A5053874809- HIV Research and Treatment
- HIV/AIDS Research and Interventions
- HIV, Drug Use, Sexual Risk
- Genomics and Phylogenetic Studies
- HIV/AIDS drug development and treatment
- RNA and protein synthesis mechanisms
- COVID-19 epidemiological studies
- Data-Driven Disease Surveillance
- Complex Network Analysis Techniques
- Evolution and Genetic Dynamics
- Vector-Borne Animal Diseases
- Animal Disease Management and Epidemiology
- T-cell and Retrovirus Studies
- SARS-CoV-2 detection and testing
- Homelessness and Social Issues
- Opinion Dynamics and Social Influence
- COVID-19 and Mental Health
- Mathematical and Theoretical Epidemiology and Ecology Models
- Machine Learning in Bioinformatics
- Opioid Use Disorder Treatment
- Virology and Viral Diseases
- Rangeland and Wildlife Management
- Antibiotic Resistance in Bacteria
- Viral Infections and Vectors
- Antibiotic Use and Resistance
CDC Foundation
2024
Centers for Disease Control and Prevention
2016-2023
National Center for HIV/AIDS Viral Hepatitis STD and TB Prevention
2017-2021
Georgia State University
2021
National Center for HIV/AIDS, Dermatology and STD
2020
Epidemic Intelligence Service
2019
Center for Surveillance, Epidemiology, and Laboratory Services
2019
Pennsylvania State University
2012-2014
University of California, San Diego
2014
Center for Disease Dynamics, Economics & Policy
2012-2013
Objectives. To describe and control an outbreak of HIV infection among people who inject drugs (PWID). Methods. The investigation included diagnosed with during 2015 to 2018 linked 2 cities in northeastern Massachusetts epidemiologically or through molecular analysis. Field activities qualitative interviews regarding service availability risk behaviors. Results. We identified 129 meeting the case definition; 116 (90%) reported injection drug use. Molecular surveillance added 36 cases not...
Opioid overdose deaths have increased rapidly in northeastern Massachusetts since 2013, with postmortem fentanyl detection increasing statewide. Molecular data indicate multiple introductions of human immunodeficiency virus (HIV) among persons who inject drugs as well recent and rapid transmission the context some longstanding HIV infections.
Detecting recent and rapid spread of HIV can help prioritize prevention early treatment for those at highest risk transmission. genetic sequence data identify transmission clusters, but previous approaches have not distinguished clusters recent, We assessed an analytic approach to such in the United States.We analyzed 156,553 partial HIV-1 polymerase sequences reported National Surveillance System inferred using 2 distance thresholds (0.5% 1.5%) periods diagnoses (all years 2013-2015, ie,...
We demonstrate that integration of laboratory, phylogenetic, and epidemiologic data sources allow detailed reconstruction an outbreak. High-resolution outbreak phylodynamics allows prevention intervention strategies to be tailored community needs.
Preventing transmission of SARS-CoV-2, the virus that causes coronavirus disease 2019 , in colleges and universities requires mitigation strategies address on-and off-campus congregate living settings as well extracurricular activities other social gatherings (1-4).At start academic year, sorority fraternity organizations host a series recruitment known rush week; week culminates with bid day, when selections are announced.At university A Arkansas, (for women) was held during August 17-22,...
Social network analysis is now widely used to investigate the dynamics of infectious disease spread. Vaccination dramatically disrupts transmission on a contact network, and indeed, high vaccination rates can potentially halt altogether. Here, we build mounting evidence that health behaviors - such as vaccination, refusal thereof spread across social networks through process complex contagion requires reinforcement. Using simulations model behavior spread, find under otherwise identical...
Rapidly evolving RNA viruses continuously produce minority haplotypes that can become dominant if they are drug-resistant or better evade the immune system. Therefore, early detection and identification of viral may help to promptly adjust patient's treatment plan preventing potential disease complications. Minority be identified using next-generation sequencing, but sequencing noise hinders accurate identification. The elimination is a non-trivial task still remains open. Here we propose...
Characteristic No. (%), [rate] † Total Marshallese Hispanic/Latino White, non-Hispanic Other, Population 7,712 § (2) 86,581 (17) 365,839 (72) 49,437 (10) 509,569 Laboratory-confirmed cases 647 (19) [8,390] 1,554 (45) [1,795] 432 (13) [118] 803 (23) [1,620] 3,436 [670] Sex ¶ Female 331 (52) 811 214 (50) 371 (46) 1,727 (51) Male 310 (48) 738 217 427 (54) 1,692 (49) Age group (yrs) <18 165 (26) 275 (18) 34 (8) 174 (22) 648 18-24 74 (11) 194 (12) 51 103
Outbreak investigations use data from interviews, healthcare providers, laboratories and surveillance systems. However, integrated of multiple sources requires a patchwork software that present challenges in usability, interoperability, confidentiality, cost. Rapid integration, visualization analysis can guide effective public health interventions. We developed MicrobeTrace to facilitate rapid responses by overcoming barriers integration exploration molecular epidemiology. is web-based,...
A recent human immunodeficiency virus (HIV) outbreak among people who inject drugs in Cabell County, West Virginia, underscores the importance of HIV prevention, diagnosis, and care communities with high rates substance use disorder.
Abstract HIV molecular epidemiology can identify clusters of individuals with elevated rates transmission. These variable transmission are primarily driven by host risk behavior; however, the effect viral traits on is poorly understood. Viral load, concentration in blood, a heritable trait that influences infectiousness and disease progression. Here, we reconstruct genetic using data from United States National Surveillance System report viruses clusters, inferred to be frequently...
Abstract We investigated transmission dynamics of a large human immunodeficiency virus (HIV) outbreak among persons who inject drugs (PWID) in KY and OH during 2017–20 by using detailed phylogenetic, network, recombination, cluster dating analyses. Using polymerase (pol) sequences from 193 people associated with the investigation, we document high HIV-1 diversity, including Subtype B (44.6 per cent); numerous circulating recombinant forms (CRFs) CRF02_AG (2.5 cent) CRF02_AG-like (21.8 many...
Molecular cluster detection analyzes HIV sequences to identify rapid transmission and inform public health responses. We describe changes in the capability detect molecular clusters geographic variation dynamics. examined reporting completeness of HIV-1 polymerase quarterly National Surveillance System datasets from December 2015 2019. Priority were identified quarterly. To understand populations recently affected by transmission, we described risk race/ethnicity people first detected...
Tailoring public health responses to growing HIV transmission clusters depends on accurately mapping the risk network through which it spreads and identifying acute infections that represent leading edge of cluster growth. links, especially those involving persons with infection (AHI), can be difficult uncover, or confirm during partner services investigations. We integrated molecular, epidemiologic, serologic behavioral data infer evaluate linkages between participants a prospective study...
The evolution of antibiotic resistance in microbes poses one the greatest challenges to management human health. Because addressing problem experimentally has been difficult, research on strategies slow through rational use antibiotics resorted mathematical and computational models. However, despite many advances, several questions remain unsettled. Here we present a population model for usage by adding three key features that have overlooked: 1) maximization frequency uninfected patients...
ABSTRACT Rapidly evolving RNA viruses continuously produce minority haplotypes that can become dominant if they are drug-resistant or better evade the immune system. Therefore, early detection and identification of viral may help to promptly adjust patient's treatment plan preventing potential disease complications. Minority be identified using next-generation sequencing (NGS), but noise hinders accurate identification. The elimination is a non-trivial task still remains open. Here we...
Abstract Background The Massachusetts Department of Public Health and the Centers for Disease Control Prevention collaborated to characterize a human immunodeficiency virus (HIV) outbreak in northeastern prevent further transmission. We determined contributions HIV sequence data defining outbreak. Methods Human surveillance partner services were analyzed understand social molecular links within Cases defined as infections diagnosed during 2015–2018 among people who inject drugs with...
HIV-1 subtype B is the predominant strain in Bulgaria, yet little known about molecular epidemiology of these infections, including its origin and transmissibility. We used a phylodynamics approach by combining analyzing 663 polymerase (pol) sequences collected from persons diagnosed with HIV/AIDS between 1988–2018 associated epidemiologic data to better understand this sub-epidemic Bulgaria. Using network analyses at 1.5% genetic distance threshold (d) we found several large phylogenetic...
The Democratic Republic of the Congo (DRC) has a history nonhuman primate (NHP) consumption and exposure to simian retroviruses yet little is known about extent zoonotic retroviral infections in DRC. We examined prevalence human T-lymphotropic viruses (HTLV), retrovirus group origin, large population persons with frequent NHP exposures foamy virus infection. screened plasma from 3,051 living rural villages central DRC using HTLV EIA western blot (WB). PCR amplification tax LTR sequences...
HIV-1 subtype CRF01_AE is the second most predominant strain in Bulgaria, yet little known about molecular epidemiology of its origin and transmissibility. We used a phylodynamics approach to better understand this sub-epidemic by analyzing 270 polymerase (pol) sequences collected from persons diagnosed with HIV/AIDS between 1995 2019. Using network analyses at 1.5% genetic distance threshold (d), we found large 154-member outbreak cluster composed mostly who inject drugs (PWID) that were...
Hantaviruses zoonotically infect humans worldwide with pathogenic consequences and are mainly spread by rodents that shed aerosolized virus particles in urine feces. Bioinformatics methods for hantavirus diagnostics, genomic surveillance epidemiology currently lacking a comprehensive approach data sharing, integration, visualization, analytics reporting. With the possibility of cases going undetected spreading over international borders, significant reporting delay can miss linked...
Abstract Motivation Outbreak investigations use data from interviews, healthcare providers, laboratories and surveillance systems. However, integrated of multiple sources requires a patchwork software that present challenges in usability, interoperability, confidentiality, cost. Rapid integration, visualization analysis can guide effective public health interventions. Results We developed MicrobeTrace to facilitate rapid responses by overcoming barriers integration exploration molecular...