andrews, St Andrews, UK
- Specialist Virology Laboratory, Royal Infirmary of Edinburgh, Edinburgh, UK
- Regional Infectious Diseases Unit, Western General Hospital, Edinburgh, UK
| | - Marc Lipsitch
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115 USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115 USA
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Chang MC, Kahn R, Li YA, Lee CS, Buckee CO, Chang HH. Variation in human mobility and its impact on the risk of future COVID-19 outbreaks in Taiwan. BMC Public Health 2021; 21:226. [PMID: 33504339 PMCID: PMC7838857 DOI: 10.1186/s12889-021-10260-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [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: 08/03/2020] [Accepted: 01/17/2021] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND As COVID-19 continues to spread around the world, understanding how patterns of human mobility and connectivity affect outbreak dynamics, especially before outbreaks establish locally, is critical for informing response efforts. In Taiwan, most cases to date were imported or linked to imported cases. METHODS In collaboration with Facebook Data for Good, we characterized changes in movement patterns in Taiwan since February 2020, and built metapopulation models that incorporate human movement data to identify the high risk areas of disease spread and assess the potential effects of local travel restrictions in Taiwan. RESULTS We found that mobility changed with the number of local cases in Taiwan in the past few months. For each city, we identified the most highly connected areas that may serve as sources of importation during an outbreak. We showed that the risk of an outbreak in Taiwan is enhanced if initial infections occur around holidays. Intracity travel reductions have a higher impact on the risk of an outbreak than intercity travel reductions, while intercity travel reductions can narrow the scope of the outbreak and help target resources. The timing, duration, and level of travel reduction together determine the impact of travel reductions on the number of infections, and multiple combinations of these can result in similar impact. CONCLUSIONS To prepare for the potential spread within Taiwan, we utilized Facebook's aggregated and anonymized movement and colocation data to identify cities with higher risk of infection and regional importation. We developed an interactive application that allows users to vary inputs and assumptions and shows the spatial spread of the disease and the impact of intercity and intracity travel reduction under different initial conditions. Our results can be used readily if local transmission occurs in Taiwan after relaxation of border control, providing important insights into future disease surveillance and policies for travel restrictions.
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Affiliation(s)
- Meng-Chun Chang
- Department of Life Science & Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Rebecca Kahn
- Department of Epidemiology & the Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Yu-An Li
- Department of Life Science & Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Cheng-Sheng Lee
- Department of Life Science & Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Caroline O Buckee
- Department of Epidemiology & the Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Hsiao-Han Chang
- Department of Life Science & Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan.
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32
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Greene SK, McGough SF, Culp GM, Graf LE, Lipsitch M, Menzies NA, Kahn R. Nowcasting for Real-Time COVID-19 Tracking in New York City: An Evaluation Using Reportable Disease Data From Early in the Pandemic. JMIR Public Health Surveill 2021; 7:e25538. [PMID: 33406053 PMCID: PMC7812916 DOI: 10.2196/25538] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 12/31/2020] [Accepted: 01/04/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Nowcasting approaches enhance the utility of reportable disease data for trend monitoring by correcting for delays, but implementation details affect accuracy. OBJECTIVE To support real-time COVID-19 situational awareness, the New York City Department of Health and Mental Hygiene used nowcasting to account for testing and reporting delays. We conducted an evaluation to determine which implementation details would yield the most accurate estimated case counts. METHODS A time-correlated Bayesian approach called Nowcasting by Bayesian Smoothing (NobBS) was applied in real time to line lists of reportable disease surveillance data, accounting for the delay from diagnosis to reporting and the shape of the epidemic curve. We retrospectively evaluated nowcasting performance for confirmed case counts among residents diagnosed during the period from March to May 2020, a period when the median reporting delay was 2 days. RESULTS Nowcasts with a 2-week moving window and a negative binomial distribution had lower mean absolute error, lower relative root mean square error, and higher 95% prediction interval coverage than nowcasts conducted with a 3-week moving window or with a Poisson distribution. Nowcasts conducted toward the end of the week outperformed nowcasts performed earlier in the week, given fewer patients diagnosed on weekends and lack of day-of-week adjustments. When estimating case counts for weekdays only, metrics were similar across days when the nowcasts were conducted, with Mondays having the lowest mean absolute error of 183 cases in the context of an average daily weekday case count of 2914. CONCLUSIONS Nowcasting using NobBS can effectively support COVID-19 trend monitoring. Accounting for overdispersion, shortening the moving window, and suppressing diagnoses on weekends-when fewer patients submitted specimens for testing-improved the accuracy of estimated case counts. Nowcasting ensured that recent decreases in observed case counts were not overinterpreted as true declines and supported officials in anticipating the magnitude and timing of hospitalizations and deaths and allocating resources geographically.
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Affiliation(s)
- Sharon K Greene
- Bureau of Communicable Disease, New York City Department of Health and Mental Hygiene, Long Island City, NY, United States
| | - Sarah F McGough
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA, United States
- Genentech, Inc, South San Francisco, CA, United States
| | - Gretchen M Culp
- Bureau of Epidemiology Services, New York City Department of Health and Mental Hygiene, Long Island City, NY, United States
| | - Laura E Graf
- Bureau of Communicable Disease, New York City Department of Health and Mental Hygiene, Long Island City, NY, United States
| | - Marc Lipsitch
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA, United States
| | - Nicolas A Menzies
- Department of Global Health and Population, Harvard TH Chan School of Public Health, Boston, MA, United States
| | - Rebecca Kahn
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA, United States
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Gostic KM, McGough L, Baskerville EB, Abbott S, Joshi K, Tedijanto C, Kahn R, Niehus R, Hay JA, De Salazar PM, Hellewell J, Meakin S, Munday JD, Bosse NI, Sherrat K, Thompson RN, White LF, Huisman JS, Scire J, Bonhoeffer S, Stadler T, Wallinga J, Funk S, Lipsitch M, Cobey S. Practical considerations for measuring the effective reproductive number, Rt. PLoS Comput Biol 2020; 16:e1008409. [PMID: 33301457 PMCID: PMC7728287 DOI: 10.1371/journal.pcbi.1008409] [Citation(s) in RCA: 229] [Impact Index Per Article: 57.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Estimation of the effective reproductive number Rt is important for detecting changes in disease transmission over time. During the Coronavirus Disease 2019 (COVID-19) pandemic, policy makers and public health officials are using Rt to assess the effectiveness of interventions and to inform policy. However, estimation of Rt from available data presents several challenges, with critical implications for the interpretation of the course of the pandemic. The purpose of this document is to summarize these challenges, illustrate them with examples from synthetic data, and, where possible, make recommendations. For near real-time estimation of Rt, we recommend the approach of Cori and colleagues, which uses data from before time t and empirical estimates of the distribution of time between infections. Methods that require data from after time t, such as Wallinga and Teunis, are conceptually and methodologically less suited for near real-time estimation, but may be appropriate for retrospective analyses of how individuals infected at different time points contributed to the spread. We advise caution when using methods derived from the approach of Bettencourt and Ribeiro, as the resulting Rt estimates may be biased if the underlying structural assumptions are not met. Two key challenges common to all approaches are accurate specification of the generation interval and reconstruction of the time series of new infections from observations occurring long after the moment of transmission. Naive approaches for dealing with observation delays, such as subtracting delays sampled from a distribution, can introduce bias. We provide suggestions for how to mitigate this and other technical challenges and highlight open problems in Rt estimation.
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Affiliation(s)
- Katelyn M. Gostic
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, United States of America
| | - Lauren McGough
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, United States of America
| | - Edward B. Baskerville
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, United States of America
| | - Sam Abbott
- Centre for Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Keya Joshi
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, United States of America
| | - Christine Tedijanto
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, United States of America
| | - Rebecca Kahn
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, United States of America
| | - Rene Niehus
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, United States of America
| | - James A. Hay
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, United States of America
| | - Pablo M. De Salazar
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, United States of America
| | - Joel Hellewell
- Centre for Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Sophie Meakin
- Centre for Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - James D. Munday
- Centre for Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Nikos I. Bosse
- Centre for Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Katharine Sherrat
- Centre for Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Robin N. Thompson
- Centre for Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Mathematical Institute, University of Oxford, Oxford, United Kingdom
| | - Laura F. White
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, United States of America
| | - Jana S. Huisman
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
- Department of Biosystems Science and Engineering, ETH Zürich, Switzerland
| | - Jérémie Scire
- Department of Biosystems Science and Engineering, ETH Zürich, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | | | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zürich, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Jacco Wallinga
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
- Department of Biomedical Data Sciences, Leiden University Medical Centre, Leiden, the Netherlands
| | - Sebastian Funk
- Centre for Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Marc Lipsitch
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, United States of America
| | - Sarah Cobey
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, United States of America
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Greene SK, McGough SF, Culp GM, Graf LE, Lipsitch M, Menzies NA, Kahn R. Evaluation of Nowcasting for Real-Time COVID-19 Tracking - New York City, March-May 2020. medRxiv 2020:2020.10.18.20209189. [PMID: 33106814 PMCID: PMC7587834 DOI: 10.1101/2020.10.18.20209189] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 11/28/2022]
Abstract
To account for delays between specimen collection and report, the New York City Department of Health and Mental Hygiene used a time-correlated Bayesian nowcasting approach to support real-time COVID-19 situational awareness. We retrospectively evaluated nowcasting performance for case counts among residents diagnosed during March-May 2020, a period when the median reporting delay was 2 days. Nowcasts with a 2-week moving window and a negative binomial distribution had lower mean absolute error, lower relative root mean square error, and higher 95% prediction interval coverage than nowcasts conducted with a 3-week moving window or with a Poisson distribution. Nowcasts conducted toward the end of the week outperformed nowcasts performed earlier in the week, given fewer patients diagnosed on weekends and lack of day-of-week adjustments. When estimating case counts for weekdays only, metrics were similar across days the nowcasts were conducted, with Mondays having the lowest mean absolute error, of 183 cases in the context of an average daily weekday case count of 2,914. Nowcasting ensured that recent decreases in observed case counts were not overinterpreted as true declines and supported health department leadership in anticipating the magnitude and timing of hospitalizations and deaths and allocating resources geographically.
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Affiliation(s)
- Sharon K. Greene
- Bureau of Communicable Disease, New York City Department of Health and Mental Hygiene, Long Island City, NY
| | - Sarah F. McGough
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA
- Genentech, Inc., South San Francisco, CA
| | - Gretchen M. Culp
- Bureau of Epidemiology Services, New York City Department of Health and Mental Hygiene, Long Island City, NY
| | - Laura E. Graf
- Bureau of Communicable Disease, New York City Department of Health and Mental Hygiene, Long Island City, NY
| | - Marc Lipsitch
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Nicolas A. Menzies
- Department of Global Health and Population, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Rebecca Kahn
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA
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Lackner A, Li X, Kahn R, Baltich NB, Krinsky H, Mei E, Badiner N, Caputo T, Holcomb K, Chapman-Davis E, Nitecki R, Rauh-Hain J, Sharaf R, Frey M. Cascade testing für erbliche Tumorerkrankungen: Eine Meta-Analyse. Geburtshilfe Frauenheilkd 2020. [DOI: 10.1055/s-0040-1718159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Affiliation(s)
| | - X Li
- New York Presbyterian Hospital – Weill Cornell, Gynecologic Oncology
| | - R Kahn
- New York Presbyterian Hospital – Weill Cornell, Gynecologic Oncology
| | - Nelson B Baltich
- New York Presbyterian Hospital – Weill Cornell, Gynecologic Oncology
| | - H Krinsky
- New York Presbyterian Hospital – Weill Cornell, Gynecologic Oncology
| | - E Mei
- New York Presbyterian Hospital – Weill Cornell, Gynecologic Oncology
| | - N Badiner
- New York Presbyterian Hospital – Weill Cornell, Gynecologic Oncology
| | - T.A Caputo
- New York Presbyterian Hospital – Weill Cornell, Gynecologic Oncology
| | - K Holcomb
- New York Presbyterian Hospital – Weill Cornell, Gynecologic Oncology
| | - E Chapman-Davis
- New York Presbyterian Hospital – Weill Cornell, Gynecologic Oncology
| | - R Nitecki
- New York Presbyterian Hospital – Weill Cornell, Gynecologic Oncology
| | - J.A Rauh-Hain
- New York Presbyterian Hospital – Weill Cornell, Gynecologic Oncology
| | - R Sharaf
- New York Presbyterian Hospital – Weill Cornell, Gynecologic Oncology
| | - M.K Frey
- New York Presbyterian Hospital – Weill Cornell, Gynecologic Oncology
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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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Chin T, Kahn R, Li R, Chen JT, Krieger N, Buckee CO, Balsari S, Kiang MV. US-county level variation in intersecting individual, household and community characteristics relevant to COVID-19 and planning an equitable response: a cross-sectional analysis. BMJ Open 2020. [PMID: 32873684 DOI: 10.1101/2020.04.08.20058248v1] [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] [MESH Headings] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/16/2023] Open
Abstract
OBJECTIVES To illustrate the intersections of, and intercounty variation in, individual, household and community factors that influence the impact of COVID-19 on US counties and their ability to respond. DESIGN We identified key individual, household and community characteristics influencing COVID-19 risks of infection and survival, guided by international experiences and consideration of epidemiological parameters of importance. Using publicly available data, we developed an open-access online tool that allows county-specific querying and mapping of risk factors. As an illustrative example, we assess the pairwise intersections of age (individual level), poverty (household level) and prevalence of group homes (community-level) in US counties. We also examine how these factors intersect with the proportion of the population that is people of colour (ie, not non-Hispanic white), a metric that reflects histories of US race relations. We defined 'high' risk counties as those above the 75th percentile. This threshold can be changed using the online tool. SETTING US counties. PARTICIPANTS Analyses are based on publicly available county-level data from the Area Health Resources Files, American Community Survey, Centers for Disease Control and Prevention Atlas file, National Center for Health Statistic and RWJF Community Health Rankings. RESULTS Our findings demonstrate significant intercounty variation in the distribution of individual, household and community characteristics that affect risks of infection, severe disease or mortality from COVID-19. About 9% of counties, affecting 10 million residents, are in higher risk categories for both age and group quarters. About 14% of counties, affecting 31 million residents, have both high levels of poverty and a high proportion of people of colour. CONCLUSION Federal and state governments will benefit from recognising high intrastate, intercounty variation in population risks and response capacity. Equitable responses to the pandemic require strategies to protect those in counties at highest risk of adverse COVID-19 outcomes and their social and economic impacts.
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Affiliation(s)
- Taylor Chin
- Epidemiology, Harvard University T H Chan School of Public Health, Boston, Massachusetts, USA
| | - Rebecca Kahn
- Epidemiology, Harvard University T H Chan School of Public Health, Boston, Massachusetts, USA
| | - Ruoran Li
- Epidemiology, Harvard University T H Chan School of Public Health, Boston, Massachusetts, USA
| | - Jarvis T Chen
- Social and Behavioral Sciences, Harvard TH Chan School of Public Health, Boston, MA, United States
| | - Nancy Krieger
- Social and Behavioral Sciences, Harvard TH Chan School of Public Health, Boston, MA, United States
| | - Caroline O Buckee
- Epidemiology, Harvard University T H Chan School of Public Health, Boston, Massachusetts, USA
| | - Satchit Balsari
- Emergency Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
- FXB Center for Health and Human Rights, Harvard University, Cambridge, Massachusetts, USA
| | - Mathew V Kiang
- FXB Center for Health and Human Rights, Harvard University, Cambridge, Massachusetts, USA
- Center for Population Health Sciences, Stanford University, Palo Alto, California, USA
- Epidemiology and Population Health, Stanford University, Stanford, California, USA
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Peak CM, Kahn R, Grad YH, Childs LM, Li R, Lipsitch M, Buckee CO. Individual quarantine versus active monitoring of contacts for the mitigation of COVID-19: a modelling study. Lancet Infect Dis 2020; 20:1025-1033. [PMID: 32445710 PMCID: PMC7239635 DOI: 10.1016/s1473-3099(20)30361-3] [Citation(s) in RCA: 128] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 03/25/2020] [Accepted: 04/16/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND Voluntary individual quarantine and voluntary active monitoring of contacts are core disease control strategies for emerging infectious diseases such as COVID-19. Given the impact of quarantine on resources and individual liberty, it is vital to assess under what conditions individual quarantine can more effectively control COVID-19 than active monitoring. As an epidemic grows, it is also important to consider when these interventions are no longer feasible and broader mitigation measures must be implemented. METHODS To estimate the comparative efficacy of individual quarantine and active monitoring of contacts to control severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), we fit a stochastic branching model to reported parameters for the dynamics of the disease. Specifically, we fit a model to the incubation period distribution (mean 5·2 days) and to two estimates of the serial interval distribution: a shorter one with a mean serial interval of 4·8 days and a longer one with a mean of 7·5 days. To assess variable resource settings, we considered two feasibility settings: a high-feasibility setting with 90% of contacts traced, a half-day average delay in tracing and symptom recognition, and 90% effective isolation; and a low-feasibility setting with 50% of contacts traced, a 2-day average delay, and 50% effective isolation. FINDINGS Model fitting by sequential Monte Carlo resulted in a mean time of infectiousness onset before symptom onset of 0·77 days (95% CI -1·98 to 0·29) for the shorter serial interval, and for the longer serial interval it resulted in a mean time of infectiousness onset after symptom onset of 0·51 days (95% CI -0·77 to 1·50). Individual quarantine in high-feasibility settings, where at least 75% of infected contacts are individually quarantined, contains an outbreak of SARS-CoV-2 with a short serial interval (4·8 days) 84% of the time. However, in settings where the outbreak continues to grow (eg, low-feasibility settings), so too will the burden of the number of contacts traced for active monitoring or quarantine, particularly uninfected contacts (who never develop symptoms). When resources are prioritised for scalable interventions such as physical distancing, we show active monitoring or individual quarantine of high-risk contacts can contribute synergistically to mitigation efforts. Even under the shorter serial interval, if physical distancing reduces the reproductive number to 1·25, active monitoring of 50% of contacts can result in overall outbreak control (ie, effective reproductive number <1). INTERPRETATION Our model highlights the urgent need for more data on the serial interval and the extent of presymptomatic transmission to make data-driven policy decisions regarding the cost-benefit comparisons of individual quarantine versus active monitoring of contacts. To the extent that these interventions can be implemented, they can help mitigate the spread of SARS-CoV-2. FUNDING National Institute of General Medical Sciences, National Institutes of Health.
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Affiliation(s)
- Corey M Peak
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T H Chan School of Public Health, Boston, MA, USA.
| | - Rebecca Kahn
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T H Chan School of Public Health, Boston, MA, USA
| | - Yonatan H Grad
- Department of Immunology and Infectious Diseases, Harvard T H Chan School of Public Health, Boston, MA, USA; Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Lauren M Childs
- Department of Mathematics, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Ruoran Li
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T H Chan School of Public Health, Boston, MA, USA
| | - Marc Lipsitch
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T H Chan School of Public Health, Boston, MA, USA; Department of Immunology and Infectious Diseases, Harvard T H Chan School of Public Health, Boston, MA, USA
| | - Caroline O Buckee
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T H Chan School of Public Health, Boston, MA, USA
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39
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Chin T, Kahn R, Li R, Chen JT, Krieger N, Buckee CO, Balsari S, Kiang MV. US-county level variation in intersecting individual, household and community characteristics relevant to COVID-19 and planning an equitable response: a cross-sectional analysis. BMJ Open 2020; 10:e039886. [PMID: 32873684 PMCID: PMC7467554 DOI: 10.1136/bmjopen-2020-039886] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/13/2020] [Accepted: 08/17/2020] [Indexed: 12/19/2022] Open
Abstract
OBJECTIVES To illustrate the intersections of, and intercounty variation in, individual, household and community factors that influence the impact of COVID-19 on US counties and their ability to respond. DESIGN We identified key individual, household and community characteristics influencing COVID-19 risks of infection and survival, guided by international experiences and consideration of epidemiological parameters of importance. Using publicly available data, we developed an open-access online tool that allows county-specific querying and mapping of risk factors. As an illustrative example, we assess the pairwise intersections of age (individual level), poverty (household level) and prevalence of group homes (community-level) in US counties. We also examine how these factors intersect with the proportion of the population that is people of colour (ie, not non-Hispanic white), a metric that reflects histories of US race relations. We defined 'high' risk counties as those above the 75th percentile. This threshold can be changed using the online tool. SETTING US counties. PARTICIPANTS Analyses are based on publicly available county-level data from the Area Health Resources Files, American Community Survey, Centers for Disease Control and Prevention Atlas file, National Center for Health Statistic and RWJF Community Health Rankings. RESULTS Our findings demonstrate significant intercounty variation in the distribution of individual, household and community characteristics that affect risks of infection, severe disease or mortality from COVID-19. About 9% of counties, affecting 10 million residents, are in higher risk categories for both age and group quarters. About 14% of counties, affecting 31 million residents, have both high levels of poverty and a high proportion of people of colour. CONCLUSION Federal and state governments will benefit from recognising high intrastate, intercounty variation in population risks and response capacity. Equitable responses to the pandemic require strategies to protect those in counties at highest risk of adverse COVID-19 outcomes and their social and economic impacts.
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Affiliation(s)
- Taylor Chin
- Epidemiology, Harvard University T H Chan School of Public Health, Boston, Massachusetts, USA
| | - Rebecca Kahn
- Epidemiology, Harvard University T H Chan School of Public Health, Boston, Massachusetts, USA
| | - Ruoran Li
- Epidemiology, Harvard University T H Chan School of Public Health, Boston, Massachusetts, USA
| | - Jarvis T Chen
- Social and Behavioral Sciences, Harvard TH Chan School of Public Health, Boston, MA, United States
| | - Nancy Krieger
- Social and Behavioral Sciences, Harvard TH Chan School of Public Health, Boston, MA, United States
| | - Caroline O Buckee
- Epidemiology, Harvard University T H Chan School of Public Health, Boston, Massachusetts, USA
| | - Satchit Balsari
- Emergency Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
- FXB Center for Health and Human Rights, Harvard University, Cambridge, Massachusetts, USA
| | - Mathew V Kiang
- FXB Center for Health and Human Rights, Harvard University, Cambridge, Massachusetts, USA
- Center for Population Health Sciences, Stanford University, Palo Alto, California, USA
- Epidemiology and Population Health, Stanford University, Stanford, California, USA
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Gostic KM, McGough L, Baskerville EB, Abbott S, Joshi K, Tedijanto C, Kahn R, Niehus R, Hay J, De Salazar PM, Hellewell J, Meakin S, Munday J, Bosse NI, Sherrat K, Thompson RN, White LF, Huisman JS, Scire J, Bonhoeffer S, Stadler T, Wallinga J, Funk S, Lipsitch M, Cobey S. Practical considerations for measuring the effective reproductive number, R t. medRxiv 2020:2020.06.18.20134858. [PMID: 32607522 PMCID: PMC7325187 DOI: 10.1101/2020.06.18.20134858] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [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: 12/13/2022]
Abstract
Estimation of the effective reproductive number, R t , is important for detecting changes in disease transmission over time. During the COVID-19 pandemic, policymakers and public health officials are using R t to assess the effectiveness of interventions and to inform policy. However, estimation of R t from available data presents several challenges, with critical implications for the interpretation of the course of the pandemic. The purpose of this document is to summarize these challenges, illustrate them with examples from synthetic data, and, where possible, make recommendations. For near real-time estimation of R t , we recommend the approach of Cori et al. (2013), which uses data from before time t and empirical estimates of the distribution of time between infections. Methods that require data from after time t, such as Wallinga and Teunis (2004), are conceptually and methodologically less suited for near real-time estimation, but may be appropriate for retrospective analyses of how individuals infected at different time points contributed to spread. We advise against using methods derived from Bettencourt and Ribeiro (2008), as the resulting R t estimates may be biased if the underlying structural assumptions are not met. Two key challenges common to all approaches are accurate specification of the generation interval and reconstruction of the time series of new infections from observations occurring long after the moment of transmission. Naive approaches for dealing with observation delays, such as subtracting delays sampled from a distribution, can introduce bias. We provide suggestions for how to mitigate this and other technical challenges and highlight open problems in R t estimation.
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Affiliation(s)
- Katelyn M. Gostic
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Lauren McGough
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | | | - Sam Abbott
- Centre for Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - Keya Joshi
- Center for Communicable Disease Dynamics, Department of Epidemiology, T.H. Chan School of Public Health, Harvard University, Cambridge, MA, USA
| | - Christine Tedijanto
- Center for Communicable Disease Dynamics, Department of Epidemiology, T.H. Chan School of Public Health, Harvard University, Cambridge, MA, USA
| | - Rebecca Kahn
- Center for Communicable Disease Dynamics, Department of Epidemiology, T.H. Chan School of Public Health, Harvard University, Cambridge, MA, USA
| | - Rene Niehus
- Center for Communicable Disease Dynamics, Department of Epidemiology, T.H. Chan School of Public Health, Harvard University, Cambridge, MA, USA
| | - James Hay
- Center for Communicable Disease Dynamics, Department of Epidemiology, T.H. Chan School of Public Health, Harvard University, Cambridge, MA, USA
| | - Pablo M. De Salazar
- Center for Communicable Disease Dynamics, Department of Epidemiology, T.H. Chan School of Public Health, Harvard University, Cambridge, MA, USA
| | - Joel Hellewell
- Centre for Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - Sophie Meakin
- Centre for Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - James Munday
- Centre for Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - Nikos I. Bosse
- Centre for Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - Katharine Sherrat
- Centre for Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - Robin N. Thompson
- Centre for Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
- Mathematical Institute, University of Oxford, Oxford, UK
| | - Laura F. White
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Jana S. Huisman
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
- Department of Biosystems Science and Engineering, ETH Zürich, Switzerland
| | - Jérémie Scire
- Department of Biosystems Science and Engineering, ETH Zürich, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | | | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zürich, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Jacco Wallinga
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Department of Biomedical Data Sciences, Leiden University Medical Centre, Leiden, The Netherlands
| | - Sebastian Funk
- Centre for Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - Marc Lipsitch
- Center for Communicable Disease Dynamics, Department of Epidemiology, T.H. Chan School of Public Health, Harvard University, Cambridge, MA, USA
| | - Sarah Cobey
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
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Chang MC, Kahn R, Li YA, Lee CS, Buckee CO, Chang HH. Variation in human mobility and its impact on the risk of future COVID-19 outbreaks in Taiwan. medRxiv 2020:2020.04.07.20053439. [PMID: 32817972 PMCID: PMC7430617 DOI: 10.1101/2020.04.07.20053439] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 11/26/2022]
Abstract
Background As COVID-19 continues to spread around the world, understanding how patterns of human mobility and connectivity affect outbreak dynamics, especially before outbreaks establish locally, is critical for informing response efforts. In Taiwan, most cases to date were imported or linked to imported cases. Methods In collaboration with Facebook Data for Good, we characterized changes in movement patterns in Taiwan since February 2020, and built metapopulation models that incorporate human movement data to identify the high risk areas of disease spread and assess the potential effects of local travel restrictions in Taiwan. Results We found that mobility changed with the number of local cases in Taiwan in the past few months. For each city, we identified the most highly connected areas that may serve as sources of importation during an outbreak. We showed that the risk of an outbreak in Taiwan is enhanced if initial infections occur around holidays. Intracity travel reductions have a higher impact on the risk of an outbreak than intercity travel reductions, while intercity travel reductions can narrow the scope of the outbreak and help target resources. The timing, duration, and level of travel reduction together determine the impact of travel reductions on the number of infections, and multiple combinations of these can result in similar impact. Conclusions To prepare for the potential spread within Taiwan, we utilized Facebook's aggregated and anonymized movement and colocation data to identify cities with higher risk of infection and regional importation. We developed an interactive application that allows users to vary inputs and assumptions and shows the spatial spread of the disease and the impact of intercity and intracity travel reduction under different initial conditions. Our results can be used readily if local transmission occurs in Taiwan after relaxation of border control, providing important insights into future disease surveillance and policies for travel restrictions.
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Affiliation(s)
- Meng-Chun Chang
- Department of Life Science & Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Rebecca Kahn
- Department of Epidemiology & the Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Yu-An Li
- Department of Life Science & Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Cheng-Sheng Lee
- Department of Life Science & Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Caroline O. Buckee
- Department of Epidemiology & the Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Hsiao-Han Chang
- Department of Life Science & Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
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Lackner A, Li X, Kahn R, Baltich Nelson B, Krinsky H, Mei E, Badiner N, Caputo TA, Holcomb K, Chapman-Davis E, Nitecki R, Rauh-Hain JA, Sharaf R, Frey MK. Cascade testing für erbliche Tumorerkrankungen: Eine Meta-Analyse. Geburtshilfe Frauenheilkd 2020. [DOI: 10.1055/s-0040-1713236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Affiliation(s)
- A Lackner
- Universitätsklinik für Frauenheilkunde, Medizinische Universität Wien, Wien, Österreich
| | - X Li
- Division of Gynecologic Oncology, Weill Cornell Medicine, New York, NY, USA
| | - R Kahn
- Division of Gynecologic Oncology, Weill Cornell Medicine, New York, NY, USA
| | - B Baltich Nelson
- Division of Gynecologic Oncology, Weill Cornell Medicine, New York, NY, USA
| | - H Krinsky
- Division of Gynecologic Oncology, Weill Cornell Medicine, New York, NY, USA
| | - E Mei
- Division of Gynecologic Oncology, Weill Cornell Medicine, New York, NY, USA
| | - N Badiner
- Division of Gynecologic Oncology, Weill Cornell Medicine, New York, NY, USA
| | - T A Caputo
- Division of Gynecologic Oncology, Weill Cornell Medicine, New York, NY, USA
| | - K Holcomb
- Division of Gynecologic Oncology, Weill Cornell Medicine, New York, NY, USA
| | - E Chapman-Davis
- Division of Gynecologic Oncology, Weill Cornell Medicine, New York, NY, USA
| | - R Nitecki
- Division of Gynecologic Oncology, Weill Cornell Medicine, New York, NY, USA
| | - J A Rauh-Hain
- Division of Gynecologic Oncology, Weill Cornell Medicine, New York, NY, USA
| | - R Sharaf
- Division of Gynecologic Oncology, Weill Cornell Medicine, New York, NY, USA
| | - M K Frey
- Division of Gynecologic Oncology, Weill Cornell Medicine, New York, NY, USA
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Abstract
The extent and duration of immunity following SARS-CoV-2 infection are critical outstanding questions about the epidemiology of this novel virus, and studies are needed to evaluate the effects of serostatus on reinfection. Understanding the potential sources of bias and methods to alleviate biases in these studies is important for informing their design and analysis. Confounding by individual-level risk factors in observational studies like these is relatively well appreciated. Here, we show how geographic structure and the underlying, natural dynamics of epidemics can also induce noncausal associations. We take the approach of simulating serologic studies in the context of an uncontrolled or a controlled epidemic, under different assumptions about whether prior infection does or does not protect an individual against subsequent infection, and using various designs and analytic approaches to analyze the simulated data. We find that in studies assessing the efficacy of serostatus on future infection, comparing seropositive individuals to seronegative individuals with similar time-dependent patterns of exposure to infection, by stratifying or matching on geographic location and time of enrollment, is essential to prevent bias.
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44
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Peak CM, Kahn R, Grad YH, Childs LM, Li R, Lipsitch M, Buckee CO. Comparative Impact of Individual Quarantine vs. Active Monitoring of Contacts for the Mitigation of COVID-19: a modelling study. medRxiv 2020:2020.03.05.20031088. [PMID: 32511440 PMCID: PMC7239061 DOI: 10.1101/2020.03.05.20031088] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/17/2023]
Abstract
Background Voluntary individual quarantine and voluntary active monitoring of contacts are core disease control strategies for emerging infectious diseases, such as COVID-19. Given the impact of quarantine on resources and individual liberty, it is vital to assess under what conditions individual quarantine can more effectively control COVID-19 than active monitoring. As an epidemic grows, it is also important to consider when these interventions are no longer feasible, and broader mitigation measures must be implemented. Methods To estimate the comparative efficacy of these case-based interventions to control COVID-19, we fit a stochastic branching model to reported parameters for the dynamics of the disease. Specifically, we fit to the incubation period distribution and each of two sets of the serial interval distribution: a shorter one with a mean serial interval of 4.8 days and a longer one with a mean of 7.5 days. To assess variable resource settings, we consider two feasibility settings: a high feasibility setting with 90% of contacts traced, a half-day average delay in tracing and symptom recognition, and 90% effective isolation; and low feasibility setting with 50% of contacts traced, a two-day average delay, and 50% effective isolation. Findings Our results suggest that individual quarantine in high feasibility settings where at least three-quarters of infected contacts are individually quarantined contains an outbreak of COVID-19 with a short serial interval (4.8 days) 84% of the time. However, in settings where this performance is unrealistically high and the outbreak continues to grow, so too will the burden of the number of contacts traced for active monitoring or quarantine. When resources are prioritized for scalable interventions such as social distancing, we show active monitoring or individual quarantine of high-risk contacts can contribute synergistically to mitigation efforts. Interpretation Our model highlights the urgent need for more data on the serial interval and the extent of presymptomatic transmission in order to make data-driven policy decisions regarding the cost-benefit comparisons of individual quarantine vs. active monitoring of contacts. To the extent these interventions can be implemented they can help mitigate the spread of COVID-19.
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Affiliation(s)
- Corey M. Peak
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Rebecca Kahn
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Yonatan H. Grad
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Division of Infectious Diseases, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Lauren M. Childs
- Department of Mathematics, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, Virginia, United States of America
| | - Ruoran Li
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Marc Lipsitch
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Caroline O. Buckee
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
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Chin T, Kahn R, Li R, Chen JT, Krieger N, Buckee CO, Balsari S, Kiang MV. U.S. county-level characteristics to inform equitable COVID-19 response. medRxiv 2020:2020.04.08.20058248. [PMID: 32511610 PMCID: PMC7276037 DOI: 10.1101/2020.04.08.20058248] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [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: 01/03/2023]
Abstract
Background The spread of Coronavirus Disease 2019 (COVID-19) across the United States confirms that not all Americans are equally at risk of infection, severe disease, or mortality. A range of intersecting biological, demographic, and socioeconomic factors are likely to determine an individual's susceptibility to COVID-19. These factors vary significantly across counties in the United States, and often reflect the structural inequities in our society. Recognizing this vast inter-county variation in risks will be critical to mounting an adequate response strategy. Methods and Findings Using publicly available county-specific data we identified key biological, demographic, and socioeconomic factors influencing susceptibility to COVID-19, guided by international experiences and consideration of epidemiological parameters of importance. We created bivariate county-level maps to summarize examples of key relationships across these categories, grouping age and poverty; comorbidities and lack of health insurance; proximity, density and bed capacity; and race and ethnicity, and premature death. We have also made available an interactive online tool that allows public health officials to query risk factors most relevant to their local context.Our data demonstrate significant inter-county variation in key epidemiological risk factors, with a clustering of counties in certain states, which will result in an increased demand on their public health system. While the East and West coast cities are particularly vulnerable owing to their densities (and travel routes), a large number of counties in the Southeastern states have a high proportion of at-risk populations, with high levels of poverty, comorbidities, and premature death at baseline, and low levels of health insurance coverage.The list of variables we have examined is by no means comprehensive, and several of them are interrelated and magnify underlying vulnerabilities. The online tool allows readers to explore additional combinations of risk factors, set categorical thresholds for each covariate, and filter counties above different population thresholds. Conclusion COVID-19 responses and decision making in the United States remain decentralized. Both the federal and state governments will benefit from recognizing high intra-state, inter-county variation in population risks and response capacity. Many of the factors that are likely to exacerbate the burden of COVID-19 and the demand on healthcare systems are the compounded result of long-standing structural inequalities in US society. Strategies to protect those in the most vulnerable counties will require urgent measures to better support communities' attempts at social distancing and to accelerate cooperation across jurisdictions to supply personnel and equipment to counties that will experience high demand.
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Affiliation(s)
- Taylor Chin
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA
| | - Rebecca Kahn
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA
| | - Ruoran Li
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA
| | - Jarvis T Chen
- Department of Social and Behavioral Sciences, Harvard TH Chan School of Public Health, Boston, MA
| | - Nancy Krieger
- Department of Social and Behavioral Sciences, Harvard TH Chan School of Public Health, Boston, MA
| | - Caroline O Buckee
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA
| | - Satchit Balsari
- Emergency Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School
- FXB Center for Health and Human Rights, Harvard University
| | - Mathew V Kiang
- FXB Center for Health and Human Rights, Harvard University
- Center for Population Health Sciences, Stanford University School of Medicine, Palo Alto, CA
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA
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Abstract
Bipolar disorder (BPD) is a highly debilitating psychiatric disorder. The underlying molecular mechanisms of BPD remain largely unknown. Studies targeting postmortem brain tissues of BPD patients have identified very few consistently replicated differences in the expression levels of protein-coding RNAs across different areas of the brain. Since differential expression of the human genome produces a wide spectrum of protein-coding and noncoding RNAs, we hypothesized that major molecular deficits associated with BPD could reflect dysregulation of multiple classes of RNA. To test this hypothesis, we obtained postmortem human medial frontal gyrus tissue from BPD patients and healthy controls (n = 16). To survey the implication of both protein-coding and long non-coding RNAs (lncRNAs) in BPD, we then performed RNA sequencing, PCR validation and replication experiments adopting a case-control design. Thirty-six genes and fifteen lncRNA transcripts not previously implicated in BPD were detected as differentially expressed (FDR < 0.1). Functional analyses identified enrichments of angiogenesis, vascular system development and histone H3-K4 demethylation. In addition, we report extensive alternative splicing defects in the brains of BPD subjects compared to controls. Finally, we describe for the first time a large reservoir of circular RNAs (circRNAs) that populate the medial frontal gyrus and report significantly altered levels of two circular transcripts (cNEBL and cEPHA3) from the NEBL and EPHA3 loci in BPD. Our findings may not only contribute to gain insight into the pathophysiology of BPD but may be tested in the near future as potential biomarkers for diagnostics.Disclosure of interestThe authors have not supplied their declaration of competing interest.
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Kahn R, Bangura S, Hann K, Salvi A, Gassimu J, Kabba A, Mesman AW, Dierberg KL, Marsh RH. Strengthening provision of essential medicines to women and children in post-Ebola Sierra Leone. J Glob Health 2020; 9:010307. [PMID: 31217949 PMCID: PMC6551484 DOI: 10.7189/jogh.09.010307] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Rebecca Kahn
- Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
| | - Sheriff Bangura
- Partners In Health, Freetown, Sierra Leone.,Harvard Medical School, Harvard University, Boston, Massachusetts, USA
| | | | | | | | - Alpha Kabba
- Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Annelies W Mesman
- Harvard Medical School, Harvard University, Boston, Massachusetts, USA
| | - Kerry L Dierberg
- New York University School of Medicine, Division of Infectious Diseases, New York, New York, USA
| | - Regan H Marsh
- Harvard Medical School, Harvard University, Boston, Massachusetts, USA.,Partners In Health, Boston, Massachusetts, USA
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Kahn R, Peak CM, Fernández-Gracia J, Hill A, Jambai A, Ganda L, Castro MC, Buckee CO. Incubation periods impact the spatial predictability of cholera and Ebola outbreaks in Sierra Leone. Proc Natl Acad Sci U S A 2020; 117:5067-5073. [PMID: 32054785 PMCID: PMC7060667 DOI: 10.1073/pnas.1913052117] [Citation(s) in RCA: 17] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Forecasting the spatiotemporal spread of infectious diseases during an outbreak is an important component of epidemic response. However, it remains challenging both methodologically and with respect to data requirements, as disease spread is influenced by numerous factors, including the pathogen's underlying transmission parameters and epidemiological dynamics, social networks and population connectivity, and environmental conditions. Here, using data from Sierra Leone, we analyze the spatiotemporal dynamics of recent cholera and Ebola outbreaks and compare and contrast the spread of these two pathogens in the same population. We develop a simulation model of the spatial spread of an epidemic in order to examine the impact of a pathogen's incubation period on the dynamics of spread and the predictability of outbreaks. We find that differences in the incubation period alone can determine the limits of predictability for diseases with different natural history, both empirically and in our simulations. Our results show that diseases with longer incubation periods, such as Ebola, where infected individuals can travel farther before becoming infectious, result in more long-distance sparking events and less predictable disease trajectories, as compared to the more predictable wave-like spread of diseases with shorter incubation periods, such as cholera.
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Affiliation(s)
- Rebecca Kahn
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115
| | - Corey M Peak
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115
| | - Juan Fernández-Gracia
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115
- Institute for Cross-Disciplinary Physics and Complex Systems, Universitat de les Illes Balears - Consell Superior d'Investigacions Científiques, E-07122 Palma de Mallorca, Spain
| | - Alexandra Hill
- Disease Control in Humanitarian Emergencies, World Health Organization, CH-1211 Geneva 27, Switzerland
| | - Amara Jambai
- Disease Control and Prevention, Sierra Leone Ministry of Health and Sanitation, Freetown, Sierra Leone FPGG+89
| | - Louisa Ganda
- Country Office, World Health Organization, Freetown, Sierra Leone FPGG+89
| | - Marcia C Castro
- Department of Global Health and Population, Harvard T.H. Chan School of Public Health, Boston, MA 02115
| | - Caroline O Buckee
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115;
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Cormier M, Schwartzman K, N'Diaye DS, Boone CE, Dos Santos AM, Gaspar J, Cazabon D, Ghiasi M, Kahn R, Uppal A, Morris M, Oxlade O. Proximate determinants of tuberculosis in Indigenous peoples worldwide: a systematic review. Lancet Glob Health 2019; 7:e68-e80. [PMID: 30554764 DOI: 10.1016/s2214-109x(18)30435-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 08/29/2018] [Accepted: 09/05/2018] [Indexed: 01/30/2023]
Abstract
BACKGROUND Indigenous peoples worldwide carry a disproportionate tuberculosis burden. There is an increasing awareness of the effect of social determinants and proximate determinants such as alcohol use, overcrowding, type 1 and type 2 diabetes, substance misuse, HIV, food insecurity and malnutrition, and smoking on the burden of tuberculosis. We aimed to understand the potential contribution of such determinants to tuberculosis in Indigenous peoples and to document steps taken to address them. METHODS We did a systematic review using seven databases (MEDLINE, Embase, CINAHL, Global Health, BIOSIS Previews, Web of Science, and the Cochrane Library). We identified English language articles published from Jan 1, 1980, to Dec 20, 2017, reporting the prevalence of proximate determinants of tuberculosis and preventive programmes targeting these determinants in Indigenous communities worldwide. We included any randomised controlled trials, controlled studies, cohort studies, cross-sectional studies, case reports, and qualitative research. Exclusion criteria were articles in languages other than English, full text not available, population was not Indigenous, focused exclusively on children or older people, and studies that focused on pharmacological interventions. FINDINGS Of 34 255 articles identified, 475 were eligible for inclusion. Most studies confirmed a higher prevalence of proximate determinants in Indigenous communities than in the general population. Diabetes was more frequent in Indigenous communities within high-income countries versus in low-income countries. The prevalence of alcohol use was generally similar to that among non-Indigenous groups, although patterns of drinking often differed. Smoking prevalence and smokeless tobacco consumption were commonly higher in Indigenous groups than in non-Indigenous groups. Food insecurity was highly prevalent in most Indigenous communities evaluated. Substance use was more frequent in Indigenous inhabitants of high-income countries than of low-income countries, with wide variation across Indigenous communities. The literature pertaining to HIV, crowding, and housing conditions among Indigenous peoples was too scant to draw firm conclusions. Preventive programmes that are culturally appropriate targeting these determinants appear feasible, although their effectiveness is largely unproven. INTERPRETATION Indigenous peoples were generally reported to have a higher prevalence of several proximate determinants of tuberculosis than non-Indigenous peoples, with wide variation across Indigenous communities. These findings emphasise the need for community-led, culturally appropriate strategies to address smoking, food insecurity, and diabetes in Indigenous populations as important public health goals in their own right, and also to reduce the burden of tuberculosis. FUNDING Canadian Institutes of Health Research.
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Affiliation(s)
- Maxime Cormier
- Respiratory Epidemiology and Clinical Research Unit, Montreal Chest Institute, Respiratory Division, McGill University, Montreal, QC, Canada
| | - Kevin Schwartzman
- Respiratory Epidemiology and Clinical Research Unit, Montreal Chest Institute, Respiratory Division, McGill University, Montreal, QC, Canada.
| | - Dieynaba S N'Diaye
- Respiratory Epidemiology and Clinical Research Unit, Montreal Chest Institute, Respiratory Division, McGill University, Montreal, QC, Canada
| | - Claire E Boone
- Respiratory Epidemiology and Clinical Research Unit, Montreal Chest Institute, Respiratory Division, McGill University, Montreal, QC, Canada
| | - Alexandre M Dos Santos
- Respiratory Epidemiology and Clinical Research Unit, Montreal Chest Institute, Respiratory Division, McGill University, Montreal, QC, Canada
| | - Júlia Gaspar
- Respiratory Epidemiology and Clinical Research Unit, Montreal Chest Institute, Respiratory Division, McGill University, Montreal, QC, Canada
| | - Danielle Cazabon
- Respiratory Epidemiology and Clinical Research Unit, Montreal Chest Institute, Respiratory Division, McGill University, Montreal, QC, Canada
| | - Marzieh Ghiasi
- Respiratory Epidemiology and Clinical Research Unit, Montreal Chest Institute, Respiratory Division, McGill University, Montreal, QC, Canada
| | - Rebecca Kahn
- Respiratory Epidemiology and Clinical Research Unit, Montreal Chest Institute, Respiratory Division, McGill University, Montreal, QC, Canada
| | - Aashna Uppal
- Respiratory Epidemiology and Clinical Research Unit, Montreal Chest Institute, Respiratory Division, McGill University, Montreal, QC, Canada
| | - Martin Morris
- Schulich Library of Physical Sciences, Life Sciences and Engineering, McGill University, Montreal, QC, Canada
| | - Olivia Oxlade
- Respiratory Epidemiology and Clinical Research Unit, Montreal Chest Institute, Respiratory Division, McGill University, Montreal, QC, Canada
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Hopman H, Chan S, Chu W, Lu H, Lam L, Mak A, Kahn R, Neggers S. Resting-state fMRI biomarkers and effects of transcranial magnetic stimulation in treatment-refractory depression. Brain Stimul 2019. [DOI: 10.1016/j.brs.2018.12.903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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