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1.
Ann Epidemiol ; 94: 81-90, 2024 May 06.
Article in English | MEDLINE | ID: mdl-38710239

ABSTRACT

PURPOSE: Identifying predictors of opioid overdose following release from prison is critical for opioid overdose prevention. METHODS: We leveraged an individually linked, state-wide database from 2015-2020 to predict the risk of opioid overdose within 90 days of release from Massachusetts state prisons. We developed two decision tree modeling schemes: a model fit on all individuals with a single weight for those that experienced an opioid overdose and models stratified by race/ethnicity. We compared the performance of each model using several performance measures and identified factors that were most predictive of opioid overdose within racial/ethnic groups and across models. RESULTS: We found that out of 44,246 prison releases in Massachusetts between 2015-2020, 2237 (5.1%) resulted in opioid overdose in the 90 days following release. The performance of the two predictive models varied. The single weight model had high sensitivity (79%) and low specificity (56%) for predicting opioid overdose and was more sensitive for White non-Hispanic individuals (sensitivity = 84%) than for racial/ethnic minority individuals. CONCLUSIONS: Stratified models had better balanced performance metrics for both White non-Hispanic and racial/ethnic minority groups and identified different predictors of overdose between racial/ethnic groups. Across racial/ethnic groups and models, involuntary commitment (involuntary treatment for alcohol/substance use disorder) was an important predictor of opioid overdose.

2.
Lancet Reg Health Am ; 32: 100709, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38510791

ABSTRACT

Background: As overdoses continue to increase worldwide, accurate estimates are needed to understand the size of the population at risk and address health disparities. Capture-recapture methods may be used in place of direct estimation at nearly any geographic level (e.g., city, state, country) to estimate the size of the population with opioid use disorder (OUD). We performed a multi-sample capture-recapture analysis with persons aged 18-64 years to estimate the prevalence of OUD in Massachusetts from 2014 to 2020, stratified by sex and race/ethnicity. Methods: We used seven statewide administrative data sources linked at the individual level. We developed log-linear models to estimate the unknown OUD-affected population. Uncertainty was characterized using 95% confidence intervals (95% CI) on the total counts and prevalence estimates. Findings: The estimated OUD prevalence increased from 5.47% (95% CI = 4.89%, 5.98%) in 2014 to 5.79% (95% CI = 5.34%, 6.19%) in 2020. Prevalence among Hispanic females doubled (2.46% in 2014 to 4.23% in 2020) and prevalence rose to nearly 10% among Black non-Hispanic males and Hispanic males from 2014 through 2019. Estimates for Black non-Hispanic females more than doubled from 2014 through 2019 (3.39% to 7.09%), and then decreased to 5.69% in 2020. Interpretation: This study is the first to provide OUD prevalence trend estimates by binary sex and race/ethnicity at a state level using capture-recapture methods. Using these methods as the international overdose crisis worsens can allow jurisdictions to appropriately allocate resources and targeted interventions to marginalised populations. Funding: NIDA.

3.
BMC Public Health ; 24(1): 595, 2024 Feb 23.
Article in English | MEDLINE | ID: mdl-38395830

ABSTRACT

Contact tracing forms a crucial part of the public-health toolbox in mitigating and understanding emergent pathogens and nascent disease outbreaks. Contact tracing in the United States was conducted during the pre-Omicron phase of the ongoing COVID-19 pandemic. This tracing relied on voluntary reporting and responses, often using rapid antigen tests due to lack of accessibility to PCR tests. These limitations, combined with SARS-CoV-2's propensity for asymptomatic transmission, raise the question "how reliable was contact tracing for COVID-19 in the United States"? We answered this question using a Markov model to examine the efficiency with which transmission could be detected based on the design and response rates of contact tracing studies in the United States. Our results suggest that contact tracing protocols in the U.S. are unlikely to have identified more than 1.65% (95% uncertainty interval: 1.62-1.68%) of transmission events with PCR testing and 1.00% (95% uncertainty interval 0.98-1.02%) with rapid antigen testing. When considering a more robust contact tracing scenario, based on compliance rates in East Asia with PCR testing, this increases to 62.7% (95% uncertainty interval: 62.6-62.8%). We did not assume presence of asymptomatic transmission or superspreading, making our estimates upper bounds on the actual percentages traced. These findings highlight the limitations in interpretability for studies of SARS-CoV-2 disease spread based on U.S. contact tracing and underscore the vulnerability of the population to future disease outbreaks, for SARS-CoV-2 and other pathogens.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , United States/epidemiology , COVID-19/diagnosis , COVID-19/epidemiology , Contact Tracing/methods , Pandemics , Disease Outbreaks
4.
J Viral Hepat ; 2024 Feb 07.
Article in English | MEDLINE | ID: mdl-38326950

ABSTRACT

Non-invasive methods have largely replaced biopsy to identify advanced fibrosis in hepatitis C virus (HCV). Guidelines vary regarding testing strategy to balance accuracy, costs and loss to follow-up. Although individual test characteristics are well-described, data comparing the accuracy of using two tests together are limited. We calculated combined test characteristics to determine the utility of combined strategies. This study synthesizes empirical data from fibrosis staging trials and the literature to estimate test characteristics for Fibrosis-4 (FIB4), APRI or a commercial serum panel (FibroSure®), followed by transient elastography (TE) or FibroSure®. We simulated two testing strategies: (1) second test only for those with intermediate first test results (staged approach), and (2) second test for all. We summarized empiric data with multinomial distributions and used this to estimate test characteristics of each strategy on a simulated population of 10,000 individuals with 4.2% cirrhosis prevalence. Negative predictive value (NPV) for cirrhosis from a single test ranged from 98.2% (95% CB 97.6-98.8%) for FIB-4 to 99.4% (95% CB 99.0-99.8%) for TE. Using a staged approach with TE second, sensitivity for cirrhosis rose to 93.3-96.9%, NPV to 99.7-99.8%, while PPV dropped to <32%. Using TE as a second test for all minimally changed estimated test characteristics compared with the staged approach. Combining two non-invasive fibrosis tests barely improves NPV and decreases or does not change PPV compared with a single test, challenging the utility of serial testing modalities. These calculated combined test characteristics can inform best methods to identify advanced fibrosis in various populations.

5.
PLoS One ; 18(10): e0292099, 2023.
Article in English | MEDLINE | ID: mdl-37851632

ABSTRACT

As the COVID-19 pandemic progresses, widespread community transmission of SARS-CoV-2 has ushered in a volatile era of viral immune evasion rather than the much-heralded stability of "endemicity" or "herd immunity." At this point, an array of viral strains has rendered essentially all monoclonal antibody therapeutics obsolete and strongly undermined the impact of vaccinal immunity on SARS-CoV-2 transmission. In this work, we demonstrate that antibody escape resulting in evasion of pre-existing immunity is highly evolutionarily favored and likely to cause waves of short-term transmission. In the long-term, invading strains that induce weak cross-immunity against pre-existing strains may co-circulate with those pre-existing strains. This would result in the formation of serotypes that increase disease burden, complicate SARS-CoV-2 control, and raise the potential for increases in viral virulence. Less durable immunity does not drive positive selection as a trait, but such strains may transmit at high levels if they establish. Overall, our results draw attention to the importance of inter-strain cross-immunity as a driver of transmission trends and the importance of early immune evasion data to predict the trajectory of the pandemic.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , Immune Evasion , Pandemics/prevention & control , Serogroup , Antibodies, Viral
6.
Epidemiology ; 34(6): 841-849, 2023 11 01.
Article in English | MEDLINE | ID: mdl-37757873

ABSTRACT

BACKGROUND: The National Survey on Drug Use and Health (NSDUH) estimated the prevalence of opioid use disorder (OUD) among the civilian, noninstitutionalized people aged 12 years or older in Massachusetts as 1.2% between 2015 and 2017. Accurate estimation of the prevalence of OUD is critical to the success of treatment and resource planning. Various indirect estimation approaches have been used but are subject to data availability and infrastructure-related issues. METHODS: We used 2015 data from the Massachusetts Public Health Data Warehouse (PHD) to compare the results of two approaches to estimating OUD prevalence in the Massachusetts population. First, we used a seven-dataset capture-recapture analysis under log-linear model parameterization, controlling for the source dependence and effects of age, sex, and county through stratification. Second, we applied a benchmark-multiplier method in a Bayesian framework by linking health care claims data to death certificate data assuming an extrapolation of death rates from observed untreated OUD to unobserved OUD. RESULTS: Our estimates for OUD prevalence among Massachusetts residents (aged 18-64 years) were 4.62% (95% CI = 4.59%, 4.64%) in the capture-recapture approach and 4.29% (95% CrI = 3.49%, 5.32%) in the Bayesian model. Both estimates were approximately four times higher than NSDUH estimates. CONCLUSION: The synthesis of our findings suggests that the disease surveillance system misses a large portion of the population with OUD. Our study also suggests that concurrent use of multiple methods improves the justification and facilitates the triangulation and interpretation of the resulting estimates. TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT04111939.


Subject(s)
Opioid-Related Disorders , Research Design , Humans , Bayes Theorem , Prevalence , Massachusetts/epidemiology , Opioid-Related Disorders/epidemiology
7.
Int J Cancer ; 153(12): 1978-1987, 2023 12 15.
Article in English | MEDLINE | ID: mdl-37555819

ABSTRACT

Evidence suggests that aspirin use reduces the occurrence of colorectal neoplasia. Few studies have investigated the association among Black Americans, who are disproportionately burdened by the disease. We assessed aspirin use in relation to colorectal adenoma among Black women. The Black Women's Health Study is a prospective cohort of self-identified Black American women established in 1995. Participants reported regular aspirin use on baseline and follow-up questionnaires. Beginning in 1999, participants reported undergoing a colonoscopy or sigmoidoscopy, the only procedures through which colorectal adenomas can be diagnosed. Multivariable logistic regression was used to estimate odds ratios (OR) and 95% confidence intervals (CI) for associations between aspirin use and colorectal adenoma among 34 397 women who reported at least 1 colonoscopy or sigmoidoscopy. From 1997 through 2018, 1913 women were diagnosed with an adenoma. Compared to nonaspirin users, regular users had 14% (OR = 0.86, 95% CI: 0.78-0.95) lower odds of adenoma. The odds of adenoma decreased with increasing duration of aspirin use (≥10 years: OR = 0.80, 95% CI: 0.66-0.96). Initiating aspirin at a younger age was associated with a reduced adenoma occurrence (age < 40 years at initiation: OR = 0.69, 95% CI: 0.55-0.86). Regular aspirin use was associated with a decreased odds of colorectal adenoma in our study of Black women. These findings support evidence demonstrating a chemopreventive impact of aspirin on colorectal neoplasia and suggest that aspirin may be a useful prevention strategy among US Black women.


Subject(s)
Adenoma , Anti-Inflammatory Agents, Non-Steroidal , Aspirin , Black or African American , Colorectal Neoplasms , Adult , Female , Humans , Acetaminophen , Adenoma/epidemiology , Adenoma/ethnology , Adenoma/prevention & control , Anti-Inflammatory Agents, Non-Steroidal/therapeutic use , Aspirin/therapeutic use , Colorectal Neoplasms/epidemiology , Colorectal Neoplasms/prevention & control , Colorectal Neoplasms/drug therapy , Prospective Studies , United States/epidemiology
8.
Res Sq ; 2023 Jun 06.
Article in English | MEDLINE | ID: mdl-37333276

ABSTRACT

Contact tracing forms a crucial part of the public-health toolbox in mitigating and understanding emergent pathogens and nascent disease outbreaks. Contact tracing in the United States was conducted during the pre-Omicron phase of the ongoing COVID-19 pandemic. This tracing relied on voluntary reporting and responses, often using rapid antigen tests (with a high false negative rate) due to lack of accessibility to PCR tests. These limitations, combined with SARS-CoV-2's propensity for asymptomatic transmission, raise the question "how reliable was contact tracing for COVID-19 in the United States"? We answered this question using a Markov model to examine the efficiency with which transmission could be detected based on the design and response rates of contact tracing studies in the United States. Our results suggest that contact tracing protocols in the U.S. are unlikely to have identified more than 1.65% (95% uncertainty interval: 1.62%-1.68%) of transmission events with PCR testing and 0.88% (95% uncertainty interval 0.86%-0.89%) with rapid antigen testing. When considering an optimal scenario, based on compliance rates in East Asia with PCR testing, this increases to 62.7% (95% uncertainty interval: 62.6%-62.8%). These findings highlight the limitations in interpretability for studies of SARS-CoV-2 disease spread based on U.S. contact tracing and underscore the vulnerability of the population to future disease outbreaks, for SARS-CoV-2 and other pathogens.

9.
Vaccines (Basel) ; 11(4)2023 Apr 06.
Article in English | MEDLINE | ID: mdl-37112718

ABSTRACT

SARS-CoV-2 vaccinations were initially shown to substantially reduce risk of severe disease and death. However, pharmacokinetic (PK) waning and rapid viral evolution degrade neutralizing antibody (nAb) binding titers, causing loss of vaccinal protection. Additionally, there is inter-individual heterogeneity in the strength and durability of the vaccinal nAb response. Here, we propose a personalized booster strategy as a potential solution to this problem. Our model-based approach incorporates inter-individual heterogeneity in nAb response to primary SARS-CoV-2 vaccination into a pharmacokinetic/pharmacodynamic (PK/PD) model to project population-level heterogeneity in vaccinal protection. We further examine the impact of evolutionary immune evasion on vaccinal protection over time based on variant fold reduction in nAb potency. Our findings suggest viral evolution will decrease the effectiveness of vaccinal protection against severe disease, especially for individuals with a less durable immune response. More frequent boosting may restore vaccinal protection for individuals with a weaker immune response. Our analysis shows that the ECLIA RBD binding assay strongly predicts neutralization of sequence-matched pseudoviruses. This may be a useful tool for rapidly assessing individual immune protection. Our work suggests vaccinal protection against severe disease is not assured and identifies a potential path forward for reducing risk to immunologically vulnerable individuals.

10.
Vaccines (Basel) ; 11(4)2023 Apr 16.
Article in English | MEDLINE | ID: mdl-37112765

ABSTRACT

The rapid emergence of immune-evading viral variants of SARS-CoV-2 calls into question the practicality of a vaccine-only public-health strategy for managing the ongoing COVID-19 pandemic. It has been suggested that widespread vaccination is necessary to prevent the emergence of future immune-evading mutants. Here, we examined that proposition using stochastic computational models of viral transmission and mutation. Specifically, we looked at the likelihood of emergence of immune escape variants requiring multiple mutations and the impact of vaccination on this process. Our results suggest that the transmission rate of intermediate SARS-CoV-2 mutants will impact the rate at which novel immune-evading variants appear. While vaccination can lower the rate at which new variants appear, other interventions that reduce transmission can also have the same effect. Crucially, relying solely on widespread and repeated vaccination (vaccinating the entire population multiple times a year) is not sufficient to prevent the emergence of novel immune-evading strains, if transmission rates remain high within the population. Thus, vaccines alone are incapable of slowing the pace of evolution of immune evasion, and vaccinal protection against severe and fatal outcomes for COVID-19 patients is therefore not assured.

11.
Cancer Epidemiol Biomarkers Prev ; 32(7): 927-935, 2023 07 05.
Article in English | MEDLINE | ID: mdl-36409509

ABSTRACT

BACKGROUND: Animal and experimental studies suggest circadian disruption increases colorectal cancer risk, but evidence in humans is limited. We examined night shift work, chronotype, and residential position within a time zone, proxies for circadian disruption, in relation to colorectal cancer risk. METHODS: Participants in the Black Women's Health Study, a prospective cohort of 59,000 Black American women established in 1995, reported history of night shift work and chronotype on follow-up questionnaires. Residential position within a time zone was estimated using participant addresses at each questionnaire cycle. Number of colorectal cancer cases and follow-up duration varied by analysis depending on timing of exposure assessment, ranging from 204 over the 2005 to 2018 night shift work study period to 452 over the 1995 to 2018 residential position study period. Cox proportional hazards regression was used to estimate multivariable-adjusted HRs and 95% confidence intervals (CI). RESULTS: Compared with never having worked a night shift, working a night shift for ≥10 years was associated with increased colorectal cancer risk (HR = 1.64; 95% CI, 1.01-2.66). However, shorter duration was not. The HR for evening versus morning chronotype was 0.96 (95% CI, 0.73-1.27). Westward position of residence within a time zone was not associated with colorectal cancer risk (HR per 5-degree longitude increase: 0.92; 95% CI, 0.82-1.03). CONCLUSIONS: Our findings suggest a possible increased risk of colorectal cancer associated with long duration night shift work; however, results require confirmation in larger studies. IMPACT: Circadian disruption from long-term night shift work may contribute to colorectal cancer development in Black women.


Subject(s)
Colorectal Neoplasms , Work Schedule Tolerance , Female , Humans , Circadian Rhythm , Colorectal Neoplasms/epidemiology , Colorectal Neoplasms/etiology , Incidence , Prospective Studies , Risk Factors , Black or African American
12.
Clin Infect Dis ; 76(3): e965-e972, 2023 02 08.
Article in English | MEDLINE | ID: mdl-35666515

ABSTRACT

BACKGROUND: Modeling studies have concluded that 60-80% of tuberculosis (TB) infections result from reinfection of previously infected persons. The annual rate of infection (ARI), a standard measure of the risk of TB infection in a community, may not accurately reflect the true risk of infection among previously infected persons. We constructed a model of infection and reinfection with Mycobacterium tuberculosis to explore the predictive accuracy of ARI and its effect on disease incidence. METHODS: We created a deterministic simulation of the progression from TB infection to disease and simulated the prevalence of TB infection at the beginning and end of a theoretical year of infection. We considered 10 disease prevalence scenarios ranging from 100/100 000 to 1000/100 000 in simulations where TB exposure probability was homogeneous across the whole simulated population or heterogeneously stratified into high-risk and low-risk groups. ARI values, rates of progression from infection to disease, and the effect of multiple reinfections were obtained from published studies. RESULTS: With homogeneous exposure risk, observed ARI values produced expected numbers of infections. However, when heterogeneous risk was introduced, observed ARI was seen to underestimate true ARI by 25-58%. Of the cases of TB disease that occurred, 36% were among previously infected persons when prevalence was 100/100 000, increasing to 79% of cases when prevalence was 1000/100 000. CONCLUSIONS: Measured ARI underestimates true ARI as a result of heterogeneous population mixing. The true force of infection in a community may be greater than previously appreciated. Hyperendemic communities likely contribute disproportionally to the global TB disease burden.


Subject(s)
Latent Tuberculosis , Mycobacterium tuberculosis , Tuberculosis , Humans , Reinfection , Incidence , Tuberculosis/epidemiology , Latent Tuberculosis/epidemiology
13.
Clin Infect Dis ; 76(3): e400-e408, 2023 02 08.
Article in English | MEDLINE | ID: mdl-35616119

ABSTRACT

BACKGROUND: The Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is highly transmissible in vaccinated and unvaccinated populations. The dynamics that govern its establishment and propensity toward fixation (reaching 100% frequency in the SARS-CoV-2 population) in communities remain unknown. Here, we describe the dynamics of Omicron at 3 institutions of higher education (IHEs) in the greater Boston area. METHODS: We use diagnostic and variant-specifying molecular assays and epidemiological analytical approaches to describe the rapid dominance of Omicron following its introduction into 3 IHEs with asymptomatic surveillance programs. RESULTS: We show that the establishment of Omicron at IHEs precedes that of the state and region and that the time to fixation is shorter at IHEs (9.5-12.5 days) than in the state (14.8 days) or region. We show that the trajectory of Omicron fixation among university employees resembles that of students, with a 2- to 3-day delay. Finally, we compare cycle threshold values in Omicron vs Delta variant cases on college campuses and identify lower viral loads among college affiliates who harbor Omicron infections. CONCLUSIONS: We document the rapid takeover of the Omicron variant at IHEs, reaching near-fixation within the span of 9.5-12.5 days despite lower viral loads, on average, than the previously dominant Delta variant. These findings highlight the transmissibility of Omicron, its propensity to rapidly dominate small populations, and the ability of robust asymptomatic surveillance programs to offer early insights into the dynamics of pathogen arrival and spread.


Subject(s)
COVID-19 , Humans , COVID-19/epidemiology , SARS-CoV-2/genetics , Universities , Boston
14.
Res Sq ; 2023 Dec 29.
Article in English | MEDLINE | ID: mdl-38234843

ABSTRACT

The basic reproductive number (R0) and superspreading potential (k) are key epidemiological parameters that inform our understanding of a disease's transmission. Often these values are estimated using the data obtained from contact tracing studies. Here we performed a simulation study to understand how incomplete data due to preferential contact tracing impacted the accuracy and inferences about the transmission of SARS-CoV-2. Our results indicate that as the number of positive contacts traced decreases, our estimates of R0 tend to decrease and our estimates of ktend to increase. Notably, when there are large amounts of positive contacts missed in the tracing process, we can conclude that there is no indication of superspreading even if we know there is. The results of this study highlight the need for a unified public health response to transmissible diseases.

15.
Front Public Health ; 10: 941773, 2022.
Article in English | MEDLINE | ID: mdl-36530725

ABSTRACT

In the face of a long-running pandemic, understanding the drivers of ongoing SARS-CoV-2 transmission is crucial for the rational management of COVID-19 disease burden. Keeping schools open has emerged as a vital societal imperative during the pandemic, but in-school transmission of SARS-CoV-2 can contribute to further prolonging the pandemic. In this context, the role of schools in driving SARS-CoV-2 transmission acquires critical importance. Here we model in-school transmission from first principles to investigate the effectiveness of layered mitigation strategies on limiting in-school spread. We examined the effect of masks and air quality (ventilation, filtration and ionizers) on steady-state viral load in classrooms, as well as on the number of particles inhaled by an uninfected person. The effectiveness of these measures in limiting viral transmission was assessed for variants with different levels of mean viral load (ancestral, Delta, Omicron). Our results suggest that a layered mitigation strategy can be used effectively to limit in-school transmission, with certain limitations. First, poorly designed strategies (insufficient ventilation, no masks, staying open under high levels of community transmission) will permit in-school spread even if some level of mitigation is present. Second, for viral variants that are sufficiently contagious, it may be difficult to construct any set of interventions capable of blocking transmission once an infected individual is present, underscoring the importance of other measures. Our findings provide practical recommendations; in particular, the use of a layered mitigation strategy that is designed to limit transmission, with other measures such as frequent surveillance testing and smaller class sizes (such as by offering remote schooling options to those who prefer it) as needed.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , COVID-19/prevention & control , COVID-19/epidemiology , Viral Load , Pandemics , Schools
16.
BMC Med Res Methodol ; 22(1): 297, 2022 11 19.
Article in English | MEDLINE | ID: mdl-36402979

ABSTRACT

BACKGROUND: The occurrence and timing of mycobacterial culture conversion is used as a proxy for tuberculosis treatment response. When researchers serially sample sputum during tuberculosis studies, contamination or missed visits leads to missing data points. Traditionally, this is managed by ignoring missing data or simple carry-forward techniques. Statistically advanced multiple imputation methods potentially decrease bias and retain sample size and statistical power. METHODS: We analyzed data from 261 participants who provided weekly sputa for the first 12 weeks of tuberculosis treatment. We compared methods for handling missing data points in a longitudinal study with a time-to-event outcome. Our primary outcome was time to culture conversion, defined as two consecutive weeks with no Mycobacterium tuberculosis growth. Methods used to address missing data included: 1) available case analysis, 2) last observation carried forward, and 3) multiple imputation by fully conditional specification. For each method, we calculated the proportion culture converted and used survival analysis to estimate Kaplan-Meier curves, hazard ratios, and restricted mean survival times. We compared methods based on point estimates, confidence intervals, and conclusions to specific research questions. RESULTS: The three missing data methods lead to differences in the number of participants achieving conversion; 78 (32.8%) participants converted with available case analysis, 154 (64.7%) converted with last observation carried forward, and 184 (77.1%) converted with multiple imputation. Multiple imputation resulted in smaller point estimates than simple approaches with narrower confidence intervals. The adjusted hazard ratio for smear negative participants was 3.4 (95% CI 2.3, 5.1) using multiple imputation compared to 5.2 (95% CI 3.1, 8.7) using last observation carried forward and 5.0 (95% CI 2.4, 10.6) using available case analysis. CONCLUSION: We showed that accounting for missing sputum data through multiple imputation, a statistically valid approach under certain conditions, can lead to different conclusions than naïve methods. Careful consideration for how to handle missing data must be taken and be pre-specified prior to analysis. We used data from a TB study to demonstrate these concepts, however, the methods we described are broadly applicable to longitudinal missing data. We provide valuable statistical guidance and code for researchers to appropriately handle missing data in longitudinal studies.


Subject(s)
Research Design , Sputum , Humans , Longitudinal Studies , Data Interpretation, Statistical , Bias
17.
PLoS Comput Biol ; 18(9): e1010434, 2022 09.
Article in English | MEDLINE | ID: mdl-36048890

ABSTRACT

The reproductive number is an important metric that has been widely used to quantify the infectiousness of communicable diseases. The time-varying instantaneous reproductive number is useful for monitoring the real-time dynamics of a disease to inform policy making for disease control. Local estimation of this metric, for instance at a county or city level, allows for more targeted interventions to curb transmission. However, simultaneous estimation of local reproductive numbers must account for potential sources of heterogeneity in these time-varying quantities-a key element of which is human mobility. We develop a statistical method that incorporates human mobility between multiple regions for estimating region-specific instantaneous reproductive numbers. The model also can account for exogenous cases imported from outside of the regions of interest. We propose two approaches to estimate the reproductive numbers, with mobility data used to adjust incidence in the first approach and to inform a formal priori distribution in the second (Bayesian) approach. Through a simulation study, we show that region-specific reproductive numbers can be well estimated if human mobility is reasonably well approximated by available data. We use this approach to estimate the instantaneous reproductive numbers of COVID-19 for 14 counties in Massachusetts using CDC case report data and the human mobility data collected by SafeGraph. We found that, accounting for mobility, our method produces estimates of reproductive numbers that are distinct across counties. In contrast, independent estimation of county-level reproductive numbers tends to produce similar values, as trends in county case-counts for the state are fairly concordant. These approaches can also be used to estimate any heterogeneity in transmission, for instance, age-dependent instantaneous reproductive number estimates. As people are more mobile and interact frequently in ways that permit transmission, it is important to account for this in the estimation of the reproductive number.


Subject(s)
COVID-19 , Communicable Diseases , Bayes Theorem , COVID-19/epidemiology , Humans , Reproduction , SARS-CoV-2
18.
Philos Trans A Math Phys Eng Sci ; 380(2233): 20210303, 2022 Oct 03.
Article in English | MEDLINE | ID: mdl-35965456

ABSTRACT

A valuable metric in understanding local infectious disease dynamics is the local time-varying reproduction number, i.e. the expected number of secondary local cases caused by each infected individual. Accurate estimation of this quantity requires distinguishing cases arising from local transmission from those imported from elsewhere. Realistically, we can expect identification of cases as local or imported to be imperfect. We study the propagation of such errors in estimation of the local time-varying reproduction number. In addition, we propose a Bayesian framework for estimation of the true local time-varying reproduction number when identification errors exist. And we illustrate the practical performance of our estimator through simulation studies and with outbreaks of COVID-19 in Hong Kong and Victoria, Australia. This article is part of the theme issue 'Technical challenges of modelling real-life epidemics and examples of overcoming these'.


Subject(s)
COVID-19 , Communicable Diseases , Bayes Theorem , COVID-19/epidemiology , Communicable Diseases/epidemiology , Disease Outbreaks , Humans , Reproduction
19.
Am J Prev Med ; 63(3): e87-e98, 2022 09.
Article in English | MEDLINE | ID: mdl-35725599

ABSTRACT

INTRODUCTION: A total of 23 state Medicaid programs continue to restrict hepatitis C virus (HCV) medication access by liver disease or substance-use criteria, creating obstacles to HCV elimination and significant care disparities. Because public insurers often set precedents for private insurer coverage and clinician practice patterns, this study sought to analyze whether spillover occurs from state Medicaid HCV treatment restrictions to HCV screening and treatment rates in commercially insured individuals. METHODS: Investigators analyzed 2014‒2017 commercial claims data across 48 U.S. states (721,961,965 person-months) and used an interrupted times series design to compare hepatitis C virus screening and treatment rates before and after state Medicaid HCV treatment policy changes, adjusting for state-level random effects, Medicaid expansion status, and state drug overdose incidence rates, in states that relaxed Medicaid policy over the study period. Analysis occurred during 2019‒2021. RESULTS: Hepatitis C virus screening rates among commercially insured individuals increased after the corresponding state Medicaid program relaxed HCV treatment policy. Among states that changed Medicaid policy, those that reduced fibrosis or both fibrosis and abstinence restrictions experienced increased HCV screening rates by the study end compared with states that changed only abstinence restrictions (rate ratio=1.29; 95% CI=1.15, 1.44; and rate ratio=1.32; 95% CI=1.17, 1.50, respectively). Similar patterns did not occur in HCV treatment rates, which declined after 2015 across groups. CONCLUSIONS: These data show that HCV screening rates increased among commercially insured individuals after the removal of Medicaid HCV treatment restrictions in the same state. This suggests that Medicaid treatment policies can spill over to affect health outcomes among commercially insured populations.


Subject(s)
Hepatitis C , Medicaid , Fibrosis , Hepacivirus , Hepatitis C/diagnosis , Hepatitis C/drug therapy , Hepatitis C/epidemiology , Humans , Policy , United States/epidemiology
20.
Cell Rep Med ; 3(3): 100556, 2022 03 15.
Article in English | MEDLINE | ID: mdl-35474742

ABSTRACT

Keeping schools open without permitting COVID-19 spread has been complicated by conflicting messages around the role of children and schools in fueling the pandemic. Here, we describe methodological limitations of research minimizing SARS-CoV-2 transmission in schools, and we review evidence for safely operating schools while reducing overall SARS-CoV-2 transmission.


Subject(s)
Automobile Driving , COVID-19 , Child , Humans , SARS-CoV-2 , Schools
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