Dataset Information

Large-scale analysis of the prevalence and geographic distribution of HIV-1 non-B variants in the United States.

ABSTRACT: The genetic diversity of human immunodeficiency virus type 1 (HIV-1) has significant implications for diagnosis, vaccine development, and clinical management of patients. Although HIV-1 subtype B is predominant in the United States, factors such as global travel, immigration, and military deployment have the potential to increase the proportion of non-subtype B infections. Limited data are available on the prevalence and distribution of non-B HIV-1 strains in the United States. We sought to retrospectively examine the prevalence, geographic distribution, diversity, and temporal trends of HIV-1 non-B infections in samples obtained by ARUP Laboratories, a national reference laboratory, from all regions of the United States. HIV-1 pol sequences from 24,386 specimens collected from 46 states between 2004 and September 2011 for drug resistance genotyping were analyzed using the REGA HIV-1 Subtyping Tool, version 2.0. Sequences refractory to subtype determination or reported as non-subtype B by this tool were analyzed by PHYLIP version 3.5 and Simplot version 3.5.1. Non-subtype B strains accounted for 3.27% (798/24,386) of specimens. The 798 non-B specimens were received from 37 states and included 5 subtypes, 23 different circulating recombinant forms (CRFs), and 39 unique recombinant forms (URFs). The non-subtype B prevalence varied from 0% in 2004 (0/54) to 4.12% in 2011 (201/4,884). This large-scale analysis reveals that the diversity of HIV-1 in the United States is high, with multiple subtypes, CRFs, and URFs circulating. Moreover, the geographic distribution of non-B variants is widespread. Data from HIV-1 drug resistance testing have the potential to significantly enhance the surveillance of HIV-1 variants in the United States.

SUBMITTER: Pyne MT

PROVIDER: S-EPMC3719628 | biostudies-literature | 2013 Aug

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Large-scale analysis of the prevalence and geographic distribution of HIV-1 non-B variants in the United States.

Pyne Michael T MT Hackett John J Holzmayer Vera V Hillyard David R DR

Journal of clinical microbiology 20130612 8

The genetic diversity of human immunodeficiency virus type 1 (HIV-1) has significant implications for diagnosis, vaccine development, and clinical management of patients. Although HIV-1 subtype B is predominant in the United States, factors such as global travel, immigration, and military deployment have the potential to increase the proportion of non-subtype B infections. Limited data are available on the prevalence and distribution of non-B HIV-1 strains in the United States. We sought to retr ...[more]

PMID: 23761148

Similar Datasets

Project description:Regionalized trauma care improves outcomes; however, access to care is not uniform across the United States. The objective was to evaluate whether geographic distribution of trauma centers correlates with injury mortality across state trauma systems.Level I or II trauma centers in the contiguous United States were mapped. State-level age-adjusted injury fatality rates per 100,000 people were obtained and evaluated for spatial autocorrelation. Nearest neighbor ratios (NNRs) were generated for each state. A NNR less than 1 indicates clustering, while a NNR greater than 1 indicates dispersion. NNRs were tested for difference from random geographic distribution. Fatality rates and NNRs were examined for correlation. Fatality rates were compared between states with trauma center clustering versus dispersion. Trauma center distribution and population density were evaluated. Spatial-lag regression determined the association between fatality rate and NNR, controlling for state-level demographics, population density, injury severity, trauma system resources, and socioeconomic factors.Fatality rates were spatially autocorrelated (Moran's I = 0.35, p < 0.01). Nine states had a clustered pattern (median NNR, 0.55; interquartile range [IQR], 0.48-0.60), 22 had a dispersed pattern (median NNR, 2.00; IQR, 1.68-3.99), and 10 had a random pattern (median NNR, 0.90; IQR, 0.85-1.00) of trauma center distribution. Fatality rate and NNR were correlated (? = 0.34, p = 0.03). Clustered states had a lower median injury fatality rate compared with dispersed states (56.9 [IQR, 46.5-58.9] vs. 64.9 [IQR, 52.5-77.1]; p = 0.04). Dispersed compared with clustered states had more counties without a trauma center that had higher population density than counties with a trauma center (5.7% vs. 1.2%, p < 0.01). Spatial-lag regression demonstrated that fatality rates increased by 0.02 per 100,000 persons for each unit increase in NNR (p < 0.01).Geographic distribution of trauma centers correlates with injury mortality, with more clustered state trauma centers associated with lower fatality rates. This may be a result of access relative to population density. These results may have implications for trauma system planning and require further study to investigate underlying mechanisms.Therapeutic/care management study, level IV.

Project description:RationaleNontuberculous mycobacteria are an important cause of morbidity in the United States, although patient outcomes vary greatly by species. Currently, nationally representative data on the distribution of mycobacterial species from clinical isolates are limited.ObjectivesUsing a national hospitalization database capturing microbiologic data for nearly 6 million patient encounters, we describe the geographic distribution of, and patient demographic features associated with, clinical mycobacterial isolates in the United States.MethodsLinked demographic and microbiologic data from the Premier Healthcare Database were extracted for all patient encounters from 2009 to 2013. Patients with at least one positive potentially pathogenic nontuberculous mycobacterial culture were identified as cases. The period prevalence was calculated, and patient-, encounter-, and hospital-level factors were analyzed. Regional differences in species distribution were analyzed; a subanalysis was conducted among patients with International Classification of Diseases, Ninth Revision, codes for pulmonary nontuberculous mycobacterial disease. Significant differences were assessed (P?<?0.05).ResultsOf 5,928,830 unique patients included during the 5-year study period, 7,812 (0.13%) had at least one positive nontuberculous mycobacterial culture. The mean age of cases was 64 years (range, <1-89 yr), and most were female (52%) and white (70%). Hospitals with cases were more often labeled "urban" (96%), "teaching" (56%), and had at least 500 beds (78%). Species distribution differed significantly by geographic area. Mycobacterium avium complex ranged from 61 to 91% of isolates and were most frequent in the South and Northeast regions; M. abscessus/M. chelonae ranged from 2 to 18% of isolates and were most frequent in the West; and other species, including M. fortuitum and M. kansasii, ranged from 7 to 26% and were also most frequent in the West.ConclusionsSignificant geographic variation exists in the distribution of nontuberculous mycobacterial species in the United States. Whereas M. avium complex was the most common species isolated in the South, M. abscessus/M. chelonae was proportionately higher in the West. Greater clinical awareness in regions with increased levels of harder-to-treat mycobacteria are needed, given differences in treatment options and implications for patient outcomes.

Dataset Information

Large-scale analysis of the prevalence and geographic distribution of HIV-1 non-B variants in the United States.

Publications

Large-scale analysis of the prevalence and geographic distribution of HIV-1 non-B variants in the United States.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets