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do Lago BV, Bezerra CS, Moreira DA, Parente TE, Portilho MM, Pessôa R, Sanabani SS, Villar LM. Genetic diversity of hepatitis B virus quasispecies in different biological compartments reveals distinct genotypes. Sci Rep 2023; 13:17023. [PMID: 37813888 PMCID: PMC10562391 DOI: 10.1038/s41598-023-43655-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 09/26/2023] [Indexed: 10/11/2023] Open
Abstract
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.
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Affiliation(s)
- Bárbara Vieira do Lago
- Laboratório de Hepatites Virais, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Cristianne Sousa Bezerra
- Laboratório de Hepatites Virais, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil
- Departamento de Educação, Instituto Federal de Educação, Ciência e Tecnologia do Ceará, Fortaleza, Ceará, Brazil
| | - Daniel Andrade Moreira
- Laboratório de Genômica Aplicada e Bioinovações, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Thiago Estevam Parente
- Laboratório de Genômica Aplicada e Bioinovações, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | | | - Rodrigo Pessôa
- Postgraduate Program in Translational Medicine, Department of Medicine, Federal University of Sao Paulo (UNIFESP), São Paulo, Brazil
| | - Sabri Saeed Sanabani
- Laboratory of Medical Investigation (LIM) 03, Clinics Hospital, Faculty of Medicine, University of São Paulo, São Paulo, Brazil
| | - Livia Melo Villar
- Laboratório de Hepatites Virais, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil.
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Jardim de Queiroz L, Cardoso Y, Jacot-des-Combes C, Bahechar IA, Lucena CA, Rapp Py-Daniel L, Sarmento Soares LM, Nylinder S, Oliveira C, Parente TE, Torrente-Vilara G, Covain R, Buckup P, Montoya-Burgos JI. Evolutionary units delimitation and continental multilocus phylogeny of the hyperdiverse catfish genus Hypostomus. Mol Phylogenet Evol 2019; 145:106711. [PMID: 31857199 DOI: 10.1016/j.ympev.2019.106711] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 10/20/2019] [Accepted: 12/14/2019] [Indexed: 10/25/2022]
Abstract
With 149 currently recognized species, Hypostomus is one of the most species-rich catfish genera in the world, widely distributed over most of the Neotropical region. To clarify the evolutionary history of this genus, we reconstructed a comprehensive phylogeny of Hypostomus based on four nuclear and two mitochondrial markers. A total of 206 specimens collected from the main Neotropical rivers were included in the present study. Combining morphology and a Bayesian multispecies coalescent (MSC) approach, we recovered 85 previously recognized species plus 23 putative new species, organized into 118 'clusters'. We presented the Cluster Credibility (CC) index that provides numerical support for every hypothesis of cluster delimitation, facilitating delimitation decisions. We then examined the correspondence between the morphologically identified species and their inter-specific COI barcode pairwise divergence. The mean COI barcode divergence between morphological sisters species was 1.3 ± 1.2%, and only in 11% of the comparisons the divergence was ≥2%. This indicates that the COI barcode threshold of 2% classically used to delimit fish species would seriously underestimate the number of species in Hypostomus, advocating for a taxon-specific COI-based inter-specific divergence threshold to be used only when approximations of species richness are needed. The phylogeny of the 108 Hypostomus species, together with 35 additional outgroup species, confirms the monophyly of the genus. Four well-supported main lineages were retrieved, hereinafter called super-groups: Hypostomus cochliodon, H. hemiurus, H. auroguttatus, and H. plecostomus super-groups. We present a compilation of diagnostic characters for each super-group. Our phylogeny lays the foundation for future studies on biogeography and on macroevolution to better understand the successful radiation of this Neotropical fish genus.
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Affiliation(s)
- Luiz Jardim de Queiroz
- Department of Genetics and Evolution, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva, Switzerland
| | - Yamila Cardoso
- Laboratorio de Sistemática y Biología Evolutiva, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, Paseo del Bosque S/N, B1900FWA, La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, Argentina
| | - Cécile Jacot-des-Combes
- Department of Genetics and Evolution, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva, Switzerland
| | - Ilham Anne Bahechar
- Department of Genetics and Evolution, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva, Switzerland
| | - Carlos Alberto Lucena
- Museu de Ciências e Tecnologia, Pontifícia Universidade Católica do Rio Grande do Sul, Av. Ipiranga 6681, 90619-900 Porto Alegre, RS, Brazil
| | - Lucia Rapp Py-Daniel
- Coordenação de Biodiversidade, Programa de Coleções Científicas e Biológicas, Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo 2936, 69060-001 Manaus, AM, Brazil
| | - Luisa Maria Sarmento Soares
- Museu de Biologia Professor Mello Leitão, Instituto Nacional da Mata Atlântica, Av. José Ruschi 4, 29650-000 Santa Teresa, ES, Brazil
| | - Stephan Nylinder
- Department of Psychology, University of Gothenburg. Haraldsgatan 1, 413 14 Gothenburg, Sweden
| | - Claudio Oliveira
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual de São Paulo, Rua Professor Doutor Antonio Celso Wagner Zanin 250, 18618-689 Botucatu, SP, Brazil
| | - Thiago Estevam Parente
- Laboratório de Toxicologia Ambiental, Laboratório de Genética Molecular de Microrganismos, Fundação Oswaldo Cruz, Av. Brasil 4365, 21040-900 Rio de Janeiro, RJ, Brazil
| | - Gislene Torrente-Vilara
- Departamento de Ciências do Mar, Universidade Federal de São Paulo, Av. Doutor Carvalho de Mendonça 144, 11070-100 Santos, SP, Brazil
| | - Raphaël Covain
- Department of Herpertology and Ichthyology, Museum of Natural History of Geneva, Route de Malagnou 1, 1211 Geneva, Switzerland
| | - Paulo Buckup
- Departamento de Vertebrados, Vista Museu Nacional do Rio de Janeiro/Universidade Federal do Rio de Janeiro, Quinta da Boa, 20940-040 Rio de Janeiro, RJ, Brazil
| | - Juan I Montoya-Burgos
- Department of Genetics and Evolution, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva, Switzerland.
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Moreira DA, Buckup PA, Furtado C, Val AL, Schama R, Parente TE. Reducing the information gap on Loricarioidei (Siluriformes) mitochondrial genomics. BMC Genomics 2017; 18:345. [PMID: 28472937 PMCID: PMC5418769 DOI: 10.1186/s12864-017-3709-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 04/19/2017] [Indexed: 01/11/2023] Open
Abstract
Background The genetic diversity of Neotropical fish fauna is underrepresented in public databases. This distortion is evident for the order Siluriformes, in which the suborders Siluroidei and Loricarioidei share equivalent proportion of species, although far less is known about the genetics of the latter clade, endemic to the Neotropical Region. Recently, this information gap was evident in a study about the structural diversity of fish mitochondrial genomes, and hampered a precise chronological resolution of Siluriformes. It has also prevented molecular ecology investigations about these catfishes, their interactions with the environment, responses to anthropogenic changes and potential uses. Results Using high-throughput sequencing, we provide the nearly complete mitochondrial genomes for 26 Loricariidae and one Callichthyidae species. Structural features were highly conserved. A notable exception was identified in the monophyletic clade comprising species of the Hemiancistrus, Hypostomini and Peckoltia-clades, a ~60 nucleotide-long deletion encompassing the seven nucleotides at the 3′ end of the Conserved Sequence Block (CSB) D of the control region. The expression of mitochondrial genes followed the usual punctuation pattern. Heteroplasmic sites were identified in most species. The retrieved phylogeny strongly corroborates the currently accepted tree, although bringing to debate the relationship between Schizolecis guntheri and Pareiorhaphis garbei, and highlighting the low genetic variability within the Peckoltia-clade, an eco-morphologically diverse and taxonomically problematic group. Conclusions Herein we have launched the use of high-throughput mitochondrial genomics in the studies of the Loricarioidei species. The new genomic resources reduce the information gap on the molecular diversity of Neotropical fish fauna, impacting the capacity to investigate a variety of aspects of the molecular ecology and evolution of these fishes. Additionally, the species showing the partial CSB-D are candidate models to study the replication and transcription of vertebrate mitochondrial genome. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3709-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daniel Andrade Moreira
- Laboratório de Toxicologia Ambiental, Escola Nacional de Saúde Pública (ENSP), Fundação Oswaldo Cruz (FIOCRUZ), Av. Brasil, 4036, Rio de Janeiro, Brasil.,Laboratório de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (FIOCRUZ), Av. Brasil, 4365, Rio de Janeiro, Brasil
| | - Paulo Andreas Buckup
- Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro (UFRJ), Quinta da Boa Vista, Rio de Janeiro, RJ, Brasil
| | - Carolina Furtado
- Unidade de Genômica, Instituto Nacional do Câncer (INCA), Rua André Cavalcanti, 37, Rio de Janeiro, Brasil
| | - Adalberto Luis Val
- Laboratório de Ecofisiologia e Evolução Molecular, Instituto Nacional de Pesquisas da Amazônia (INPA), Av. André Araújo, 2936, Manaus, Brasil
| | - Renata Schama
- Laboratório de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (FIOCRUZ), Av. Brasil, 4365, Rio de Janeiro, Brasil
| | - Thiago Estevam Parente
- Laboratório de Toxicologia Ambiental, Escola Nacional de Saúde Pública (ENSP), Fundação Oswaldo Cruz (FIOCRUZ), Av. Brasil, 4036, Rio de Janeiro, Brasil. .,Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (FIOCRUZ), Av. Brasil, 4365, Rio de Janeiro, Brasil.
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Moreira DA, Magalhães MGP, de Andrade PCC, Furtado C, Val AL, Parente TE. An RNA-based approach to sequence the mitogenome of Hypoptopoma incognitum (Siluriformes: Loricariidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3784-6. [PMID: 26370305 DOI: 10.3109/19401736.2015.1079903] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Hypoptopoma incognitum is a fish of the fifth most species-rich family of vertebrates and abundant in rivers from the Brazilian Amazon. Only two species of Loricariidae fish have their complete mitogenomes sequence deposited in the Genbank. An innovative RNA-based approach was used to assemble the complete mitogenome of H. incognitum with an average coverage depth of 5292×. The typical vertebrate mitochondrial features were found; 22 tRNA genes, two rRNA genes, 13 protein-coding genes, and a non-coding control region. Moreover, the use of this approach allowed the measurement of mtRNA expression levels, the punctuation pattern of editing, and the detection of heteroplasmies.
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Affiliation(s)
- Daniel Andrade Moreira
- a Laboratório de Toxicologia Ambiental , Fundação Oswaldo Cruz (FIOCRUZ) , Rio de Janeiro , Brasil
| | - Maithê G P Magalhães
- a Laboratório de Toxicologia Ambiental , Fundação Oswaldo Cruz (FIOCRUZ) , Rio de Janeiro , Brasil
| | - Paula C C de Andrade
- a Laboratório de Toxicologia Ambiental , Fundação Oswaldo Cruz (FIOCRUZ) , Rio de Janeiro , Brasil
| | - Carolina Furtado
- b Divisão de Genética , Instituto Nacional do Cancer (INCA) , Rio de Janeiro , Brasil , and
| | - Adalberto L Val
- c Laboratório de Ecofisiologia e Evolução Molecular , Instituto Nacional de Pesquisas da Amazônia (INPA) , Manaus , Brasil
| | - Thiago Estevam Parente
- a Laboratório de Toxicologia Ambiental , Fundação Oswaldo Cruz (FIOCRUZ) , Rio de Janeiro , Brasil
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