Hepatitis B virus subgenotype A1: evolutionary relationships between Brazilian, African and Asian isolates

Genetic diversity of hepatitis B virus quasispecies in different biological compartments reveals distinct genotypes

The selection pressure imposed by the host immune system impacts hepatitis B virus (HBV) quasispecies variability. This study evaluates HBV genetic diversity in different biological fluids. Twenty paired serum, oral fluid, and DBS samples from chronic HBV carriers were analyzed using both Sanger and next generation sequencing (NGS). The mean HBV viral load in serum was 5.19 ± 4.3 log IU/mL (median 5.29, IQR 3.01-7.93). Genotype distribution was: HBV/A1 55% (11/20), A2 15% (3/20), D3 10% (2/20), F2 15% (3/20), and F4 5% (1/20). Genotype agreement between serum and oral fluid was 100% (genetic distances 0.0-0.006), while that between serum and DBS was 80% (genetic distances 0.0-0.115). Two individuals presented discordant genotypes in serum and DBS. Minor population analysis revealed a mixed population. All samples displayed mutations in polymerase and/or surface genes. Major population analysis of the polymerase pointed to positions H122 and M129 as the most polymorphic (≥ 75% variability), followed by V163 (55%) and I253 (50%). Neither Sanger nor NGS detected any antiviral primary resistance mutations in the major populations. Minor population analysis, however, demonstrated the rtM204I resistance mutation in all individuals, ranging from 2.8 to 7.5% in serum, 2.5 to 6.3% in oral fluid, and 3.6 to 7.2% in DBS. This study demonstrated that different fluids can be used to assess HBV diversity, nonetheless, genotypic differences according to biological compartments can be observed.

Genomic Variability of Hepatitis B Virus Circulating in Brazilian Western Amazon

The emergence of clinically relevant mutations in the hepatitis B virus (HBV) genome has been a matter of great debate because of the possibility of escape from the host’s immune system, the potential to cause more severe progression of liver diseases and the emergence of treatment-resistant variants. Here we characterized the circulating variants of HBV in Rondônia State, in the north of Brazil. Serum samples of 62 chronic HBV carriers were subjected to PCR assays and clinical data were collected. Mutations and genotypes were characterized through direct sequencing. The findings show the presence of subgenotypes A1 (54.83%, 34/62), D3 (16.13%, 10/62), F2 (16.13%, 10/62), A2 (4.84%, 3/62), D2 (3.23%, 2/62), D1 (1.61%, 1/62), D4 (1.61%, 1/62) and F4 (1.61%, 1/62). Deletions in the pre-S2 region were found in 13.79% (8/58) of the samples, mutations in the S gene in 59.68% (37/62) and RT mutations in 48.39% (30/62). We found a variable genotypic distribution in different locations and important mutations related to immune escape and drug resistance in Western Amazonia, which contributed to genetic surveillance and provided important information to help control the disease.

Spacer Domain in Hepatitis B Virus Polymerase: Plugging a Hole or Performing a Role?

Hepatitis B virus (HBV) polymerase is divided into terminal protein, spacer, reverse transcriptase, and RNase domains. Spacer has previously been considered dispensable, merely acting as a tether between other domains or providing plasticity to accommodate deletions and mutations. We explore evidence for the role of spacer sequence, structure, and function in HBV evolution and lineage, consider its associations with escape from drugs, vaccines, and immune responses, and review its potential impacts on disease outcomes.

Hepatitis B in the Northwestern region of Sao Paulo State: genotypes and resistance mutations

In Brazil, few studies on the molecular aspects of hepatitis B virus (HBV) infection have been conducted in the interior regions of Sao Paulo State. This study aimed to identify HBV genotypes and evaluate strains with resistance mutations for nucleoside analogues in the Administrative Region (AR) of the municipality of Sao Jose do Rio Preto. We performed nested PCRs of 127 samples from the Health Care Services of the AR to amplify, sequence and analyze fragments of the HBV DNA, in order to identify genotypes and resistance mutations. The HBV S/Pol regions of 126 samples were successfully amplified and sequenced. Five different genotypes were found, and the main ones were A, D and F; a greater number of samples contained the subgenotypes A1 (n = 51; 40.5%), D3 (n = 36; 28.6%), A2 (n = 14; 11.1%) and F2a (n = 9; 7.1%). Resistance mutations (rtM204V/I/S) associated or not with compensatory mutations (rtL180M, rtV173L) were identified in 13.9% (5/36) of patients undergoing viral treatment and 1.1% (1/90) of naïve patients. The diversity of genotypes/subgenotypes found is probably due to the intense migration occurring in the region. These data can complement epidemiological and clinical surveillance, and can be used for a more effective management of chronic HBV patients.

Differences in prevalence of hepatitis B virus infection and genotypes between ethnic populations in Suriname, South America

Epidemiological data on hepatitis B virus (HBV) are needed to benchmark HBV elimination goals. We recently assessed prevalence of HBV infection and determinants in participants attending the Emergency Department in Paramaribo, Suriname, South America. Overall, 24.5% (95%CI = 22.7-26.4%) of participants had anti-Hepatitis B core antibodies, which was associated with older age (per year, adjusted Odds Ratio [aOR] = 1.03, 95%CI = 1.02-1.04), Afro-Surinamese (aOR = 1.84, 95%CI = 1.52-2.19) and Javanese ethnicity (aOR = 1.63, 95%CI = 1.28-2.07, compared to the grand mean). 3.2% of participants were Hepatitis B surface Ag-positive, which was also associated with older age (per year, aOR = 1.02, 95%CI = 1.00-1.04), Javanese (aOR = 4.3, 95%CI = 2.66-6.95) and Afro-Surinamese ethnicity (aOR = 2.36, 95%CI = 1.51-3.71). Sex, nosocomial or culturally-related HBV transmission risk-factors were not associated with infection. Phylogenetic analysis revealed strong ethnic clustering: Indonesian subgenotype HBV/B3 among Javanese and African subgenotypes HBV/A1, HBV/QS-A3 and HBV/E among Afro-Surinamese. Testing for HBV during adulthood should be considered for individuals living in Suriname, specifically with Javanese and Afro-Surinamese ancestry.

Temporal and geographic spreading of hepatitis B virus genotype A (HBV-A) in Brazil and the Americas

Hepatitis B virus genotype A (HBV-A) is disseminated in different countries around the world. It presents a high genetic diversity and is classified into seven subgenotypes (A1-A7). HBV-A1 and HBV-A2 are the most frequent and spread in almost all American countries. This study aimed to evaluate the molecular epidemiology of these two subgenotypes, with a special focus on the temporal and geographic spreading in the Americas and Brazil. Bayesian coalescent analyses with HBV-A1 and HBV-A2 whole-genome sequences were performed to study viral phylodynamic and phylogeography. HBV-A1 evolutionary history demonstrated that it was initially disseminated from Africa to other continents probably after the 1400s and mainly in the 17th-18th centuries. The whole viral population grew between the 1700s-1900s and then reached a stationary phase. In Brazil, HBV-A1 common ancestors dated back to the 1600s with successive introductions between the 17th-18th centuries. In contrast, HBV-A2 spread from Europe to other continents after the 1800s, with an increase in the viral population over decades. It was introduced in the 20th century in America and between the 1950s-1970s in Brazil, presenting a high increase in the viral population from the 1970s to the 1980s. The circulation continents for HBV-A1 are Africa and America, while for HBV-A2 are Europe and America. HBV-A is one of the predominant genotypes in America (including Brazil) because of the early introduction by human migration processes of the subgenotypes A1 and A2 between the 16th and 20th centuries and the continuous spreading inside the continent over time.

Precore and Basal Core Promoter Hepatitis B Virus (HBV) Variants Are Present From a Young Age and Differ Across HBV Genotypes

BACKGROUND AND AIMS

Hepatitis B virus (HBV) precore (PC) and dual basal core promoter (BCP) mutations halt and down-regulate hepatitis B e antigen (HBeAg) production respectively. PC mutation is rarely associated with HBV genotype A. We sought to examine the association of these variants with HBV genotypes, age, and HBeAg status in a racially diverse population in North America. Prospective study included 1,036 (808 adults, 228 children) participants in the Hepatitis B Research Network. PC and BCP variants were determined by Sanger sequencing, and dominant HBV species (>50%) were reported.

APPROACH AND RESULTS

Median age was 36.3 years (range, 2-80), 44.6% HBeAg(+), 74.2% Asians, 13.3% black, and 9.7% white. The dominant PC variant was present in 29.4% participants, including 20 with subgenotype A1 or A2. Seventeen of 20 participants with genotype A and PC had a compensatory C1858T mutation. In the HBeAg(+) cohort, the prevalence of PC and/or BCP variants increased from 14.4% in the first two decades to 51% after 40 years of age. Among those aged 2-18, 52% and 83% with dominant PC and BCP variants were HBeAg(+) compared to 3.8% and 29% in the >40 years age group. HBeAg clearance rates were significantly higher for those with dominant PC or BCP variants: 24.4 and 15.0 per 100 person-years compared to 6.0 in wild-type HBV (P < 0.0001).

CONCLUSIONS

PC variants can be present in HBV genotype A and are usually associated with C1858T, which preserves the pregenome encapsidation sequence. Selection of PC and BCP variants occurred at a young age, with increasing prevalence across age groups. HBeAg(+) participants with dominant PC and BCP variants progressed to the HBeAg(-) phase of chronic HBV infection significantly faster. This finding has potential clinical and therapeutic implications.

Global and regional dispersal patterns of hepatitis B virus genotype E from and in Africa: A full-genome molecular analysis

Description of the spatial characteristics of viral dispersal is important in understanding the history of infections. Nine hepatitis B virus (HBV) genotypes (A-I), and a putative 10th genotype (J), with distinct geographical distribution, are recognized. In sub-Saharan Africa (sub)-genotypes A1, D3 and E circulate, with E predominating in western Africa (WA), where HBV is hyperendemic. The low genetic diversity of genotype E (HBV/E) suggests its recent emergence. Our aim was to study the dispersal of HBV/E using full-length, non-redundant and non-recombinant sequences available in public databases. HBV/E was confirmed, and the phylogeny reconstruction performed using maximum likelihood (ML) with bootstrapping. Phylogeographic analysis was conducted by reconstruction of ancestral states using the criterion of parsimony on the estimated ML phylogeny. 46.5% of HBV/E sequences were found within monophyletic clusters. Country-wise analysis revealed the existence of 50 regional clusters. Sequences from WA were located close to the root of the tree, indicating this region as the most probable origin of the HBV/E epidemic and expanded to other geographical regions, within and outside of Africa. A localized dispersal was observed with sequences from Nigeria and Guinea as compared to other WA countries. Based on the sequences available in the databases, the phylogenetic results suggest that European strains originated primarily from WA whereas a majority of American strains originated in Western Central Africa. The differences in regional dispersal patterns of HBV/E suggest limited cross-border transmissions because of restricted population movements.

Molecular and serological characterization of occult hepatitis B among blood donors in Maputo, Mozambique

BACKGROUND

Occult hepatitis B virus (HBV) - characterized by the absence of detectable HBsAg in the presence of HBV DNA - represents a potential threat for blood safety.

OBJECTIVES

This study was conducted with the aim to investigate the serological and molecular characterization of occult HBV infection (OBI) among blood donors in Mozambique.

METHODS

1,502 blood donors were tested for HBsAg. All HBsAg-negative individuals were tested for HBV DNA. Antibodies against HBV core, surface and HBe antigen (anti-HBc, anti-HBs, HBeAg) were measured in HBV DNA positive individuals.

FINDINGS

1435 serum samples were HBsAg negative and 16 positive for HBV DNA, 14 confirmed to have OBI, corresponding to a frequency of 0.98%. Of the 14 OBI infections identified, 13/14 (92.8%) were positive for anti-HBc, 4/14 (28.5%) for anti-HBs, and no samples were reactive for HBeAg. Of the 14 OBI cases, nine samples (64.2%) were sequenced for the S/P region. Eight samples (88.9%) belonged to genotype A1 and one (11.1%) to genotype E. One escape mutation (T123A) associated with OBI and various amino acid substitutions for genotype A1 and E were observed.

MAIN CONCLUSIONS

Our results show the importance of using nucleic acid amplification test to detect occult hepatitis B infection in blood donors in Mozambique.

Hepatitis B: changes in epidemiological features of Afro-descendant communities in Central Brazil

Hepatitis B virus (HBV) infection is still a concern in vulnerable populations. In a study performed by our team in 1999–2003 in two Afro-Brazilian communities, Furnas dos Dionísios (FD) and São Benedito (SB), high prevalence rates of HBV exposure (42.7% and 16.0%, respectively), high susceptibility to HBV (55.3% and 63.0%) and low HBV vaccination like profile rates (2.0% and 21.0%) were observed. In 2015–2016, we reassessed HBV epidemiological and molecular features in these two communities to verify the impact of health actions adopted in the last years. The prevalence rate of HBV exposure among the enrolled 331 subjects was 35.3% in FD and 21.8% in SB. HBV chronic infection (5.8% in FD, 4.9% in SB) remained high. The rate of HBV vaccination like profile increased from 10.7% to 43.5% (2.0% to 45.9% in FD, 21.0% to 39.5% in SB) while susceptible subjects declined from 58.9% to 26.3% (55.3% to 18.8% in FD, 63.0% to 38.7% in SB). Among 18 HBsAg positive samples, 13 were successfully sequenced (pre-S/S region). Phylogenetic analyses showed that all isolates belong to HBV subgenotype A1, clustering within the Asian-American clade. Despite the maintenance of high prevalence rate of HBV exposure over these 13 years of surveillance, significant improvements were observed, reinforcing the importance of facilitated HBV vaccination to difficult-to-access population to close gaps in prevention.

Genetic Diversity of the Hepatitis B Virus Subgenotypes in Brazil

Hepatitis B virus (HBV) subgenotypes may be related to clinical outcomes and response to antiviral therapy. Most Brazilian studies on HBV subgenotypes are restricted to some regions and to specific population groups. Here, we provide an insight about genetic diversity of HBV subgenotypes in 321 serum samples from all five geographical regions, providing a representative overview of their circulation among chronic carriers. Overall, HBV/A1 was the most prevalent subgenotype, being found as the major one in all regions except in South Brazil. Among HBV/D samples, subgenotype D3 was the most prevalent, found in 51.5%, followed by D2 (27.3%) and D4 (21.2%). D2 and D3 were the most prevalent subgenotypes in South region, with high similarity with European strains. D4 was found in North and Northeast region and clustered with strains from Cape Verde and India. For HBV/F, the most frequent subgenotype was F2 (84.1%), followed by F4 (10.1%) and F1 (5.8%), closely related with strains from Venezuela, Argentina and Chile, respectively. Phylogeographic analyses were performed using an HBV full-length genome obtained from samples infected with genotypes rarely found in Brazil (B, C, and E). According to Bayesian inference, HBV/B2 and HBV/C2 were probably introduced in Brazil through China, and HBV/E from Guinea, all of them mostly linked to recent events of human migration. In conclusion, this study provided a comprehensive overview of the current circulation of HBV subgenotypes in Brazil. Our findings might contribute to a better understand of the dynamics of viral variants, to establish a permanent molecular surveillance on the introduction and dispersion patterns of new strains and, thus, to support public policies to control HBV dissemination in Brazil.

Molecular epidemiology of hepatitis B virus in Paraguay

Hepatitis B virus (HBV) infection is a leading cause of severe chronic liver disease worldwide. The HBV epidemiology in Latin American countries is complex and the data is still scanty and fragmentary. The aim of this study was to investigate the distribution of HBV genotypes in Paraguay and to estimate the viral population dynamic and spread pattern of the main phylogenetic group. To this end, partial and complete genome sequences were obtained from 60 blood donor candidates and analysed by phylogenetic and Bayesian phylodynamic approaches. The phylogenetic analysis based on sequences of partial Polymerase/Pre-S1 overlapping region showed a predominance of the Native American subgenotype F4 (81.7%), the presence of the European subgenotypes A2 (1.7%) and D3 (8.3%), the African subgenotype A1 (3, 5%) and the Asian subgenotypes B2 (1.7%) and C2 (1.7%). The distribution of HBV genotypes was in accordance with the ethnic composition of the population. The phylogeographic analysis of subgenotype F4 complete genomes suggests that this lineage emerged and spread in the last 300 years. Paraguay was the most probable location of the common ancestor. The lineage diverged into two main clades and spread to neighbor regions, mainly Bolivia and Northwest Argentina, and Buenos Aires. The phylogeny showed a scanty geographical structure and a complex migratory pattern. In conclusion, the HBV genotypes circulating in Paraguay reflect the ethnic origin of the population. The distribution of genotypes and the phylogeographic reconstruction showed the impact of both global and local migrations in shaping the HBV molecular epidemiology in the region.

High Prevalence of Hepatitis B Subgenotype D4 in Northeast Brazil: an Ancient Relic from African Continent?

INTRODUCTION

Hepatitis B virus (HBV) infection leads to a chronic liver disease that is distributed worldwide. The characterization of HBV into genotypes/subgenotypes is not only a mere procedure for distinguishing different HBV strains around the world because determining their geographic distribution is crucial to understanding their spread across the world.

MATERIAL AND METHODS

We characterized different HBV genotypes and subgenotypes in five municipalities located in northeastern Maranhão, in the Brazilian north Atlantic coast. 92 HBsAg-positive individuals were submitted to PCR (polymerase chain reaction). Fifty samples were sequenced using automated Sanger sequencing and classified by phylogenetic methods.

RESULTS

Subgenotypes D4 and A1 were found in 42 (84%) and eight (16%) samples, respectively. To our knowledge, this is the first study to describe a high frequency of subgenotype D4 in any population. Subgenotype A1 is frequently found across Brazil, but D4 has been rarely detected and only in a few Brazilian states. This study shows the characterization of HBV subgenotypes from a population based study in the state of Maranhão, particularly in populations that do not have frequent contact with populations from other regions of the world.

CONCLUSION

Our findings showed a HBV subgenotype profile that probably reflect the viruses that were brought with the slave trade from Africa to Maranhão. This study also reinforces the need to evaluate the status of HBV dispersion not only in large urban centers, but also in the hinterland, to enable the implementation of effective control and treatment measures.

Phylogenetic analysis and genotype distribution of Hepatitis B Virus (HBV) in Roraima, Brazil

Hepatitis B virus (HBV) infection is a serious global health problem. HBV has a high viral genetic diversity, with 10 genotypes recognized. In Brazil, the Roraima State is the third in the Northern region regarding the number of hepatitis B cases. On the other hand, few data on HBV genotyping and phylogenetic analysis are available. The purpose of this study is to characterize the HBV genotypes circulating in Roraima State. Of the 113 chronic hepatitis B patients enrolled in this study, 40 were HBV-DNA positive. A fragment of 280 bp (S gene) was amplified by PCR and submitted to nucleotide sequencing. A dataset containing the viral sequences obtained in this study, plus 130 obtained from GenBank was used for genotyping by phylogenetic analysis. The HBV subgenotype distribution found was A1 (62.5%), A2 (7.5%), D2, D3, D4 (2.5%), F2a (12.5%), and F3 (10%). We characterized the genotypes and subgenotypes of HBV circulating among patients in the State of Roraima. In addition, our study shows for the first time the HBV/F3 genotype circulating in Brazil. In conclusion, our findings showed a high diversity of HBV genotypes in Roraima, which is also found in other Brazilian geographical regions.

Relative Abundance of Integrant-Derived Viral RNAs in Infected Tissues Harvested from Chronic Hepatitis B Virus Carriers

Five matching sets of nonmalignant liver tissues and hepatocellular carcinoma (HCC) samples from individuals chronically infected with hepatitis B virus (HBV) were examined. The HBV genomic sequences were determined by using overlapping PCR amplicons covering the entire viral genome. Four pairs of tissues were infected with HBV genotype C, while one pair was infected with HBV genotype B. HBV replication markers were found in all tissues. In the majority of HCC samples, the levels of pregenomic/precore RNA (pgRNA) and covalently closed circular DNA (cccDNA) were lower than those in liver tissue counterparts. Regardless of the presence of HBV replication markers, (i) integrant-derived HBV RNAs (id-RNAs) were found in all tissues by reverse transcription-PCR (RT-PCR) analysis and were considerably abundant or predominant in 6/10 tissue samples (2 liver and 4 HCC samples), (ii) RNAs that were polyadenylated using the cryptic HBV polyadenylation signal and therefore could be produced by HBV replication or derived from integrated HBV DNA were found in 5/10 samples (3 liver and 2 HCC samples) and were considerably abundant species in 3/10 tissues (2 livers and 1 HCC), and (iii) cccDNA-transcribed RNAs polyadenylated near position 1931 were not abundant in 7/10 tissues (2 liver and 5 HCC samples) and were predominant in only two liver samples. Subsequent RNA sequencing analysis of selected liver/HCC samples also showed relative abundance of id-RNAs in most of the examined tissues. Our findings suggesting that id-RNAs could represent a significant source of HBV envelope proteins, which is independent of viral replication, are discussed in the context of the possible contribution of id-RNAs to the HBV life cycle.IMPORTANCE The relative abundance of integrant-derived HBV RNAs (id-RNAs) in chronically infected tissues suggest that id-RNAs coding for the envelope proteins may facilitate the production of a considerable fraction of surface antigens (HBsAg) in infected cells bearing HBV integrants. If the same cells support HBV replication, then a significant fraction of assembled HBV virions could bear id-RNA-derived HBsAg as a major component of their envelopes. Therefore, the infectivity of these HBV virions and their ability to facilitate virus cell-to-cell spread could be determined mainly by the properties of id-RNA-derived envelope proteins and not by the properties of replication-derived HBsAg. These interpretations suggest that id-RNAs may play a role in the maintenance of chronic HBV infection and therefore contribute to the HBV life cycle. Furthermore, the production of HBsAg from id-RNAs independently of viral replication may explain at least in part why treatment with interferon or nucleos(t)ides in most cases fails to achieve a loss of serum HBsAg.

Hepatitis B virus genotypes A1, A2 and E in Cape Verde: Unequal distribution through the islands and association with human flows

Hepatitis B virus (HBV) diversity has not been previously studied in Cape Verde. The archipelago was discovered in 1460 by Portuguese explorers, who brought African slaves to colonise the islands. In this study, we investigated the HBV characteristics from 183 HBsAg-positive Cape Verdean individuals. Phylogenetic analysis of the pre-S/S region and the full-length genomes revealed 54 isolates with HBV/A1 (57%), 21 with HBV/A2 (22%), 19 with HBV/E (20%), and one with HBV/D (1%). HBV genotypes and subgenotypes were unequally distributed through the islands. In São Vicente, the main northern island, most isolates (84%) belonged to the African-originated HBV/A1, with the remaining isolates belonging to HBV/A2, which is prevalent in Europe. Interestingly, the HBV/A1 isolates from São Vicente were closely related to Brazilian sequences into the Asian-American clade, which suggests the dissemination of common African ancestors through slave trade. In contrast, in Santiago and nearby southern islands, where a recent influx from different populations circulates, a higher diversity of HBV was observed: HBV/A1 (40%); HBV/E (32%); HBV/A2 (28%); and HBV/D (1%). HBV/E is a recent genotype disseminated in Africa that was absent in the era of the slave trade. African and European human flows at different times of the history may explain the HBV diversity in Cape Verde. The possible origin and specifics of each HBV genotype circulating in Cape Verde are discussed.

Epidemiological and molecular analysis of hepatitis B virus infection in manicurists in Central Brazil

The aim of this study was to investigate the serological and molecular prevalence of hepatitis B virus (HBV) infection in 514 manicurists/pedicurists and identify the risk factors related with this infection. Samples were tested for HBV serological markers, hepatitis C virus (HCV), and human immunodeficiency virus (HIV) by enzyme-linked immunosorbent assay (ELISA). Anti-HBc-positive samples were tested to investigate occult hepatitis B by PCR. HBsAg-positive samples were genotyped and the viral loads of HBV-DNA positive samples were quantified. The overall HBV prevalence was 5.6% (29/514) and of HBsAg was 0.4% (2/514). One case of occult hepatitis B was found. The genotypes A1 and F2 were identified in two HBsAg-positive samples. Low level of education, not being born in the State of Mato Grosso do Sul and working in the central region of the city were associated with the HBV infection. No single manicurist/pedicurist was infected by HCV or HIV. These findings suggest that despite the exposure to blood contact, this occupation was not associated to an increased risk of acquiring HBV, HCV, and HIV infections.

Distribution of HBV subgenotypes in Ribeirão Preto, Southeastern Brazil: a region with history of intense Italian immigration

Hepatitis B virus (HBV) is distributed worldwide, with geographical variations regarding prevalence of the different genotypes. The aim of this study was to determine the HBV genotypes and subgenotypes circulating in Southeast Brazil and compare the genetic sequences found with HBV sequences previously described in the world. Sequences from 166 chronic HBV carriers were analyzed using the fragment constituted by 1306 base pairs comprising surface and polymerase regions of the HBV genome. The sequences obtained were submitted to phylogenetic analysis. HBV subgenotypes A1, A2, D1-D4, F2a, and F4 were found. HBV genotype D was the most frequent, found in 99 patients (58.4%). Within this group, subgenotype D3 was the most prevalent, in 73 patients (42.9%). HBV genotype A was identified in 58 (36%) patients, subgenotype A1, in 48 (29.8%) subjects. Genotype F was identified in 9 (5.4%). According to the phylogenetic analysis, the sequences found were grouped with sequences from Europe, Asia and Middle East (subgenotypes D1, D2, D3) and sequences from Latin America and Africa (subgenotype A1). HBV D3 grouped in different clusters inside D3 clade, several of them with sequences isolated in Italy. We also identified eight families whose relatives were infected with the same HBV subgenotype, most with high similarity between sequences. In conclusion, the distribution of the HBV sequences obtained interweaved with sequences from other continents, corresponding to regions from where many immigrants came to this region, in accordance to the hypothesis that the HBV detected over there were brought during the colonization times.

Molecular epidemiology of hepatitis B virus infection in Tanzania

Despite the significant public health problems associated with hepatitis B virus (HBV) in sub-Saharan Africa, many countries in this region do not have systematic HBV surveillance or genetic information on HBV circulating locally. Here, we report on the genetic characterization of 772 HBV strains from Tanzania. Phylogenetic analysis of the S-gene sequences showed prevalence of HBV genotype A (HBV/A, n=671, 86.9 %), followed by genotypes D (HBV/D, n=95, 12.3 %) and E (HBV/E, n=6, 0.8 %). All HBV/A sequences were further classified into subtype A1, while the HBV/D sequences were assigned to a new cluster. Among the Tanzanian sequences, 84 % of HBV/A1 and 94 % of HBV/D were unique. The Tanzanian and global HBV/A1 sequences were compared and were completely intermixed in the phylogenetic tree, with the Tanzanian sequences frequently generating long terminal branches, indicating a long history of HBV/A1 infections in the country. The time to the most recent common ancestor was estimated to be 188 years ago [95 % highest posterior density (HPD): 132 to 265 years] for HBV/A1 and 127 years ago (95 % HPD: 79 to 192 years) for HBV/D. The Bayesian skyline plot showed that the number of transmissions 'exploded' exponentially between 1960-1970 for HBV/A1 and 1970-1990 for HBV/D, with the effective population of HBV/A1 having expanded twice as much as that of HBV/D. The data suggest that Tanzania is at least a part of the geographic origin of the HBV/A1 subtype. A recent increase in the transmission rate and significant HBV genetic diversity should be taken into consideration when devising public health interventions to control HBV infections in Tanzania.

A novel hepatitis B virus subgenotype D10 circulating in Ethiopia

Hepatitis B virus (HBV) is genetically highly divergent and classified in ten genotypes and forty subgenotypes in distinct ethno-geographic populations worldwide. Ethiopia is a country with high HBV prevalence; however, little is known about the genetic variability of HBV strains that circulate. Here, we characterize the complete genome of 29 HBV strains originating from five Ethiopian regions, by 454 deep sequencing and Sanger sequencing. Phylogenetically, ten strains were classified as genotype A1 and nineteen as genotype D. Fifteen genotype D strains, provisionally named subgenotype D10, showed a novel distinct cluster supported by high bootstrap value and >4% nucleotide divergence from other known subgenotypes. In addition, the novel D10 strains harboured nine unique amino acid signatures in the surface, polymerase and X genes. Seventy-two per cent of the genotype D strains had the precore premature stop codon G1896A. In addition, 63% genotype A and 33% genotype D strains had the basal core promoter mutations, A1762T/G1764A. Furthermore, four pre-S deletion variants and two recombinants were identified in this study. In conclusion, we identified a novel HBV subgenotype D10 circulating in Ethiopia, underlining the high genetic variability of HBV strains in Africa.

Identification of a new hepatitis B virus recombinant D2/D3 in the city of São Paulo, Brazil

Two hundred forty million people are chronically infected with hepatitis B virus (HBV) worldwide. The rise of globalization has facilitated the emergence of novel HBV recombinants and genotypes. We evaluated HBV genotypes and recombinants, mutations associated with resistance to antivirals (AVs), progression of hepatic illness, and inefficient hepatitis B vaccination responses in chronically infected individuals in the city of São Paulo, Brazil. Forty-five full-length and 24 partial-length sequences were obtained. The genotype distribution was as follows: A (66.7%), D (15.9%), F (11.6%) and C (4.3%). We describe a new recombinant (D2/D3), confirmed through next-generation sequencing (NGS) and reconstruction of the quasispecies sequences in silico. Primary resistance and major vaccine escape mutations were not found. We did, however, find mutations in the S region that might may be related to HBV antigenicity changes, as well as Pre-S deletions. The precore/core mutations A1762T + G1764A (40.9%) were found mostly in genotypes A and D, and G1896A (29.55%) was more frequent in genotype D than in genotype A. The genotypic distribution reflects the history of Brazilian immigration. This is the first description of recombination between genotypes D2 and D3 in Brazil. It is also the first confirmation through NGS and reconstruction of the quasispecies in silico. However, little is known about the response to treatment of recombinants. This demonstrates the need for molecular epidemiology studies involving the analysis of full-length HBV sequences.

Is Hepatitis Delta infections important in Brazil?

Background

The Hepatitis Delta Virus (HDV) can increase the incidence of fulminant hepatitis. For this infection occurs, the host must also be infected with Hepatitis B Virus. Previous studies demonstrated the endemicity and near exclusivity of this infection in the Amazon region, and as a consequence of the difficulty in accessing this area we used dried blood spots (DBS) in sample collection. The aims of this study were to investigate the presence of recombination, to analyze the epidemiology, ancestry and evolutionary pressures on HDV in Brazil.

Methods

Blood samples from 50 individuals were collected using dried-blood spots (DBS 903, Whatman), and sent via regular mail to Retrovirology Laboratory from Federal University of São Paulo, where the samples were processed. In the analysis the following software were used: PhyML, RDP, BEAST, jModelTest and CODEML.

Results

Our results confirm the prevalence of HDV-3 in the Amazon region of Brazil, with the absence of inter-genotypic recombination. It was identified a positive selection in probable epitopes of HDV on B lymphocytes that might indicate that the virus is changing to escape the humoral response of the host. The analysis of the time of the most common ancestor demonstrated the exponential growth of this virus in late 1970s that lasted until 1995, after which it remained constant. It was also observed a probable founder effect in two cities, which demonstrate the need to focus on prevention methods against HBV/HDV infection.

Conclusion

We confirmed the prevalence of HDV-3 in the Amazon region of Brazil, without inter-genotypic recombination. The analysis of the time of the most common ancestor showed that this infection remain constant in the studied area. Taking into account the probable founder effect established in the cities of Rio Branco and Porto Velho, a focus on preventive methods is recommended against these infections.

Prevalence, Risk Behaviors, and Virological Characteristics of Hepatitis B Virus Infection in a Group of Men Who Have Sex with Men in Brazil: Results from a Respondent-Driven Sampling Survey

Background

Men who have sex with men (MSM) are at increased risk of exposure to hepatitis B virus (HBV) compared with the general population. This study aims to assess the epidemiological and virological characteristics of HBV infection in a sample of MSM in Brazil, where data are scarce.

Methods

A cross-sectional study was conducted among MSM in the City of Goiânia, Central Brazil, from March to November 2014, using Respondent-Driven Sampling (RDS). After signing the consent form, participants were interviewed and a blood sample collected. All samples were tested for HBV serological markers and HBV DNA. HBV nucleotide sequence analysis was also performed.

Results

A total of 522 MSM were recruited in the study. The prevalence of HBV infection (current or past [presence of anti-HBc marker]) was 15.4% (95% CI: 8.7–25.8) and the rate of HBsAg carriers was 0.6% (95% CI: 0.2–1.6). About 40% (95% CI: 32.3–48.8) of the participants had serological evidence of previous HBV vaccination (reactive for isolated anti-HBs). In addition, 44.3% (95% CI: 36.1–52.9) were seronegative for all HBV markers. Age over 25 years old, receptive anal intercourse, previous sex with women, and history of sexually transmitted infections (STIs) were factors associated with HBV infection. HBV DNA was detected only in HBsAg-positive individuals. HBV isolates were classified into genotype A (subgenotypes A1 and A2), and some mutations were identified throughout the genome. Therefore, occult HBV infection was not observed in the study population.

Conclusions

Public health strategies should be improved for the MSM population in order to prevent HBV and other STIs, as well as to provide appropriate management of patients with active infections.

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

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.

Hepatitis B Virus Genotype D Isolates Circulating in Chapecó, Southern Brazil, Originate from Italy

Hepatitis B virus genotype A1 (HBV/A1), of African origin, is the most prevalent genotype in Brazil, while HBV/F predominates in the other South American countries. However, HBV/D is the most common in the three states of southern Brazil, where ‘islands’ of elevated prevalence, as Chapecó and other cities, have been described. In this study, 202 HBV chronic carriers attending in 2013 the viral hepatitis ambulatory of Chapecó, were investigated. In comparison with previous studies performed in the same ambulatory, a rapid aging of the HBV infected population was observed (mean age of the newly diagnosed patients increasing from 29.9 ± 10.3 years in 1996 to 44.4 ± 13.3 years in 2013), probably due to a singular vaccination schedule at Chapecó that included not only children but also adolescents. Phylogenetic and BLAST analyses (S region) classified 91 HBV isolates into genotypes A (n = 3) and D (n = 88). The majority of HBV/D isolates were closely related to D3 sequences. To understand the reasons for the absence or near absence of genotypes A and F, and how HBV/D was introduced in the south of Brazil, HBV/D infected patients were inquired about their genealogical and geographical origins. Forty-three (52%) patients have their four grandparents of Italian origin, vs. seven (8%) who have their four grandparents of Brazilian origin. At all, 65 out of 83 (78%) patients had at least one grandparent originating from Italy. Taking into consideration the fact that Italy is one of the few countries where subgenotype D3 is predominant, the results strongly suggested that HBV/D was introduced in Brazil through Italian immigration which culminated between 1870 and 1920.

HBV genotypic variability in Cuba

The genetic diversity of HBV in human population is often a reflection of its genetic admixture. The aim of this study was to explore the genotypic diversity of HBV in Cuba. The S genomic region of Cuban HBV isolates was sequenced and for selected isolates the complete genome or precore-core sequence was analyzed. The most frequent genotype was A (167/250, 67%), mainly A2 (149, 60%) but also A1 and one A4. A total of 77 isolates were classified as genotype D (31%), with co-circulation of several subgenotypes (56 D4, 2 D1, 5 D2, 7 D3/6 and 7 D7). Three isolates belonged to genotype E, two to H and one to B3. Complete genome sequence analysis of selected isolates confirmed the phylogenetic analysis performed with the S region. Mutations or polymorphisms in precore region were more common among genotype D compared to genotype A isolates. The HBV genotypic distribution in this Caribbean island correlates with the Y lineage genetic background of the population, where a European and African origin prevails. HBV genotypes E, B3 and H isolates might represent more recent introductions.