African, Amerindian and European hepatitis B virus strains circulate on the Caribbean Island of Martinique

A Glimpse into the Past: What Ancient Viral Genomes Reveal About Human History

Humans have battled viruses for millennia. However, directly linking the symptomatology of disease outbreaks to specific viral pathogens was not possible until the twentieth century. With the advent of the genomic era and the development of advanced protocols for isolation, sequencing, and analysis of ancient nucleic acids from diverse human remains, the identification and characterization of ancient viruses became feasible. Recent studies have provided invaluable information about past epidemics and made it possible to examine assumptions and inferences on the origin and evolution of certain viral families. In parallel, the study of ancient viruses also uncovered their importance in the evolution of the human lineage and their key roles in shaping major events in human history. In this review, we describe the strategies used for the study of ancient viruses, along with their limitations, and provide a detailed account of what past viral infections have revealed about human history.

Tracing the evolutionary history of hepatitis B virus genotype H endemic to Mexico

Hepatitis B virus (HBV) spreads efficiently among all human populations worldwide. HBV is classified into ten genotypes (A to J) with their geographic distribution and clinical features. In Mexico, HBV genotype H is the leading cause of hepatitis B and has been detected in indigenous populations, suggesting that HBV genotype H may be native to Mexico. However, little is known about the evolutionary history of HBV genotype H. Thus, we aimed to determine the age of HBV genotype H in Mexico using molecular dating techniques. Ninety-two HBV sequences of the reverse transcriptase (RT) domain of the polymerase gene (~1,251 bp) were analyzed; 48 were genotype H, 43 were genotype F, and the oldest HBV sequence from America was included as the root. All sequences were aligned, and the most recent common ancestor (TMRCA) time was calculated using the Bayesian Skyline Evolutionary Analysis. Our results estimate a TMRCA for the genotype H in Mexico of 2070.9 (667.5-4489.2) years before the present (YBP). We identified four major diversification events in genotype H, named H1, H2, H3, and H4. The TMRCA of H1 was 1213.0 (253.3-2638.3) YBP, followed by H2 1175.5 (557.5-2424.2) YBP, H3 949.6 (279.3-2105.0) YBP, and H4 1230.5 (336.3, 2756.7) YBP. We estimated that genotype H diverged from its sister genotype F around 8140.8 (1867.5-18012.8) YBP. In conclusion, this study found that genotype H in Mexico has an estimated age of 2070.9 (667.5-4489.2) YBP and has experienced at least four major diversification events since then.

The unexpected high prevalence of HBV subgenotype D4 in patients with chronic hepatitis B in Galicia, a northwestern Spanish region, reflects strong links with Latin America

BACKGROUND

Hepatitis B virus (HBV) comprises 9 genotypes and multiple subgenotypes that depict differences in geographic distribution, clinical outcome and response to antiviral therapy. However, the molecular epidemiology of HBV geno/subgenotypes is globally scarce. In Spain, HBV genotype D seems to be more prevalent in the northwestern regions compared to the rest of the country for unclear reasons.

METHODS

HBV genotyping was performed using geno2pheno on a S gene fragment amplified from plasma collected from all chronic hepatitis B individuals attended at one reference hospital in Santiago de Compostela, the Galicia's capital town. Phylogenetic and phylogeographic analyses using a fragment of 345 bp were performed in all viremic specimens. To avoid misleading allocation as consequence of short fragment analysis, several bioinformatic controls were used.

RESULTS

A total of 320 individuals with persistent serum HBsAg+ and detectable HBV-DNA were seen between 2000 and 2016 (male 68.4%; median age, 52 years-old; native Spaniards 83.8%). HBV genotype distribution was as follows: A 15.3%; B 1.6%; C 2.5%; D 71.6%; E 3.1%; F 2.2%; G 3.1%; and H 0.6%. HBV genotype D was mostly represented by D4 and D2 subgenotypes (33.4% and 15% of total, respectively). Compared to chronic hepatitis B patients with genotypes B, C, E and G, HBV-D4 carriers tended to be older (54.2% had >50 years-old) and HBeAg-negative (85%). Moreover, 43% were female, 4.7% had cirrhosis, 10.2% hepatitis C and 6.4% HIV coinfection. Phylogenetic analyses could be performed on 82 HBV-D4 specimens; and 79 were confirmed as HBV-D4 using PhyML. Phylogeography using FasTree suggested at least two distinct introductions of HBV-D4 in Galicia, one from the Caribbean and South America, and another from India.

CONCLUSIONS

HBV subgenotype D4 is the most prevalent HBV variant in chronic hepatitis B patients living in the northwest of Spain, representing 33.4% (107/320) of all chronic hepatitis B infections. This rate of HBV-D4 is among the highest reported worldwide. Epidemiological and phylogenetic analyses suggest a strong association with historical migrant exchanges with Latin America, and especially with the Caribbean basin.

[Prevalence of viral hepatitis B markers among blood donors in the Republic of Guinea]

INTRODUCTION

The problem of transfusion safety in relation to parenteral viral hepatitis still remains relevant. Viral hepatitis B (HB) remains the most common viral infection transmitted through transfusion procedures. One of the natural phases of chronic hepatitis B (CHB) is occult hepatitis B infection (OBI), characterized by an undetectable HBsAg (regardless of the other serological markers content) in the presence of hepatitis B virus (HBV) DNA in the liver tissue and an extremely low, up to undetectable, level of viral load in the blood. In the Republic of Guinea, as in most countries on the continent, the prevention of HBV transmission through transfusion is still based on HBsAg serological testing of donors only. In this connection, OBI remains as a potential threat to blood transfusion safety. Detection of HBV DNA is a reliable preventive measure against transmission of the virus from donors with HBsAg-negative HBV infection, especially in highly endemic regions. In this regard, the study was conducted to substantiate recommendations for improving blood safety against the background of significant HBV prevalence in the Republic of Guinea.The aim of the work was the evaluation of serological and molecular markers of HBV infection in blood donors in the Republic of Guinea.

MATERIAL AND METHODS

We examined 250 blood samples obtained from donors living in Conakry, Republic of Guinea. Samples were tested for the presence of serological (surface antigen, HBsAg; antibodies (ABs) to surface (anti-HBs IgG) and core (anti-HBc IgG) antigens) and molecular (DNA) markers of HBV infection.

RESULTS AND DISCUSSION

The overall detection rate of hepatitis B markers was 83.2%; HBsAg was detected in 16.4% of all individuals. The high incidence of HBsAg in men (19.55%) compared to women (8.45%) was shown, the relative risk of HBV infection with the formation of HBsAg-positive chronic hepatitis B in males was also significantly higher. The prevalence of the HBV DNA in the study group was 30.4%, the OBI cases accounted for 15.6%. The prevalence of this form of the disease was shown in donors aged 30-49 years (24.78%), in the group of people younger than 30 years, the incidence was lower (8.73%), and at the age of over 50 years, OBI was not detected. Based on the phylogenetic analysis of 76 virus isolates, it was shown that genotype E prevails in the examined group (85.53%).Cases of pathogen DNA detection occurred in HBsAg-negative blood donors in the presence of anti-HBs IgG (n = 4), as well as in the simultaneous presence of ABs anti-HBs IgG and anti-HBc IgG (n = 7). The viral load exceeded 200 IU/ml in OBI samples. Escape mutations were detected by sequencing in each OBI sample, contributing to the virus escaping from diagnostic based on screening for HBsAg.

CONCLUSION

Assessment of the prevalence viral hepatitis B markers in blood donors, determination of genotypes and clinically significant mutations of virus variants are necessary to ensure safe medical manipulations, control and prevention of the spread of this infectious agent.

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.

Ancient viral genomes reveal introduction of human pathogenic viruses into Mexico during the transatlantic slave trade

After the European colonization of the Americas, there was a dramatic population collapse of the Indigenous inhabitants caused in part by the introduction of new pathogens. Although there is much speculation on the etiology of the Colonial epidemics, direct evidence for the presence of specific viruses during the Colonial era is lacking. To uncover the diversity of viral pathogens during this period, we designed an enrichment assay targeting ancient DNA (aDNA) from viruses of clinical importance and applied it to DNA extracts from individuals found in a Colonial hospital and a Colonial chapel (16th-18th century) where records suggest that victims of epidemics were buried during important outbreaks in Mexico City. This allowed us to reconstruct three ancient human parvovirus B19 genomes and one ancient human hepatitis B virus genome from distinct individuals. The viral genomes are similar to African strains, consistent with the inferred morphological and genetic African ancestry of the hosts as well as with the isotopic analysis of the human remains, suggesting an origin on the African continent. This study provides direct molecular evidence of ancient viruses being transported to the Americas during the transatlantic slave trade and their subsequent introduction to New Spain. Altogether, our observations enrich the discussion about the etiology of infectious diseases during the Colonial period in Mexico.

Method for detecting hepatitis B virus in blood plasma at low viral load using real-time PCR

A method for detecting HBV DNA in peripheral blood at low viral load using real-time PCR was developed and its significance in identifying HBsAg-negative viral hepatitis B was evaluated. When developing the method, blood plasma samples and liver tissue biopsy material were used from 128 patients living in St. Petersburg, in various regions of the Russian Federation, as well as in the Central Asia countries. We also used blood plasma samples from 96 pregnant women and 37 hemodialysis center patients living in Northwestern Federal District, 199 foreign citizens undergoing medical examination to obtain work permits at the Directorate for Migration in the Northwestern Federal District, 397 conditionally healthy people living in the Socialist Republic of Vietnam. HBV was detected by nested PCR. Analytical sensitivity was tested using the stepwise dilution method. According to the method developed by us, at the first stage, the HBV DNA is amplified using at the first stage oligonucleotides flanking the genome region 2932-3182 ... 1-1846 nt., and at the second stage two oligonucleotides pairs to the genome virus regions (gene S and gene X) and corresponding oligonucleotide fluorescently labeled probes complementary to the amplified fragments regions carrying fluorophores at the 5'-end, and non-fluorescent quenchers at the 3'-end. The channel corresponding to the FAM fluorophore detects the HBV DNA S-region amplification product, and the channel corresponding to the ROX fluorophore detects the HBV DNA X-region amplification product. The method sensitivity for DNA extraction from plasma with a 100 μl volume was 10 IU/ml. Obtaining a threshold cycle Ct for only one FAM or ROX fluorophore may indicate the HBV DNA presence in a sample at a load of less than 10 IU / ml, HBV detection in this case is possible with a repeated PCR study of the corresponding sample with HBV DNA extraction from an increased plasma volume (200-1000 μl). The developed method makes it possible to identify various HBV genovariants, both characteristic and rare in the Russian Federation, circulating in other world regions. The method can be used to detect HBV in risk groups, in the population, as well as in screening blood donors in order to ensure the blood transfusions safety.

Estimating the proportion of people with chronic hepatitis B virus infection eligible for hepatitis B antiviral treatment worldwide: a systematic review and meta-analysis

BACKGROUND

In 2016, of the estimated 257 million people living with chronic hepatitis B virus (HBV) infection worldwide, only a small proportion was diagnosed and treated. The insufficiency of information on the proportion of people infected with HBV who are eligible for treatment limits the interpretation of global treatment coverage. We aimed to estimate the proportion of people with chronic HBV infection who were eligible for antiviral treatment worldwide, based on the WHO 2015 guidelines.

METHODS

In this systematic review and meta-analysis, we searched Medline, EMBASE, and the Cochrane databases from Jan 1, 2007, to Jan 31, 2018, for studies describing HBsAg-positive people in the population or health-care facilities. We extracted information from published studies using a standardised form to estimate the frequency of cirrhosis, abnormal alanine aminotransferase (ALT), HBV DNA exceeding 2000 IU/mL or 20 000 IU/mL, presence of HBeAg, and eligibility for treatment as per WHO and other guidelines as reported in the studies. We pooled proportions through meta-analysis with random effects. The study was registered with PROSPERO, CRD42020132345.

FINDINGS

Of the 13 497 studies, 162 were eligible and included in our analysis. These studies included 145 789 participants. The pooled estimate of the proportion of cirrhosis was 9% (95% CI 8-10), ranging from 6% (4-8) in community settings to 10% (9-11) in clinic settings. Examining the proportion of participants who had characteristics used to determine eligibility in the WHO guidelines, 1750 (10·1%) of 17 394 had HBV DNA exceeding 20 000 IU/mL, and 20 425 (30·8%) of 66 235 had ALT above the upper limit of normal. 32 studies reported eligibility for treatment according to WHO or any other guidelines, with a pooled estimate of eligibility at 19% (95% CI 18-20), ranging from 12% (6-18) for studies in community settings to 25% (19-30) in clinic settings.

INTERPRETATION

Many studies described people with HBV infection, but few reported information in a way that allowed assessment of eligibility for treatment. Although about one in ten of the 257 million people with HBV infection (26 million) might be in urgent need of treatment because of cirrhosis, a larger proportion (12-25%) is eligible for treatment in accordance with different guidelines. Future studies describing people with HBV infection should report on treatment eligibility, according to broadly agreed definitions.

FUNDING

WHO and US Centers for Disease Control and Prevention.

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.

[Hepatitis B virus identification in a blood plasma at a low viral load.]

To analyze the method for detecting HBV DNA in peripheral blood at low viral load and evaluate its significance in identifying HBsAg-negative viral hepatitis B. In this work, samples of blood and liver tissue biopsy material were used from 128 patients living in the Russian Federation and the Republic of Uzbekistan without CHB and with CHB confirmed detection of circle covalently closed HBV DNA in hepatocytes. Plasma viral load was measured using the «AmpliSens® HBV-Monitor-FL» kit. HBV at low viral load was detected by nested PCR. Analytical sensitivity was checked by step dilution. According to our method, at the first stage, an asymmetric PCR is carried out using extended oligonucleotide primers with different melting points, complementary to the hepatitis B different genotypes genomes greatest similarity region. To increase the sensitivity, a second PCR is performed using the first reaction amplification product and internal primers. The sensitivity of the method for DNA extraction from 100 μl of plasma was 5 IU / ml, specificity 100%. Since, in spite of the HBV genotypes characteristic geographical distribution, the detection of "alien" genovariants for certain territories is becoming more frequent, we tested the method in geographically remote but active international relations with the Russian Federation regions with a high frequency of hepatotropic viruses. The developed method for detecting HBV DNA in blood plasma at low viral load based on PCR technology allows the various HBV gene variants identification and genotyping, both characteristic and rare in the Russian Federation, circulating in other world regions. The method can be used to detect HBV in risk groups, in a population, as well as when screening blood donors in order to ensure the blood transfusions safety.

Variety of the hepatitis B virus genovariants in the military

Aim. To estimate the distribution of genotypes and subgenotypes of the hepatitis B virus among military personnel with chronic viral hepatitis B. Materials and methods. The work used samples of blood plasma and biopsy material obtained from 90 active or retired military personnel with chronic viral hepatitis B with various degrees of fibrosis undergoing treatment in St. Petersburg. Primary detection of HBV was carried out by isolating nucleic acids (NK) from the blood plasma using the «AmplePrime Ribo-prep» commercial kit (FBIS CRIE, Moscow). Specific primers were used for the amplification and sequencing reaction. Overlapping primer pairs were used, jointly flanking 1475 base pairs (bp) fragment, including the recommended for HBV genotyping the 1169 bp Pre-S1/Pre-S2/S. Results. Among 90 samples from patients with chronic viral hepatitis B from different regions of the Russian Federation, HBV subgenotypes are represented in the following ratios: D2 = 45.6% (n=41), D1 = 32.2% (n=29), D3 = 13.3% (n=12), A2 = 6.7% (n=6), D4 and A1 by 1.1%, respectively. The distribution of HBV subgenotypes from the North Caucasian federal district (D1 – 63.6%, D2, D3, D4, A2 – by 9.1%) was significantly different from the distribution among patients from the Central and North-Western federal districts (D1-20, 9%, D2 – 58%, D3 – 16.3%, A2 – 4.8%) (χ2=11,9приp=0,0076, df=3). Uncharacteristic for the Russian Federation subgenotypes D4 and A1, representing single imported cases. The tendency to shift the distribution of genovariants due to imports of the corresponding HBV subgenotypes from other countries, including the Central Asian countries, is discussed. Conclusion. A systematic study of the HBV isolates phylogeny provides new information about the HBV subgenotypes distribution among certain population groups, including military personnel.

Integrated HIV surveillance finds recent adult hepatitis B virus (HBV) transmission and intermediate HBV prevalence among military in uncharacterized Caribbean country

Background

Guyana expanded its HIV response in 2005 but the epidemiology of hepatitis B virus (HBV) and hepatitis C virus (HCV) infections has not been characterized.

Methods

The 2011 Seroprevalence and Behavioral Epidemiology Risk Survey for HIV and STIs collected biologic specimens with demographic and behavioral data from a representative sample of Guyana military personnel. Diagnostics included commercial serum: HIV antibody; total antibody to hepatitis B core (anti-HBc); IgM anti-HBc; hepatitis B surface antigen (HBsAg); anti-HBs; antibody to HCV with confirmatory testing; and HBV DNA sequencing with S gene fragment phylogenetic analysis. Chi-square, p-values and prevalence ratios determined statistical significance.

Results

Among 480 participants providing serologic specimens, 176 (36.7%) tested anti-HBc-positive. Overall, 19 (4.0%) participants tested HBsAg-positive; 17 (89.5%) of the HBsAg-positive participants also had detectable anti-HBc, including 1 (5.3%) IgM anti-HBc-positive male. Four (6.8%) females with available HBV testing were HBsAg-positive, all aged 23–29 years. Sixteen (16, 84.2%) HBsAg-positive participants had sufficient specimen for DNA testing. All 16 had detectable HBV DNA, 4 with viral load >2x10⁴IU/ml. Sequencing found: 12 genotype (gt) A1 with 99.9% genetic identity between 1 IgM anti-HBc-positive and 1 anti-HBc-negative; 2 gtD1; and 2 with insufficient specimen. No statistically significant associations between risk factors and HBV infection were identified.

Conclusions

Integrated HIV surveillance identified likely recent adult HBV transmission, current HBV infection among females of reproductive age, moderate HBV infection prevalence (all gtA1 and D1), no HCV infections and low HIV frequency among Guyana military personnel. Integrated HIV surveillance helped characterize HBV and HCV epidemiology, including probable recent transmission, prompting targeted responses to control ongoing HBV transmission and examination of hepatitis B vaccine policies.

Reconstruction of the spatial and temporal dynamics of hepatitis B virus genotype D in the Americas

Hepatitis B virus (HBV) genotype D (HBV/D) is globally widespread, and ten subgenotypes (D1 to D10) showing distinct geographic distributions have been described to date. The evolutionary history of HBV/D and its subgenotypes, for which few complete genome sequences are available, in the Americas is not well understood. The main objective of the current study was to determine the full-length genomic sequences of HBV/D isolates from Brazil and frequency, origin and spread of HBV/D subgenotypes in the Americas. Complete HBV/D genomes isolated from 39 Brazilian patients infected with subgenotypes D1 (n = 1), D2 (n = 10), D3 (n = 27), and D4 (n = 1) were sequenced and analyzed together with reference sequences using the Bayesian coalescent and phylogeographic framework. A search for HBV/D sequences available in GenBank revealed 209 complete and 926 partial genomes from American countries (Argentina, Brazil, Canada, Chile, Colombia, Cuba, Haiti, Martinique, Mexico, USA and Venezuela), with the major circulating subgenotypes identified as D1 (26%), D2 (17%), D3 (36%), D4 (21%), and D7 (1%) within the continent. The detailed evolutionary history of HBV/D in the Americas was investigated by using different evolutionary time scales. Spatiotemporal reconstruction analyses using short-term substitution rates suggested times of the most recent common ancestor for the American HBV/D subgenotypes coincident with mass migratory movements to Americas during the 19^th and 20^th centuries. In particular, significant linkages between Argentina and Syria (D1), Brazil and Central/Eastern Europe (D2), USA and India (D2), and Brazil and Southern Europe (D3) were estimated, consistent with historical and epidemiological data.

THE PREVALENCE OF OCCULT HEPATITIS B AMONG HBSAG-NEGATIVE PERSONS WITH HIV IN VELIKY NOVGOROD

Aim: to estimate the prevalence of the occult hepatitis B virus among HIV-infected patients with the virological ineffectiveness of antiretroviral therapy in Veliky Novgorod. Materials and methods. Blood plasma samples from 76 HBsAg-negative HIVinfected patients with virological inefficiency of antiretroviral therapy from Veliky Novgorod were used in the work. For the detection of the hepatitis B virus, nucleic acids were isolated using the commercial kit AmplePrime Ribo-prep. For amplification and sequencing, overlapping pairs of specific primers were used, jointly flanking a 1475 base pair fragment including the 1169 base pair Pre-S1/Pre-S2/S region recommended for genotyping the hepatitis B virus. Results. Among 76 samples of hepatitis B virus DNA, 44 samples were found, which was 57,89%. None of the patients had HBsAg, and 6 patients (13,63%) had HBcor IgG and HBe IgG antibodies. On the basis of phylogenetic analysis, it was shown that only genotype D, which is the most common genotype of the hepatitis B virus in the Russian Federation, was detected in the examined group. The subgenotype D2 (47,72%) prevailed in comparison with the subgenotype D1 (34,09%) and the subgenotype D3 (18,18%). The distribution possible ways of the subgenotype D1 hepatitis B virus, which is uncharacteristic for the region, are discussed. Only one isolate of hepatitis B virus with mutations of drug resistance to nucleotide / nucleoside analogue therapy has been identified — amino acid substitution in the polymerase gene of the virus (L180M, M204V) associated with the development of resistance to lamivudine, entecavir, telbivudine and tenofovir. Conclusion. The high prevalence of occult hepatitis B among HIVinfected patients indicates a lack current tests for the diagnosis of chronic HBV infections. The identification of occult hepatitis B in HIV-infected individuals seems appropriate for timely treatment of patients and requires the use more sensitive methods.

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.

Prevalence of occult hepatitis B in a population from the Brazilian Amazon region

In the present study, we evaluated the prevalence of occult hepatitis B (OBI) in a population from the Brazilian Amazon region, identify circulating genotypes, and mutations in the S gene. One hundred eighty-one patients with negative serology for HBsAg and anti-HBs and positive serology for anti-HBc participated in the study. Detection of viral DNA, genotyping by sequencing, and analysis of nucleotide sequences to detect possible mutations were performed. HBV DNA was detected in 14.36% of the patients. Genotyping revealed genotype A in 88.46% of HBV DNA-positive subjects, with subgenotype A1 being the most prevalent (78.26%) followed by subgenotype A2 (21.74%). Genotype F was detected in 11.54% (all of them subgenotype F2). Amino acid substitutions were observed in the amplified S gene in individuals with OBI compared to HBsAg-positive individuals (evident infection). In conclusion, the results show a high prevalence of OBI in the population studied, with a pattern of genotypes A and F that circulate in the Brazilian Amazon region. Amino acid substitutions were detected in part of the S gene in patients with OBI. Further studies on the molecular epidemiology of HBV in this region are important to identify patients considered healthy but who are potential transmitters of the disease.

MOLECULAR-BIOLOGICAL MARKERS OF HEPATITIS В IN PATIENTS WITH LIVER FIBROSIS/CIRRHOSIS IN UZBEKISTAN

Aim. Evaluate prevalence of genetic variants of hepatitis В viruses in population of various regions of Uzbekistan with hepatitis of various genesis and different severity levels of liver fibrosis and cirrhosis. Materials and methods. Blood plasma and liver biopsy from 39 patients with different severity levels of liver fibrosis and cirrhosis served as study material. Genotyping based on direct sequencing of Pre-Sl/Pre-S2/S HBV DNA region was applied. Results. Hepatitis В virus was detected in 32 samples ofthe 39 provided, frequency of occurrence - 82%, respectively. Phylogenetic analysis has shown, that only genotype D was detected among the examined patients, hepatitis В virus subtype D1 predominated (84.38%) compared with D2 (3.12%) and D3 (12.5%) subtypes. Conclusion. Large-scale sequencing of HBV in Central Asia will allow to evaluate routes of transmission and time of evolutionary separation of virus isolates. Understanding the epidemiology of the infectious process is important for development of programs for prophylaxis and therapy of the infection.

Molecular characterization of hepatitis B virus among chronic hepatitis B patients from Pointe Noire, Republic of Congo

BACKGROUND

Chronic Hepatitis B infection is a major health problem in Republic of Congo therefore molecular analysis of HBV strains is important to detect the patients at high risk of disease progression.

METHODS

Serum samples were obtained from 111 chronic HBV patients in Pointe Noire. HBsAg, HBeAg and HBeAb were detected. A fragment of the preS1 region of HBV was amplified and sequenced to determine genotypes, subgenotypes and to identify mutations.

RESULTS

Of the 111 samples analyzed, 35 patients were asymptomatic carriers (ASC), 24 with a chronic active hepatitis (CAH), 33 with liver cirrhosis (LC) and 19 have a hepatocellular carcinoma (HCC). The mean age were 45 ± 13 year, 88 (79.3 %) were male and 23 (20.7 %) female. The prevalence of HBeAg was 15.3 % and 73 % of subjects were anti-HBe positive. The mean serum level of alanine aminotransferase transaminase (ALT) and aspartate transaminase (AST) was 25.1 ± 9 IU/L and 28.6 ± 10 IU/L respectively. Eighty two samples out of 111 (73.9 %) were genotyped by the analyzing of the S region of HBV, 58 (70.7 %) cases belonged to HBV genotype E and 24 (29.3 %) were genotype A with three subgenotypes; A3 (66.7 %), A4 (20.8 %) and A6 (12.5 %). Prevalence of genotype A was relatively high in CAH (33.3 %) and HCC (31.6 %) patients in comparison with other groups. The most prevalent amino acids substitutions were R38K found in 14 (17.1 %) sequences, following by H44L in 11 (13.4 %), K13E in 8 (9.8 %), N29K in 8 (9.8 %), A35E in 8 (9.8 %), V80I in 7 (8.5 %) and in 6 (7.3 %) sequences for S90T. Different substitutions located in the hepatocyte binding site were higher among patients with LC and HCC (p < 0.05).

CONCLUSIONS

This study have shown that HBV genotype E and A were the most frequent strains circulating in Republic of Congo patients. HBV pres1 substitutions found in this study were associated with severe clinical forms of liver diseases. This data have shown the importance of implementing an effective program to fight HBV infection.

The hepatitis delta genotype 8 in Northeast Brazil: The North Atlantic slave trade as the potential route for infection

Hepatitis Delta virus (HDV) is not well known, even though HDV and Hepatitis B virus (HBV) co-infection leads to severe forms of acute and chronic liver diseases. HDV is endemic in the Western Amazon region. Recently, the HDV genotype 8 was found in chronic patients followed at the center for liver studies in the Northeast Brazil, Maranhão. Previous studies suggested that this genotype was introduced in Maranhão during the slave trade. The presence of HDV in that study, which was done outside the Amazon region, led us to investigate whether the virus is found infecting individuals in other regions of Maranhão as well. Thus, we screened ninety-two HBsAg positive individuals from five Municipalities of Maranhão for anti-HD antibody and eight were found positive (8.7%). These eight positive individuals were submitted to polymerase chain reaction (PCR) to investigate active HDV infection. Half of them were positive for a fragment sequence of the delta antigen; their sequence samples were submitted to genotype characterization by phylogenetic analysis. All sequences clustered in a unique branch of the tree separated from the other branch described in Africa. Our study confirmed the presence of HDV-8 in Maranhão. These infected individuals had no evidence of contact with African people. Furthermore, we found individuals infected with HDV-8 in two more different municipalities. More studies like ours are urgent because the co-infection HBV/HDV is more difficult to treat. Identification of the endemic regions and implementation of healthy policies for preventing this infection are urgent in this region.

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.

Epidemiology of HBV subgenotypes D

The natural history of hepatitis B virus infection is not uniform and affected from several factors including, HBV genotype. Genotype D is a widely distributed genotype. Among genotype D, several subgenotypes differentiate epidemiologically and probably clinically. D1 is predominant in Middle East and North Africa, and characterized by early HBeAg seroconversion and low viral load. D2 is seen in Albania, Turkey, Brazil, western India, Lebanon, and Serbia. D3 was reported from Serbia, western India, and Indonesia. It is a predominant subgenotype in injection drug use-related acute HBV infections in Europe and Canada. D4 is relatively rare and reported from Haiti, Russia and Baltic region, Brazil, Kenya, Morocco and Rwanda. Subgenotype D5 seems to be common in Eastern India. D6 has been reported as a rare subgenotype from Indonesia, Kenya, Russia and Baltic region. D7 is the main genotype in Morocco and Tunisia. D8 and D9 are recently described subgenotypes and reported from Niger and India, respectively. Subgenotypes of genotype D may have clinical and/or viral differences. More subgenotype studies are required to conclude on subgenotype and its clinical/viral characteristics.

A rare HBV subgenotype D4 with unique genomic signatures identified in north-eastern India--an emerging clinical challenge?

BACKGROUND/AIMS

HBV has been classified into ten genotypes (A-J) and multiple subgenotypes, some of which strongly influence disease outcome and their distribution also correlate with human migration. HBV infection is highly prevalent in India and its diverse population provides an excellent opportunity to study the distinctiveness of HBV, its evolution and disease biology in variegated ethnic groups. The North-East India, having international frontiers on three sides, is one of the most ethnically and linguistically diverse region of the country. Given the paucity of information on molecular epidemiology of HBV in this region, the study aimed to carry out an in-depth genetic characterization of HBV prevailing in North-East state of Tripura.

METHODS

From sera of chronically HBV infected patients biochemical/serological tests, HBV DNA quantification, PCR-amplification, sequencing of PreS/S or full-length HBV genomes were done. HBV genotype/subgenotype determination and sequence variability were assessed by MEGA5-software. The evolutionary divergence times of different HBV subgenotypes were estimated by DNAMLK/PHYLIP program while jpHMM method was used to detect any recombination event in HBV genomes.

RESULTS

HBV genotypes D (89.5%), C (6.6%) and A (3.9%) were detected among chronic carriers. While all HBV/A and HBV/C isolates belonged to subgenotype-A1 and C1 respectively, five subgenotypes of HBV/D (D1-D5) were identified including the first detection of rare D4. These non-recombinant Indian D4 (IndD4) formed a distinct phylogenetic clade, had 2.7% nucleotide divergence and recent evolutionary radiation than other global D4. Ten unique amino acids and 9 novel nucleotide substitutions were identified as IndD4 signatures. All IndD4 carried T120 and R129 in ORF-S that may cause immune/vaccine/diagnostic escape and N128 in ORF-P, implicated as compensatory Lamivudine resistance mutation.

CONCLUSIONS

IndD4 has potential to undermine vaccination programs or anti-viral therapy and its introduction to North-East India is believed to be linked with the settlement of ancient Tibeto-Burman migrants from East-Asia.

A rare HBV subgenotype D4 with unique genomic signatures identified in north-eastern India--an emerging clinical challenge?

Background/Aims

HBV has been classified into ten genotypes (A–J) and multiple subgenotypes, some of which strongly influence disease outcome and their distribution also correlate with human migration. HBV infection is highly prevalent in India and its diverse population provides an excellent opportunity to study the distinctiveness of HBV, its evolution and disease biology in variegated ethnic groups. The North-East India, having international frontiers on three sides, is one of the most ethnically and linguistically diverse region of the country. Given the paucity of information on molecular epidemiology of HBV in this region, the study aimed to carry out an in-depth genetic characterization of HBV prevailing in North-East state of Tripura.

Methods

From sera of chronically HBV infected patients biochemical/serological tests, HBV DNA quantification, PCR-amplification, sequencing of PreS/S or full-length HBV genomes were done. HBV genotype/subgenotype determination and sequence variability were assessed by MEGA5-software. The evolutionary divergence times of different HBV subgenotypes were estimated by DNAMLK/PHYLIP program while jpHMM method was used to detect any recombination event in HBV genomes.

Results

HBV genotypes D (89.5%), C (6.6%) and A (3.9%) were detected among chronic carriers. While all HBV/A and HBV/C isolates belonged to subgenotype-A1 and C1 respectively, five subgenotypes of HBV/D (D1–D5) were identified including the first detection of rare D4. These non-recombinant Indian D4 (IndD4) formed a distinct phylogenetic clade, had 2.7% nucleotide divergence and recent evolutionary radiation than other global D4. Ten unique amino acids and 9 novel nucleotide substitutions were identified as IndD4 signatures. All IndD4 carried T¹²⁰ and R¹²⁹ in ORF-S that may cause immune/vaccine/diagnostic escape and N¹²⁸ in ORF-P, implicated as compensatory Lamivudine resistance mutation.

Conclusions

IndD4 has potential to undermine vaccination programs or anti-viral therapy and its introduction to North-East India is believed to be linked with the settlement of ancient Tibeto-Burman migrants from East-Asia.

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

Brazil is a country of low hepatitis B virus (HBV) endemicity in which the genotype A of HBV (HBV/A) is the most prevalent. The complete nucleotide sequences of 26 HBV/A isolates, originating from eight Brazilian states, were determined. All were adw2. Twenty-three belonged to subgenotype A1 and three to A2. By phylogenetic analysis, it was shown that all the 23 HBV/A1 isolates clustered together with isolates from Bangladesh, India, Japan, Nepal, the Philippines and United Arab Emirates, but not with those of Congo, Kenya, Malawi, Rwanda, South Africa, Tanzania, Uganda and Zimbabwe. Four amino acid residues in the polymerase (His138 in the terminal protein domain, Pro18 and His90 in the spacer, and Ser109 in the reverse transcriptase), and one (Phe17) in the precore region, predominated in Latin American and Asian HBV/A1 isolates, but were rarely encountered in African isolates, with the exception of those from Somalia. Specific variations of two adjacent amino acids in the C-terminal domain of the HBx protein, namely Ala146 and Pro147, were found in all the Brazilian, but rarely in the other HBV/A1 isolates. By Bayesian analysis, the existence of an 'Asian-American' clade within subgenotype A1 was supported by a posterior probability value of 0.996. The close relatedness of the Brazilian, Asian and Somalian isolates suggests that the HBV/A1 strains predominant in Brazil did not originate from the five million slaves who were imported from Central and Western Africa from 1551 to 1840, but rather from the 300-400,000 captives forcibly removed from southeast Africa at the middle of the 19th century.

Analysis of complete nucleotide sequences of Angolan hepatitis B virus isolates reveals the existence of a separate lineage within genotype E

Hepatitis B virus genotype E (HBV/E) is highly prevalent in Western Africa. In this work, 30 HBV/E isolates from HBsAg positive Angolans (staff and visitors of a private hospital in Luanda) were genetically characterized: 16 of them were completely sequenced and the pre-S/S sequences of the remaining 14 were determined. A high proportion (12/30, 40%) of subjects tested positive for both HBsAg and anti-HBs markers. Deduced amino acid sequences revealed the existence of specific substitutions and deletions in the B- and T-cell epitopes of the surface antigen (pre-S1- and pre-S2 regions) of the virus isolates derived from 8/12 individuals with concurrent HBsAg/anti-HBs. Phylogenetic analysis performed with 231 HBV/E full-length sequences, including 16 from this study, showed that all isolates from Angola, Namibia and the Democratic Republic of Congo (n = 28) clustered in a separate lineage, divergent from the HBV/E isolates from nine other African countries, namely Cameroon, Central African Republic, Côte d'Ivoire, Ghana, Guinea, Madagascar, Niger, Nigeria and Sudan, with a Bayesian posterior probability of 1. Five specific mutations, namely small S protein T57I, polymerase Q177H, G245W and M612L, and X protein V30L, were observed in 79-96% of the isolates of the separate lineage, compared to a frequency of 0–12% among the other HBV/E African isolates.

Bayesian inference of the evolution of HBV/E

Despite its wide spread and high prevalence in sub-Saharan Africa, hepatitis B virus genotype E (HBV/E) has a surprisingly low genetic diversity, indicating an only recent emergence of this genotype in the general African population. Here, we performed extensive phylogeographic analyses, including Bayesian MCMC modeling. Our results indicate a mutation rate of 1.9×10⁻⁴ substitutions per site and year (s/s/y) and confirm a recent emergence of HBV/E, most likely within the last 130 years, and only after the transatlantic slave-trade had come to an end. Our analyses suggest that HBV/E originated from the area of Nigeria, before rapidly spreading throughout sub-Saharan Africa. Interestingly, viral strains found in Haiti seem to be the result of multiple introductions only in the second half of the 20th century, corroborating an absence of a significant number of HBV/E strains in West Africa several centuries ago. Our results confirm that the hyperendemicity of HBV(E) in today's Africa is a recent phenomenon and likely the result of dramatic changes in the routes of viral transmission in a relatively recent past.