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Angelice GP, Barros TM, Marques VA, Villar LM, Lago BV, Mello FCA. Exploring genetic diversity of hepatitis D virus full-length genome in Brazil: Discovery of a novel HDV-8 subgenotype beyond African borders. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024:105671. [PMID: 39299539 DOI: 10.1016/j.meegid.2024.105671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 09/13/2024] [Accepted: 09/16/2024] [Indexed: 09/22/2024]
Abstract
Hepatitis D virus (HDV) is currently classified into 8 genotypes (1 to 8) and several subgenotypes, with distinct distribution worldwide. However, due to the scarcity of complete genome sequences in databases, this classification is constantly being updated and tends to be regularly revisited in upcoming years as more sequence data becomes available. Aiming to increase knowledge about the genetic variability of HDV, this study presents the full-length genomes of 11 HDV samples collected in Brazil in endemic and non-endemic regions, including the first complete genomes of the genotypes 5 and 8 obtained outside Africa. We also determined the co-infecting HBV genotypes to investigate their prevalence among the HDV-infected individuals throughout the country. Whole genome sequencing confirmed our previous findings based on a partial fragment of the HDV genome, in which HDV subgenoypes 3c (9/11; 81.8 %), 5b (1/11; 9.1 %) and one HDV-8 sequence (1/11; 9.1 %) were detected. As previously observed, HDV-8 formed a distinct branch apart from subgenotypes 8a and 8b, a monophyletic clade representing a novel HDV-8 subgenotype, designated as 8c. Among HDV-3 samples, the main co-infecting HBV genotype found was HBV-F (4/8; 50 %), reflecting the higher incidence of this native South American genotype in the endemic Amazon Basin. Both samples infected with HDV-5 and HDV-8 were coinfected with HBV genotype E, also a genotype with African origin. Our findings based on complete genome sequence of HDV corroborated our results based on a partial region of the HDV genome of a novel HDV-8 subgenotype and reinforced the need to use full-length genomes to properly subdivide genotypes with very low intragroup genetic variability, such as HDV-3. The provision of these complete genomes is expected to contribute to the enrichment of sequence databases for future molecular and evolutionary investigations of HDV.
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Affiliation(s)
- Giovana P Angelice
- Laboratory of Viral Hepatitis, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Tairine M Barros
- Laboratory of Viral Hepatitis, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Vanessa A Marques
- Laboratory of Viral Hepatitis, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Livia M Villar
- Laboratory of Viral Hepatitis, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Barbara V Lago
- Laboratory of Viral Hepatitis, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Francisco C A Mello
- Laboratory of Viral Hepatitis, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
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Ding Y, Guo H, Hong X, Li Q, Miao Z, Pan Q, Zheng K, Wang W. The distinct spatiotemporal evolutionary landscape of HBV and HDV largely determines the unique epidemic features of HDV globally. Mol Phylogenet Evol 2024; 197:108114. [PMID: 38825156 DOI: 10.1016/j.ympev.2024.108114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 05/07/2024] [Accepted: 05/26/2024] [Indexed: 06/04/2024]
Abstract
Chronic infection of hepatitis B virus (HBV) and hepatitis D virus (HDV) causes the most severe form of viral hepatitis. Due to the dependence on HBV, HDV was deemed to co-evolve and co-migrate with HBV. However, we previously found that the naturally occurred HDV/HBV combinations do not always reflect the most efficient virological adaptation (Wang et al., 2021). Moreover, regions with heavy HBV burden do not always correlate with high HDV prevalence (e.g., East Asia), and vice versa (e.g., Central Asia). Herein, we systematically elucidated the spatiotemporal evolutionary landscape of HDV to understand the unique epidemic features of HDV. We found that the MRCA of HDV was from South America around the late 13th century, was globally dispersed mainly via Central Asia, and evolved into eight genotypes from the 19th to 20th century. In contrast, the MRCA of HBV was from Europe ∼23.7 thousand years ago (Kya), globally dispersed mainly via Africa and East Asia, and evolved into eight genotypes ∼1100 years ago. When HDV stepped in, all present-day HBV genotypes had already formed and its global genotypic distribution had stayed stable geographically. Nevertheless, regionalized HDV adapted to local HBV genotypes and human lineages, contributing to the global geographical separation of HDV genotypes. Additionally, a sharp increase in HDV infections was observed after the 20th century. In conclusion, HDV exhibited a distinct spatiotemporal distribution path compared with HBV. This unique evolutionary relationship largely fostered the unique epidemic features we observe nowadays. Moreover, HDV infections may continue to ramp up globally, thus more efforts are urgently needed to combat this disease.
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Affiliation(s)
- Yibo Ding
- Department of Pathogen Biology and Immunology, Jiangsu Key Laboratory of Immunity and Metabolism, Jiangsu International Laboratory of Immunity and Metabolism, Xuzhou Medical University, Xuzhou, China
| | - Hongbo Guo
- Department of Pathogen Biology and Immunology, Jiangsu Key Laboratory of Immunity and Metabolism, Jiangsu International Laboratory of Immunity and Metabolism, Xuzhou Medical University, Xuzhou, China.
| | - Xinfang Hong
- Second Medical Center of PLA General Hospital, Beijing, China
| | - Qiudi Li
- Department of Pathogen Biology and Immunology, Jiangsu Key Laboratory of Immunity and Metabolism, Jiangsu International Laboratory of Immunity and Metabolism, Xuzhou Medical University, Xuzhou, China
| | - Zhijiang Miao
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Qiuwei Pan
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands.
| | - Kuiyang Zheng
- Department of Pathogen Biology and Immunology, Jiangsu Key Laboratory of Immunity and Metabolism, Jiangsu International Laboratory of Immunity and Metabolism, Xuzhou Medical University, Xuzhou, China.
| | - Wenshi Wang
- Department of Pathogen Biology and Immunology, Jiangsu Key Laboratory of Immunity and Metabolism, Jiangsu International Laboratory of Immunity and Metabolism, Xuzhou Medical University, Xuzhou, China.
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Passos-Silva AM, Silva EDCE, Borzacov LMP, Araújo A, Porto AS, Salcedo JMV, Vieira D. Molecular genetic association of rs8099917 and rs1800795 polymorphisms in the progression of hepatitis Delta virus liver disease. J Venom Anim Toxins Incl Trop Dis 2024; 30:e20230025. [PMID: 38221914 PMCID: PMC10786575 DOI: 10.1590/1678-9199-jvatitd-2023-0025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 11/23/2023] [Indexed: 01/16/2024] Open
Abstract
Background The relationship between viral infections and host factors holds high hopes for identifying the role of Interferon Lambda 3 (IFNL3) and Interleukin 6 (IL-6) polymorphisms in the development of Chronic Liver Disease (CLD) in patients infected with hepatitis Delta virus (HDV) in the Western Brazilian Amazon. Methods Cross-sectional study conducted with a cohort of 40 chronic HDV patients, 27 with CLD and 13 without evident liver damage. Biological samples from the participants were analyzed using the polymerase chain reaction (PCR) technique, followed by sequencing by the automated Sanger method. Results The rs8099917 T allele, from the IFNL3 gene, showed a higher frequency in both groups; however, it was not possible to establish an association with HDV infection [OR = 1.42 (0.42 - 4.75; p = 0.556 (95% CI). For IL-6, the rs1800795 G allele was superior to rs1800795 C. Analyzing both distributions in the studied groups, any association with HDV was absent (p > 0.05). Conclusion The results suggest that the rs8099917 T/G (IFNL3) and rs1800795 G/C (IL-6) polymorphisms are not associated with the evolution of HDV in the studied population.
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Affiliation(s)
- Ana Maísa Passos-Silva
- Molecular Virology Laboratory, Oswaldo Cruz Foundation Rondonia -
FIOCRUZ/RO, Porto Velho, RO, Brazil
- Postgraduate Program in Experimental Biology, Federal University of
Rondonia, UNIR/FIOCRUZ-RO, Porto Velho, RO, Brazil
- Tropical Medicine Research Center - CEPEM, Porto Velho, RO,
Brazil
- National Institute of Epidemiology of the Western Amazon, INCT
EpiAmO, Porto Velho, RO, Brazil
| | | | | | - Adrhyan Araújo
- Molecular Virology Laboratory, Oswaldo Cruz Foundation Rondonia -
FIOCRUZ/RO, Porto Velho, RO, Brazil
- Tropical Medicine Research Center - CEPEM, Porto Velho, RO,
Brazil
- National Institute of Epidemiology of the Western Amazon, INCT
EpiAmO, Porto Velho, RO, Brazil
| | - Anita Sperandio Porto
- Federal University of Rondonia, UNIR, Porto Velho, RO,
Brazil
- Unir Pathology Laboratory, UNIR/RO, Porto Velho, RO, Brazil
| | - Juan Miguel Villalobos Salcedo
- Federal University of Rondonia, UNIR, Porto Velho, RO,
Brazil
- Tropical Medicine Research Center - CEPEM, Porto Velho, RO,
Brazil
- National Institute of Epidemiology of the Western Amazon, INCT
EpiAmO, Porto Velho, RO, Brazil
| | - Deusilene Vieira
- Molecular Virology Laboratory, Oswaldo Cruz Foundation Rondonia -
FIOCRUZ/RO, Porto Velho, RO, Brazil
- Postgraduate Program in Experimental Biology, Federal University of
Rondonia, UNIR/FIOCRUZ-RO, Porto Velho, RO, Brazil
- Tropical Medicine Research Center - CEPEM, Porto Velho, RO,
Brazil
- National Institute of Epidemiology of the Western Amazon, INCT
EpiAmO, Porto Velho, RO, Brazil
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Montoya-Guzman M, Martinez J, Castro-Arroyave D, Rojas C, Navas MC. Epidemiology and Genetic Diversity of Hepatitis B Virus and Hepatitis Delta Virus Infection in Indigenous Communities in Colombia. Microorganisms 2023; 11:1739. [PMID: 37512911 PMCID: PMC10386745 DOI: 10.3390/microorganisms11071739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/20/2023] [Accepted: 06/28/2023] [Indexed: 07/30/2023] Open
Abstract
Despite the universal vaccination program, there are still regions and territories with a high prevalence of Hepatitis B Virus infection (HBV), such as the Amazon basin, where several indigenous communities live. Additionally, Hepatitis Delta Virus (HDV) is a defective that requires the hepatitis B surface antigen (HBsAg) for the assembly and release of de novo viral particles. Therefore, hepatitis D could be the result of HBV/HDV coinfection or HDV superinfection in individuals with chronic hepatitis B. Among the high prevalence HDV populations are indigenous communities of America. This study aims to describe and characterize the frequency of HBV and HDV infection, viral genotypes and HBV immune escape mutants in indigenous populations from different regions of Colombia. The diagnosis of hepatitis B and hepatitis D was confirmed by serological markers. Moreover, the HBV and HDV genome were amplified by PCR and RT-PCR, respectively, and, subsequently, the phylogenetic analysis was performed. We characterized 47 cases of chronic hepatitis B, 1 case of reactivation and 2 cases of occult hepatitis B infection (OBI). Furthermore, a high prevalence of HDV infection was identified in the study population (29.33%, 22/75) and the circulation of several HBV genotypes and subgenotypes (F1b, F3, F4, and D). Interestingly, this is the first report of the HDV genotype I circulation in this country. These findings demonstrated that HBV and HDV infections are still public health problems in indigenous communities in Colombia.
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Affiliation(s)
- Melissa Montoya-Guzman
- Grupo Gastrohepatología, Facultad de Medicina, Universidad de Antioquia, Calle 70 No. 52-21, Medellín 050010, Colombia
| | - Jaime Martinez
- Grupo Epidemiología, Facultad Nacional de Salud Pública, Universidad de Antioquia, Calle 70 No. 52-21, Medellín 050010, Colombia
| | - Diana Castro-Arroyave
- Grupo de Estudio en Pedagogía, Infancia y Desarrollo Humano (GEPIDH), Facultad de Educación, Universidad de Antioquia, Calle 70 No. 52-21, Medellín 050010, Colombia
| | - Carlos Rojas
- Grupo Epidemiología, Facultad Nacional de Salud Pública, Universidad de Antioquia, Calle 70 No. 52-21, Medellín 050010, Colombia
| | - Maria-Cristina Navas
- Grupo Gastrohepatología, Facultad de Medicina, Universidad de Antioquia, Calle 70 No. 52-21, Medellín 050010, Colombia
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Mello FCA, Barros TM, Angelice GP, Costa VD, Mello VM, Pardini MIMC, Lampe E, Lago BV, Villar LM. Circulation of HDV Genotypes in Brazil: Identification of a Putative Novel HDV-8 Subgenotype. Microbiol Spectr 2023; 11:e0396522. [PMID: 37074189 PMCID: PMC10269522 DOI: 10.1128/spectrum.03965-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 03/09/2023] [Indexed: 04/20/2023] Open
Abstract
Hepatitis D virus (HDV) is classified into 8 genotypes (1 to 8) and several subgenotypes. In Brazil, HDV-3 and HDV-1 predominate; however, most of the diagnosis efforts and molecular studies are directed to the area of endemicity of the Amazon Basin. Here, we determined the molecular epidemiological profile of circulating HDV in Brazilian HBsAg-positive patients between 2013 and 2015 in areas of endemicity and non-areas of endemicity. From 38 anti-HDV-positive individuals, 13 (34.2%) had detectable HDV-RNA and 11 (28.9%) were successfully sequenced. Partial HDAg (~320 nt) sequencing followed by phylogenetic analysis with reference sequences resulted in the identification of HDV-3 (9/11; 81.8%), HDV-5 (1/11; 9.1%), and HDV-8 (1/11; 9.1%). Most HDV-3 samples (8/9; 88.9%) were found in the endemic North region, while one was found in Central-West Brazil, a non-area of endemicity. HDV-5 and 8, genotypes native from African countries, were found in São Paulo, a cosmopolitan city from Southeast Brazil with a high circulation of immigrants. Phylogenetic analysis of HDV-8 strains indicated that the sample determined in our study, along with previously reported sequences from Brazil, formed a highly supported monophyletic clade, likely representing a putative novel HDV-8 subgenotype. IMPORTANCE Considered a neglected pathogen until the last 2 decades, an increase in the availability of genetic data of hepatitis D virus (HDV) strains around the world has been noticed recently, resulting in the proposition of different classifications. Our study aimed to determine the molecular epidemiological profile of HDV isolates circulating in areas of endemicity and non-areas of endemicity in Brazil. Based on the analyzed fragment, HDV-8 sequences clustered out of the clades formed by subgenotypes 8a and 8b might suggest the identification of a novel subgenotype, putatively designated subgenotype 8c. Our findings demonstrate the importance of continuous epidemiological surveillance to map HDV spread pathways and the introduction of imported variants. It also reinforces that as the amount of HDV genomes generated and reported increases, we will have changes in viral classification and, consequently, in our understanding of the dynamics of variability of this viral agent.
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Affiliation(s)
- Francisco C. A. Mello
- Laboratório de Hepatites Virais, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Tairine M. Barros
- Laboratório de Hepatites Virais, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Giovana P. Angelice
- Laboratório de Hepatites Virais, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Vanessa D. Costa
- Laboratório de Hepatites Virais, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Vinicius M. Mello
- Laboratório de Hepatites Virais, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Maria Inês M. C. Pardini
- Universidade Estadual Paulista (Unesp), Faculdade de Medicina (FMB), Divisão Hemocentro, Laboratório de Biologia Molecular, Campus de Botucatu, Botucatu, São Paulo, Brazil
| | - Elisabeth Lampe
- Laboratório de Hepatites Virais, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Barbara V. Lago
- Laboratório de Hepatites Virais, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
- Instituto de Tecnologia em Imunobiológicos (Bio-Manguinhos), FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Livia M. Villar
- Laboratório de Hepatites Virais, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
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Isaeva OV, Kyuregyan KK, Karlsen AA, Kuzmin OV, Potemkin IA, Kichatova VS, Asadi Mobarkhan FA, Mullin EV, Kozhanova TV, Manuylov VA, Pochtovyy AA, Gushchin VA, Saryglar AA, Ilchenko LY, Mikhailov MI. Silent HDV epidemics culminates in high levels of liver cirrhosis in endemic region despite 20 years of HBV vaccination. J Viral Hepat 2023; 30:182-194. [PMID: 36478630 DOI: 10.1111/jvh.13783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 05/23/2022] [Accepted: 12/02/2022] [Indexed: 02/16/2023]
Abstract
The hepatitis delta virus (HDV) is believed to be a vanishing infection in countries with successful hepatitis B virus (HBV) vaccination programs. We assessed the current status of HDV infection in Tuva, a region of the Russia that has been highly endemic for HBV. The proportion of HDV-infected patients among HBsAg-positive patients in the regional registry in 2020 was 32.7% (786/2401). An analysis of the medical records of 514 HDV patients demonstrated that 37.5% (193/514) had liver cirrhosis at the first doctor's visit, and 7.4% of patients lived in families where another family member had HDV. All HDV patients were infected with genotype HDV-1, 94.5% had HBV genotype D, and 5.5% had genotype A. A serosurvey conducted among 1170 healthy volunteers showed that the average detection rate of HBsAg with anti-HDV was 1.0% (95% CI: 0.57-1.81%). No anti-HDV positive samples were detected in participants aged under 30 years. The HBsAg/anti-HDV positivity rate peaked at 7.4% in patients aged 50-59 years, which was significantly higher than in a similar age cohort surveyed in 2008 (1.6%, p < .0001). A Bayesian analysis showed that HDV circulation in Tuva resulted from two waves of introduction, the first in the 1810s (95% HPD: 1741-1834) from Central Asia, and the second in the 1960s (95% HPD: 1953-1979) from Russia. HBV has a much longer history of circulation in Tuva with the MRCA for the predominant genotype HBV-D dated to 972 (95% HPD: 535-1253) for subtype D1, 1274 (95% HPD: 936-1384) for D2, and 1173 (95% HPD: 1005-1618) for D3. A SkyGrid reconstruction of population dynamics showed an increase in the intensity of HDV spread in recent decades. This situation shows the need for HDV screening and prevention measures among people living with HBV.
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Affiliation(s)
- Olga V Isaeva
- Department of Viral Hepatitis, Russian Medical Academy of Continuous Professional Education, Moscow, Russia.,Laboratory of Viral Hepatitis, Mechnikov Research Institute of Vaccines and Sera, Moscow, Russia
| | - Karen K Kyuregyan
- Department of Viral Hepatitis, Russian Medical Academy of Continuous Professional Education, Moscow, Russia.,Laboratory of Viral Hepatitis, Mechnikov Research Institute of Vaccines and Sera, Moscow, Russia.,Scientific and Educational Resource Center for High-Performance Methods of Genomic Analysis, Peoples' Friendship University of Russia (RUDN University), Moscow, Russia
| | - Anastasia A Karlsen
- Department of Viral Hepatitis, Russian Medical Academy of Continuous Professional Education, Moscow, Russia.,Laboratory of Viral Hepatitis, Mechnikov Research Institute of Vaccines and Sera, Moscow, Russia.,Scientific and Educational Resource Center for High-Performance Methods of Genomic Analysis, Peoples' Friendship University of Russia (RUDN University), Moscow, Russia
| | - Oleg V Kuzmin
- Laboratory of Viral Hepatitis, Mechnikov Research Institute of Vaccines and Sera, Moscow, Russia
| | - Ilya A Potemkin
- Department of Viral Hepatitis, Russian Medical Academy of Continuous Professional Education, Moscow, Russia.,Laboratory of Viral Hepatitis, Mechnikov Research Institute of Vaccines and Sera, Moscow, Russia
| | - Vera S Kichatova
- Department of Viral Hepatitis, Russian Medical Academy of Continuous Professional Education, Moscow, Russia.,Laboratory of Viral Hepatitis, Mechnikov Research Institute of Vaccines and Sera, Moscow, Russia
| | - Fedor A Asadi Mobarkhan
- Laboratory of Viral Hepatitis, Mechnikov Research Institute of Vaccines and Sera, Moscow, Russia
| | - Eugeniy V Mullin
- Laboratory of Viral Hepatitis, Mechnikov Research Institute of Vaccines and Sera, Moscow, Russia
| | - Tatyana V Kozhanova
- Pirogov Russian National Research Medical University, Moscow, Russia.,Chumakov Federal Scientific Center for Research and Development of Immunobiological Products of Russian Academy of Sciences, Moscow, Russia
| | - Victor A Manuylov
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ivanovsky Institute of Virology, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Andrey A Pochtovyy
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ivanovsky Institute of Virology, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Vladimir A Gushchin
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ivanovsky Institute of Virology, Ministry of Health of the Russian Federation, Moscow, Russia
| | | | - Lyudmila Yu Ilchenko
- Laboratory of Viral Hepatitis, Mechnikov Research Institute of Vaccines and Sera, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia
| | - Mikhail I Mikhailov
- Department of Viral Hepatitis, Russian Medical Academy of Continuous Professional Education, Moscow, Russia.,Laboratory of Viral Hepatitis, Mechnikov Research Institute of Vaccines and Sera, Moscow, Russia
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7
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Bahoussi AN, Wang PH, Guo YY, Rabbani N, Wu C, Xing L. Global Distribution and Natural Recombination of Hepatitis D Virus: Implication of Kyrgyzstan Emerging HDVs in the Clinical Outcomes. Viruses 2022; 14:v14071467. [PMID: 35891448 PMCID: PMC9323457 DOI: 10.3390/v14071467] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 06/28/2022] [Accepted: 06/30/2022] [Indexed: 02/05/2023] Open
Abstract
Discrepancies in human hepatitis delta virus (HDV) genotypes impact the virus’ biological behavior, clinical manifestation, and treatment response. Herein, this report aims to explore the role of recombination in the worldwide genotypic distribution and genetic diversity of HDV. Three-hundred-forty-eight human HDV full-length genomic sequences of ~1678 nt in length, isolated in twenty-eight countries worldwide between 1986 and 2018, were analysed. Similarity analysis and recombination mapping were performed, and forty-eight recombination events were identified, twenty-nine of which were isolated from Kyrgyzstan and determined to be involved in the diversity and extension of HDV sub-genotypes. HDV recombination occurred only between the genetically close genotypes (genotype 5 and genotype 2) or mainly within genotype 1, suggesting the complex replicative molecular mechanisms of HDV-RNA. The global distribution and classification of HDV genotypes have been updated, indicating that HDV recombination is one of the driving forces behind the biodiversity and the evolution of human HDV genomes. The outcome analysis suggests that the expansion of HDV sub-genotypes and the complex recombination networks might be related to the genomic character of Kyrgyzstan circulating strains and extensive mobility within countries and across borders. These findings will be of great importance in formulating more effective public health HDV surveillance strategies and guiding future molecular and epidemiological research to achieve better clinical outcomes.
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Affiliation(s)
- Amina Nawal Bahoussi
- Institutes of Biomedical Sciences, Shanxi University, 92 Wucheng Road, Taiyuan 030006, China; (A.N.B.); (P.-H.W.); (Y.-Y.G.); (N.R.); (C.W.)
| | - Pei-Hua Wang
- Institutes of Biomedical Sciences, Shanxi University, 92 Wucheng Road, Taiyuan 030006, China; (A.N.B.); (P.-H.W.); (Y.-Y.G.); (N.R.); (C.W.)
| | - Yan-Yan Guo
- Institutes of Biomedical Sciences, Shanxi University, 92 Wucheng Road, Taiyuan 030006, China; (A.N.B.); (P.-H.W.); (Y.-Y.G.); (N.R.); (C.W.)
| | - Nighat Rabbani
- Institutes of Biomedical Sciences, Shanxi University, 92 Wucheng Road, Taiyuan 030006, China; (A.N.B.); (P.-H.W.); (Y.-Y.G.); (N.R.); (C.W.)
| | - Changxin Wu
- Institutes of Biomedical Sciences, Shanxi University, 92 Wucheng Road, Taiyuan 030006, China; (A.N.B.); (P.-H.W.); (Y.-Y.G.); (N.R.); (C.W.)
- The Key Laboratory of Medical Molecular Cell Biology of Shanxi Province, Shanxi University, 92 Wucheng Road, Taiyuan 030006, China
- Shanxi Provincial Key Laboratory for Prevention and Treatment of Major Infectious Diseases, 92 Wucheng Road, Taiyuan 030006, China
| | - Li Xing
- Institutes of Biomedical Sciences, Shanxi University, 92 Wucheng Road, Taiyuan 030006, China; (A.N.B.); (P.-H.W.); (Y.-Y.G.); (N.R.); (C.W.)
- The Key Laboratory of Medical Molecular Cell Biology of Shanxi Province, Shanxi University, 92 Wucheng Road, Taiyuan 030006, China
- Shanxi Provincial Key Laboratory for Prevention and Treatment of Major Infectious Diseases, 92 Wucheng Road, Taiyuan 030006, China
- Correspondence: ; Tel.: +86-351-701-025
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8
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Karlsen AA, Kyuregyan KK, Isaeva OV, Kichatova VS, Asadi Mobarkhan FA, Bezuglova LV, Netesova IG, Manuylov VA, Pochtovyi AA, Gushchin VA, Sleptsova SS, Ignateva ME, Mikhailov MI. Different evolutionary dynamics of hepatitis B virus genotypes A and D, and hepatitis D virus genotypes 1 and 2 in an endemic area of Yakutia, Russia. BMC Infect Dis 2022; 22:452. [PMID: 35550023 PMCID: PMC9097355 DOI: 10.1186/s12879-022-07444-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 04/29/2022] [Indexed: 11/16/2022] Open
Abstract
Background The geographic distribution of the hepatitis B virus (HBV) and the hepatitis D virus (HDV) genotypes is uneven. We reconstructed the temporal evolution of HBV and HDV in Yakutia, one of the regions of Russia most affected by HBV and HDV, in an attempt to understand the possible mechanisms that led to unusual for Russia pattern of viral genotypes and to identify current distribution trends. Methods HBV and HDV genotypes were determined in sera collected in 2018–2019 in Yakutia from randomly selected 140 patients with HBV monoinfection and 59 patients with HBV/HDV. Total 86 HBV and 88 HDV genomic sequences isolated in Yakutia between 1997 and 2019 were subjected to phylodynamic and philogeographic Bayesian analysis using BEAST v1.10.4 software package. Bayesian SkyGrid reconstruction and Birth–Death Skyline analysis were applied to estimate HBV and HDV population dynamics. Results Currently, HBV-A and HDV-D genotypes are prevalent in Yakutia, in both monoinfected and HDV-coinfected patients. Bayesian analysis has shown that the high prevalence of HBV-A in Yakutia, which is not typical for Russia, initially emerged after the genotype was introduced from Eastern Europe in the fifteenth century (around 600 (95% HPD: 50–715) years ago). The acute hepatitis B epidemics in the 1990s in Yakutia were largely associated with this particular genotype, as indicated by temporal changes in HBV-A population dynamics. HBV-D had a longer history in Yakutia and demonstrated stable population dynamics, indicating ongoing viral circulation despite vaccination. No correlation between HBV and HDV genotypes was observed for coinfected patients in Yakutia (r = − 0.016069332). HDV-2b circulates in Russia in Yakutia only and resulted from a single wave of introduction from Central Asia 135 years ago (95% HPD: 60–350 years), while HDV-1 strains resulted from multiple introductions from Europe, the Middle East, Central Asia, and different parts of Russia starting 180 years ago (95% HPD: 150–210 years) and continuing to the present day. The population dynamics of HDV-1 and HDV-2 show no signs of decline despite 20 years of HBV vaccination. The Birth–Death Skyline analysis showed an increase in the viral population in recent years for both HDV genotypes, indicating ongoing HDV epidemics. Conclusions Taken together, these data call for strict control of HBV vaccination quality and coverage, and implementation of HBV and HDV screening programs in Yakutia. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-022-07444-w.
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Affiliation(s)
- Anastasia A Karlsen
- Department of Viral Hepatitis, Russian Medical Academy of Continuous Professional Education, Moscow, Russia, 125993.,Laboratory of Viral Hepatitis, Mechnikov Research Institute of Vaccines and Sera, Moscow, Russia, 105064.,Scientific and Educational Resource Center for High-Performance Methods of Genomic Analysis, Peoples' Friendship University of Russia (RUDN University), Moscow, Russia, 117198
| | - Karen K Kyuregyan
- Department of Viral Hepatitis, Russian Medical Academy of Continuous Professional Education, Moscow, Russia, 125993. .,Laboratory of Viral Hepatitis, Mechnikov Research Institute of Vaccines and Sera, Moscow, Russia, 105064. .,Scientific and Educational Resource Center for High-Performance Methods of Genomic Analysis, Peoples' Friendship University of Russia (RUDN University), Moscow, Russia, 117198.
| | - Olga V Isaeva
- Department of Viral Hepatitis, Russian Medical Academy of Continuous Professional Education, Moscow, Russia, 125993.,Laboratory of Viral Hepatitis, Mechnikov Research Institute of Vaccines and Sera, Moscow, Russia, 105064
| | - Vera S Kichatova
- Department of Viral Hepatitis, Russian Medical Academy of Continuous Professional Education, Moscow, Russia, 125993.,Laboratory of Viral Hepatitis, Mechnikov Research Institute of Vaccines and Sera, Moscow, Russia, 105064
| | - Fedor A Asadi Mobarkhan
- Department of Viral Hepatitis, Russian Medical Academy of Continuous Professional Education, Moscow, Russia, 125993.,Laboratory of Viral Hepatitis, Mechnikov Research Institute of Vaccines and Sera, Moscow, Russia, 105064
| | - Lyudmila V Bezuglova
- JSC «Vector-Best», Research and Production Area, building 36, Koltsovo, Novosibirsk region, Russia, 630559
| | - Irina G Netesova
- JSC «Vector-Best», Research and Production Area, building 36, Koltsovo, Novosibirsk region, Russia, 630559
| | - Victor A Manuylov
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ivanovsky Institute of Virology, Ministry of Health of the Russian Federation, Moscow, Russia, 123098
| | - Andrey A Pochtovyi
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ivanovsky Institute of Virology, Ministry of Health of the Russian Federation, Moscow, Russia, 123098
| | - Vladimir A Gushchin
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ivanovsky Institute of Virology, Ministry of Health of the Russian Federation, Moscow, Russia, 123098
| | - Snezhana S Sleptsova
- Medical Institute, M.K. Ammosov North-Eastern Federal University, Yakutsk, Russia, 677010
| | - Margarita E Ignateva
- The Sakha Republic (Yakutia) Regional Department of Rospotrebnadzor, Yakutsk, Russia, 677027
| | - Mikhail I Mikhailov
- Department of Viral Hepatitis, Russian Medical Academy of Continuous Professional Education, Moscow, Russia, 125993.,Laboratory of Viral Hepatitis, Mechnikov Research Institute of Vaccines and Sera, Moscow, Russia, 105064.,Medical Faculty, Belgorod State National Research University, Belgorod, Russia, 308015
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9
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Silva RJS, do Nascimento RS, Oliveira-Neto JAJ, Silva FQ, Piauiense JNF, Gomes CM, Pinheiro LML, Resque RL, Pinho JRR, Kupek E, Fischer B, Machado LFA, Martins LC, Lemos JAR, Oliveira-Filho AB. Detection and Genetic Characterization of Hepatitis B and D Viruses: A Multi-Site Cross-Sectional Study of People Who Use Illicit Drugs in the Amazon Region. Viruses 2021; 13:v13071380. [PMID: 34372586 PMCID: PMC8310228 DOI: 10.3390/v13071380] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 07/03/2021] [Accepted: 07/06/2021] [Indexed: 02/06/2023] Open
Abstract
Hepatitis B (HBV) and delta (HDV) viruses are endemic in the Amazon region, but vaccine coverage against HBV is still limited. People who use illicit drugs (PWUDs) represent a high-risk group due to common risk behavior and socioeconomic factors that facilitate the acquisition and transmission of pathogens. The present study assessed the presence of HBV and HBV-HDV co-infection, identified viral sub-genotypes, and verified the occurrence of mutations in coding regions for HBsAg and part of the polymerase in HBV-infected PWUDs in municipalities of the Brazilian states of Amapá and Pará, in the Amazon region. In total, 1074 PWUDs provided blood samples and personal data in 30 municipalities of the Brazilian Amazon. HBV and HDV were detected by enzyme-linked immunosorbent assay and polymerase chain reaction. Viral genotypes were identified by nucleotide sequencing followed by phylogenetic analysis, whereas viral mutations were analyzed by specialized software. High rates of serological (32.2%) and molecular (7.2%) markers for HBV were detected, including cases of occult HBV infection (2.5%). Sub-genotypes A1, A2, D4, and F2a were most frequently found. Escape mutations due to vaccine and antiviral resistance were identified. Among PWUDs with HBV DNA, serological (19.5%) and molecular (11.7%) HDV markers were detected, such as HDV genotypes 1 and 3. These are worrying findings, presenting clear implications for urgent prevention and treatment needs for the carriers of these viruses.
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Affiliation(s)
- Ronylson José S. Silva
- Programa de Pós-Graduação em Biologia Ambiental, Universidade Federal do Pará, Bragança 68600-000, PA, Brazil; (R.J.S.S.); (R.S.d.N.); (C.M.G.)
| | - Raquel Silva do Nascimento
- Programa de Pós-Graduação em Biologia Ambiental, Universidade Federal do Pará, Bragança 68600-000, PA, Brazil; (R.J.S.S.); (R.S.d.N.); (C.M.G.)
| | - José Augusto J. Oliveira-Neto
- Instituto de Estudos Costeiros, Universidade Federal do Pará, Bragança 68600-000, PA, Brazil; (J.A.J.O.-N.); (F.Q.S.)
| | - Fabricio Quaresma Silva
- Instituto de Estudos Costeiros, Universidade Federal do Pará, Bragança 68600-000, PA, Brazil; (J.A.J.O.-N.); (F.Q.S.)
| | - Juliana Nádia F. Piauiense
- Programa de Pós-Graduação em Saúde na Amazônia, Universidade Federal do Pará, Belém 66055-240, PA, Brazil; (J.N.F.P.); (L.C.M.)
| | - Camila Moraes Gomes
- Programa de Pós-Graduação em Biologia Ambiental, Universidade Federal do Pará, Bragança 68600-000, PA, Brazil; (R.J.S.S.); (R.S.d.N.); (C.M.G.)
| | - Luiz Marcelo L. Pinheiro
- Faculdade de Ciências Biológicas, Campus do Marajó, Universidade Federal do Pará, Soure 68870-000, PA, Brazil;
| | - Rafael Lima Resque
- Departamento de Ciências Biológicas e da Saúde, Universidade Federal do Amapá, Macapá 68903-419, AP, Brazil;
| | - João Renato R. Pinho
- Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo 05403-000, SP, Brazil;
| | - Emil Kupek
- Departamento de Saúde Pública, Universidade Federal de Santa Catarina, Florianópolis 88040-900, SC, Brazil;
| | - Benedikt Fischer
- Centre for Applied Research in Mental Health and Addiction, Faculty of Health Sciences, Simon Fraser University, Vancouver, BC V6B 5K3, Canada;
- Faculty of Medical and Health Sciences, University of Auckland, Auckland 1023, New Zealand
- Departamento de Psiquiatria, Universidade Federal de São Paulo, São Paulo 04038-000, SP, Brazil
| | - Luiz Fernando A. Machado
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, PA, Brazil; (L.F.A.M.); (J.A.R.L.)
| | - Luísa Caricio Martins
- Programa de Pós-Graduação em Saúde na Amazônia, Universidade Federal do Pará, Belém 66055-240, PA, Brazil; (J.N.F.P.); (L.C.M.)
- Núcleo de Medicina Tropical, Universidade Federal do Pará, Belém 66055-240, PA, Brazil
| | - José Alexandre R. Lemos
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, PA, Brazil; (L.F.A.M.); (J.A.R.L.)
| | - Aldemir B. Oliveira-Filho
- Programa de Pós-Graduação em Biologia Ambiental, Universidade Federal do Pará, Bragança 68600-000, PA, Brazil; (R.J.S.S.); (R.S.d.N.); (C.M.G.)
- Instituto de Estudos Costeiros, Universidade Federal do Pará, Bragança 68600-000, PA, Brazil; (J.A.J.O.-N.); (F.Q.S.)
- Correspondence: ; Tel.: +55-91-3425-1209
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10
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Cabezas C, Braga W. Hepatitis B Virus and Delta Infection: Special Considerations in the Indigenous and Isolated Riverside Populations in the Amazon Region. Clin Liver Dis (Hoboken) 2020; 16:117-122. [PMID: 33005393 PMCID: PMC7508778 DOI: 10.1002/cld.1009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 07/08/2020] [Accepted: 07/12/2020] [Indexed: 02/04/2023] Open
Affiliation(s)
- César Cabezas
- Faculty of MedicineUniversidad Nacional Mayor de San MarcosLimaPeru,National Public Health CenterInstituto Nacional de SaludLimaPerú
| | - Wornei Braga
- Fundação de Medicina Tropical Dr. Heitor Vieira DouradoManausAmazon State, PABrazil
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