Dataset Information

Characterizing HIV transmission networks across the United States.

ABSTRACT:

Background

Clinically, human immunodeficiency virus type 1 (HIV-1) pol sequences are used to evaluate for drug resistance. These data can also be used to evaluate transmission networks and help describe factors associated with transmission risk.

Methods

HIV-1 pol sequences from participants at 5 sites in the CFAR Network of Integrated Clinical Systems (CNICS) cohort from 2000-2009 were analyzed for genetic relatedness. Only the first available sequence per participant was included. Inferred transmission networks ("clusters") were defined as ?2 sequences with ?1.5% genetic distance. Clusters including ?3 patients ("networks") were evaluated for clinical and demographic associations.

Results

Of 3697 sequences, 24% fell into inferred clusters: 155 clusters of 2 individuals ("dyads"), 54 clusters that included 3-14 individuals ("networks"), and 1 large cluster that included 336 individuals across all study sites. In multivariable analyses, factors associated with being in a cluster included not using antiretroviral (ARV) drugs at time of sampling (P < .001), sequence collected after 2004 (P < .001), CD4 cell count >350 cells/mL (P < .01), and viral load 10,000-100,000 copies/mL (P < .001) or >100,000 copies/mL (P < .001). In networks, women were more likely to cluster with other women (P < .001), and African Americans with other African Americans (P < .001).

Conclusions

Molecular epidemiology can be applied to study HIV transmission networks in geographically and demographically diverse cohorts. Clustering was associated with lack of ARV use and higher viral load, implying transmission may be interrupted by earlier diagnosis and treatment. Observed female and African American networks reinforce the importance of diagnosis and prevention efforts targeted by sex and race.

SUBMITTER: Aldous JL

PROVIDER: S-EPMC3529609 | biostudies-literature | 2012 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Characterizing HIV transmission networks across the United States.

Aldous Jeannette L JL Pond Sergei Kosakovsky SK Poon Art A Jain Sonia S Qin Huifang H Kahn James S JS Kitahata Mari M Rodriguez Benigno B Dennis Ann M AM Boswell Stephen L SL Haubrich Richard R Smith Davey M DM

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 20120710 8

<h4>Background</h4>Clinically, human immunodeficiency virus type 1 (HIV-1) pol sequences are used to evaluate for drug resistance. These data can also be used to evaluate transmission networks and help describe factors associated with transmission risk.<h4>Methods</h4>HIV-1 pol sequences from participants at 5 sites in the CFAR Network of Integrated Clinical Systems (CNICS) cohort from 2000-2009 were analyzed for genetic relatedness. Only the first available sequence per participant was included ...[more]

PMID: 22784872

Similar Datasets

Project description:Involvement of clinical pharmacists in the ICU attenuates costs, avoids adverse drug events, and reduces morbidity and mortality. This survey assessed services and activities of ICU pharmacists.DesignA 27-question, pretested survey.Setting1,220 U.S. institutions.SubjectsCritical care pharmacists.InterventionsElectronic questionnaire of pharmacy services and activities across clinical practice, education, scholarship, and administration.Measurements and main resultsA total of 401 (response rate of 35.4%) surveys representing 493 ICUs were completed. Median daily ICU census was 12 (interquartile range, 6-20) beds with 1 (interquartile range, 1-1.5) pharmacist full-time equivalent per ICU. Direct clinical ICU pharmacy services were available in 70.8% of ICUs. Pharmacists attended rounds 5 days (interquartile range, 4-5 d) per week with a median patient-to-pharmacist ratio of 17 (interquartile range, 12-26). The typical workweek consisted of 50% (interquartile range, 40-60%) direct ICU patient care, 10% (interquartile range, 8-16%) teaching, 8% (interquartile range, 5-18%) order processing, 5% (interquartile range, 0-20%) direct non-ICU patient care, 5% (interquartile range, 2-10%) administration, 5% (interquartile range, 0-10%) scholarship, and 0% (interquartile range, 0-5%) drug distribution. Common clinical activities as a percentage of the workweek were reviewing drug histories (28.5%); assessing adverse events (27.6%); and evaluating (26.1%), monitoring (23.8%), and managing (21.4%) drug therapies. Services were less likely to occur overnight or on weekends. Telemedicine was rarely employed. Dependent prescriptive authority (per protocol or via practice agreements) was available to 51.1% of pharmacists and independent prescriptive authority was provided by 13.4% of pharmacists. Educational services most frequently provided were inservices (97.6%) and experiential training of students or residents (89%). Education of ICU healthcare members was provided at a median of 5 times/mo (interquartile range, 3-15 times/mo). Most respondents were involved with ICU or departmental policies/guidelines (84-86.8%) and 65.7% conducted some form of scholarship.ConclusionsICU pharmacists have diverse and versatile responsibilities and provide several key clinical and nonclinical services. Initiatives to increase the availability of services are warranted.

Project description:Nonnative plants are widely recognized as stressors to wetlands and other ecosystems. They may compete with native plant species or communities and alter ecosystem properties, which can affect ecological condition, posing challenges to resource managers. As part of the United States Environmental Protection Agency's National Wetland Condition Assessment (NWCA), we characterized the status of nonnative plants in wetlands across the conterminous United States (US). Our primary goals were to (1) document the composition of nonnative taxa at 1138 NWCA sites sampled in 2011 and (2) estimate the areal extent of wetland under stress from nonnative plants within the NWCA 2011 sampled population of ~?25 million ha of wetland (represented by 967 sampled probability sites and the NWCA survey design). A total of 443 unique nonnative taxa were observed, encompassing a species pool adapted to diverse ecological conditions. For individual sites, the number of nonnative taxa ranged from 0 to 29, and total absolute cover of nonnatives ranged from 0 to 160%. We devised the nonnative plant indicator (NNPI) as a categorical indicator of stress (low to very high) from the collective set of nonnative plant taxa occurring at a particular location, based on a decision matrix of exceedance values for nonnative richness, relative frequency, and relative cover. Wetland area of the sampled population occurring in each NNPI category was estimated at the scale of the conterminous US and within five large ecoregions and four broad wetland types. Potential stress from nonnative plants, as indicated by the NNPI category, was low for approximately 61% (~?15.3 million ha), moderate for about 20% (~?5.2 million ha), high for about 10% (~?2.48 million ha), and very high for about 9% (~?2.2 million ha) of the wetland area in the entire sampled population. Percent of wetland area with high and very high NNPI varied by ecoregional subpopulations: greater within interior and western ecoregions (~?29 to 87%) than within ecoregions in the eastern half of the nation (~?11%). Among wetland type subpopulations, greater percent of wetland area with high and very high NNPI was observed for herbaceous vs. woody types and for inland vs. estuarine types. Estimates of wetland area by NNPI categories are expected to be useful to policy makers or resource managers for prioritizing management actions by identifying situations where stress from nonnative plants is most extensive. We also considered four exploratory analyses aimed at providing ecological information useful in interpreting NNPI extent results. We conducted three population-scale analyses examining ecoregional and wetland type population means for (1) the three NNPI metrics, (2) absolute cover of growth-habit groups of nonnative plants, and (3) metrics describing human-mediated disturbance. Finally, we examined ecological relationships with site-level NNPI status using a random forest (RF) analysis with NNPI as the response variable and predictor variables including ecoregion, wetland type, and a variety of characteristics describing natural vegetation structure, environment, and human-mediated disturbance.

Dataset Information

Characterizing HIV transmission networks across the United States.

Background

Methods

Results

Conclusions

Publications

Characterizing HIV transmission networks across the United States.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets