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Weng Y, Tian L, Boothroyd D, Lee J, Zhang K, Lu D, Lindan CP, Bollyky J, Huang B, Rutherford GW, Maldonado Y, Desai M. Adjusting Incidence Estimates with Laboratory Test Performances: A Pragmatic Maximum Likelihood Estimation-Based Approach. Epidemiology 2024; 35:295-307. [PMID: 38465940 PMCID: PMC11022996 DOI: 10.1097/ede.0000000000001725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 01/28/2024] [Indexed: 03/12/2024]
Abstract
Understanding the incidence of disease is often crucial for public policy decision-making, as observed during the COVID-19 pandemic. Estimating incidence is challenging, however, when the definition of incidence relies on tests that imperfectly measure disease, as in the case when assays with variable performance are used to detect the SARS-CoV-2 virus. To our knowledge, there are no pragmatic methods to address the bias introduced by the performance of labs in testing for the virus. In the setting of a longitudinal study, we developed a maximum likelihood estimation-based approach to estimate laboratory performance-adjusted incidence using the expectation-maximization algorithm. We constructed confidence intervals (CIs) using both bootstrapped-based and large-sample interval estimator approaches. We evaluated our methods through extensive simulation and applied them to a real-world study (TrackCOVID), where the primary goal was to determine the incidence of and risk factors for SARS-CoV-2 infection in the San Francisco Bay Area from July 2020 to March 2021. Our simulations demonstrated that our method converged rapidly with accurate estimates under a variety of scenarios. Bootstrapped-based CIs were comparable to the large-sample estimator CIs with a reasonable number of incident cases, shown via a simulation scenario based on the real TrackCOVID study. In more extreme simulated scenarios, the coverage of large-sample interval estimation outperformed the bootstrapped-based approach. Results from the application to the TrackCOVID study suggested that assuming perfect laboratory test performance can lead to an inaccurate inference of the incidence. Our flexible, pragmatic method can be extended to a variety of disease and study settings.
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Affiliation(s)
- Yingjie Weng
- From the Quantitative Sciences Unit, Department of Medicine, Stanford University, Palo Alto, CA
| | - Lu Tian
- Biomedical Data Science, Department of Medicine, Stanford University, Palo Alto, CA
| | - Derek Boothroyd
- From the Quantitative Sciences Unit, Department of Medicine, Stanford University, Palo Alto, CA
| | - Justin Lee
- From the Quantitative Sciences Unit, Department of Medicine, Stanford University, Palo Alto, CA
| | - Kenny Zhang
- From the Quantitative Sciences Unit, Department of Medicine, Stanford University, Palo Alto, CA
| | - Di Lu
- From the Quantitative Sciences Unit, Department of Medicine, Stanford University, Palo Alto, CA
| | - Christina P. Lindan
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA
- Institute for Global Health Sciences, University of California San Francisco, San Francisco, CA
| | - Jenna Bollyky
- Division of Primary Care & Population Health, School of Medicine, Stanford University, Stanford, CA
| | - Beatrice Huang
- Department of Family and Community Medicine, University of California, San Francisco, CA
| | - George W. Rutherford
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA
- Institute for Global Health Sciences, University of California San Francisco, San Francisco, CA
| | - Yvonne Maldonado
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
| | - Manisha Desai
- From the Quantitative Sciences Unit, Department of Medicine, Stanford University, Palo Alto, CA
- Biomedical Data Science, Department of Medicine, Stanford University, Palo Alto, CA
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May F, Ginige S, Firman E, Li YS, Soonarane YK, Smoll N, Hunter I, Pery B, Macfarlane B, Bladen T, Allen T, Green T, Walker J, Slinko V, Stickley M, Khandaker G, Anuradha S, Wattiaux A. Estimating the incidence of COVID-19, influenza and respiratory syncytial virus infection in three regions of Queensland, Australia, winter 2022: findings from a novel longitudinal testing-based sentinel surveillance programme. BMJ Open 2024; 14:e081793. [PMID: 38653507 PMCID: PMC11043701 DOI: 10.1136/bmjopen-2023-081793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 04/10/2024] [Indexed: 04/25/2024] Open
Abstract
OBJECTIVE The 2022 Australian winter was the first time that COVID-19, influenza and respiratory syncytial virus (RSV) were circulating in the population together, after two winters of physical distancing, quarantine and borders closed to international travellers. We developed a novel surveillance system to estimate the incidence of COVID-19, influenza and RSV in three regions of Queensland, Australia. DESIGN We implemented a longitudinal testing-based sentinel surveillance programme. Participants were provided with self-collection nasal swabs to be dropped off at a safe location at their workplace each week. Swabs were tested for SARS-CoV-2 by PCR. Symptomatic participants attended COVID-19 respiratory clinics to be tested by multiplex PCR for SARS-CoV-2, influenza A and B and RSV. Rapid antigen test (RAT) results reported by participants were included in the analysis. SETTING AND PARTICIPANTS Between 4 April 2022 and 3 October 2022, 578 adults were recruited via their workplace. Due to rolling recruitment, withdrawals and completion due to positive COVID-19 results, the maximum number enrolled in any week was 423 people. RESULTS A total of 4290 tests were included. Participation rates varied across the period ranging from 25.9% to 72.1% of enrolled participants. The total positivity of COVID-19 was 3.3%, with few influenza or RSV cases detected. Widespread use of RAT may have resulted in few symptomatic participants attending respiratory clinics. The weekly positivity rate of SARS-CoV-2 detected during the programme correlated with the incidence of notified cases in the corresponding communities. CONCLUSION This testing-based surveillance programme could estimate disease trends and be a useful tool in settings where testing is less common or accessible. Difficulties with recruitment meant the study was underpowered. The frontline sentinel nature of workplaces meant participants were not representative of the general population but were high-risk groups providing early warning of disease.
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Affiliation(s)
- Fiona May
- Gold Coast Public Health Unit, Gold Coast Hospital and Health Service, Southport, Queensland, Australia
| | - Shamila Ginige
- Gold Coast Public Health Unit, Gold Coast Hospital and Health Service, Southport, Queensland, Australia
| | - Elise Firman
- Gold Coast Public Health Unit, Gold Coast Hospital and Health Service, Southport, Queensland, Australia
| | - Yee Sum Li
- Metro South Public Health Unit, Metro South Hospital and Health Service, Woolloongabba, Queensland, Australia
| | - Yudish Kumar Soonarane
- Metro South Public Health Unit, Metro South Hospital and Health Service, Woolloongabba, Queensland, Australia
| | - Nicolas Smoll
- Central Queensland Public Health Unit, Central Queensland Hospital and Health Service, Rockhampton, Queensland, Australia
| | - Ian Hunter
- Gold Coast Public Health Unit, Gold Coast Hospital and Health Service, Southport, Queensland, Australia
| | - Brielle Pery
- Gold Coast Public Health Unit, Gold Coast Hospital and Health Service, Southport, Queensland, Australia
| | - Bonnie Macfarlane
- Metro South Public Health Unit, Metro South Hospital and Health Service, Woolloongabba, Queensland, Australia
| | - Tracy Bladen
- Gold Coast Public Health Unit, Gold Coast Hospital and Health Service, Southport, Queensland, Australia
| | - Terresa Allen
- Gold Coast Public Health Unit, Gold Coast Hospital and Health Service, Southport, Queensland, Australia
| | - Trevor Green
- Metro South Public Health Unit, Metro South Hospital and Health Service, Woolloongabba, Queensland, Australia
| | - Jacina Walker
- Central Queensland Public Health Unit, Central Queensland Hospital and Health Service, Rockhampton, Queensland, Australia
| | - Vicki Slinko
- Gold Coast Public Health Unit, Gold Coast Hospital and Health Service, Southport, Queensland, Australia
- School of Public Health, The University of Queensland, Herston, Queensland, Australia
| | - Mark Stickley
- Metro South Public Health Unit, Metro South Hospital and Health Service, Woolloongabba, Queensland, Australia
| | - Gulam Khandaker
- Central Queensland Public Health Unit, Central Queensland Hospital and Health Service, Rockhampton, Queensland, Australia
| | - Satyamurthy Anuradha
- Metro South Public Health Unit, Metro South Hospital and Health Service, Woolloongabba, Queensland, Australia
- School of Public Health, The University of Queensland, Herston, Queensland, Australia
| | - Andre Wattiaux
- Gold Coast Public Health Unit, Gold Coast Hospital and Health Service, Southport, Queensland, Australia
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Gwaikolo C, Sackie-Wapoe Y, Badio M, Glidden DV, Lindan C, Martin J. Prevalence and determinants of post-acute sequelae of COVID-19 in Liberia. Int J Epidemiol 2024; 53:dyad167. [PMID: 38052015 PMCID: PMC10859153 DOI: 10.1093/ije/dyad167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Indexed: 12/07/2023] Open
Abstract
BACKGROUND Evidence from resource-rich settings indicates that many people continue to have persistent symptoms following acute SARS-CoV-2 infection, called post-acute sequelae of COVID-19 (PASC). Only a few studies have described PASC in sub-Saharan Africa (SSA). We aimed to describe PASC in Liberia. METHODS We randomly sampled all people who were reported from the most populous county to the Liberian Ministry of Health (MOH) as having a laboratory-confirmed SARS-CoV-2 infection from June to August 2021. We interviewed individuals by phone 3 to 6 months later. Those with persistence of at least one symptom were considered to have PASC. RESULTS From among 2848 people reported to the MOH from Montserrado County during the period of interest, we randomly selected 650; of these, 548 (84.3%) were reached and 505 (92.2%) of those who were contacted were interviewed. The median age was 38 years (interquartile range (IQR), 30-49), and 43.6% were female. During acute infection, 40.2% were asymptomatic, 53.9% had mild/moderate disease and 6.9% had severe/critical disease. Among the 59.8% (n = 302) who were initially symptomatic, 50.2% (n = 152) reported at least one persistent symptom; the most common persistent symptoms were fatigue (21.2%), headache (16.2%) and cough (12.6%); 40.1% reported that PASC significantly affected their daily activities. Being hospitalized with moderate disease [adjusted prevalence ratio (aPR), 2.00 (95% CI, 1.59 to 2.80] or severe/critical disease [aPR, 2.11 (95% CI, 1.59 to 2.80)] was associated with PASC, compared with those not hospitalized. Females were more likely than males to report persistent fatigue [aPR, 1.67 (95% CI, 1.08 to 2.57)]. CONCLUSIONS Our findings suggest that persistent symptoms may have affected a large proportion of people with initially symptomatic COVID-19 in west Africa and highlight the need to create awareness among infected people and health care professionals.
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Affiliation(s)
- Cozie Gwaikolo
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | | | - Moses Badio
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
- Partnership for Research on Vaccines and Infectious Diseases in Liberia (PREVAIL), Monrovia, Liberia
| | - David V Glidden
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Christina Lindan
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
- Institute for Global Health Sciences, University of California, San Francisco, CA, USA
| | - Jeffrey Martin
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
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Judson TJ, Zhang S, Lindan CP, Boothroyd D, Grumbach K, Bollyky JB, Sample HA, Huang B, Desai M, Gonzales R, Maldonado Y, Rutherford G. Association of protective behaviors with SARS-CoV-2 infection: results from a longitudinal cohort study of adults in the San Francisco Bay Area. Ann Epidemiol 2023; 86:1-7. [PMID: 37524216 DOI: 10.1016/j.annepidem.2023.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 07/20/2023] [Accepted: 07/24/2023] [Indexed: 08/02/2023]
Abstract
PURPOSE In an effort to decrease transmission during the first years of the COVID-19 pandemic, public health officials encouraged masking, social distancing, and working from home, and restricted travel. However, many studies of the effectiveness of these measures had significant methodologic limitations. In this analysis, we used data from the TrackCOVID study, a longitudinal cohort study of a population-based sample of 3846 adults in the San Francisco Bay Area, to evaluate the association between self-reported protective behaviors and incidence of SARS-CoV-2 infection. METHODS Participants without SARS-CoV2 infection were enrolled from August to December 2020 and followed monthly with testing and surveys (median of four visits). RESULTS A total of 118 incident infections occurred (3.0% of participants). At baseline, 80.0% reported always wearing a mask; 56.0% avoided contact with nonhousehold members some/most of the time; 9.6% traveled outside the state; and 16.0% worked 20 or more hours per week outside the home. Factors associated with incident infection included being Black or Latinx, having less than a college education, and having more household residents. The only behavioral factor associated with incident infection was working outside the home (adjusted hazard ratio 1.62, 95% confidence interval 1.02-2.59). CONCLUSIONS Focusing on protecting people who cannot work from home could help prevent infections during future waves of COVID-19, or future pandemics from respiratory viruses. This focus must be balanced with the known importance of directing resources toward those at risk of severe infections.
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Affiliation(s)
- Timothy J Judson
- Department of Medicine, University of California San Francisco, San Francisco.
| | - Shiqi Zhang
- Quantitative Sciences Unit, Department of Medicine, Stanford University, Palo Alto, CA
| | - Christina P Lindan
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco
| | - Derek Boothroyd
- Quantitative Sciences Unit, Department of Medicine, Stanford University, Palo Alto, CA
| | - Kevin Grumbach
- Department of Family and Community Medicine, University of California San Francisco, San Francisco
| | - Jennifer B Bollyky
- Department of Pediatrics, School of Medicine, Stanford University, Stanford, CA
| | - Hannah A Sample
- David Geffen School of Medicine, University of California Los Angeles, Los Angeles
| | - Beatrice Huang
- Department of Medicine, University of California San Francisco, San Francisco
| | - Manisha Desai
- Quantitative Sciences Unit, Department of Medicine, Stanford University, Palo Alto, CA
| | - Ralph Gonzales
- Division of General Internal Medicine, Department of Medicine, University of California San Francisco, San Francisco
| | - Yvonne Maldonado
- Department of Pediatrics, School of Medicine, Stanford University, Stanford, CA; Department of Medicine, School of Medicine, Stanford University, Stanford, CA
| | - George Rutherford
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco
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Gerlee P, Jöud A, Spreco A, Timpka T. Computational models predicting the early development of the COVID-19 pandemic in Sweden: systematic review, data synthesis, and secondary validation of accuracy. Sci Rep 2022; 12:13256. [PMID: 35918476 PMCID: PMC9345013 DOI: 10.1038/s41598-022-16159-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 07/05/2022] [Indexed: 11/25/2022] Open
Abstract
Computational models for predicting the early course of the COVID-19 pandemic played a central role in policy-making at regional and national levels. We performed a systematic review, data synthesis, and secondary validation of studies that reported on prediction models addressing the early stages of the COVID-19 pandemic in Sweden. A literature search in January 2021 based on the search triangle model identified 1672 peer-reviewed articles, preprints and reports. After applying inclusion criteria 52 studies remained out of which 12 passed a Risk of Bias Opinion Tool. When comparing model predictions with actual outcomes only 4 studies exhibited an acceptable forecast (mean absolute percentage error, MAPE < 20%). Models that predicted disease incidence could not be assessed due to the lack of reliable data during 2020. Drawing conclusions about the accuracy of the models with acceptable methodological quality was challenging because some models were published before the time period for the prediction, while other models were published during the prediction period or even afterwards. We conclude that the forecasting models involving Sweden developed during the early stages of the COVID-19 pandemic in 2020 had limited accuracy. The knowledge attained in this study can be used to improve the preparedness for coming pandemics.
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Affiliation(s)
- Philip Gerlee
- Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden. .,Mathematical Sciences, University of Gothenburg, Gothenburg, Sweden.
| | - Anna Jöud
- Department of Laboratory Medicine, Lund University, Lund, Sweden.,Department of Research and Development, Skåne University Hospital, Lund, Sweden
| | - Armin Spreco
- Department of Health, Medicine and Caring Sciences, Linköping University, Linköping, Sweden.,Regional Executive Office, Region Östergötland, Linköping, Sweden
| | - Toomas Timpka
- Department of Health, Medicine and Caring Sciences, Linköping University, Linköping, Sweden.,Regional Executive Office, Region Östergötland, Linköping, Sweden
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Weng Y, Lu D, Bollyky J, Jain V, Desai M, Lindan C, Boothroyd D, Judson T, Doernberg SB, Holubar M, Sample H, Huang B, Maldonado Y, Rutherford GW, Grumbach K. Race-ethnicity and COVID-19 Vaccination Beliefs and Intentions: A Cross-Sectional Study among the General Population in the San Francisco Bay Area. Vaccines (Basel) 2021; 9:1406. [PMID: 34960152 PMCID: PMC8705240 DOI: 10.3390/vaccines9121406] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 11/20/2021] [Accepted: 11/22/2021] [Indexed: 11/17/2022] Open
Abstract
OBJECTIVE The study was designed to compare intentions to receive COVID-19 vaccination by race-ethnicity, to identify beliefs that may mediate the association between race-ethnicity and intention to receive the vaccine and to identify the demographic factors and beliefs most strongly predictive of intention to receive a vaccine. DESIGN Cross-sectional survey conducted from November 2020 to January 2021, nested within a longitudinal cohort study of the prevalence and incidence of SARS-CoV-2 among a general population-based sample of adults in six San Francisco Bay Area counties (called TrackCOVID). Study Cohort: In total, 3161 participants among the 3935 in the TrackCOVID parent cohort responded. RESULTS Rates of high vaccine willingness were significantly lower among Black (41%), Latinx (55%), Asian (58%), Multi-racial (59%), and Other race (58%) respondents than among White respondents (72%). Black, Latinx, and Asian respondents were significantly more likely than White respondents to endorse lack of trust of government and health agencies as a reason not to get vaccinated. Participants' motivations and concerns about COVID-19 vaccination only partially explained racial-ethnic differences in vaccination willingness. Concerns about a rushed government vaccine approval process and potential bad reactions to the vaccine were the two most important factors predicting vaccination intention. CONCLUSIONS Vaccine outreach campaigns must ensure that the disproportionate toll of COVID-19 on historically marginalized racial-ethnic communities is not compounded by inequities in vaccination. Efforts must emphasize messages that speak to the motivations and concerns of groups suffering most from health inequities to earn their trust to support informed decision making.
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Affiliation(s)
- Yingjie Weng
- Quantitative Sciences Unit, Department of Medicine, Stanford University, Palo Alto, CA 94304, USA; (D.L.); (M.D.); (D.B.)
| | - Di Lu
- Quantitative Sciences Unit, Department of Medicine, Stanford University, Palo Alto, CA 94304, USA; (D.L.); (M.D.); (D.B.)
| | - Jenna Bollyky
- Division of Primary Care & Population Health, School of Medicine, Stanford University, Stanford, CA 94305, USA;
| | - Vivek Jain
- Division of HIV, Infectious Diseases & Global Medicine, San Francisco General Hospital, San Francisco, CA 94110, USA;
| | - Manisha Desai
- Quantitative Sciences Unit, Department of Medicine, Stanford University, Palo Alto, CA 94304, USA; (D.L.); (M.D.); (D.B.)
| | - Christina Lindan
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA 94134, USA; (C.L.); (G.W.R.)
- Institute for Global Health Sciences, University of California San Francisco, San Francisco, CA 94134, USA
| | - Derek Boothroyd
- Quantitative Sciences Unit, Department of Medicine, Stanford University, Palo Alto, CA 94304, USA; (D.L.); (M.D.); (D.B.)
| | - Timothy Judson
- Division of Hospital Medicine, Department of Medicine, University of California,
San Francisco, CA 94117, USA;
| | - Sarah B. Doernberg
- Division of Infectious Diseases, Department of Medicine, University of California, San Francisco CA 94117, USA;
| | - Marisa Holubar
- Division of Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA;
| | - Hannah Sample
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco CA 94134, USA;
| | - Beatrice Huang
- Department of Family and Community Medicine, University of California, San Francisco, CA 94110, USA; (B.H.); (K.G.)
| | - Yvonne Maldonado
- Division of Pediatric Infectious Diseases, Stanford University School of Medicine , Stanford, CA 94305, USA;
| | - George W. Rutherford
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA 94134, USA; (C.L.); (G.W.R.)
- Institute for Global Health Sciences, University of California San Francisco, San Francisco, CA 94134, USA
| | - Kevin Grumbach
- Department of Family and Community Medicine, University of California, San Francisco, CA 94110, USA; (B.H.); (K.G.)
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