High prevalence of HBV/A1 subgenotype in native south Americans may be explained by recent economic developments in the Amazon

Highlights

• HBV screening in 1070 Native Americans resulted in a high prevalence (10.2%).

• The most frequent HBV genotype was A1 (94.3%), followed by F2a and F4 (2.8% each).

• Expansion of HBV/A1 in the Amazon occurred between 1945–1965.

• Developmental policies may facilitate viral dispersal into isolated populations.

Abstract

Native American populations present the highest prevalence of Hepatitis B Virus (HBV) infection in the Americas, which may be associated to severe disease outcomes. Ten HBV genotypes (A–J) have been described, displaying a remarkable geographic structure, which most likely reflects historic patterns of human migrations. In this study, we characterize the HBV strains circulating in a historical sample of Native South Americans to characterize the historical viral dynamics in this population. The sample consisted of 1070 individuals belonging to 38 populations collected between 1965 and 1997. Presence of HBV DNA was checked by quantitative real-time PCR, and determination of HBV genotypes and subgenotypes was performed through sequencing and phylogenetic analysis of a fragment including part of HBsAg and Pol coding regions (S/Pol). A Bayesian Skyline Plot analysis was performed to compare the viral population dynamics of HBV/A1 strains found in Native Americans and in the general Brazilian population. A total of 109 individuals were positive for HBV DNA (~ 10%), and 70 samples were successfully sequenced and genotyped. Subgenotype A1 (HBV/A1), related to African populations and the African slave trade, was the most prevalent (66–94%). The Skyline Plot analysis showed a marked population expansion of HBV/A1 in Native Americans occurring more recently (1945–1965) than in the general Brazilian population. Our results suggest that historic processes that contributed to formation of HBV/A1 circulating in Native American are related with more recent migratory waves towards the Amazon basin, which generated a different viral dynamics in this region.

Introduction

Despite the availability of a vaccine, which produced a significant reduction in the overall rates of infection (Zanetti et al., 2008), there are currently 240 million people chronically infected with HBV, and more than 780,000 people die every year due to complications of the disease, maintaining HBV as a serious problem of public health (WHO, 2014). This pathogen, which belongs to the Hepadnaviridae family, has marked tropism for hepatocytes (Ganem and Prince, 2004), which explains the consequences of HBV infection that ranges from asymptomatic infection to chronic hepatitis and can progress to complications such as liver cirrhosis and hepatocellular carcinoma (HCC) (Dandri and Locarnini, 2012). The transmission can occur vertically – from mother to child – and horizontally – by parenteral or sexual way, due to the high concentrations that HBV reaches in body fluids (Alvarado-Mora and Pinho, 2013a).

The encapsulated viral genome presents a partially double stranded circular DNA with approximately 3200 bp that displays four overlapping open reading frames (Wei et al., 2010). The comparison between sequences and phylogenetic groups led to the classification of 10 different lineages of HBV (A to J), named “genotypes”, which show more than 7.5% of nucleotide divergence at the whole genome level (Kramvis et al., 2008). Some of these genotypes are further divided into “subgenotypes”, according to inter-genotypic divergences between 4% and 7.5% (Alvarado-Mora and Pinho, 2013b). HBV genotypes and subgenotypes present a strong geographic structure, where specific genotypes are associated with specific regions or ethnic profiles, reflecting historical aspects and migration patterns of human populations (Andernach, I.E., et al., 2009, Campos, R.H., et al., 2005, Paraskevis, D., et al., 2013).

In South America, the most endemic area comprises the Amazon basin, and the highest prevalence rates have been observed in Native American populations (Braga, W.S., et al., 2001, Devesa, M. and Pujol, F.H., 2007, Duarte, M.C., et al., 2010, Parana, R. and Almeida, D., 2005, Tanaka, J., 2000). The isolated location, hygiene and sanitation conditions, and some cultural practices are part of the factors that can contribute to this figure (Coimbra Júnior et al., 1996). In addition, these populations have been associated with high rates of superinfection with hepatitis delta virus, as well as fulminant hepatitis occurring as a consequence (Braga, W. S., 2004, Casey, J.L., et al., 1996, Gomes-Gouvêa, M.S., et al., 2009, Hadler, S.C., et al., 1984, Manock, S.R., et al., 2000, Quintero, A., et al., 2001), suggesting a possible relationship between the genetic background present in these populations, the combination of viral genotypes and the severity of disease (Casey, J.L., et al., 1996, Devesa, M. and Pujol, F.H., 2007, Gomes-Gouvêa, M.S., et al., 2009, Nakano, T., et al., 2001). Typically, this region has been reported as having a high prevalence of genotype HBV/F, considered as autochthonous to South America and related to Native American populations (Alvarado-Mora, M.V. and Pinho, J.R.R., 2013b, Devesa, M. and Pujol, F.H., 2007, Mello, F.C., et al., 2007, Nakano, T., et al., 2001). Nonetheless, the complex way of Latin America colonization has altered these patterns, creating a mosaic of HBV genotypes, with an influx of European, African, and Asian HBV genotypes due to population migration since the colonial epoch (Alvarado-Mora, M.V. and Pinho, J.R.R., 2013b, Barros, L.M., et al., 2014, Bertolini, D.A., et al., 2012, Mello, F.C., et al., 2007, Moraes, M.T.B., et al., 1999). One example is the A1 subgenotype (HBV/A1), which has an African background, but is common in many Brazilian regions due to the African slave trade during the colonial period (Alvarado-Mora, M.V., et al., 2011, Araujo, N.M., et al., 2004, Barros, L.M., et al., 2014, Kramvis, A. and Paraskevis, D., 2013, Matos, M.A., et al., 2009, Motta-Castro, A.R., et al., 2008, Moura, I.F., et al., 2013, Oliveira, C.M., et al., 2008, Santos, A.O., et al., 2010, Zehender, G., et al., 2015), most probably during the 19th century (Lago et al., 2014).

In this context, the association of HBV genotypes with different disease outcomes and response to antiviral therapy (Kim, B.K., et al., 2011, Liu, C.J. and Kao, J.H., 2013, Tanwar, S. and Dusheiko, G., 2012) makes important the characterization of the HBV lineages in a given region or population. The aim of this study is to perform a molecular characterization of HBV circulating in a large historical sample of Native South Americans to provide more information about the epidemiologic situation of HBV and to better understand the historic processes that contributed to the viral dynamics in these populations.