Molecular characterization of the Hepatitis B virus genotypes in Colombia: A Bayesian inference on the genotype F

Abstract

Hepatitis B is a worldwide health problem affecting about 2 billion people and more than 350 million are chronic carriers of the virus. Nine HBV genotypes (A to I) have been described. The geographical distribution of HBV genotypes is not completely understood due to the limited number of samples from some parts of the world. One such example is Colombia, in which few studies have described the HBV genotypes. In this study, we characterized HBV genotypes in 143 HBsAg-positive volunteer blood donors from Colombia. A fragment of 1306 bp partially comprising HBsAg and the DNA polymerase coding regions (S/POL) was amplified and sequenced. Bayesian phylogenetic analyses were conducted using the Markov Chain Monte Carlo (MCMC) approach to obtain the maximum clade credibility (MCC) tree using BEAST v.1.5.3. Of all samples, 68 were positive and 52 were successfully sequenced. Genotype F was the most prevalent in this population (77%) - subgenotypes F3 (75%) and F1b (2%). Genotype G (7.7%) and subgenotype A2 (15.3%) were also found. Genotype G sequence analysis suggests distinct introductions of this genotype in the country. Furthermore, we estimated the time of the most recent common ancestor (TMRCA) for each HBV/F subgenotype and also for Colombian F3 sequences using two different datasets: (i) 77 sequences comprising 1306 bp of S/POL region and (ii) 283 sequences comprising 681 bp of S/POL region. We also used two other previously estimated evolutionary rates: (i) 2.60 × 10(-4)s/s/y and (ii) 1.5 × 10(-5)s/s/y. Here we report the HBV genotypes circulating in Colombia and estimated the TMRCA for the four different subgenotypes of genotype F.

Distribution of hepatitis B virus subgenotype F2a in São Paulo, Brazil

“…HBV genotypes F and H are considered indigenous to the American continent [15,17,18]. An HBV strain isolated from woolly monkey (a New World monkey) is closer to genotype F but with a noteworthy phylogenic distance from other strains of HBV [19].…”

“…These samples were initially subgenotyped using a system developed in the Clinical Laboratory [23] and were then selected for a longer fragment (1306 bp) amplification using other previously described primers [18]. …”

Molecular characterization of occult hepatitis B virus infection in patients with end-stage liver disease in Colombia

“…The studies of HBV genotyping in different populations revealed that in the Andean region of Colombia, genotype F, subgenotype F3, is the most prevalent, while genotype F1b is the most frequent in Amazonas state (South East) and genotype A is the most common in the Pacific region of the country; even though genotypes D, C, G and E have also been described in the Colombian populations [32, 61, 88–91]. In the present study, the genetic analysis of the viral genome revealed the predominance of genotype F (three cases); subgenotype F1 was identified in one case while F3 was identified in two cases.…”

Molecular Characterization of the Measles Virus Genotypes in JiLin Province, China

“…Each Bayesian MCMC analysis was run for 20 million states and sampled at every 10,000 states. Posterior probabilities were calculated with a burn-in of 2 million states and checked for convergence using Tracer (v1.5 [30]). …”