title: [Genome epidemiology and tropical spastic paraparesis associated with human T-cell lymphotropic virus type 1].
abstract: OBJECTIVE
  Characterize the genomic environment of the sequences adjacent to human T-cell lymphotropic virus type 1 (HTLV-1) in patients with HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) in different regions of Colombia and Japan.
  
  
  METHODS
  A total of 71 recombinant clones with human genome sequences adjacent to 5' LTR in patients with HAM/TSP were compared to the Genome Browser and GenBank databases. Sixteen structural and compositional genome variables were identified, and statistical analysis was conducted in the R computer program, version 2.8.1, in a 0.5 Mb window.
  
  
  RESULTS
  A total of 43.0% of the proviruses were located in the group C chromosomes; 74% of the sequences were located in the telomeric and subtelomeric regions (P < 0.05). A cluster analysis was used to establish the hierarchical relations between the genome characteristics included in the study. The analysis of principal components identified the components that defined the preferred genome environments for proviral integration in cases of HAM/TSP.
  
  
  CONCLUSIONS
  HTLV-1 was integrated more often in chromatin regions rich in CpG islands with a high density of genes and LINE type repetitions, and DNA transposons which, overall, would form the genomic environments targeted for integration. This new scenario will promote substantial changes in the field of public health and in epidemiological management of infectious diseases. It will also foster the development of powerful tools for increasing the efficiency of epidemiological surveillance.
authors.affiliation: Departamento de Ciencias Fisiológicas, Laboratorio de Biología Molecular y Patogénesis, Escuela de Ciencias Básicas, Universidad del Valle, Cali, Colombia.
authors.forename: Mercedes
authors.initials: M
authors.lastname: Salcedo-Cifuentes
authors.forename: Martha C
authors.initials: MC
authors.lastname: Domínguez
authors.forename: Felipe
authors.initials: F
authors.lastname: García-Vallejo
mesh_terms: D000328:Adult; D000368:Aged; D002874:Chromosome Mapping; D002877:Chromosomes, Human / Q000235:genetics; D003105:Colombia / Q000453:epidemiology; D018899:CpG Islands; D004274:DNA, Recombinant / Q000235:genetics; D005260:Female; D015894:Genome, Human; D015368:Human T-lymphotropic virus 1 / Q000235:genetics*; D006801:Humans; D008297:Male; D008875:Middle Aged; D015493:Paraparesis, Tropical Spastic / Q000453:epidemiology / Q000235:genetics* / Q000821:virology; D011533:Proviruses / Q000235:genetics*; D018626:Retroelements / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D012689:Sequence Homology, Nucleic Acid; D020079:Terminal Repeat Sequences / Q000235:genetics*; D016662:Virus Integration / Q000235:genetics*
chemical_list: D004274:DNA, Recombinant; D018626:Retroelements