A5042124068- COVID-19 epidemiological studies
- Tuberculosis Research and Epidemiology
- Mycobacterium research and diagnosis
- SARS-CoV-2 and COVID-19 Research
- Pneumonia and Respiratory Infections
- Evolution and Genetic Dynamics
- Bacillus and Francisella bacterial research
- Poxvirus research and outbreaks
- Vaccine Coverage and Hesitancy
- COVID-19 Clinical Research Studies
- SARS-CoV-2 detection and testing
- Advanced Causal Inference Techniques
- Food Security and Health in Diverse Populations
- Viral Infections and Outbreaks Research
- Healthcare Policy and Management
- Data-Driven Disease Surveillance
- HIV/AIDS Impact and Responses
- Stuttering Research and Treatment
- Virology and Viral Diseases
- Plant Virus Research Studies
- HIV Research and Treatment
- COVID-19 and healthcare impacts
- Misinformation and Its Impacts
- Bayesian Methods and Mixture Models
- Health Education and Validation
Yale University
2019-2025
Ministério da Saúde
2021
Estimates of the reproductive number for novel pathogens, such as severe acute respiratory syndrome coronavirus 2, are essential understanding potential trajectory epidemics and levels intervention that needed to bring under control. However, most methods estimating basic (R0) time-varying effective (Rt) assume fraction cases detected reported is constant through time. We explored impact secular changes in diagnostic testing reporting on estimates R0 Rt using simulated data. then compared...
Reported COVID-19 cases and deaths provide a delayed incomplete picture of SARS-CoV-2 infections in the United States (US). Accurate estimates both timing magnitude are needed to characterize viral transmission dynamics better understand disease burden. We estimated time trends other outcomes for every county US, from first reported case January 13, 2020 through 1, 2021. To do so we employed Bayesian modeling approach that explicitly accounts reporting delays variation ascertainment,...
Abstract Background Although a substantial fraction of the US population was infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during December 2021–February 2022, subsequent evolution immunity reflects competing influences waning protection over time and acquisition or restoration through additional infections vaccinations. Methods Using Bayesian evidence synthesis model reported disease 2019 (COVID-19) data (diagnoses, hospitalizations), vaccinations, patterns for...
The incidence of multidrug-resistant tuberculosis (MDR-TB) remains critically high in countries the former Soviet Union, where >20% new cases and >50% previously treated have resistance to rifampin isoniazid. Transmission resistant strains, as opposed selected through inadequate treatment drug-susceptible (TB), is main driver incident MDR-TB these countries.We conducted a prospective, genomic analysis all culture-positive TB diagnosed 2018 2019 Republic Moldova. We used phylogenetic methods...
While a substantial fraction of the US population was infected with SARS-CoV-2 during December 2021 - February 2022, subsequent evolution immunity against Omicron variants reflects competing influences waning protection over time and acquisition or restoration through additional infections vaccinations.
Abstract The projected trajectory of multidrug resistant tuberculosis (MDR-TB) epidemics depends on the reproductive fitness circulating strains MDR M. (Mtb) . Previous efforts to characterize Mtb have found that Beijing sublineage (Lineage 2.2.1) may be more prone develop resistance and retain in presence resistance-conferring mutations than other lineages. Using genome sequences from all culture-positive cases collected over two years Moldova, we estimate Ural 4.2) strains, lineages which...
Abstract SARS-CoV-2 infection rates displayed striking temporal and spatial variation during the emergence of new variants globally within United States. While spatiotemporal “waves” have been observed, quantitative assessments their spread remain limited. Here, we estimate compare speed extent first two major waves in States, illustrating these dynamics through detailed visualizations. Our findings reveal that origins coincide with large gatherings relaxation masking mandates. Notably,...
Abstract Background Mixed infection with multiple strains of the same pathogen in a single host can present clinical and analytical challenges. Whole genome sequence (WGS) data identify signals samples, though precision previous methods be improved. Here, we MixInfect2, new tool to accurately detect mixed samples from Mycobacterium tuberculosis short-read WGS data. We then evaluate three approaches for reconstructing underlying constituent strain sequences. This allows these included...
Abstract Estimates of the reproductive number for novel pathogens such as SARS-CoV-2 are essential understanding potential trajectory epidemic and level intervention that is needed to bring under control. However, most methods estimating basic ( R 0 ) time-varying effective t assume fraction cases detected reported constant through time. We explore impact secular changes in diagnostic testing reporting on estimates using simulated data. then compare these patterns data COVID-19 practices...
Reported COVID-19 cases and deaths provide a delayed incomplete picture of SARS-CoV-2 infections in the United States (US). Accurate estimates both timing magnitude are needed to characterize viral transmission dynamics better understand disease burden. We estimated time trends other outcomes for every county US, from first reported case January 13, 2020 through 1, 2021. To do so we employed Bayesian modeling approach that explicitly accounts reporting delays variation ascertainment,...
This decision analytic model estimates the levels of community testing, contract tracing, and vaccination required to reduce effective reproduction number mpox virus among high-risk group men who have sex with men.
Both severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and disease 2019 (COVID-19) vaccination contribute to population-level immunity against SARS-CoV-2. This study estimated the immunological exposure effective protection future SARS-CoV-2 in each US state county over 2020-2021 how this changed with introduction of Omicron variant.We used a Bayesian model synthesize estimates daily infections, data relative rates conditional on status estimate fraction population (1)...
Omicron surged as a variant of concern in late 2021. Several distinct variants appeared and overtook each other. We combined frequencies infection estimates from nowcasting model for US state to estimate variant-specific infections, attack rates, effective reproduction numbers (R
Infectious disease dynamics are driven by the complex interplay of epidemiological, ecological, and evolutionary processes. Accurately modeling these interactions is crucial for understanding pathogen spread informing public health strategies. However, existing simulators often fail to capture dynamic between processes, resulting in oversimplified models that do not fully reflect real-world complexities which pathogen's genetic evolution dynamically influences transmission. We introduce...
Background: In spring and summer 2022, an outbreak of mpox occurred worldwide, largely confined to men who have sex with (MSM). There was concern that could break swiftly into congregate settings populations high levels regular frequent physical contact, like university campus communities. Objective: To estimate the likelihood potential effect mitigation measures in a residential college setting. Design: A stochastic dynamic SEIR (susceptible, exposed but not infectious, or recovered) model...
Policy makers need decision tools to determine when use physical distancing interventions maximize the control of COVID-19 while minimizing economic and social costs these interventions. We describe a pragmatic tool characterize adaptive policies that combine real-time surveillance data with clear rules guide trigger, continue, or stop during current pandemic. In model-based experiments, we find characterized by our proposed approach prevent more deaths require shorter overall duration than...
Abstract Understanding factors that contribute to the increased likelihood of pathogen transmission between two individuals is important for infection control. However, analyzing measures relatedness estimate these associations complicated due correlation arising from presence same individual across multiple dyadic outcomes, potential spatial caused by unmeasured dynamics, and distinctive distributional characteristics some outcomes. We develop novel hierarchical Bayesian methods genetic...
Abstract Initial projections from the first generation of COVID-19 models focused public attention on worst-case scenarios in absence decisive policy action. These underscored imperative for strong and immediate measures to slow spread infection. In coming weeks, however, as policymakers continue enlisting inform decisions COVID-19, answers most difficult pressing questions will be much more sensitive underlying uncertainties. this study, we demonstrate a model-based approach assessing...
Reliable subnational estimates of TB incidence would allow national policy makers to focus disease control resources in areas highest need. We developed an approach for generating small area incidence, and the fraction individuals missed by routine case detection, based on available notification mortality data. demonstrate feasibility this creating municipality-level burden Brazil. a mathematical model describing relationship between notifications deaths, allowing known biases each these...
Abstract Background Mixed infection with multiple strains of the same pathogen in a single host can present clinical and analytical challenges. Whole genome sequence (WGS) data identify signals samples, though precision previous methods be improved. Here, we MixInfect2, new tool to accurately detect mixed samples from Mycobacterium tuberculosis WGS data. We then evaluate three approaches for reconstructing underlying constituent strain sequences. This allows these included downstream...
Abstract Background Delays in identifying and treating individuals with infectious tuberculosis (TB) contribute to poor health outcomes allow ongoing community transmission of M. ( Mtb ). Current recommendations for screening specify characteristics (e.g., areas high local prevalence) that can be used target within the general population. However, higher burden are not necessarily rates transmission. We investigated genomic diversity using high-resolution surveillance data Blantyre, Malawi....
Prior infection and vaccination both contribute to population-level SARS-CoV-2 immunity. We used a Bayesian model synthesize evidence estimate population immunity prevalent variants in the United States over course of epidemic until December 1, 2021, how this changed with introduction Omicron variant. daily estimates coverage data for each US state county. estimated relative rates conditional on previous status using Census Bureau’s Household Pulse Survey. published natural vaccine-induced...
Abstract The projected trajectory of multidrug resistant tuberculosis (MDR-TB) epidemics depends on the reproductive fitness circulating strains MDR M. (Mtb) . Previous efforts to characterize Mtb have found that Beijing sublineage (Lineage 2.2.1) may be more prone develop resistance and retain in presence resistance-conferring mutations than other lineages. Using genome sequences from all culture-positive cases collected over two years Moldova, we estimate Ural 4.2) strains, lineages which...
Evidence on local disease burden and the completeness of case detection represent important information for TB control programs. We present a new method estimating subnational incidence fraction individuals with incident who are diagnosed treated in Brazil. compiled data notifications TB-related mortality Brazil specified an analytic model approximating as number exiting untreated active (sum treatment initiation, death before treatment, self-cure). employed Bayesian inference approach to...
Background Limited access to drug-susceptibility tests (DSTs) and delays in receiving DST results are challenges for timely appropriate treatment of multi-drug resistant tuberculosis (TB) many low-resource settings. We investigated whether data collected as part routine, national TB surveillance could be used develop predictive models identify additional resistance fluoroquinolones (FLQs), a critical second-line class anti-TB agents, at the time diagnosis with rifampin-resistant TB. Methods...