title: Temporal trends in the Swedish HIV-1 epidemic: increase in non-B subtypes and recombinant forms over three decades.
abstract: BACKGROUND
  HIV-1 subtype B (HIV-1B) still dominates in resource-rich countries but increased migration contributes to changes in the global subtype distribution. Also, spread of non-B subtypes within such countries occurs. The trend of the subtype distribution from the beginning of the epidemic in the country has earlier not been reported in detail. Thus the primary objective of this study is to describe the temporal trend of the subtype distribution from the beginning of the HIV-1 epidemic in Sweden over three decades.
  
  
  METHODS
  HIV-1 pol sequences from patients (n = 3967) diagnosed in Sweden 1983-2012, corresponding to >40% of patients ever diagnosed, were re-subtyped using several automated bioinformatics tools. The temporal trends of subtypes and recombinants during three decades were described by a multinomial logistic regression model.
  
  
  RESULTS
  All eleven group M HIV-1 subtypes and sub-subtypes (78%), 17 circulating recombinant forms (CRFs) (19%) and 32 unique recombinants forms (URF) (3%) were identified. When all patients were analysed, there was an increase of newly diagnosed HIV-1C (RR, 95%CI: 1.10, 1.06-1.14), recombinants (1.20, 1.17-1.24) and other pure subtypes (1.11, 1.07-1.16) over time compared to HIV-1B. The same pattern was found when all patients infected in Sweden (n = 1165) were analysed. Also, for MSM patients infected in Sweden (n = 921), recombinant forms and other pure subtypes increased.
  
  
  CONCLUSIONS
  Sweden exhibits one of the most diverse subtype epidemics outside Africa. The increase of non-B subtypes is due to migration and to a spread among heterosexually infected patients and MSM within the country. This viral heterogeneity may become a hotspot for development of more diverse and complex recombinant forms if the epidemics converge.
authors.affiliation: Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden.
authors.forename: Ujjwal
authors.initials: U
authors.lastname: Neogi
authors.affiliation: Unit of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden; Department of Infectious Diseases, County Council of Gävleborg, Gävle, Sweden.
authors.forename: Amanda
authors.initials: A
authors.lastname: Häggblom
authors.affiliation: Unit of Biostatistics, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.
authors.forename: Michele
authors.initials: M
authors.lastname: Santacatterina
authors.affiliation: Department of Clinical Science and Education, Venhälsan, Stockholm South General Hospital, Stockholm, Sweden.
authors.forename: Göran
authors.initials: G
authors.lastname: Bratt
authors.affiliation: Department of Infectious Diseases, University of Gothenburg, Gothenburg, Sweden.
authors.forename: Magnus
authors.initials: M
authors.lastname: Gisslén
authors.affiliation: Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
authors.forename: Jan
authors.initials: J
authors.lastname: Albert
authors.affiliation: Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden; Unit of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden.
authors.forename: Anders
authors.initials: A
authors.lastname: Sonnerborg
mesh_terms: D019992:Databases as Topic; D003710:Demography; D058872:Epidemics / Q000706:statistics & numerical data*; D005260:Female; D015658:HIV Infections / Q000175:diagnosis / Q000453:epidemiology* / Q000821:virology*; D015497:HIV-1 / Q000145:classification / Q000235:genetics*; D006801:Humans; D008297:Male; D008969:Molecular Sequence Data; D011995:Recombination, Genetic; D013548:Sweden / Q000453:epidemiology; D013997:Time Factors