title: Phylogenetic analysis of the emergence of main hepatitis C virus subtypes in São Paulo, Brazil.
abstract: BACKGROUND
  It is recognized that hepatitis C virus subtypes (1a, 1b, 2a, 2b, 2c and 3a) originated in Africa and Asia and spread worldwide exponentially during the Second World War (1940) through the transfusion of contaminated blood products, invasive medical and dental procedures, and intravenous drug use. The entry of hepatitis C virus subtypes into different regions occurred at distinct times, presenting exponential growth rates of larger or smaller spread. Our study estimated the growth and spread of the most prevalent subtypes currently circulating in São Paulo.
  
  
  METHODS
  A total of 465 non-structural region 5B sequences of hepatitis C virus covering a 14-year time-span were used to reconstruct the population history and estimate the population dynamics and Time to Most Recent Common Ancestor of genotypes using the Bayesian Markov Chain Monte Carlo approach implemented in BEAST (Bayesian evolutionary analysis by sampling tree software/program).
  
  
  RESULTS
  Evolutionary analysis demonstrated that the different hepatitis C virus subtypes had distinct growth patterns. The introduction of hepatitis C virus-1a and -3a were estimated to be circa 1979 and 1967, respectively, whereas hepatitis C virus-1b appears to have a more ancient entry, circa 1923. Hepatitis C virus-1b phylogenies suggest that different lineages circulate in São Paulo, and four well-supported groups (i.e., G1, G2, G3 and G4) were identified. Hepatitis C virus-1a presented the highest growth rate (r=0.4), but its spread became less marked after the 2000s. Hepatitis C virus-3a grew exponentially until the 1990s and had an intermediate growth rate (r=0.32). An evident exponential growth (r=0.26) was found for hepatitis C virus-1b between 1980 and the mid-1990s.
  
  
  CONCLUSIONS
  After an initial period of exponential growth, the expansion of the three main subtypes began to decrease. Hepatitis C virus-1b presented inflated genetic diversity, and its transmission may have been sustained by different generations and transmission routes other than blood transfusion. Hepatitis C virus-1a and -3a showed no group stratification, most likely due to their recent entry.
authors: Fundação Pró-Sangue/Hemocentro de São Paulo, São Paulo, SP, Brazil; Infectious Diseases Division (DIPA), Universidade Federal de São Paulo (UNIFESP), São Paulo, SP, Brazil. Electronic address: a_nishiya@hotmail.com.
authors: Anna Shoko
authors: AS
authors: Nishiya
authors: Fundação Pró-Sangue/Hemocentro de São Paulo, São Paulo, SP, Brazil; Discipline of Medical Science, Faculdade de Medicina, Universidade de São Paulo (USP), São Paulo, SP, Brazil.
authors: César de
authors: Cd
authors: Almeida-Neto
authors: Laboratory of Virology, Department of Infectious and Parasitic Diseases, Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina, Universidade de São Paulo (USP), São Paulo, SP, Brazil.
authors: Camila Malta
authors: CM
authors: Romano
authors: Infectious Diseases Division (DIPA), Universidade Federal de São Paulo (UNIFESP), São Paulo, SP, Brazil; Lim 03 Medical Research Laboratory, Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo (USP), São Paulo, SP, Brazil.
authors: Cecília Salete
authors: CS
authors: Alencar
authors: Fundação Pró-Sangue/Hemocentro de São Paulo, São Paulo, SP, Brazil; Infectious Diseases Division (DIPA), Universidade Federal de São Paulo (UNIFESP), São Paulo, SP, Brazil.
authors: Suzete Cleusa
authors: SC
authors: Ferreira
authors: Universidade São João Del Rei, São João Del Rei, MG, Brazil.
authors: Claudia
authors: C
authors: Di-Lorenzo-Oliveira
authors: Fundação Pró-Sangue/Hemocentro de São Paulo, São Paulo, SP, Brazil.
authors: José Eduardo
authors: JE
authors: Levi
authors: Fundação Pró-Sangue/Hemocentro de São Paulo, São Paulo, SP, Brazil.
authors: Nanci Alves
authors: NA
authors: Salles
authors: Fundação Pró-Sangue/Hemocentro de São Paulo, São Paulo, SP, Brazil.
authors: Alfredo
authors: A
authors: Mendrone-Junior
authors: Infectious Diseases Division (DIPA), Universidade Federal de São Paulo (UNIFESP), São Paulo, SP, Brazil; Department of Infectious Disease, Faculdade de Medicina, Universidade de São Paulo (USP), São Paulo, SP, Brazil.
authors: Ester Cerdeira
authors: EC
authors: Sabino
mesh_terms: D001938:Brazil / Q000453:epidemiology; D005838:Genotype; D016174:Hepacivirus / Q000235:genetics*; D006526:Hepatitis C / Q000453:epidemiology / Q000821:virology*; D006801:Humans; D010802:Phylogeny; D015995:Prevalence; D012367:RNA, Viral / Q000235:genetics*; D017422:Sequence Analysis, DNA
chemical_list: D012367:RNA, Viral
keywords: Growth rate; HCV; Phylogenetic analysis; Subtypes